IndraLab
Statements
sparser
"In ABT-737–resistant cancer cells, the interaction between USP9X and Mcl-1 ( xref ), which was increased by ABT-737 treatment, could be disrupted by gemcitabine, thus resulting in enhanced ubiquitination and the subsequent degradation of Mcl-1 ultimately provoking synergism of this two drug combination ( xref )."
reach
"Some cancers, including primary breast cancer, demonstrate an association between Usp9x and Mcl-1, a prosurvival BCL2 family member that is essential for stem and progenitor cell survival and is known to confer chemo- and radioresistance in a variety of tumors including lymphoma, breast, renal, lung, bladder, and prostate cancer XREF_BIBR, XREF_BIBR, XREF_BIBR."
USP9X is modified
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103
USP9X is phosphorylated.
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61
sparser
"To investigate the possibility that WT1 is involved in mitotic transcription and to identify cell cycle-specific target genes that are dependent on USP9X phosphorylation and activity, we conducted RNA-sequencing analyses (RNA-Seq) in two different experimental settings: first, we performed RNA-Seq from control versus WT1 knockdown cells, in order to identify genes transcribed in a WT1-dependent manner."
sparser
"To investigate the functional consequences of USP9X phosphorylation at serine 2563, we first performed DUB activity assays of USP9X WT and its non-phosphorylatable mutant USP9X S2563A . The first respective approach was based upon the detection of active DUBs that are captured as soon as they act on the recombinant substrate HA(Hemagglutinin)-Ubiquitin-Vinyl Sulfone."
sparser
"For further experiments, we produced mouse FAM84A specific anti-serum using the C-terminal peptide of FAM84A. We also produced an anti-serum to detect the phosphorylation of serine 38 of mouse FAM84A, since it has been reported that serine 38 is a target site for phosphorylation of human FAM84A, which is involved in changes in cell morphology ( xref )."
USP9X is methylated.
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33
USP9X is ubiquitinated.
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6
sparser
"Mass spectrometry studies led the authors to discover that FBXW11 (a ubiquitin ligase subunit known as “F-box and WD repeat domain containing 11”) ubiquitinates PTENα/β and USP9X (a deubiquitinase known as “ubiquitin specific peptidase 9 X-linked”) deubiquitinates PTENα/β, but not canonical PTEN."
USP9X is palmitoylated.
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3
sparser
"The unlabelled SHH peptide or SHH(FL) substrates were employed as competitive inhibitors of SHH-FAM palmitoylation, affording IC 50 values of 370 nM (95% CI 300–470 nM) and 440 nM (95% CI 350–570 nM), respectively ( xref ), which corresponded to approximately 50% of the SHH-FAM concentration."
sparser
"In ABT-737–resistant cancer cells, the interaction between USP9X and Mcl-1 ( xref ), which was increased by ABT-737 treatment, could be disrupted by gemcitabine, thus resulting in enhanced ubiquitination and the subsequent degradation of Mcl-1 ultimately provoking synergism of this two drug combination ( xref )."
reach
"Some cancers, including primary breast cancer, demonstrate an association between Usp9x and Mcl-1, a prosurvival BCL2 family member that is essential for stem and progenitor cell survival and is known to confer chemo- and radioresistance in a variety of tumors including lymphoma, breast, renal, lung, bladder, and prostate cancer XREF_BIBR, XREF_BIBR, XREF_BIBR."
sparser
"Its hepatotoxicity has been verified in mouse models. xref , xref To observe if FAF–Rapa induced any systemic toxicity during our therapeutic study, serum alanine aminotransferase (ALT), alkaline phosphatase (ALP) (indicators of liver damage), blood urea nitrogen (BUN), and creatinine levels (indicators of kidney damage) were analyzed. xref , xref As compared in xref , there was no apparent nephro or hepatotoxicities upon FAF–Rapa treatment in this study."
eidos
"At molecular level , USP9X induces beta-catenin signaling to mediate HCC progression.124 Therefore , mediating GSK-3beta degradation and triggering beta-catenin nuclear translocation can significantly enhance proliferation rate of HCC cells.125 Besides , activation of beta-catenin signaling induces resistance of HCC cells toward apoptosis.126 Histone deacetylase 6 ( HDAC6 ) acts as tumor-suppressor and diminishes beta-catenin expression to induce apoptosis in HCC cells ."
reach
"At molecular level, USP9X induces β-catenin signaling to mediate HCC progression.124 Therefore, mediating GSK-3β degradation and triggering β-catenin nuclear translocation can significantly enhance proliferation rate of HCC cells.125 Besides, activation of β-catenin signaling induces resistance of HCC cells toward apoptosis.126 Histone deacetylase 6 (HDAC6) acts as tumor-suppressor and diminishes β-catenin expression to induce apoptosis in HCC cells."
reach
"USP9X has also been reported to increase the levels of beta-catenin, a transcription factor linked to the growth of brain tumors XREF_BIBR, XREF_BIBR, and overexpression of USP9X has been reported to enhance the half-life and expression of beta-catenin in mouse L cells and MCF7 cells, respectively XREF_BIBR, XREF_BIBR."
sparser
"On the other hand inhibition of ERK and USP9x with pharmaceutical or genetic approach in breast cancer cells abolishes FFA promotion of TGF-β–induced SMAD4-USP9x interaction, SMAD4 nuclear retention, SMAD3/SMAD4 complex formation, and target gene expression, resulting in decrease in cancer cell invasion and metastasis ( xref )."
sparser
"We also found that FFA/ERK-induced SMAD4 T277 phosphorylation is indispensable in SMAD4-USP9x interaction and its deubiquitination as well as subsequent nuclear accumulation, which is required for TGF-β–induced breast cancer invasion and metastasis under the high FFA/obesity conditions."
"Multiple mono-ubiquitination of SMAD3 can be removed by USP15 and mono-ubiquitination of SMAD4 seems to be removed by FAM/USP9X."
"Smad4 is monoubiquitinated in lysine 519 in vivo, a modification that inhibits smad4 by impeding association with phospho-smad2. Fam reverts this negative modification, re-empowering smad4 function;control of smad4 is a good way to regulate bone formation. Fam and ectodermin/tif1gamma (ecto) were reported to respectively regulate the de-ubiquitination and ubiquitination of smad4."
"Smad4 is monoubiquitinated in lysine 519 in vivo, a modification that inhibits smad4 by impeding association with phospho-smad2. Fam reverts this negative modification, re-empowering smad4 function;control of smad4 is a good way to regulate bone formation. Fam and ectodermin/tif1gamma (ecto) were reported to respectively regulate the de-ubiquitination and ubiquitination of smad4."
"Smad4 is monoubiquitinated in lysine 519 in vivo, a modification that inhibits smad4 by impeding association with phospho-smad2. Fam reverts this negative modification, re-empowering smad4 function;control of smad4 is a good way to regulate bone formation. Fam and ectodermin/tif1gamma (ecto) were reported to respectively regulate the de-ubiquitination and ubiquitination of smad4."
"Smad4 is monoubiquitinated in lysine 519 in vivo, a modification that inhibits smad4 by impeding association with phospho-smad2. Fam reverts this negative modification, re-empowering smad4 function;control of smad4 is a good way to regulate bone formation. Fam and ectodermin/tif1gamma (ecto) were reported to respectively regulate the de-ubiquitination and ubiquitination of smad4."
"Smad4 is monoubiquitinated in lysine 519 in vivo, a modification that inhibits smad4 by impeding association with phospho-smad2. Fam reverts this negative modification, re-empowering smad4 function;control of smad4 is a good way to regulate bone formation. Fam and ectodermin/tif1gamma (ecto) were reported to respectively regulate the de-ubiquitination and ubiquitination of smad4."
USP9X affects Partial Remission
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USP9X binds Partial Remission. 10 / 64
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sparser
"While more and more evidence has emerged in recent years in favour of positive effects of short- and long-term treatment with PR-FAM on ambulatory function [ xref , xref ], data demonstrating a possible long-term effect of the drug on non-walking functional outcomes are either still limited or discordant."
sparser
"Apart from one randomized, placebo-controlled study describing PR-FAM’s beneficial effects on different cognitive domains as well as on fatigue and depression over 2 years in a cohort of MS patients [ xref ], most studies conducted so far, utilizing a randomized, placebo-controlled design, have failed to demonstrate fampridine’s benefits in such non-walking outcomes [ xref – xref ]."
USP9X affects apoptotic process
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1
USP9X inhibits apoptotic process.
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USP9X activates apoptotic process.
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sparser
"While the YAP1–TEAD interaction is essential for YAP1-MAMLD1 -driven tumorigenesis (Fig. xref ), electroporated animals carrying a putative NLS-conjugated YAP1 domain (YAP1ΔC-MYC(NLS)) as well as YAP1-FAM118B did not develop tumors despite their nuclear localization (Fig. xref ; Supplementary Figs. xref and xref ), implying that the MAMLD1 domain may have other roles in transforming primary cells, in addition to nuclear shuttling."
sparser
"The oncogenicity of YAP1-MAMLD1 and YAP1-FAM118B has been demonstrated via gene transfer of the full-length fusions or wild-type fusion partners to target RGCs/NSCs in the embryonal cerebral ventricular zone (VZ) using in utero electroporation [ xref ], as well as the RCAS/tv-a system [ xref ] or lentivirus injections [ xref ] in mouse neonatal brains."
| PMC
reach
"Similarly, depletion of USP9X in cells using two specific shRNAs significantly decreased YAP1 protein levels (XREF_FIG) and increased cellular sensitivity to MMC, cisplatin and etoposide (XREF_FIG), while reconstituting USP9X depleted cells with FLAG-YAP1 reversed chemotherapy drugs hypersensitivity (XREF_FIG)."
USP9X affects cell population proliferation
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USP9X activates cell population proliferation.
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USP9X inhibits cell population proliferation.
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sparser
"While the YAP1–TEAD interaction is essential for YAP1-MAMLD1 -driven tumorigenesis (Fig. xref ), electroporated animals carrying a putative NLS-conjugated YAP1 domain (YAP1ΔC-MYC(NLS)) as well as YAP1-FAM118B did not develop tumors despite their nuclear localization (Fig. xref ; Supplementary Figs. xref and xref ), implying that the MAMLD1 domain may have other roles in transforming primary cells, in addition to nuclear shuttling."
sparser
"The oncogenicity of YAP1-MAMLD1 and YAP1-FAM118B has been demonstrated via gene transfer of the full-length fusions or wild-type fusion partners to target RGCs/NSCs in the embryonal cerebral ventricular zone (VZ) using in utero electroporation [ xref ], as well as the RCAS/tv-a system [ xref ] or lentivirus injections [ xref ] in mouse neonatal brains."
| PMC
reach
"We observed that when the cellular levels of USP9X were reduced by siRNA, the TDRD3 ubiquitination levels markedly increased (XREF_FIG, upper panel -- compare lane 2 to lane 5) and inhibition of the proteasome greatly augmented this difference (XREF_FIG, upper panel -- compare lane 3 to lane 6), suggesting that USP9X is necessary to suppress TDRD3 ubiquitination."
reach
"Interestingly, the C terminus of USP9X has been reported to mediate the interactions with its de-ubiquitination substrates, including FOXO3, MIB1 and VMP1 [XREF_BIBR], suggesting that USP9X may target TDRD3 for de-ubiquitination; we have tested this hypothesis extensively in the next sections."
sparser
"As illustrated in a detailed view
of the time evolution of FAM134B-RHD clusters during a representative
budding event for Δ N = 300 and n = 9 ( xref ), we
found that budding is initiated at the site of a spontaneously formed
FAM134B-RHD cluster (yellow) consisting of three proteins."
sparser
"Second, our observation of
FAM134B-RHD-induced membrane budding explains the “membrane
shredding” action of FAM134B-RHD, which results in the formation
of tiny vesicular structures. xref , xref Highlighting the biological
relevance of FAM134B-RHD in ER-phagy, we note that Zika and Dengue
viruses proteolytically target FAM134B-RHD to evade host responses
during infection. xref "
sparser
"Budding is associated with a sharp decrease in the box
width L x as membrane
area is absorbed into the nascent bud ( xref A), making L x an excellent reporter on membrane shape changes. xref B shows the initial
flat membrane and final budded state in an MD simulation with n = 9 FAM134B-RHDs and a leaflet asymmetry of Δ N = 300."
sparser
"Overall, LT-FH and Fam-meta had higher power than CC-GWAS in simulations, especially using phenotypes that were more prevalent in older age groups, and both methods detected known genetic variants with lower P -values in real data application, highlighting the benefits of including family history in genetic association studies."
WP1130 affects USP9X
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sparser
"On the other hand inhibition of ERK and USP9x with pharmaceutical or genetic approach in breast cancer cells abolishes FFA promotion of TGF-β–induced SMAD4-USP9x interaction, SMAD4 nuclear retention, SMAD3/SMAD4 complex formation, and target gene expression, resulting in decrease in cancer cell invasion and metastasis ( xref )."
sparser
"We also found that FFA/ERK-induced SMAD4 T277 phosphorylation is indispensable in SMAD4-USP9x interaction and its deubiquitination as well as subsequent nuclear accumulation, which is required for TGF-β–induced breast cancer invasion and metastasis under the high FFA/obesity conditions."
sparser
"Immunofluorescent microscopy analysis revealed that in G 1 /S/G 2 phases of the cell cycle USP9X is distributed not only in the cytoplasm but also in the centrosome, where it is physically and functionally associated with CEP131, indicating that USP9X is an integral component of the centrosome."
sparser
"To confirm the association of USP9X with CEP131, co-immunoprecipitation experiments were performed with HeLa cell extracts and the results showed that USP9X was efficiently co-immunoprecipitated with CEP131, but not with another centrosomal protein CP110 (ref. xref ), although USP33, another DUB protein, could be effectively co-immunoprecipitated with CP110 (ref. xref ; xref )."
reach
"In vitro deubiquitination assays revealed that, while USP9X was able to remove ubiquitins of CEP131 and K504R, but not that of CEP131 and K254R (XREF_FIG), favouring the argument that USP9X targets K254 of CEP131 for deubiquitination, although polyubiquitin chains conjugated onto CEP131 and K254R and CEP131 and K504R were both dramatically reduced (XREF_FIG)."
reach
"Combining the findings that mildly disrupted centrosomal localization of PCM1 has minimal effect on CEP131 recruitment and the observations that USP9X directly interacts with CEP131 and opposes its polyubiquitin linkages in vitro, we get the conclusion that the effect of USP9X on CEP131 stabilization is attributed to the interplay between these two molecules but not through USP9X targeting other substrates like PCM1, and USP9X regulated PCM1 stabilization on centrosome activity, if it does so, seems to be independent of USP9X promoted CEP131 stabilization."
reach
"To investigate whether and how other substrates of USP9X might affect the cellular function of USP9X promoted CEP131 stabilization, we analysed by WB analysis the expression of IPO5, PRMT5 and PPM1B, which were also identified as interactors of USP9X (XREF_SUPPLEMENTARY), and the results indicate that the protein abundance of these proteins was essentially unchanged upon USP9X knockdown (XREF_SUPPLEMENTARY)."
reach
"Although we currently do not know the mechanism by which AGS3 modulates the structure or function of the late Golgi compartments, the observations that USP9x interacts with AGS3 and regulates the level of AGS3 are consistent with a role of ubiquitination and deubiquitination of AGS3 in this process."
reach
"Relative to the full-length USP9x, which increased the AGS3 staining primarily in cells expressing a high level of transfected USP9x-HA (~ 30% of these cells), the UCH domain led to enhanced AGS3 staining in almost all transfected cells displaying a moderate-to-high level of overexpression (XREF_FIG)."
sparser
"The diagnosis of COVID-19 was made by monitoring the signs and symptoms of the participants to finally confirm the infection status by RT-PCR (SuperScript III Platinum, Invitrogen, EEUU; Integrated DNA Technologies, Coralville, EEUU) and the kit 2019-nCoV ValuPanel Reagents (2019-nCoV_N1 Probe: FAM-ACC CCG CAT TAC GTT TGG TGG ACC-BHQ1, 2019-nCoV_N1 Forward Primer: GAC CCC AAA ATC AGC GAA AT, 2019-nCoV_N1 Reverse Primer: TCT GGT TAC TGC CAG TTG AAT CTG; 2019-nCoV_N2 Probe: FAM-ACA ATT TGC CCC CAG CGC TTC AG-BHQ1, 2019-nCoV_N2 Forward Primer: TTA CAA ACA TTG GCC GCA AA, 2019-nCoV_N2 Reverse Primer: GCG CGA CAT TCC GAA GAA; 2019-nCoV_N3 Probe: FAM-AYC ACA TTG GCA CCC GCA ATC CTG-BHQ1, 2019-nCoV_N3 Forward Primer: GGG AGC CTT GAA TAC ACC AAA A, 2019-nCoV_N3 Reverse Primer: TGT AGC ACG ATT GCA GCA TTG)
70 nasal rinse made by 64 participants; weekly number of contacts with patients diagnosed with COVID-19 or atypical pneumonia during the study period: (0-860, 169 on average) in the experimental group and (0 to 729, 146 on average) in the control group; percentage of individuals who presented symptoms of respiratory tract infection (RTI's) at some point during the study; 18.4% in the experimental group and 35.8% in the control group; no adverse reactions were reported by performing mouthwash and nose rinse with AgNPs."
sparser
"Primer and probe sequences for SARS-CoV-2 (N1 and N2 targets) and OC43 Target Primer/Probe Sequences Reference SARS-CoV-2 N1 F: 5'-GAC CCC AAA ATC AGC GAA AT-3' R: 5'-TCT GGT TAC TGC CAG TTG AAT CTG-3' P: 5'-FAM-ACC CCG CAT TAC GTT TGG TGG ACC-BHQ1-3' Pdouble: FAM-ACC CCG CAT /ZEN/ TAC GTT TGG TGG ACC-3IABkFQ 2019-nCoV CDC EUA Kit, IDT Catalog No."
| DOI
sparser
"The diagnosis of COVID-19 was made by monitoring the signs and symptoms of the participants to finally confirm the infection status by RT-PCR (SuperScript III Platinum, Invitrogen, EEUU; Integrated DNA Technologies, Coralville, EEUU) and the kit 2019-nCoV ValuPanel Reagents (2019-nCoV_N1 Probe: FAM-ACC CCG CAT TAC GTT TGG TGG ACC-BHQ1, 2019-nCoV_N1 Forward Primer: GAC CCC AAA ATC AGC GAA AT, 2019-nCoV_N1 Reverse Primer: TCT GGT TAC TGC CAG TTG AAT CTG; 2019-nCoV_N2 Probe: FAM-ACA ATT TGC CCC CAG CGC TTC AG-BHQ1, 2019-nCoV_N2 Forward Primer: TTA CAA ACA TTG GCC GCA AA, 2019-nCoV_N2 Reverse Primer: GCG CGA CAT TCC GAA GAA; 2019-nCoV_N3 Probe: FAM-AYC ACA TTG GCA CCC GCA ATC CTG-BHQ1, 2019-nCoV_N3 Forward Primer: GGG AGC CTT GAA TAC ACC AAA A, 2019-nCoV_N3 Reverse Primer: TGT AGC ACG ATT GCA GCA TTG)."
sparser
"Sequences of the primers and probe used : 2019-nCoV_N1 Forward Primer: GAC CCC AAA ATC AGC GAA AT 2019-nCoV_N1 Reverse Primer : TCT GGT TAC TGC CAG TTG AAT CTG 2019-nCoV_N1 Probe: FAM-ACC CCG CAT /ZEN/ TAC GTT TGG TGG ACCRemove an aliquot of the Twist Synthetic SARS-CoV-2 RNA Control 1 (Twist Biosciences Cat."
sparser
"1B R: GTG AGT AGG AGA GGT GAG AGAGG FAM-ACA CCA ATG CCC AAC TGC CTG CCT -TAMRA 109 F: GGG ATC TGA AAC AAC ATT CAT GTG IL-2 R: AGT CAG TGT TGA GAT GAT GCT TTG FAM -TGA TGA GAC AGC AACCA -TAMRA 88 F: TGC TGC CTC CAA GAA CAC AAC IL-4 R: GTC CTT CTC ATG GTG GCT GTAG FAM-CCG GAG CAC AGT CGC AGC CCT-TAMRA 160 F: ATG CAA TAA CCA CCC CTG ACC IL-6 R: CCA TGC TAC ATT TGC CGA AGAG FAM-ACC ACA AAT GCC AGC CTG CTG ACG -TAMRA 77 F: CGG AAG GAA CCA TCT CAC TGTG IL-8 R: AGA AAT CAG GAA GGC TGC CAAG FAM-TGA CTT CCA AGC TGG CCG TGG CTC -TAMRA 176 F: CAG CAA GAG ATC CTG GTC CTG IL-17 R: GGT CGG CTC TCC ATA GTC TAAC FAM-AGC CTC CAC ACT GCC CCA ACT CCT -TAMRA 96 F: GGC AAG GCT ATG TGA TTA CAAGG IFN-G R: CAT CAA GTG AAA TAA ACA CAC AAC CC FAM-AGG GGC CAA CTA GGC AGC CAA CCT -TAMRA 101 F: GCT CCA CGG AGA AGA ACT GC TGF-B R: GTT GGC ATG GTA GCC CTT GG FAM-CCA CTT CCA GCC GAG GTC CTT GCG -TAMRA 97 F: TCC ACC CAT GTG CTC CTC AC TNF-A R: TCT GGC AGG GGC TCT TGA TG FAM-CTA CCG AGT CCG TGT CTA CCA -TAMRA
depicts the relative expression levels of cytokine coding genes in COVID-19 patients and healthy subjects using box plot
Heatmap showing the correlation between expression amounts of cytokine coding genes and clinical/ demographic information among COVID-19 patients (red and blue colors indicate positive and negative correlations, respectively with dark colors showing stronger correlations)
ROC curves depicted by three machine learning models showing the power of cytokine coding genes in in distinguishing between COVID-19 patients and healthy controls (A) and between ICU-admitted patients and other patients (B) Fig. 4 ROC curves depicted by the linear discriminant analysis (LDA), showing the power of cytokine coding genes in in distinguishing between COVID-19 patients and healthy controls (A) and between ICU-admitted patients and other patients (B)
Correlation
Paraclinical parameters of the COVID-19 group Details of expression results of cytokine transcripts in study groups
Parameters obtained from ROC curve analysis for assessment of the diagnostic power of cytokine coding genes in COVID-19 AUC Sensitivity Specificity AUC Sensitivity Specificity AUC Sensitivity Specificity AUC Sensitivity Specificity AUC AUC Sensitivity Specificity AUC Sensitivity Specificity AUC Sensitivity Specificity AUC Sensitivity Specificity AUC"
sparser
"Sequences were identical to the 2019-nCoV_N1 CDC assay for SARS-CoV-2 detection (2019-nCoV_N1 Forward Primer GAC CCC AAA ATC AGC GAA AT None 500nM; 2019-nCoV_N1 Reverse Primer TCT GGT TAC TGC CAG TTG AAT CTG None 500nM; 2019-nCoV_N1 Probe FAM-ACC CCG CAT TAC GTT TGG TGG ACC-BHQ1)."
sparser
"CDC Primers, which were synthesized at Eurofins Scientific SE (Luxenburg), were used in a concentration of 0.4 µM and the Probe of 0.2 µM. The qPCR primers were as follows: N1 forward GAC CCC AAA ATC AGC GAA AT, N1 reverse TCT GGT TAC TGC CAG TTG AAT CTG, and N1 Probe FAM-ACC CCG CAT TAC GTT TGG TGG ACC-BHQ1."
sparser
"The fluorescence micrographs of FFPE tissues of human liver fibrosis,
liver cancer, rectal cancer, and esophageal cancer stained with FAM-GFO
and DAPI demonstrated that FAM-GFO could highly sensitively and selectively
target denatured collagen in different types of pathological connective
tissues ( xref )."
sparser
"Spine heads, which include ankyrin-G, Usp9X, and PLA nanodomains concurrently, showed the same phenotype whether TGF-β treated or not, suggesting that TGF-β treatment increases the number of ankyrin-G-containing spines and spine head size through upregulation of the interaction between Usp9X and ankyrin-G."
sparser
"Using structured illumination microscopy (SIM), we found that ankyrin-G and Usp9X localize to distinct nanostructures within spines, the number of which correlates to mushroom spine head size, while proximity ligation assay (PLA)/SIM confirmed that TGF-β increases ankyrin-G’s interaction with Usp9X. These data reveal that TGF-β can enhance stabilization of ankyrin-G in spines through the increase of Usp9X binding ability toward its target substrate."
sparser
"To investigate the role of phosphorylation in regulating the Usp9X and ankyrin-G interaction, we predicted possible models based on the crystal structure of Usp9X. Structural reports have identified the inner groove of the ANKRD as a promiscuous protein-protein interaction site ( xref )."
sparser
"Our results indicate that induced Usp9X phosphorylation within the peptidase domain strengthens its interaction with ankyrin-G. Upregulation of this Usp9X-ankyrin-G interaction appears to facilitate the deubiquitination of ankyrin-G, inhibiting proteasomal degradation and stabilizing ankyrin-G levels within synapses."
reach
"Using in situ proximity ligation combined with structured illumination superresolution microscopy, we characterize the postsynaptic spatial organization of phosphorylation dependent regulation of Usp9X and ankyrin-G interactions in dendrites and its quantitative relationship with spine morphology and number."
sparser
"Sample size calculation was carried out with the software PASS 2015, using two independent proportions and is based on the assumed increase in the proportion of non-conspicuous parent among the initially conspicuous parents according to SCID-I criteria between the patients treated with CARE-FAM and patients that did not receive CARE-FAM at18 months after randomization."
sparser
"Given a power of 80% and a type I error rate of 5% (two-sided hypothesis), 74 initially conspicuous parents per treatment combination group (296 in total) are needed to detect a difference of 11.2% (91.2% of the CARE-FAM patients and 80% of the non-CARE-FAM patients) in the proportion of non-conspicuous parents between both groups."
sparser
"Here, we present the ZBTB38 interactome and report that ZBTB38 interacts with the deubiquitinase USP9X; that this interaction controls the stability of ZBTB38; that both proteins are coordinately stabilized by oxidative stress; that together they control the basal level of ROS in cells; and that together they are necessary for cells to mount a proper response to oxidative stress."
USP9X affects Cell Survival
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USP9X activates Cell Survival.
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USP9X activates Cell Survival. 10 / 21
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eidos
"USP9X Modulates Cell Survival in Response to High-LET IR Following siRNA screening , we aimed to validate that depletion of USP9X caused a decrease in cell survival following high-LET radiation , but had no impact in response to low-LET protons , in both HeLa cells and also cells derived from head and neck squamous cell carcinoma ."
reach
"USP9X is involved in fundamental processes such as pre-implantation development and is considered to particularly enhance cell survival by stabilizing different pro survival substrates such as beta-catenin and the pro survival BCL2 family member MCL1 (Taya etal, 1999; Murray etal, 2004; Sacco etal, 2010; Schwickart etal, 2010; Vucic etal, 2011)."
USP9X inhibits Cell Survival.
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3
sparser
"A fluorescent aptasensor coupled with conformational switch-induced hybridization was established to detect AβO. The fluorescent aptasensor is based on the interaction of fluorophore-labeled AβO-specific aptamer (FAM-Apt) against its partly complementary DNA sequence on the surface of magnetic beads (cDNA-MBs)."
sparser
"Arachidonic acid, aspirin, BWA4C, dimethylammonio]-1-propanesulfonate hydrate, CJ-13,610, creatine phosphate, DAPI (4′,6-Diamidine-2-phenylindole), dexamethasone, FAF-BSA (fatty acid-free bovine serum albumin), IL-1β, indomethacin, LPS (bacterial lipopolysaccharide), Mowiol 4-88, NDGA (nordihydroguaiaretic acid), PFA (paraformaldehyde), rofecoxib, SC-560 and Tween 20 were purchased from Sigma-Aldrich (Munich, Germany)."
sparser
"Palmitic acid (≥99% pure), bovine serum albumin-fatty acid-free (FAF-BSA), Dulbecco's
modified Eagle's medium (DMEM; Sigma Aldrich); fetal bovine serum (FBS; ByProductos);
Lipofectamine 2000 (Life Technologies); full-length human SERCA2b cDNA clone (ID
5503508) in pCMV-SPORT6 vector (Invitrogen); full-length human RGS2 3xHA-tagged cDNA
(CloneID RGS020TN00) in the pcDNA3.1+ vector (cDNA Resource Center); anti-SERCA2 (Thermo
Scientific), anti-RGS2, anti-Actin and mitomycin C (Santa Cruz Biotechnology)."
sparser
"Basal media BE1: MCDB131 (Invitrogen) with 0.8 g/l glucose (Sigma), 1.174 g/l sodium bicarbonate (Sigma), 0.5% fatty acid free BSA (Proliant), 2 mM l-Glutamine; BE3: MCDB131 with 3.32 g/l glucose, 1.754 g/l sodium bicarbonate, 2% FAF-BSA, 2 mM l-Glutamine, 44 mg/l l-Ascorbic acid, 0.5% ITS-X.
For differentiation, culture plates were coated with growth factor reduced Matrigel (BD, 354230) and 300,000 hESCs per 24-well were seeded in mTESR1 containing 10 µM ROCK inhibitor."
sparser
"To determine the unesterified cholesterol content, the lipids in isopropanol were mixed with 10 times volumes of cholesterol assay buffer (CAB): 0.1% FAF-BSA, 2 mM sodium taurocholate, 50 mM Tris-HCl, pH 7.5, 0.3 mM Na2EDTA, 5% isopropanol, and 250 mM sucrose, with freshly added 0.5 U/mL horseradish peroxidase (HRP) and 0.02 U/mL cholesterol oxidase in the presence of 30–50 µM scopoletin [107] (excitation 360, emission 460)."
USP9X affects NCIT:C95408
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USP9X binds NCIT:C95408. 10 / 19
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sparser
"All rights reserved.) U VEITIS CAN BE OF INFECTIOUS OR NONINFECTIOUS
A(G/C)G G(G/C)G T(A/G)C GCA GGT A AGA A(G/C)G GTG T(A/G)C GCA GAT A Probe FAM-ACC ACG TCG AAA ACT TCG AA-MGBNFQ FAM-ACC ACG TCG AAA ACT TCA AA-MGBNFQ FAM-ACA CCG CGG CGT CA-MGBNFQ Coronavirus 229E Forward CAG TCA AAT GGG CTG ATG CA Reverse CAA AGG GCT ATA AAG AGA ATA AGG TAT TCT ND 53 Probe FAM-CCC TGA CGA CCA CGT TGT GGT TCA -TAMRA Coronavirus NL63 Forward AAG GGT TTT CCA CAG CTT GCT AAA GGT TTT CCA CAG CTT GCT ND 53 Reverse ATC ACC CAC TTC ATC AGT GCT AAC Probe FAM-TCA CTA TCA AAG AAT AAC GCA GCC TGA TTA GGA A -TAMRA Coronavirus OC43 Forward CGA TGA GGC TAT TCC GAC TAG GT Reverse CCT TCC TGA GCC TTC AAT ATA GTA ACC ND 53 Probe FAM-TCC GCC TGG CAC GGT ACT CCC T -TAMRA Enteroviruses Forward TCC TCC GGC CCC TGA Reverse AAT TGT CAC CAT AAG CAG CCA GAT TGT CAC CAT AAG CAG CCA ND 50 Probe FAM-CGG AAC CGA CTA CTT TGG GTG ACC GT -TAMRA FAM-CGG AAC CGA CTA CTT TGG GTG TCC GT -TAMRA Epstein-Barr virus Forward GGA ACC TGG TCA TCC TTT GC Reverse ACG TGC ATG GAC CGG TTA AT 50 copies/mL 42 Probe FAM-CGC AGG CAC TCG TAC TGC TCG CT -TAMRA Human herpesvirus 6 Forward GAA GCA GCA ATC GCA 160 copies/mL 42 Reverse ACA CA ATG TAA CTC Probe GGT GTA CGG TGT CTA FAM-AAC CCG TGC GCC GCT -TAMRA Human metapneumovirus Forward CAT ATA AGC ATG CTA TAT TAA AAG AGT CTC ND 49 Reverse CCT ATT TCT GCA GCA TAT TTG TAA TCA G Probe FAM-TG(C/T) AAT GAT GAG GGT GTC ACT GCG GTT G -TAMRA Influenza virus A Forward AAG ACC AAT CCT GTC ACC TCT GA Reverse CAA AGC GTC TAC GCT GCA GTC C ND 52 Probe FAM-TTT GTG TTC ACG CTC ACC GTG CC -TAMRA Influenza virus B Forward AAA TAC GGT GGA TTA AAC AAA AGC AA Reverse CCA GCA ATA GCT CCG AAG AAA ND 52 Probe FAM-CAC CCA TAT TGG GCA ATT TCC TAT GGC -TAMRA Parainfluenza virus 1 Forward TGA TTT AAA CCC GGT AAT TTC TCA T Reverse CCT TGT TCC TGC AGC TAT TAC AGA ND 51 Probe FAM-ACG ACA ACA GGA AAT C -TAMRA Parainfluenza virus 2 Forward AGG ACT ATG AAA ACC ATT TAC CTA AGT GA Reverse AAG CAA GTC TCA GTT CAG CTA GAT CA ND 51 Probe FAM-ATC AAT CGC AAA AGC TGT TCA GTC ACT GCT ATA C -TAMRA Parainfluenza virus 3 Forward TGA TGA AAG ATC AGA TTA TGC AT Reverse CCG GGA CAC CCA GTT GTG ND 51 Probe FAM-TGG ACC AGG GAT ATA CTA CAA AGG CAA AAT AAT ATT TCT C -TAMRA Continued on next page
FAM-GTA TCA TCA TCT GCC AAA TCG GCA ATT AAA CA -TAMRA Human parechovirus Forward TGC AAA CAC TAG TGG TA(A/T) GGC CC Reverse 1 TCA GAT CCA TAG TG(C/T) CAC TTG TTA CCT Reverse 2 TCA GAT CCA CAG TGT CTC TTG TTA CCT 1 TCID50/mL Forthcoming Probe FAM-CGA AGG ATG CCC AGA AGG TAC CCG -TAMRA Respiratory syncytial virus A Forward AGA TCA ACT TCT GTC ATC CAG CAA Reverse TTC TGA ACA TCA TAA TTA GGA GTA TCA AT ND 54 Probe FAM-CAC CAT CCA ACG GAG CAC AGG AGA T -TAMRA Respiratory syncytial virus B Forward AAG ATG CAA ATC ATA AAT TCA CAG GA Reverse TGA TAT CCA GCA TCT TTA AGT ATC TTT ATA GTG ND 54 Probe FAM-TCC CCT TCC TAA CCT GGA CAT AGC ATA TAA CAT ACC T -TAMRA Rubella virus Forward CAC GCC GCA CGG ACA Reverse 1 CAC CGG GAC TG(C/T) TG(A/G) TTG C 1.7 PFU/mL Forthcoming Reverse 2 CAC CGG GAC TGT TGG TTG C Probe FAM-AGG TCC CGC CCG AC-MGBNFQ Mycoplasma pneumoniae Forward GGT CAA TCT GGC GTG CAT CT Reverse TGG TAA CTG CCC CAC AAG C 50 CCU/mL 34 Probe FAM-TCC CCC GTT GAA AAA GTG AGT GGG T -TAMRA Chlamydia pneumoniae Forward TCC GCA TTG CTC AGC C Reverse AAA CAA TTT GCA TGA AGT CTG AGA A 4.9 IFU/mL 34 Probe FAM-TAA ACT TAA CTG CAT GGA ACC CTT CTT TAC TAG G -TAMRA CCU ϭ color-changing units; FAM ϭ 6-carboxyfluorescein fluorescent label; IFU ϭ inclusion-forming units; MGBNFQ ϭ minor groove binding nonfluorescent quencher; ND ϭ not determined; PFU ϭ plaque-forming units; TAMRA ϭ tetramethylrhodamine quencher; TCID50 ϭ tissue culture infectious dose 50."
sparser
"10006606 SARS-CoV-2 N2 F: 5'-TTA CAA ACA TTG GCC GCA AA-3' R: 5'-GCG CGA CAT TCC GAA GAA-3' P: 5'-FAM-ACA ATT TGC CCC CAG CGC TTC AG-BHQ1-3' Pdouble: FAM-ACA ATT TGC /ZEN/ CCC CAG CGC TTC AG
Recovery-corrected SARS-CoV-2 concentrations (N1 and N2 targets) at Plant 1 measured by each SOP."
| DOI
sparser
"The diagnosis of COVID-19 was made by monitoring the signs and symptoms of the participants to finally confirm the infection status by RT-PCR (SuperScript III Platinum, Invitrogen, EEUU; Integrated DNA Technologies, Coralville, EEUU) and the kit 2019-nCoV ValuPanel Reagents (2019-nCoV_N1 Probe: FAM-ACC CCG CAT TAC GTT TGG TGG ACC-BHQ1, 2019-nCoV_N1 Forward Primer: GAC CCC AAA ATC AGC GAA AT, 2019-nCoV_N1 Reverse Primer: TCT GGT TAC TGC CAG TTG AAT CTG; 2019-nCoV_N2 Probe: FAM-ACA ATT TGC CCC CAG CGC TTC AG-BHQ1, 2019-nCoV_N2 Forward Primer: TTA CAA ACA TTG GCC GCA AA, 2019-nCoV_N2 Reverse Primer: GCG CGA CAT TCC GAA GAA; 2019-nCoV_N3 Probe: FAM-AYC ACA TTG GCA CCC GCA ATC CTG-BHQ1, 2019-nCoV_N3 Forward Primer: GGG AGC CTT GAA TAC ACC AAA A, 2019-nCoV_N3 Reverse Primer: TGT AGC ACG ATT GCA GCA TTG)
70 nasal rinse made by 64 participants; weekly number of contacts with patients diagnosed with COVID-19 or atypical pneumonia during the study period: (0-860, 169 on average) in the experimental group and (0 to 729, 146 on average) in the control group; percentage of individuals who presented symptoms of respiratory tract infection (RTI's) at some point during the study; 18.4% in the experimental group and 35.8% in the control group; no adverse reactions were reported by performing mouthwash and nose rinse with AgNPs."
sparser
"The diagnosis of COVID-19 was made by monitoring the signs and symptoms of the participants to finally confirm the infection status by RT-PCR (SuperScript III Platinum, Invitrogen, EEUU; Integrated DNA Technologies, Coralville, EEUU) and the kit 2019-nCoV ValuPanel Reagents (2019-nCoV_N1 Probe: FAM-ACC CCG CAT TAC GTT TGG TGG ACC-BHQ1, 2019-nCoV_N1 Forward Primer: GAC CCC AAA ATC AGC GAA AT, 2019-nCoV_N1 Reverse Primer: TCT GGT TAC TGC CAG TTG AAT CTG; 2019-nCoV_N2 Probe: FAM-ACA ATT TGC CCC CAG CGC TTC AG-BHQ1, 2019-nCoV_N2 Forward Primer: TTA CAA ACA TTG GCC GCA AA, 2019-nCoV_N2 Reverse Primer: GCG CGA CAT TCC GAA GAA; 2019-nCoV_N3 Probe: FAM-AYC ACA TTG GCA CCC GCA ATC CTG-BHQ1, 2019-nCoV_N3 Forward Primer: GGG AGC CTT GAA TAC ACC AAA A, 2019-nCoV_N3 Reverse Primer: TGT AGC ACG ATT GCA GCA TTG)."
USP9X affects ASPS
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19
sparser
"Considering that average B12 and folate concentrations of ASPS, ASPS-Fam and PRODEM participants were well within the respective reference ranges, it can be concluded that differences of these vitamins within the respective reference ranges are unlikely to modify the risk of dementia and brain volume loss."
sparser
"The ASPS-Fam is funded by the Austrian Science Fund (FWF) project I904),the EU Joint Programme -Neurodegenerative Disease Research (JPND) in frame of the BRIDGET project (Austria, Ministry of Science) and the Medical University of Graz and the Steiermrkische Krankenanstalten Gesellschaft."
| DOI
sparser
"Despite the fact that none of the study participants of ASPS, ASPS-Fam and PRODEM used vitamin supplements, the majority of participants were well within the respective reference range of folate, B12, active B12 and MMA suggesting an adequate B-vitamin status in the Austrian population."
NCIT:C95408 affects USP9X
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19
USP9X binds NCIT:C95408. 10 / 19
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19
sparser
"All rights reserved.) U VEITIS CAN BE OF INFECTIOUS OR NONINFECTIOUS
A(G/C)G G(G/C)G T(A/G)C GCA GGT A AGA A(G/C)G GTG T(A/G)C GCA GAT A Probe FAM-ACC ACG TCG AAA ACT TCG AA-MGBNFQ FAM-ACC ACG TCG AAA ACT TCA AA-MGBNFQ FAM-ACA CCG CGG CGT CA-MGBNFQ Coronavirus 229E Forward CAG TCA AAT GGG CTG ATG CA Reverse CAA AGG GCT ATA AAG AGA ATA AGG TAT TCT ND 53 Probe FAM-CCC TGA CGA CCA CGT TGT GGT TCA -TAMRA Coronavirus NL63 Forward AAG GGT TTT CCA CAG CTT GCT AAA GGT TTT CCA CAG CTT GCT ND 53 Reverse ATC ACC CAC TTC ATC AGT GCT AAC Probe FAM-TCA CTA TCA AAG AAT AAC GCA GCC TGA TTA GGA A -TAMRA Coronavirus OC43 Forward CGA TGA GGC TAT TCC GAC TAG GT Reverse CCT TCC TGA GCC TTC AAT ATA GTA ACC ND 53 Probe FAM-TCC GCC TGG CAC GGT ACT CCC T -TAMRA Enteroviruses Forward TCC TCC GGC CCC TGA Reverse AAT TGT CAC CAT AAG CAG CCA GAT TGT CAC CAT AAG CAG CCA ND 50 Probe FAM-CGG AAC CGA CTA CTT TGG GTG ACC GT -TAMRA FAM-CGG AAC CGA CTA CTT TGG GTG TCC GT -TAMRA Epstein-Barr virus Forward GGA ACC TGG TCA TCC TTT GC Reverse ACG TGC ATG GAC CGG TTA AT 50 copies/mL 42 Probe FAM-CGC AGG CAC TCG TAC TGC TCG CT -TAMRA Human herpesvirus 6 Forward GAA GCA GCA ATC GCA 160 copies/mL 42 Reverse ACA CA ATG TAA CTC Probe GGT GTA CGG TGT CTA FAM-AAC CCG TGC GCC GCT -TAMRA Human metapneumovirus Forward CAT ATA AGC ATG CTA TAT TAA AAG AGT CTC ND 49 Reverse CCT ATT TCT GCA GCA TAT TTG TAA TCA G Probe FAM-TG(C/T) AAT GAT GAG GGT GTC ACT GCG GTT G -TAMRA Influenza virus A Forward AAG ACC AAT CCT GTC ACC TCT GA Reverse CAA AGC GTC TAC GCT GCA GTC C ND 52 Probe FAM-TTT GTG TTC ACG CTC ACC GTG CC -TAMRA Influenza virus B Forward AAA TAC GGT GGA TTA AAC AAA AGC AA Reverse CCA GCA ATA GCT CCG AAG AAA ND 52 Probe FAM-CAC CCA TAT TGG GCA ATT TCC TAT GGC -TAMRA Parainfluenza virus 1 Forward TGA TTT AAA CCC GGT AAT TTC TCA T Reverse CCT TGT TCC TGC AGC TAT TAC AGA ND 51 Probe FAM-ACG ACA ACA GGA AAT C -TAMRA Parainfluenza virus 2 Forward AGG ACT ATG AAA ACC ATT TAC CTA AGT GA Reverse AAG CAA GTC TCA GTT CAG CTA GAT CA ND 51 Probe FAM-ATC AAT CGC AAA AGC TGT TCA GTC ACT GCT ATA C -TAMRA Parainfluenza virus 3 Forward TGA TGA AAG ATC AGA TTA TGC AT Reverse CCG GGA CAC CCA GTT GTG ND 51 Probe FAM-TGG ACC AGG GAT ATA CTA CAA AGG CAA AAT AAT ATT TCT C -TAMRA Continued on next page
FAM-GTA TCA TCA TCT GCC AAA TCG GCA ATT AAA CA -TAMRA Human parechovirus Forward TGC AAA CAC TAG TGG TA(A/T) GGC CC Reverse 1 TCA GAT CCA TAG TG(C/T) CAC TTG TTA CCT Reverse 2 TCA GAT CCA CAG TGT CTC TTG TTA CCT 1 TCID50/mL Forthcoming Probe FAM-CGA AGG ATG CCC AGA AGG TAC CCG -TAMRA Respiratory syncytial virus A Forward AGA TCA ACT TCT GTC ATC CAG CAA Reverse TTC TGA ACA TCA TAA TTA GGA GTA TCA AT ND 54 Probe FAM-CAC CAT CCA ACG GAG CAC AGG AGA T -TAMRA Respiratory syncytial virus B Forward AAG ATG CAA ATC ATA AAT TCA CAG GA Reverse TGA TAT CCA GCA TCT TTA AGT ATC TTT ATA GTG ND 54 Probe FAM-TCC CCT TCC TAA CCT GGA CAT AGC ATA TAA CAT ACC T -TAMRA Rubella virus Forward CAC GCC GCA CGG ACA Reverse 1 CAC CGG GAC TG(C/T) TG(A/G) TTG C 1.7 PFU/mL Forthcoming Reverse 2 CAC CGG GAC TGT TGG TTG C Probe FAM-AGG TCC CGC CCG AC-MGBNFQ Mycoplasma pneumoniae Forward GGT CAA TCT GGC GTG CAT CT Reverse TGG TAA CTG CCC CAC AAG C 50 CCU/mL 34 Probe FAM-TCC CCC GTT GAA AAA GTG AGT GGG T -TAMRA Chlamydia pneumoniae Forward TCC GCA TTG CTC AGC C Reverse AAA CAA TTT GCA TGA AGT CTG AGA A 4.9 IFU/mL 34 Probe FAM-TAA ACT TAA CTG CAT GGA ACC CTT CTT TAC TAG G -TAMRA CCU ϭ color-changing units; FAM ϭ 6-carboxyfluorescein fluorescent label; IFU ϭ inclusion-forming units; MGBNFQ ϭ minor groove binding nonfluorescent quencher; ND ϭ not determined; PFU ϭ plaque-forming units; TAMRA ϭ tetramethylrhodamine quencher; TCID50 ϭ tissue culture infectious dose 50."
sparser
"10006606 SARS-CoV-2 N2 F: 5'-TTA CAA ACA TTG GCC GCA AA-3' R: 5'-GCG CGA CAT TCC GAA GAA-3' P: 5'-FAM-ACA ATT TGC CCC CAG CGC TTC AG-BHQ1-3' Pdouble: FAM-ACA ATT TGC /ZEN/ CCC CAG CGC TTC AG
Recovery-corrected SARS-CoV-2 concentrations (N1 and N2 targets) at Plant 1 measured by each SOP."
| DOI
sparser
"The diagnosis of COVID-19 was made by monitoring the signs and symptoms of the participants to finally confirm the infection status by RT-PCR (SuperScript III Platinum, Invitrogen, EEUU; Integrated DNA Technologies, Coralville, EEUU) and the kit 2019-nCoV ValuPanel Reagents (2019-nCoV_N1 Probe: FAM-ACC CCG CAT TAC GTT TGG TGG ACC-BHQ1, 2019-nCoV_N1 Forward Primer: GAC CCC AAA ATC AGC GAA AT, 2019-nCoV_N1 Reverse Primer: TCT GGT TAC TGC CAG TTG AAT CTG; 2019-nCoV_N2 Probe: FAM-ACA ATT TGC CCC CAG CGC TTC AG-BHQ1, 2019-nCoV_N2 Forward Primer: TTA CAA ACA TTG GCC GCA AA, 2019-nCoV_N2 Reverse Primer: GCG CGA CAT TCC GAA GAA; 2019-nCoV_N3 Probe: FAM-AYC ACA TTG GCA CCC GCA ATC CTG-BHQ1, 2019-nCoV_N3 Forward Primer: GGG AGC CTT GAA TAC ACC AAA A, 2019-nCoV_N3 Reverse Primer: TGT AGC ACG ATT GCA GCA TTG)
70 nasal rinse made by 64 participants; weekly number of contacts with patients diagnosed with COVID-19 or atypical pneumonia during the study period: (0-860, 169 on average) in the experimental group and (0 to 729, 146 on average) in the control group; percentage of individuals who presented symptoms of respiratory tract infection (RTI's) at some point during the study; 18.4% in the experimental group and 35.8% in the control group; no adverse reactions were reported by performing mouthwash and nose rinse with AgNPs."
sparser
"The diagnosis of COVID-19 was made by monitoring the signs and symptoms of the participants to finally confirm the infection status by RT-PCR (SuperScript III Platinum, Invitrogen, EEUU; Integrated DNA Technologies, Coralville, EEUU) and the kit 2019-nCoV ValuPanel Reagents (2019-nCoV_N1 Probe: FAM-ACC CCG CAT TAC GTT TGG TGG ACC-BHQ1, 2019-nCoV_N1 Forward Primer: GAC CCC AAA ATC AGC GAA AT, 2019-nCoV_N1 Reverse Primer: TCT GGT TAC TGC CAG TTG AAT CTG; 2019-nCoV_N2 Probe: FAM-ACA ATT TGC CCC CAG CGC TTC AG-BHQ1, 2019-nCoV_N2 Forward Primer: TTA CAA ACA TTG GCC GCA AA, 2019-nCoV_N2 Reverse Primer: GCG CGA CAT TCC GAA GAA; 2019-nCoV_N3 Probe: FAM-AYC ACA TTG GCA CCC GCA ATC CTG-BHQ1, 2019-nCoV_N3 Forward Primer: GGG AGC CTT GAA TAC ACC AAA A, 2019-nCoV_N3 Reverse Primer: TGT AGC ACG ATT GCA GCA TTG)."
reach
"Although we currently do not know the mechanism by which AGS3 modulates the structure or function of the late Golgi compartments, the observations that USP9x interacts with AGS3 and regulates the level of AGS3 are consistent with a role of ubiquitination and deubiquitination of AGS3 in this process."
sparser
"Immunofluorescent microscopy analysis revealed that in G 1 /S/G 2 phases of the cell cycle USP9X is distributed not only in the cytoplasm but also in the centrosome, where it is physically and functionally associated with CEP131, indicating that USP9X is an integral component of the centrosome."
sparser
"To confirm the association of USP9X with CEP131, co-immunoprecipitation experiments were performed with HeLa cell extracts and the results showed that USP9X was efficiently co-immunoprecipitated with CEP131, but not with another centrosomal protein CP110 (ref. xref ), although USP33, another DUB protein, could be effectively co-immunoprecipitated with CP110 (ref. xref ; xref )."
ASPS affects USP9X
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19
sparser
"Considering that average B12 and folate concentrations of ASPS, ASPS-Fam and PRODEM participants were well within the respective reference ranges, it can be concluded that differences of these vitamins within the respective reference ranges are unlikely to modify the risk of dementia and brain volume loss."
sparser
"The ASPS-Fam is funded by the Austrian Science Fund (FWF) project I904),the EU Joint Programme -Neurodegenerative Disease Research (JPND) in frame of the BRIDGET project (Austria, Ministry of Science) and the Medical University of Graz and the Steiermrkische Krankenanstalten Gesellschaft."
| DOI
sparser
"Despite the fact that none of the study participants of ASPS, ASPS-Fam and PRODEM used vitamin supplements, the majority of participants were well within the respective reference range of folate, B12, active B12 and MMA suggesting an adequate B-vitamin status in the Austrian population."
sparser
"A substrate concentration of 25 μM for BV, BV-PEG-FAM , and BV-(PEG-FAM)2 was chosen because BV and BV dimethyl ester saturated smURFP-tag at 25 μM. The labeling time was 4 hours because fluorescence rise fit a first-order, exponential rate equation, and BV saturation is expected after ≤1.3 hours. xref Four hours ensures ample time to saturate the smURFP-tag with the substrates."
USP9X affects cell death
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1
14
USP9X inhibits cell death.
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1
8
USP9X inhibits cell death. 9 / 9
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1
8
reach
"Moreover, USP9x silencing resulted in significantly increased cell death in BaF3 and p210 cells (XREF_SUPPLEMENTARY), suggesting that the ITC induced inhibition of USP9x can, at least partially, account for the reduced viability and increased cell death observed upon ITC treatment."
reach
"However, taking this speculation aside, at the minimum, increased Noxa levels will facilitate release of BAK and BIM from Mcl-1, thereby driving BAX/BAK mediated intrinsic apoptosis.In seeking to identify others forms of cell death produced by Usp9X inhibition in MPNST cells, TEM analysis showed morphological features of paraptosis with extensive cytoplasmic vacuolization, swelling of ER and mitochondria and only minimal features of apoptosis ."
USP9X activates cell death.
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6
sparser
"Given that NPHP5 is ubiquitinated in cells and that a relatively large number of unique peptides corresponding to USP9X were identified in our proteomic screen ( xref ), we focused on verifying the interaction between NPHP5 and USP9X. We expressed Flag-NPHP5 in HEK293 cells, performed anti-Flag immunoprecipitations, and showed that recombinant NPHP5 and endogenous USP9X are co-precipitated ( xref )."
sparser
"The imaging experiments were also performed on the APP 3′UTR rG4mut region, and we found that green fluorescence was detected ( xref ), showing the successful transfection of corresponding RNA and hybridization of FAM-APP probes in cells, however, very low red fluorescence was detected ( xref ), suggesting no rG4 formation in the APP 3′UTR rG4mut region."
sparser
"On the other hand inhibition of ERK and USP9x with pharmaceutical or genetic approach in breast cancer cells abolishes FFA promotion of TGF-β–induced SMAD4-USP9x interaction, SMAD4 nuclear retention, SMAD3/SMAD4 complex formation, and target gene expression, resulting in decrease in cancer cell invasion and metastasis ( xref )."
sparser
"We also found that FFA/ERK-induced SMAD4 T277 phosphorylation is indispensable in SMAD4-USP9x interaction and its deubiquitination as well as subsequent nuclear accumulation, which is required for TGF-β–induced breast cancer invasion and metastasis under the high FFA/obesity conditions."
reach
"For example : the DUB BRCC36 together with the RING E3 ligase BRCA1 regulates the DNA damage response; the RBR E3 ligase Parkin and the DUB USP30 contribute to mitophagy; the DUB Ubp2 can impede yeast growth by antagonizing the function of the HECT E3 Rsp5; the DUB FAM and USP9x interacts with and stabilizes SMURF1 and this impacts on cell motility."
| PMC
sparser
"The putative Prickle-Usp9x interaction was of particular interest because Usp9x physically interacts with Smurf1 (to date, one of the few Prickle interactors identified in neural tissues[ xref ] and both are implicated in neurite extension).[ xref ] Moreover, since ubiquitination plays a role in cancer pathogenesis, a variety of reagents that modulate this system are already commercially available and in clinical trials.[ xref ] The combination of previously identified Prickle-interacting partners with the present studies are depicted in the Prickle-interactome ( xref ) that we utilize to identify new seizure-modifying targets."
sparser
"Here, we present the ZBTB38 interactome and report that ZBTB38 interacts with the deubiquitinase USP9X; that this interaction controls the stability of ZBTB38; that both proteins are coordinately stabilized by oxidative stress; that together they control the basal level of ROS in cells; and that together they are necessary for cells to mount a proper response to oxidative stress."
USP9X affects Neoplasm Invasiveness
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1
12
2
USP9X activates Neoplasm Invasiveness.
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1
8
USP9X inhibits Neoplasm Invasiveness.
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4
2
USP9X inhibits Neoplasm Invasiveness. 6 / 6
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4
2
reach
"The depletion and pharmacological inhibition of USP9X by WP1130, an inhibitor of USP9X, downregulate endogenous Snail1 protein, inhibit cell migration, invasion, metastasis, and increase cellular sensitivity to cisplatin and paclitaxel both in vitro and in vivo, whereas the reconstitution of Snail1 in cells with USP9X depletion at least partially reverses these phenotypes."
sparser
"This internally controlled quantitative real-time PCR assay targets the hexon gene of adenovirus, and is validated for detection Table 1 Nucleotide sequences of primers and probes used in this study
Sequence (5′ to 3′) Reference
CCA GGA CGC CTC GGA GTA [18] AdV2R AAA CTT GTT ATT CAG GCT GAA GTA CGT [18] AdV2pr FAM-AGT TTG CCC GCG CCA CCA CCG -BHQ1 * [18] AdV4F GGA CAG GAC GCT TCG GAG TA [18] AdV4R CTT GTT CCC CAG ACT GAA GTA GGT [18] AdV4pr FAM-CAG TTC GCC CGY GCM ACA G -BHQ1 * [ of types 1 to 52 [7] ."
sparser
"Together, these findings indicate that (1) WW domain scaffolding partially contributes to the interaction between WWP1 and USP9X, (2) WW domain interactions are required for WWP1 engagement with DVL2, and (3) the WW domains of WWP1 function redundantly for interaction with both DVL2 and USP9X."
sparser
"For example, the WNT signal transducing protein disheveled (DVL2) is subject to complex regulation by multiple E3 ubiquitin ligases and DUBs [ xref , xref – xref ], and it was recently reported that an interaction between USP9X and WWP1 regulates DVL2 participation in canonical WNT and non-canonical WNT signaling pathways [ xref ]."
reach
"Moreover, USP9X can increase MAPT phosphorylation via a second mechanism, by deubiquitinating the protein alpha-synuclein (SNCA) [XREF_BIBR], which functions as a connecting mediator between the glycogen synthase kinase 3beta (GSK3B) and MAPT and has been shown to stimulate MAPT phosphorylation via GSK3B in vitro [XREF_BIBR]."
reach
"In the brain tissues of PD patients, USP9X colocalises with alpha-synuclein inclusions, and in vitro studies show a functional interaction; whilst monoubiquitylated alpha-synuclein is degraded by the proteasome, USP9X deubiquitylation of alpha-synuclein directs its degradation by the less efficient autophagy pathway [XREF_BIBR]."
"Deubiquitination of α-synuclein by USP9X impairs SIAH-dependent α-synuclein proteasomal degradation and promotes degradation by autophagy"
"We recently found that USP9X deubiquitinates α-synuclein, and that this process determines the partition of α-synuclein between the proteasomal and autophagy pathways."
reach
"Although these findings point toward low pH of acidic organelles not being necessary in Rapa release from FAF/Rapa, such conclusions can be made only after confirming lysosomal basification under the treatment conditions employed.Another possible mechanism that hasn’t been explored is a release-independent pathway wherein FAF/Rapa directly binds to mTOR and inhibits its kinase activity."
sparser
"Binding of galectin-7 to protein FAF was examined in a slot binding assay together with proteins PAB and SufA, other potential virulence factors in F. magna , see Fig. xref A. This blot shows a concentration dependent binding of galectin-7 to FAF, but no interaction with SufA and protein PAB."
sparser
"In order to map the binding of galectin-7 to a particular region of protein FAF, various recombinantly expressed FAF fragments were applied onto a PVDF membrane and probed with galectin-7, see Fig. xref B. The fragments, which were constructed in another study, correspond to the N-terminal FAF I (amino acids 28–115, 10 kDa) and FAF II (amino acids 28–317, 32 kDa) and the C-terminal FAF III (amino acids 239–616, 42 kDa) ( xref )."
sparser
"Binding of galectin-7 to protein FAF was examined in a slot binding assay together with proteins PAB and SufA, other potential virulence factors in F. magna , see Fig. xref A. This blot shows a concentration dependent binding of galectin-7 to FAF, but no interaction with SufA and protein PAB."
sparser
"In order to map the binding of galectin-7 to a particular region of protein FAF, various recombinantly expressed FAF fragments were applied onto a PVDF membrane and probed with galectin-7, see Fig. xref B. The fragments, which were constructed in another study, correspond to the N-terminal FAF I (amino acids 28–115, 10 kDa) and FAF II (amino acids 28–317, 32 kDa) and the C-terminal FAF III (amino acids 239–616, 42 kDa) ( xref )."
sparser
"Given that NPHP5 is ubiquitinated in cells and that a relatively large number of unique peptides corresponding to USP9X were identified in our proteomic screen ( xref ), we focused on verifying the interaction between NPHP5 and USP9X. We expressed Flag-NPHP5 in HEK293 cells, performed anti-Flag immunoprecipitations, and showed that recombinant NPHP5 and endogenous USP9X are co-precipitated ( xref )."
sparser
"Together, these findings indicate that (1) WW domain scaffolding partially contributes to the interaction between WWP1 and USP9X, (2) WW domain interactions are required for WWP1 engagement with DVL2, and (3) the WW domains of WWP1 function redundantly for interaction with both DVL2 and USP9X."
sparser
"Although individual WW domains were dispensable for interaction with DVL2 and USP9X, we found that a WWP1 variant with point mutations disrupting each WW domain ( wwp1–4ww ) exhibited significantly decreased interaction with USP9X and complete loss of interaction with DVL2 ( xref and xref )."
USP9X affects CPH
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13
sparser
"Since the level of comorbidity and inflammatory biomarkers was relatively high in the FAM-CPH cohort and there was a strong and significant association of signs of dysphagia and the three sarcopenia-related parameters at 56-week follow-up, it cannot be excluded that the presence of signs of dysphagia at 56-week follow-up was influenced by sarcopenia."
sparser
"Together, these findings indicate that (1) WW domain scaffolding partially contributes to the interaction between WWP1 and USP9X, (2) WW domain interactions are required for WWP1 engagement with DVL2, and (3) the WW domains of WWP1 function redundantly for interaction with both DVL2 and USP9X."
sparser
"Although individual WW domains were dispensable for interaction with DVL2 and USP9X, we found that a WWP1 variant with point mutations disrupting each WW domain ( wwp1–4ww ) exhibited significantly decreased interaction with USP9X and complete loss of interaction with DVL2 ( xref and xref )."
CPH affects USP9X
|
13
sparser
"Since the level of comorbidity and inflammatory biomarkers was relatively high in the FAM-CPH cohort and there was a strong and significant association of signs of dysphagia and the three sarcopenia-related parameters at 56-week follow-up, it cannot be excluded that the presence of signs of dysphagia at 56-week follow-up was influenced by sarcopenia."
P3 affects USP9X
|
12
sparser
"The fluorescence intensities corresponding to Cy5-P1 and FAM-P3 were increased (red and green) when mRNA biosensor was mixed with chemically synthesized AlinOBP14-T1 and AlinOBP14-T3, indicating that the PNA probes conjugated with Cy5 and FAM hybridized with AlinOBP14-T1 and AlinOBP14-T3, respectively ( xref f1–f3)."
sparser
"The fluorescence intensities corresponding to Cy5-P1, ROX-P2, and FAM-P3 were increased (red, blue, and green) when mRNA biosensor was mixed with chemically synthesized AlinOBP14-T1, AlinOBP14-T2, and AlinOBP14-T3, indicating that the PNA probes conjugated with Cy5, ROX, and FAM hybridized with AlinOBP14-T1, AlinOBP14-T2, and AlinOBP14-T3, respectively ( xref g1–g3)."
sparser
"The fluorescence intensities corresponding to ROX-P2 and FAM-P3 were increased (blue and green) when mRNA biosensor was mixed with chemically synthesized AlinOBP14-T2 and AlinOBP14-T3, indicating that the PNA probes conjugated with ROX and FAM hybridized with AlinOBP14-T2 and AlinOBP14-T3, respectively ( xref e1–e3)."
reach
"Among the compounds targeting USP9X, a non specific inhibitor of USP9X, named (EOAI3402143) G9, belonging to the USP9X-second generation inhibitors, has been shown to destabilize the pro survival protein MCL1 and increased p53 levels, promoting apoptosis in a dose dependent manner and reducing tumor growth of human myeloma xenograft [XREF_BIBR]."
USP9X affects Circulin-C
|
12
sparser
"In this study, we dissected the structural aspects of the ATG9A-FAM134B and ATG9A-SEC62 interaction, resolved the ATG9A interactome , and took advantage of AT-1 S113R/+ and AT-1 sTg mice to discover two ATG9A-interacting proteins—calreticulin (CALR) and heat shock protein beta 1 (HSPB1)—which engage from the lumenal and cytosolic sides of the ER membrane, respectively, to regulate the induction of reticulophagy."
sparser
"In this study, we dissected the structural aspects of the ATG9A-FAM134B and ATG9A-SEC62 interaction, resolved the ATG9A interactome , and took advantage of AT-1 S113R/+ and AT-1 sTg mice to discover two ATG9A-interacting proteins—calreticulin (CALR) and heat shock protein beta 1 (HSPB1)—which engage from the lumenal and cytosolic sides of the ER membrane, respectively, to regulate the induction of reticulophagy."
Circulin-C affects USP9X
|
12
sparser
"In this study, we dissected the structural aspects of the ATG9A-FAM134B and ATG9A-SEC62 interaction, resolved the ATG9A interactome , and took advantage of AT-1 S113R/+ and AT-1 sTg mice to discover two ATG9A-interacting proteins—calreticulin (CALR) and heat shock protein beta 1 (HSPB1)—which engage from the lumenal and cytosolic sides of the ER membrane, respectively, to regulate the induction of reticulophagy."
sparser
"In this study, we dissected the structural aspects of the ATG9A-FAM134B and ATG9A-SEC62 interaction, resolved the ATG9A interactome , and took advantage of AT-1 S113R/+ and AT-1 sTg mice to discover two ATG9A-interacting proteins—calreticulin (CALR) and heat shock protein beta 1 (HSPB1)—which engage from the lumenal and cytosolic sides of the ER membrane, respectively, to regulate the induction of reticulophagy."
sparser
"The evidence we have uncovered in the present experiments suggests that binding of FAM46C to Plk4 may occur predominantly within the kinase domain of the latter, but is not dependent on kinase activity, and does not result in phosphorylation of FAM46C. Further investigation of the mechanism of inhibition of Plk4 kinase activity will determine its dependence on direct physical interaction."
sparser
"Interestingly, comparing hFAM46C to paralogs FAM46A, B and D, there is greater divergence in the N terminal versus the C terminal sequence, an observation that, taken together with the failure of the C terminal fragment to bind to or inhibit the kinase activity of Plk4, could underlie the specific interaction of FAM46C with Plk4 (Fig. xref ; Supplementary Fig. xref )."
sparser
"The localization of FAM46C and Plk4 to centrioles throughout the cell cycle (Supplementary Fig. xref ; xref , xref ), in addition to the physical interaction of FAM46C with Plk4 observed in co-immunoprecipitation experiments, taken together with the rosette-like centriolar configuration conferred by depletion of FAM46C, suggested that FAM46C might normally function to limit Plk4 activity and/or abundance."
reach
"Furthermore, the expression level of USP9X is positively related to LATS expression but negatively associated with the expression of YAP/TAZ in multiple tumor tissues, such as pancreatic cancer and breast cancer, demonstrating that USP9X potentiates LATS kinase in suppressing tumor growth (Toloczko et al., 2017)."
USP9X affects Neoplasm Metastasis
|
10
USP9X activates Neoplasm Metastasis.
|
7
USP9X inhibits Neoplasm Metastasis.
|
3
USP9X inhibits Neoplasm Metastasis. 3 / 3
|
3
reach
"The depletion and pharmacological inhibition of USP9X by WP1130, an inhibitor of USP9X, downregulate endogenous Snail1 protein, inhibit cell migration, invasion, metastasis, and increase cellular sensitivity to cisplatin and paclitaxel both in vitro and in vivo, whereas the reconstitution of Snail1 in cells with USP9X depletion at least partially reverses these phenotypes."
sparser
"Binding of a compound or of excess of unlabeled IRE oligonucleotide (0.5 µM, positive control, IRE) to the FOXO3-DBD protein causes an increase of unbound, highly rotating IRE-FAM oligonucleotide and depolarisation of the emitted light, thereby leading to a reduction of the millipolarization (mP) value."
sparser
"The binding affinity (Ki)-value of RPG was assessed by the equation of Nikolovska-Coleska [ xref ] based on the measured IC 50 -values, the K-value of the protein/oligonucleotide complex (FOXO3-DBD/IRE-FAM oligonucleotide [ xref ]), the concentration of the FOXO3-DBD protein (25 nM), and the IRE-FAM oligonucleotide (5 nM) used in the assay."
sparser
"The binding affinity (K i )-value of CBX was assessed by the equation of Nikolovska–Coleska [ xref ] based on the measured IC50-values, the K d -value of the protein/oligonucleotide complex (FOXO3-DBD/IRE-FAM oligonucleotide), the concentration of the FOXO3-DBD protein (25 nM), as well as the IRE-FAM oligonucleotide (5 nM) used in the assay."
sparser
"The basis of the designed paper-supported aptasensor was the specific complexation of Cd 2+ with the aptamer strand, adsorption of fluorescein-labeled complementary (FAM-CP) strand on the ZIF-8 surface, and fluorescence quenching of FAM molecule after the leakage of the injected target solution on the sample zone of the paper substrate to the detection part."
sparser
"The FINC-NA questionnaire has four subscales: family as a resource in nursing care (Fam-RNC) with 10 items, score range 10 to 50, assesses positive attitudes toward family members and the value of their presence in nursing care (e.g., “Family members should be invited to actively take part in the patient’s nursing care”); family as a conversational partner (Fam-CP) with eight items, score range 8 to 40, assesses attitudes toward the importance of acknowledging the patient’s family members and having dialogue with them (e.g., “I ask family members to take part in discussions from the very first contact, when a patient comes into my care”); family as a burden (Fam-B) with four items, score range 4 to 20, assesses negative attitudes toward the presence family members and time to take care of families (e.g., “The presence of family members makes me feel that they are checking up on me”); and family as its own resource (Fam-OR) with four items, score range 4 to 20, assesses attitudes toward family members as having their own resources for coping (e.g., “I consider family members as co-operating partners”; Benzein, Johansson, Arestedt, Berg, & Saveman, 2008)."
sparser
"The FINC-NA questionnaire has four subscales: family as a resource in nursing care (Fam-RNC) with 10 items, score range 10 to 50, assesses positive attitudes toward family members and the value of their presence in nursing care (e.g., "Family members should be invited to actively take part in the patient's nursing care"); family as a conversational partner (Fam-CP) with eight items, score range 8 to 40, assesses attitudes toward the importance of acknowledging the patient's family members and having dialogue with them (e.g., "I ask family members to take part in discussions from the very first contact, when a patient comes into my care"); family as a burden (Fam-B) with four items, score range 4 to 20, assesses negative attitudes toward the presence family members and time to take care of families (e.g., "The presence of family members makes me feel that they are checking up on me"); and family as its own resource (Fam-OR) with four items, score range 4 to 20, assesses attitudes toward family members as having their own resources for coping (e.g., "I consider family members as co-operating partners"; Benzein, Johansson, Arestedt, Berg, & Saveman, 2008) ."
sparser
"The evidence we have uncovered in the present experiments suggests that binding of FAM46C to Plk4 may occur predominantly within the kinase domain of the latter, but is not dependent on kinase activity, and does not result in phosphorylation of FAM46C. Further investigation of the mechanism of inhibition of Plk4 kinase activity will determine its dependence on direct physical interaction."
sparser
"Interestingly, comparing hFAM46C to paralogs FAM46A, B and D, there is greater divergence in the N terminal versus the C terminal sequence, an observation that, taken together with the failure of the C terminal fragment to bind to or inhibit the kinase activity of Plk4, could underlie the specific interaction of FAM46C with Plk4 (Fig. xref ; Supplementary Fig. xref )."
sparser
"The localization of FAM46C and Plk4 to centrioles throughout the cell cycle (Supplementary Fig. xref ; xref , xref ), in addition to the physical interaction of FAM46C with Plk4 observed in co-immunoprecipitation experiments, taken together with the rosette-like centriolar configuration conferred by depletion of FAM46C, suggested that FAM46C might normally function to limit Plk4 activity and/or abundance."
sparser
"Binding of a compound or of excess of unlabeled IRE oligonucleotide (0.5 µM, positive control, IRE) to the FOXO3-DBD protein causes an increase of unbound, highly rotating IRE-FAM oligonucleotide and depolarisation of the emitted light, thereby leading to a reduction of the millipolarization (mP) value."
sparser
"The binding affinity (Ki)-value of RPG was assessed by the equation of Nikolovska-Coleska [ xref ] based on the measured IC 50 -values, the K-value of the protein/oligonucleotide complex (FOXO3-DBD/IRE-FAM oligonucleotide [ xref ]), the concentration of the FOXO3-DBD protein (25 nM), and the IRE-FAM oligonucleotide (5 nM) used in the assay."
sparser
"The binding affinity (K i )-value of CBX was assessed by the equation of Nikolovska–Coleska [ xref ] based on the measured IC50-values, the K d -value of the protein/oligonucleotide complex (FOXO3-DBD/IRE-FAM oligonucleotide), the concentration of the FOXO3-DBD protein (25 nM), as well as the IRE-FAM oligonucleotide (5 nM) used in the assay."
sparser
"The basis of the designed paper-supported aptasensor was the specific complexation of Cd 2+ with the aptamer strand, adsorption of fluorescein-labeled complementary (FAM-CP) strand on the ZIF-8 surface, and fluorescence quenching of FAM molecule after the leakage of the injected target solution on the sample zone of the paper substrate to the detection part."
sparser
"The FINC-NA questionnaire has four subscales: family as a resource in nursing care (Fam-RNC) with 10 items, score range 10 to 50, assesses positive attitudes toward family members and the value of their presence in nursing care (e.g., “Family members should be invited to actively take part in the patient’s nursing care”); family as a conversational partner (Fam-CP) with eight items, score range 8 to 40, assesses attitudes toward the importance of acknowledging the patient’s family members and having dialogue with them (e.g., “I ask family members to take part in discussions from the very first contact, when a patient comes into my care”); family as a burden (Fam-B) with four items, score range 4 to 20, assesses negative attitudes toward the presence family members and time to take care of families (e.g., “The presence of family members makes me feel that they are checking up on me”); and family as its own resource (Fam-OR) with four items, score range 4 to 20, assesses attitudes toward family members as having their own resources for coping (e.g., “I consider family members as co-operating partners”; Benzein, Johansson, Arestedt, Berg, & Saveman, 2008)."
sparser
"The FINC-NA questionnaire has four subscales: family as a resource in nursing care (Fam-RNC) with 10 items, score range 10 to 50, assesses positive attitudes toward family members and the value of their presence in nursing care (e.g., "Family members should be invited to actively take part in the patient's nursing care"); family as a conversational partner (Fam-CP) with eight items, score range 8 to 40, assesses attitudes toward the importance of acknowledging the patient's family members and having dialogue with them (e.g., "I ask family members to take part in discussions from the very first contact, when a patient comes into my care"); family as a burden (Fam-B) with four items, score range 4 to 20, assesses negative attitudes toward the presence family members and time to take care of families (e.g., "The presence of family members makes me feel that they are checking up on me"); and family as its own resource (Fam-OR) with four items, score range 4 to 20, assesses attitudes toward family members as having their own resources for coping (e.g., "I consider family members as co-operating partners"; Benzein, Johansson, Arestedt, Berg, & Saveman, 2008) ."
OAβ affects USP9X
|
10
USP9X affects PRC2_complex
|
2
4
4
USP9X binds PRC2_complex.
|
1
4
USP9X deubiquitinates PRC2_complex.
|
3
USP9X activates PRC2_complex.
|
2
USP9X affects E3_Ub_ligase
|
8
2
USP9X binds E3_Ub_ligase.
|
6
2
USP9X inhibits E3_Ub_ligase.
|
2
USP9X affects DT
|
10
sparser
"Forward ATT-CGC-AGT-CCC-CAA-CCT-CCA-ATC-ACT-AAT-ACC-ACA-TCA-TCC-ATA-TAA-CTR-AAA-GCC 755-726 Shen et al. P1F-HBV Forward AAC-CTC-CAA-TCA-CTC-ACC-AAC-CTC-T 322-346 Yi et al. P1R-HBV Reverse GAT-AGT-CCA-GAA-GAA-CCA-ACA-AGA-AGA 455-429 Yi et al. EXO_HBV Forward CCA-AYT-TGT-CCT-GGC-TAT-CGY-TGG-ATG-[dT-FAM]-G[THF]-C[dT-BHQ1]G-CGG-CGT-TTT-ATC-AT-[Spacer C3] 353-399 This study RPA-NFO Kit: Primers, Probe, and Synthetic Control HBV-Fc Forward ATT-CGC-AGT-CCC-CAA-CCT-CCA-ATC-ACT-FAM-GAT-AGT-CCA-GAA-GAA-CCA-ACA-AGA-AGA 455-429 Yi et al. HBV probe Forward Biotin-CCA-AYT-TGT-CCT-GGC-TAT-CGY-TGG-ATG-TG[THF]-CTG-CGG-CGT-TTT-ATC-AT--CGA-TCA-TGC-CCA-TCA-GCA-GCT-TAT-GAT-CAA-T[THF]T-GAT-CCA-AAC-CGA-GGC-G-[Spacer C3] This study Probe modifications: FAM: 6-carboxyfuorescein; THF: tetrahydrofuran; BHQ: black hole quencher; spacer-C3: 3 phosphate blocker."
sparser
"The 50 μL reaction mixture consisted of 25 μL of 2 × 1 Step Buffer, 2 μL of 1 Step Enzyme Mix (Takara, Dalian, China), 0.5 μL of N-forward primer (20 μmol/L), Table 1 Sequence of primers and probes for CDV RT-PCR, real-time RT-PCR and RT--RPA-F GCTTACTTCAGACTCGGGCAAGAAATGGTTA 154 CDV-RPA-R CAGTAGCTCGAATTGTCCGGTCCTCTGTTGT CDV-RPA-P CTTGGCATCACCAAGGAGGAAGCTCAGCTGG (FAM-dT) (THF)(BHQ1-dT)CAGAAATAGCATCCA-C3spacer
Analytical specificity of the CDV RT-RPA assay."
sparser
"Ebola EBOV Primer forward primer [A/5'-CTA CTG TAT TTC ATA AGA AGA GAG TTG AAC C-3'/5'-AAT TGT TGT TCT ACT GAT CCA CAA GTC TTA C-3'/5'-ATA TGT CCG ACC TTG AAA AAA GGA TTT TTG [FAM-dT][THF][BHQ1-dT] GAC AGT AGT TTT TGC [3'-phosphate]/160 bp] reverse primer [B/5'-CTA CTG AGT CCA GTA TAG AGT CAG AAA TAG TA-3'/5'-CTG AGT TGT TAA GAA TAA TCT CAA TTT GGT-3'/5'-AAT GAC TAC TCC TAG GAT GCT TCT ACC TGT [FAM-dT][THF][BHQ1-dT] GTC AAA ATT CCA TAA [3'-phosphate]/127 bp] probe [C/5'-GAC GAC AAT CCT GGC CAT CAA GAT GAT GAT CC -3'/5'-CGT CCT CGT CTA GAT CGA ATA GGA CCA AGT C -3'/5'-GAT GAT GGA AGC TAC GGC GAA TAC CAG AG [FAM-dT] T [THF] C [BHQ1-dT] CGG AAA ACG GCA TG [3'-phosphate]/168 bp] [51] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ."
sparser
"RSV-P0 a CAT CCT GAT ATA AGA TAT ATT TAC AGAAG[T(FAM-dT)][Y(THF)][T(BHQ-dT)]GAA AGA TTG CAA TGA[C3-spacer] 47 P-IC a GTA AGG TGC TAG ACT AAA ATT GTT GGGAC[T(HEX-dT)][T(THF)][T(BHQ-dT)]GAA TCT CTG AAG TAA AAG G[TTA TRG TGT CTT CYC TTC CTA ACC 30 qPCR-P FAM-TAA TAG GTA TGT TAT ATG CKATGTC-BHQ 25
The oligonucleotides used for RT-PCR, rtRAA, and RT-qPCR
The reproducibility of singleplex-rtRAA and duplex-rtRAA a Each dilution was tested in a total of 8 replicates"
sparser
"Some other NF-κB associated lncRNAs
include Tmevpg1 in T helper type 1 cells [ xref ]; HOXA-AS2 in breast cancer [ xref ]; BANCR in gastric cancer [ xref ]; FAM3D-AS1 in colorectal cancer [ xref ]; TP73-AS1 in hepatocellular carcinoma [ xref ]; GAS5 in colorectal cancer [ xref ], osteosarcoma [ xref ], chondrocytes [ xref ], and in cardiomyocytes [ xref ]; MIAT in ischemia/reperfusion injury model [ xref ]; lnc-SLC4A1–1 in unexplained recurrent
pregnancy loss (URPL) patients [ xref ];
CYTOR in cardiac hypertrophy model [ xref ]; XIST in the bovine mammary epithelial cells [ xref ]; SRA in the polycystic ovary syndrome model
[ xref ]; H19 in multiple myeloma
[ xref ], melanoma [ xref ], osteosarcoma [ xref ], and in atherosclerosis model [ xref ]; IFNG-AS1 in human T cells [ xref ]; lncRNA-POIR during osteogenic differentiation [ xref ]; lnc-DILC in liver cancer stem cells
[ xref ]; UCA1 in the hippocampus of
rats [ xref ]; and CUDR in hepatocyte-like
stem cells [ xref ]."
sparser
"Among the overall 90 DEL, 10 were shared by all the three subject categories (AC109460.3, AL031429.1, AL139260.1, APTR, FAM198B-AS1, LINC00968, LINC01106, LINC01348, MIR4435-2HG, SNHG16), 6 were shared by NwCRC and Ob patients (AC008105.3, AC021092.1, HIF1A-AS1, LINC00926, RASSF8-AS1, ZNF883), 12 were shared by NwCRC and ObCRC patients (AC009022.1, AC010457.1, AC016582.2, AC068888.1, AL356056.1, AP000317.2, FAM27E3, MINCR, MIR100HG, SLC14A2-AS1, STAG3L5P-PVRIG2P-PILRB, TPTEP1), and only one was shared by Ob and ObCRC patients (AC022007.1)."
E3_Ub_ligase affects USP9X
|
8
2
E3_Ub_ligase binds USP9X.
|
6
2
E3_Ub_ligase inhibits USP9X.
|
2
DT affects USP9X
|
10
sparser
"Forward ATT-CGC-AGT-CCC-CAA-CCT-CCA-ATC-ACT-AAT-ACC-ACA-TCA-TCC-ATA-TAA-CTR-AAA-GCC 755-726 Shen et al. P1F-HBV Forward AAC-CTC-CAA-TCA-CTC-ACC-AAC-CTC-T 322-346 Yi et al. P1R-HBV Reverse GAT-AGT-CCA-GAA-GAA-CCA-ACA-AGA-AGA 455-429 Yi et al. EXO_HBV Forward CCA-AYT-TGT-CCT-GGC-TAT-CGY-TGG-ATG-[dT-FAM]-G[THF]-C[dT-BHQ1]G-CGG-CGT-TTT-ATC-AT-[Spacer C3] 353-399 This study RPA-NFO Kit: Primers, Probe, and Synthetic Control HBV-Fc Forward ATT-CGC-AGT-CCC-CAA-CCT-CCA-ATC-ACT-FAM-GAT-AGT-CCA-GAA-GAA-CCA-ACA-AGA-AGA 455-429 Yi et al. HBV probe Forward Biotin-CCA-AYT-TGT-CCT-GGC-TAT-CGY-TGG-ATG-TG[THF]-CTG-CGG-CGT-TTT-ATC-AT--CGA-TCA-TGC-CCA-TCA-GCA-GCT-TAT-GAT-CAA-T[THF]T-GAT-CCA-AAC-CGA-GGC-G-[Spacer C3] This study Probe modifications: FAM: 6-carboxyfuorescein; THF: tetrahydrofuran; BHQ: black hole quencher; spacer-C3: 3 phosphate blocker."
sparser
"The 50 μL reaction mixture consisted of 25 μL of 2 × 1 Step Buffer, 2 μL of 1 Step Enzyme Mix (Takara, Dalian, China), 0.5 μL of N-forward primer (20 μmol/L), Table 1 Sequence of primers and probes for CDV RT-PCR, real-time RT-PCR and RT--RPA-F GCTTACTTCAGACTCGGGCAAGAAATGGTTA 154 CDV-RPA-R CAGTAGCTCGAATTGTCCGGTCCTCTGTTGT CDV-RPA-P CTTGGCATCACCAAGGAGGAAGCTCAGCTGG (FAM-dT) (THF)(BHQ1-dT)CAGAAATAGCATCCA-C3spacer
Analytical specificity of the CDV RT-RPA assay."
sparser
"Ebola EBOV Primer forward primer [A/5'-CTA CTG TAT TTC ATA AGA AGA GAG TTG AAC C-3'/5'-AAT TGT TGT TCT ACT GAT CCA CAA GTC TTA C-3'/5'-ATA TGT CCG ACC TTG AAA AAA GGA TTT TTG [FAM-dT][THF][BHQ1-dT] GAC AGT AGT TTT TGC [3'-phosphate]/160 bp] reverse primer [B/5'-CTA CTG AGT CCA GTA TAG AGT CAG AAA TAG TA-3'/5'-CTG AGT TGT TAA GAA TAA TCT CAA TTT GGT-3'/5'-AAT GAC TAC TCC TAG GAT GCT TCT ACC TGT [FAM-dT][THF][BHQ1-dT] GTC AAA ATT CCA TAA [3'-phosphate]/127 bp] probe [C/5'-GAC GAC AAT CCT GGC CAT CAA GAT GAT GAT CC -3'/5'-CGT CCT CGT CTA GAT CGA ATA GGA CCA AGT C -3'/5'-GAT GAT GGA AGC TAC GGC GAA TAC CAG AG [FAM-dT] T [THF] C [BHQ1-dT] CGG AAA ACG GCA TG [3'-phosphate]/168 bp] [51] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ."
sparser
"RSV-P0 a CAT CCT GAT ATA AGA TAT ATT TAC AGAAG[T(FAM-dT)][Y(THF)][T(BHQ-dT)]GAA AGA TTG CAA TGA[C3-spacer] 47 P-IC a GTA AGG TGC TAG ACT AAA ATT GTT GGGAC[T(HEX-dT)][T(THF)][T(BHQ-dT)]GAA TCT CTG AAG TAA AAG G[TTA TRG TGT CTT CYC TTC CTA ACC 30 qPCR-P FAM-TAA TAG GTA TGT TAT ATG CKATGTC-BHQ 25
The oligonucleotides used for RT-PCR, rtRAA, and RT-qPCR
The reproducibility of singleplex-rtRAA and duplex-rtRAA a Each dilution was tested in a total of 8 replicates"
sparser
"Some other NF-κB associated lncRNAs
include Tmevpg1 in T helper type 1 cells [ xref ]; HOXA-AS2 in breast cancer [ xref ]; BANCR in gastric cancer [ xref ]; FAM3D-AS1 in colorectal cancer [ xref ]; TP73-AS1 in hepatocellular carcinoma [ xref ]; GAS5 in colorectal cancer [ xref ], osteosarcoma [ xref ], chondrocytes [ xref ], and in cardiomyocytes [ xref ]; MIAT in ischemia/reperfusion injury model [ xref ]; lnc-SLC4A1–1 in unexplained recurrent
pregnancy loss (URPL) patients [ xref ];
CYTOR in cardiac hypertrophy model [ xref ]; XIST in the bovine mammary epithelial cells [ xref ]; SRA in the polycystic ovary syndrome model
[ xref ]; H19 in multiple myeloma
[ xref ], melanoma [ xref ], osteosarcoma [ xref ], and in atherosclerosis model [ xref ]; IFNG-AS1 in human T cells [ xref ]; lncRNA-POIR during osteogenic differentiation [ xref ]; lnc-DILC in liver cancer stem cells
[ xref ]; UCA1 in the hippocampus of
rats [ xref ]; and CUDR in hepatocyte-like
stem cells [ xref ]."
sparser
"Among the overall 90 DEL, 10 were shared by all the three subject categories (AC109460.3, AL031429.1, AL139260.1, APTR, FAM198B-AS1, LINC00968, LINC01106, LINC01348, MIR4435-2HG, SNHG16), 6 were shared by NwCRC and Ob patients (AC008105.3, AC021092.1, HIF1A-AS1, LINC00926, RASSF8-AS1, ZNF883), 12 were shared by NwCRC and ObCRC patients (AC009022.1, AC010457.1, AC016582.2, AC068888.1, AL356056.1, AP000317.2, FAM27E3, MINCR, MIR100HG, SLC14A2-AS1, STAG3L5P-PVRIG2P-PILRB, TPTEP1), and only one was shared by Ob and ObCRC patients (AC022007.1)."
sparser
"The interaction of FAM122A with PP2A complex promoted us to detect whether FAM122A modulates the phosphatase activity of PP2A. For this purpose, an in vitro phosphatase assay was applied to the anti-PP2A-Cα antibody-pulled down precipitates from equal amounts of 293T cells respectively with ectopic expression of Flag-tagged FAM122A and CIP2A (a known PP2A inhibitor) or with the treatment of 50 nM of okadaic acid (OA, a chemical PP2A inhibitor) [ xref ]."
sparser
"Considering that FAM122A is previously identified as an endogenous inhibitor of PP2A, we asked whether FAM122A regulating HCC cell growth is associated with PP2A. The results showed FAM122A can also modulate PP2A activity in HCC cells although the modulated effect is relatively slight, however, treatment with a PP2A inhibitor okadaic acid did not rescue the inhibitory effects of cell growth and proliferation in FAM122A deletion cells, indicating that FAM122A may support HCC cell growth independent of its ability to modulate PP2A. Collectively, these results suggest that FAM122A is required for maintaining HCC cell growth, and its elimination combined with chemotherapy may represent a potential novel therapeutic strategy for HCC patients."
reach
"Others have recently utilized LC-MS to identify nitric oxide-mediated S-nitrosylation of 217 proteins in cultured VICs, and subsequently demonstrated that S-nitrosylation of the deubiquitinase USP9X modulates NOTCH signaling in VICs, prevents murine valvular calcification, and is reduced in human valves with CAVD."
sparser
"The lack of significant difference between physiological (10 and 100 pM) and pharmacology (1000 pM) concentrations suggests that the tran-endothelial transport of GLP-1-FAM does not appear to be concentration dependent ( xref ), suggesting endothelial transport of GLP-1 is a regulated process."
sparser
"To further characterize the pharmacological properties of the non-canonically substituted GLP-1-CYA variant we measured relative receptor binding and ERK1/2 activity, another signaling axis triggered by activation of GLP-1R. To measure binding, a competition assay was performed with CHO-K1 cells expressing exogenous GLP-1R in which either unlabeled GLP-1 or GLP-1-CYA was used to compete off GLP-1 labeled at the C-terminus with 6-carboxyfluorescein (GLP-1-FAM)."
sparser
"Peptide
probes FAM-GYO and FAM-GFO containing aromatic residues Tyr and Phe
at the X position showed similarly high binding affinity and tissue-staining
efficacy as the well-established peptide probe FAM-GPO, while peptide
probes FAM-GDO and FAM-GAO with the corresponding charged residue
Asp and the hydrophobic residue Ala indicated much weaker binding
affinity and tissue-staining capability."
sparser
"In order to solve the problem shown in Fig. 2(a), we fabricated magnetic Fe3O4 GO nanoparticles (see Fig. 2(b)–(d)) to completely remove free TBA-conjugated 6-FAM in aqueous solution containing G-quadruplex TBA-conjugated 6-FAM bound with thrombin that does not interact with magnetic Fe3O4 GO nanoparticles."
sparser
"In conclusion, it is impossible to develop a G-quardruplex DNA aptasensor with guanine chemiluminescence detection using magnetic Fe 3 O 4 GO nanoparticles due to the mechanism shown in xref even though magnetic Fe 3 O 4 GO nanoparticles can completely remove free TBA-conjugated 6-FAM remaining in the solution after the reaction to form G-quadruplex TBA-conjugated 6-FAM bound with thrombin."
sparser
"In order to solve the problem shown in xref (a), we fabricated magnetic Fe 3 O 4 GO nanoparticles (see xref (b)–(d)) to completely remove free TBA-conjugated 6-FAM in aqueous solution containing G-quadruplex TBA-conjugated 6-FAM bound with thrombin that does not interact with magnetic Fe 3 O 4 GO nanoparticles."
sparser
"In conclusion, it is impossible to develop a G-quardruplex DNA aptasensor with guanine chemiluminescence detection using magnetic Fe3O4 GO nanoparticles due to the mechanism shown in Fig. S2 even though magnetic Fe3O4 GO nanoparticles can completely remove free TBA-conjugated 6-FAM remaining in the solution after the reaction to form G-quadruplex TBA-conjugated 6-FAM bound with thrombin."
reach
"For example : the DUB BRCC36 together with the RING E3 ligase BRCA1 regulates the DNA damage response; the RBR E3 ligase Parkin and the DUB USP30 contribute to mitophagy; the DUB Ubp2 can impede yeast growth by antagonizing the function of the HECT E3 Rsp5; the DUB FAM and USP9x interacts with and stabilizes SMURF1 and this impacts on cell motility."
| PMC
sparser
"The putative Prickle-Usp9x interaction was of particular interest because Usp9x physically interacts with Smurf1 (to date, one of the few Prickle interactors identified in neural tissues[ xref ] and both are implicated in neurite extension).[ xref ] Moreover, since ubiquitination plays a role in cancer pathogenesis, a variety of reagents that modulate this system are already commercially available and in clinical trials.[ xref ] The combination of previously identified Prickle-interacting partners with the present studies are depicted in the Prickle-interactome ( xref ) that we utilize to identify new seizure-modifying targets."
sparser
"The interaction of FAM122A with PP2A complex promoted us to detect whether FAM122A modulates the phosphatase activity of PP2A. For this purpose, an in vitro phosphatase assay was applied to the anti-PP2A-Cα antibody-pulled down precipitates from equal amounts of 293T cells respectively with ectopic expression of Flag-tagged FAM122A and CIP2A (a known PP2A inhibitor) or with the treatment of 50 nM of okadaic acid (OA, a chemical PP2A inhibitor) [ xref ]."
sparser
"Considering that FAM122A is previously identified as an endogenous inhibitor of PP2A, we asked whether FAM122A regulating HCC cell growth is associated with PP2A. The results showed FAM122A can also modulate PP2A activity in HCC cells although the modulated effect is relatively slight, however, treatment with a PP2A inhibitor okadaic acid did not rescue the inhibitory effects of cell growth and proliferation in FAM122A deletion cells, indicating that FAM122A may support HCC cell growth independent of its ability to modulate PP2A. Collectively, these results suggest that FAM122A is required for maintaining HCC cell growth, and its elimination combined with chemotherapy may represent a potential novel therapeutic strategy for HCC patients."
reach
"Although these findings point toward low pH of acidic organelles not being necessary in Rapa release from FAF/Rapa, such conclusions can be made only after confirming lysosomal basification under the treatment conditions employed.Another possible mechanism that hasn’t been explored is a release-independent pathway wherein FAF/Rapa directly binds to mTOR and inhibits its kinase activity."
sparser
"The lack of significant difference between physiological (10 and 100 pM) and pharmacology (1000 pM) concentrations suggests that the tran-endothelial transport of GLP-1-FAM does not appear to be concentration dependent ( xref ), suggesting endothelial transport of GLP-1 is a regulated process."
sparser
"To further characterize the pharmacological properties of the non-canonically substituted GLP-1-CYA variant we measured relative receptor binding and ERK1/2 activity, another signaling axis triggered by activation of GLP-1R. To measure binding, a competition assay was performed with CHO-K1 cells expressing exogenous GLP-1R in which either unlabeled GLP-1 or GLP-1-CYA was used to compete off GLP-1 labeled at the C-terminus with 6-carboxyfluorescein (GLP-1-FAM)."
sparser
"Peptide
probes FAM-GYO and FAM-GFO containing aromatic residues Tyr and Phe
at the X position showed similarly high binding affinity and tissue-staining
efficacy as the well-established peptide probe FAM-GPO, while peptide
probes FAM-GDO and FAM-GAO with the corresponding charged residue
Asp and the hydrophobic residue Ala indicated much weaker binding
affinity and tissue-staining capability."
sparser
"In order to solve the problem shown in Fig. 2(a), we fabricated magnetic Fe3O4 GO nanoparticles (see Fig. 2(b)–(d)) to completely remove free TBA-conjugated 6-FAM in aqueous solution containing G-quadruplex TBA-conjugated 6-FAM bound with thrombin that does not interact with magnetic Fe3O4 GO nanoparticles."
sparser
"In conclusion, it is impossible to develop a G-quardruplex DNA aptasensor with guanine chemiluminescence detection using magnetic Fe 3 O 4 GO nanoparticles due to the mechanism shown in xref even though magnetic Fe 3 O 4 GO nanoparticles can completely remove free TBA-conjugated 6-FAM remaining in the solution after the reaction to form G-quadruplex TBA-conjugated 6-FAM bound with thrombin."
sparser
"In order to solve the problem shown in xref (a), we fabricated magnetic Fe 3 O 4 GO nanoparticles (see xref (b)–(d)) to completely remove free TBA-conjugated 6-FAM in aqueous solution containing G-quadruplex TBA-conjugated 6-FAM bound with thrombin that does not interact with magnetic Fe 3 O 4 GO nanoparticles."
sparser
"In conclusion, it is impossible to develop a G-quardruplex DNA aptasensor with guanine chemiluminescence detection using magnetic Fe3O4 GO nanoparticles due to the mechanism shown in Fig. S2 even though magnetic Fe3O4 GO nanoparticles can completely remove free TBA-conjugated 6-FAM remaining in the solution after the reaction to form G-quadruplex TBA-conjugated 6-FAM bound with thrombin."
SiSPAG5 affects USP9X
|
8
sparser
"In addition, in the FeSiNTs/FAM-siSPAG5 treated group, the fluorescence distribution area was significantly larger than then that for the naked FAM-siSPAG5 treatment, which demonstrated the excellent tumor tissue penetration ability of FeSiNTs carrying FAM-siSPAG5 and its subsequent distribution over a large tumor area."
SiFGL1 affects USP9X
|
8
sparser
"The FINC-NA questionnaire has four subscales: family as a resource in nursing care (Fam-RNC) with 10 items, score range 10 to 50, assesses positive attitudes toward family members and the value of their presence in nursing care (e.g., "Family members should be invited to actively take part in the patient's nursing care"); family as a conversational partner (Fam-CP) with eight items, score range 8 to 40, assesses attitudes toward the importance of acknowledging the patient's family members and having dialogue with them (e.g., "I ask family members to take part in discussions from the very first contact, when a patient comes into my care"); family as a burden (Fam-B) with four items, score range 4 to 20, assesses negative attitudes toward the presence family members and time to take care of families (e.g., "The presence of family members makes me feel that they are checking up on me"); and family as its own resource (Fam-OR) with four items, score range 4 to 20, assesses attitudes toward family members as having their own resources for coping (e.g., "I consider family members as co-operating partners"; Benzein, Johansson, Arestedt, Berg, & Saveman, 2008) ."
sparser
"The FINC-NA questionnaire has four subscales: family as a resource in nursing care (Fam-RNC) with 10 items, score range 10 to 50, assesses positive attitudes toward family members and the value of their presence in nursing care (e.g., “Family members should be invited to actively take part in the patient’s nursing care”); family as a conversational partner (Fam-CP) with eight items, score range 8 to 40, assesses attitudes toward the importance of acknowledging the patient’s family members and having dialogue with them (e.g., “I ask family members to take part in discussions from the very first contact, when a patient comes into my care”); family as a burden (Fam-B) with four items, score range 4 to 20, assesses negative attitudes toward the presence family members and time to take care of families (e.g., “The presence of family members makes me feel that they are checking up on me”); and family as its own resource (Fam-OR) with four items, score range 4 to 20, assesses attitudes toward family members as having their own resources for coping (e.g., “I consider family members as co-operating partners”; Benzein, Johansson, Arestedt, Berg, & Saveman, 2008)."
USP9X affects siSPAG5
|
8
sparser
"In addition, in the FeSiNTs/FAM-siSPAG5 treated group, the fluorescence distribution area was significantly larger than then that for the naked FAM-siSPAG5 treatment, which demonstrated the excellent tumor tissue penetration ability of FeSiNTs carrying FAM-siSPAG5 and its subsequent distribution over a large tumor area."
USP9X affects siFGL1
|
8
sparser
"The FINC-NA questionnaire has four subscales: family as a resource in nursing care (Fam-RNC) with 10 items, score range 10 to 50, assesses positive attitudes toward family members and the value of their presence in nursing care (e.g., "Family members should be invited to actively take part in the patient's nursing care"); family as a conversational partner (Fam-CP) with eight items, score range 8 to 40, assesses attitudes toward the importance of acknowledging the patient's family members and having dialogue with them (e.g., "I ask family members to take part in discussions from the very first contact, when a patient comes into my care"); family as a burden (Fam-B) with four items, score range 4 to 20, assesses negative attitudes toward the presence family members and time to take care of families (e.g., "The presence of family members makes me feel that they are checking up on me"); and family as its own resource (Fam-OR) with four items, score range 4 to 20, assesses attitudes toward family members as having their own resources for coping (e.g., "I consider family members as co-operating partners"; Benzein, Johansson, Arestedt, Berg, & Saveman, 2008) ."
sparser
"The FINC-NA questionnaire has four subscales: family as a resource in nursing care (Fam-RNC) with 10 items, score range 10 to 50, assesses positive attitudes toward family members and the value of their presence in nursing care (e.g., “Family members should be invited to actively take part in the patient’s nursing care”); family as a conversational partner (Fam-CP) with eight items, score range 8 to 40, assesses attitudes toward the importance of acknowledging the patient’s family members and having dialogue with them (e.g., “I ask family members to take part in discussions from the very first contact, when a patient comes into my care”); family as a burden (Fam-B) with four items, score range 4 to 20, assesses negative attitudes toward the presence family members and time to take care of families (e.g., “The presence of family members makes me feel that they are checking up on me”); and family as its own resource (Fam-OR) with four items, score range 4 to 20, assesses attitudes toward family members as having their own resources for coping (e.g., “I consider family members as co-operating partners”; Benzein, Johansson, Arestedt, Berg, & Saveman, 2008)."
sparser
"However, in the presence of SMZ, FAM-SMZ1S specifically bound SMZ and would thus not be adsorbed by Fe 3 O 4 /Au/g-C 3 N 4 , which prevented quenching of the fluorescence from FAM-SMZ1S. Therefore, the higher the SMZ concentration, the higher the fluorescence value in the supernatant after magnetic separation."
sparser
"In brief, a one-step method was adopted using Platinum ® Quantitative PCR Super-Mix-UDG (Invitrogen srl, Milan, Italy) and the following 50-μl mixture: 25 μl of master mix, 300 nM of primers FcoV1128f (GAT TTG ATT TGG CAA TGC TAG ATT T) and FcoV1229r (AAC AAT CAC TAG ATC CAG ACG TTA GCT), 200 nM of probe FCoV1200p (FAM-TCC ATT GTT GGC TCG TCA TAG CGG A-BHQ1) and 10 μl of template NA."
sparser
"AGA GCT GCT CCT TAT AT CTC CAC TTC CGT CTT CCA GTT C FAM-TCC GGA GAT GAC CAC GCC CC-ATA GCC GGC GTG GTA CCC GGC CAC AGA TCA AGT ACT TA FAM-ATC CAA CTC CGG AGG AGG AGG A-TAMRAł (59) T. gondii first round NN1 NN2 TCA ACC TTT GAA TCC AAA CGA GCC AAG ACA TCC ATT (72) T. gondii second round Tg-NP1 Tg-NP2 GTG ATA GTA TCG AAA GGT AT ACT CTC TCT CAA ATG TTC CT (72) A. vasorum Nad3-F1 Nad3-R1 ATC GTG AGA TAG AAT TGT TTA TCT TG CCA ACT CTA CAC CAA TCA CAT CAA C
N2, H&E stain, 100×: Inflammation of the superficial grey matter with primarily lymphocytic infiltrates (non-suppurative polioencephalitis; arrowhead) with meningitis (arrow)."
sparser
"Transcript levels of host genes were detected with SYBR Premix Ex Taq (Tli RNaseH Plus) (TaKaRa) and QuantiTect primers (human IFNB, QT00203763; RRN18S, QT00199367; Qiagen), whereas viral genomic segments were detected with Premix Ex Taq (Probe qPCR) (TaKaRa) and previously published primers and probes for the SFSV and RVFV S and L segments (for SFSV S, fwd, 5ʹ-TGC ACT CAT CCA AGC TAT GTG-3ʹ, rev, 5ʹ-GAG GGC TAC AAA CAA GGG ATC-3ʹ, probe, 6-carboxyfluorescein [FAM]-TCC CCC ATT CTC AGA ATG TAA GAC ATT AGC-black hole quencher 1 [BHQ-1] [89]; for SFSV L, fwd, 5ʹ-TCT GAG AAC TGA GCT ACA AGT GTT TAT TA-3ʹ, rev, 5ʹ-TTC CCA TCT CTC TTC TGA AGA GTG-3ʹ, probe, FAM-AGG TCA TAG ACA GTA TCA TGA GAA TTG CTA GGT G-BHQ-1 [4]; for RVFV S, fwd, 5ʹ-TGC CAC GAG TYA GAG CCA-3ʹ, rev, 5ʹ-GTG GGT CCG AGA GTY TGC-3ʹ, probe, FAM-TCC TTC TCC CAG TCA GCC CCA C-BHQ-1 [89])."
sparser
"Transcript levels of host genes were detected with SYBR Premix Ex Taq (Tli RNaseH Plus) (TaKaRa) and QuantiTect primers (human IFNB, QT00203763; RRN18S, QT00199367; Qiagen), whereas viral genomic segments were detected with Premix Ex Taq (Probe qPCR) (TaKaRa) and previously published primers and probes for the SFSV and RVFV S and L segments (for SFSV S, fwd, 5=-TGC ACT CAT CCA AGC TAT GTG-3=, rev, 5=-GAG GGC TAC AAA CAA GGG ATC-3=, probe, 6-carboxyfluorescein [FAM]-TCC CCC ATT CTC AGA ATG TAA GAC ATT AGC-black hole quencher 1 [BHQ-1] [89]; for SFSV L, fwd, 5=-TCT GAG AAC TGA GCT ACA AGT GTT TAT TA-3=, rev, 5=-TTC CCA TCT CTC TTC TGA AGA GTG-3=, probe, FAM-AGG TCA TAG ACA GTA TCA TGA GAA TTG CTA GGT G-BHQ-1 [4]; for RVFV S, fwd, 5=-TGC CAC GAG TYA GAG CCA-3=, rev, 5=-GTG GGT CCG AGA GTY TGC-3=, probe, FAM-TCC TTC TCC CAG TCA GCC CCA C-BHQ-1 [89])."
sparser
"All rights reserved.) U VEITIS CAN BE OF INFECTIOUS OR NONINFECTIOUS
A(G/C)G G(G/C)G T(A/G)C GCA GGT A AGA A(G/C)G GTG T(A/G)C GCA GAT A Probe FAM-ACC ACG TCG AAA ACT TCG AA-MGBNFQ FAM-ACC ACG TCG AAA ACT TCA AA-MGBNFQ FAM-ACA CCG CGG CGT CA-MGBNFQ Coronavirus 229E Forward CAG TCA AAT GGG CTG ATG CA Reverse CAA AGG GCT ATA AAG AGA ATA AGG TAT TCT ND 53 Probe FAM-CCC TGA CGA CCA CGT TGT GGT TCA -TAMRA Coronavirus NL63 Forward AAG GGT TTT CCA CAG CTT GCT AAA GGT TTT CCA CAG CTT GCT ND 53 Reverse ATC ACC CAC TTC ATC AGT GCT AAC Probe FAM-TCA CTA TCA AAG AAT AAC GCA GCC TGA TTA GGA A -TAMRA Coronavirus OC43 Forward CGA TGA GGC TAT TCC GAC TAG GT Reverse CCT TCC TGA GCC TTC AAT ATA GTA ACC ND 53 Probe FAM-TCC GCC TGG CAC GGT ACT CCC T -TAMRA Enteroviruses Forward TCC TCC GGC CCC TGA Reverse AAT TGT CAC CAT AAG CAG CCA GAT TGT CAC CAT AAG CAG CCA ND 50 Probe FAM-CGG AAC CGA CTA CTT TGG GTG ACC GT -TAMRA FAM-CGG AAC CGA CTA CTT TGG GTG TCC GT -TAMRA Epstein-Barr virus Forward GGA ACC TGG TCA TCC TTT GC Reverse ACG TGC ATG GAC CGG TTA AT 50 copies/mL 42 Probe FAM-CGC AGG CAC TCG TAC TGC TCG CT -TAMRA Human herpesvirus 6 Forward GAA GCA GCA ATC GCA 160 copies/mL 42 Reverse ACA CA ATG TAA CTC Probe GGT GTA CGG TGT CTA FAM-AAC CCG TGC GCC GCT -TAMRA Human metapneumovirus Forward CAT ATA AGC ATG CTA TAT TAA AAG AGT CTC ND 49 Reverse CCT ATT TCT GCA GCA TAT TTG TAA TCA G Probe FAM-TG(C/T) AAT GAT GAG GGT GTC ACT GCG GTT G -TAMRA Influenza virus A Forward AAG ACC AAT CCT GTC ACC TCT GA Reverse CAA AGC GTC TAC GCT GCA GTC C ND 52 Probe FAM-TTT GTG TTC ACG CTC ACC GTG CC -TAMRA Influenza virus B Forward AAA TAC GGT GGA TTA AAC AAA AGC AA Reverse CCA GCA ATA GCT CCG AAG AAA ND 52 Probe FAM-CAC CCA TAT TGG GCA ATT TCC TAT GGC -TAMRA Parainfluenza virus 1 Forward TGA TTT AAA CCC GGT AAT TTC TCA T Reverse CCT TGT TCC TGC AGC TAT TAC AGA ND 51 Probe FAM-ACG ACA ACA GGA AAT C -TAMRA Parainfluenza virus 2 Forward AGG ACT ATG AAA ACC ATT TAC CTA AGT GA Reverse AAG CAA GTC TCA GTT CAG CTA GAT CA ND 51 Probe FAM-ATC AAT CGC AAA AGC TGT TCA GTC ACT GCT ATA C -TAMRA Parainfluenza virus 3 Forward TGA TGA AAG ATC AGA TTA TGC AT Reverse CCG GGA CAC CCA GTT GTG ND 51 Probe FAM-TGG ACC AGG GAT ATA CTA CAA AGG CAA AAT AAT ATT TCT C -TAMRA Continued on next page
FAM-GTA TCA TCA TCT GCC AAA TCG GCA ATT AAA CA -TAMRA Human parechovirus Forward TGC AAA CAC TAG TGG TA(A/T) GGC CC Reverse 1 TCA GAT CCA TAG TG(C/T) CAC TTG TTA CCT Reverse 2 TCA GAT CCA CAG TGT CTC TTG TTA CCT 1 TCID50/mL Forthcoming Probe FAM-CGA AGG ATG CCC AGA AGG TAC CCG -TAMRA Respiratory syncytial virus A Forward AGA TCA ACT TCT GTC ATC CAG CAA Reverse TTC TGA ACA TCA TAA TTA GGA GTA TCA AT ND 54 Probe FAM-CAC CAT CCA ACG GAG CAC AGG AGA T -TAMRA Respiratory syncytial virus B Forward AAG ATG CAA ATC ATA AAT TCA CAG GA Reverse TGA TAT CCA GCA TCT TTA AGT ATC TTT ATA GTG ND 54 Probe FAM-TCC CCT TCC TAA CCT GGA CAT AGC ATA TAA CAT ACC T -TAMRA Rubella virus Forward CAC GCC GCA CGG ACA Reverse 1 CAC CGG GAC TG(C/T) TG(A/G) TTG C 1.7 PFU/mL Forthcoming Reverse 2 CAC CGG GAC TGT TGG TTG C Probe FAM-AGG TCC CGC CCG AC-MGBNFQ Mycoplasma pneumoniae Forward GGT CAA TCT GGC GTG CAT CT Reverse TGG TAA CTG CCC CAC AAG C 50 CCU/mL 34 Probe FAM-TCC CCC GTT GAA AAA GTG AGT GGG T -TAMRA Chlamydia pneumoniae Forward TCC GCA TTG CTC AGC C Reverse AAA CAA TTT GCA TGA AGT CTG AGA A 4.9 IFU/mL 34 Probe FAM-TAA ACT TAA CTG CAT GGA ACC CTT CTT TAC TAG G -TAMRA CCU ϭ color-changing units; FAM ϭ 6-carboxyfluorescein fluorescent label; IFU ϭ inclusion-forming units; MGBNFQ ϭ minor groove binding nonfluorescent quencher; ND ϭ not determined; PFU ϭ plaque-forming units; TAMRA ϭ tetramethylrhodamine quencher; TCID50 ϭ tissue culture infectious dose 50."
sparser
"We recently reported that the acetylation status of ATG9A regulates its ability to interact with FAM134B (also referred to as RETREG1) and SEC62 ( xref ), two ER membrane-bound proteins that can act as receptors for LC3B through their LC3B-interacting region (LIR) ( xref ; xref ; xref ; xref )."
sparser
"In this study, we dissected the structural aspects of the ATG9A-FAM134B and ATG9A-SEC62 interaction, resolved the ATG9A interactome , and took advantage of AT-1 S113R/+ and AT-1 sTg mice to discover two ATG9A-interacting proteins—calreticulin (CALR) and heat shock protein beta 1 (HSPB1)—which engage from the lumenal and cytosolic sides of the ER membrane, respectively, to regulate the induction of reticulophagy."
USP9X affects NP
|
8
sparser
"In 2011, the groups of Frangioni and Nguyen reported the use of fluorescently tagged nerve tracers, namely, GE3082 and FAM-NP41, for the visualization of sciatic nerves. xref , xref In 2017, the group of Gibbs reported a dual fluorophore tissue staining method that reduced fluorescence background signals and aided in nerve-specific visualization. xref Parallel to this work, the Chin lab reported the use of [ 18 F]FTC-146 for the visualization of nerve injuries in a neuropathic pain model via targeting of the sigma-1 receptor. xref In 2013, Du Bois and colleagues reported the use of 18 F-labeled saxitoxin for the imaging of neuromas in a rat model of spared-nerve injury. xref While this represented the first small-molecule positron emission tomography (PET) imaging agent capable of targeting voltage-gated sodium channels, the reagent lacked specificity for a particular sodium channel subtype."
sparser
"To this end, 145-nucleosomes, 185-nucleosomes and oligonucleosomes were reconstituted using 5′-fluorescein (FAM)-labelled 145-dsDNA, 185-dsDNA and 2,450-dsDNA, respectively, and isolated HeLa nucleosomes were chemically labelled through the reaction of 5(6)-carboxyfluorescein N -hydroxysuccinimide ester (FAM-NHS) with Lys residues of histones."
| PMC
sparser
"Here, we detail
a protocol to label WWP2 at the N-terminus using Fluorescein NHS ester
(5/6-carboxyfluorescein succinimidyl ester, FAM-NHS ester) adopting a stepwise
labeling procedure (Basic Protocol 1 and 2), and then use the labeled FAM-WWP2 to
measure its binding affinity to its requisite E2 (UbcH5c) enzyme by performing MST
binding assays (Basic Protocol 3)."
sparser
"Bevacizumab-loaded tetra-PEG gel and 5-Carboxyfluorescein N-succinimidyl ester (FAM-NHS)-labeled IgG-loaded tetra-PEG gel were prepared by mixing tetra-PEG with thiol termini (tetra-PEG-SH) solution, maleimide termini (tetra-PEG-MA) solution, and bevacizumab or FAM-NHS labeled IgG."
sparser
"In the absence of GST–hPXR-LBD, these FAM-SRC1 peptides interacted with the Tb–anti-GST only very weakly, and these weak interactions correlated positively with the respective FAM-SRC1 peptide concentrations in a linear manner ( xref , lower curves with data points shown as closed triangles)."
sparser
"With the addition of the hPXR agonist T0901317 (10 μM), the total interactions (10 μM T0901317–mediated total bindings) between individual FAM-SRC1 peptides and the complex of Tb–anti-GST and GST–hPXR-LBD increased further, first in an exponential manner when the FAM-SRC1 peptide concentrations were low and then in a linear manner when the FAM-SRC1 peptide concentrations increased ( xref , upper curves with data points shown as closed squares)."
sparser
"These T0901317-induced specific interactions between FAM-SRC1 peptides and hPXR could be quantified by the relative areas ( xref , gray areas, calculated by using the GraphPad software Prism) between the respective T0901317 curves ( xref , upper curves) and DMSO curves ( xref , middle curve) in the presence of Tb–anti-GST and GST–hPXR-LBD, with areas of 7,764,875, 16,729,790, and 10,406,140 for FAM-SRC1-A, FAM-SRC1-B, and FAM-SRC1-C, respectively, with FAM-SRC1-B giving the largest induction among the three peptides tested."
reach
"Although G9 treatment reduced human MIAPACA2 tumor burden in vivo, in mouse pancreatic cancer cell lines established from constitutive (8041) and doxycycline inducible (4668) KrasG12D and Tp53R172H mouse pancreatic tumors, Usp9x inhibition increased and sustained the 3D colony growth and showed no significant effect on tumor growth in 8041-xenografts."
sparser
"However, in the presence of SMZ, FAM-SMZ1S specifically bound SMZ and would thus not be adsorbed by Fe 3 O 4 /Au/g-C 3 N 4 , which prevented quenching of the fluorescence from FAM-SMZ1S. Therefore, the higher the SMZ concentration, the higher the fluorescence value in the supernatant after magnetic separation."
sparser
"In brief, a one-step method was adopted using Platinum ® Quantitative PCR Super-Mix-UDG (Invitrogen srl, Milan, Italy) and the following 50-μl mixture: 25 μl of master mix, 300 nM of primers FcoV1128f (GAT TTG ATT TGG CAA TGC TAG ATT T) and FcoV1229r (AAC AAT CAC TAG ATC CAG ACG TTA GCT), 200 nM of probe FCoV1200p (FAM-TCC ATT GTT GGC TCG TCA TAG CGG A-BHQ1) and 10 μl of template NA."
sparser
"AGA GCT GCT CCT TAT AT CTC CAC TTC CGT CTT CCA GTT C FAM-TCC GGA GAT GAC CAC GCC CC-ATA GCC GGC GTG GTA CCC GGC CAC AGA TCA AGT ACT TA FAM-ATC CAA CTC CGG AGG AGG AGG A-TAMRAł (59) T. gondii first round NN1 NN2 TCA ACC TTT GAA TCC AAA CGA GCC AAG ACA TCC ATT (72) T. gondii second round Tg-NP1 Tg-NP2 GTG ATA GTA TCG AAA GGT AT ACT CTC TCT CAA ATG TTC CT (72) A. vasorum Nad3-F1 Nad3-R1 ATC GTG AGA TAG AAT TGT TTA TCT TG CCA ACT CTA CAC CAA TCA CAT CAA C
N2, H&E stain, 100×: Inflammation of the superficial grey matter with primarily lymphocytic infiltrates (non-suppurative polioencephalitis; arrowhead) with meningitis (arrow)."
sparser
"Transcript levels of host genes were detected with SYBR Premix Ex Taq (Tli RNaseH Plus) (TaKaRa) and QuantiTect primers (human IFNB, QT00203763; RRN18S, QT00199367; Qiagen), whereas viral genomic segments were detected with Premix Ex Taq (Probe qPCR) (TaKaRa) and previously published primers and probes for the SFSV and RVFV S and L segments (for SFSV S, fwd, 5ʹ-TGC ACT CAT CCA AGC TAT GTG-3ʹ, rev, 5ʹ-GAG GGC TAC AAA CAA GGG ATC-3ʹ, probe, 6-carboxyfluorescein [FAM]-TCC CCC ATT CTC AGA ATG TAA GAC ATT AGC-black hole quencher 1 [BHQ-1] [89]; for SFSV L, fwd, 5ʹ-TCT GAG AAC TGA GCT ACA AGT GTT TAT TA-3ʹ, rev, 5ʹ-TTC CCA TCT CTC TTC TGA AGA GTG-3ʹ, probe, FAM-AGG TCA TAG ACA GTA TCA TGA GAA TTG CTA GGT G-BHQ-1 [4]; for RVFV S, fwd, 5ʹ-TGC CAC GAG TYA GAG CCA-3ʹ, rev, 5ʹ-GTG GGT CCG AGA GTY TGC-3ʹ, probe, FAM-TCC TTC TCC CAG TCA GCC CCA C-BHQ-1 [89])."
sparser
"Transcript levels of host genes were detected with SYBR Premix Ex Taq (Tli RNaseH Plus) (TaKaRa) and QuantiTect primers (human IFNB, QT00203763; RRN18S, QT00199367; Qiagen), whereas viral genomic segments were detected with Premix Ex Taq (Probe qPCR) (TaKaRa) and previously published primers and probes for the SFSV and RVFV S and L segments (for SFSV S, fwd, 5=-TGC ACT CAT CCA AGC TAT GTG-3=, rev, 5=-GAG GGC TAC AAA CAA GGG ATC-3=, probe, 6-carboxyfluorescein [FAM]-TCC CCC ATT CTC AGA ATG TAA GAC ATT AGC-black hole quencher 1 [BHQ-1] [89]; for SFSV L, fwd, 5=-TCT GAG AAC TGA GCT ACA AGT GTT TAT TA-3=, rev, 5=-TTC CCA TCT CTC TTC TGA AGA GTG-3=, probe, FAM-AGG TCA TAG ACA GTA TCA TGA GAA TTG CTA GGT G-BHQ-1 [4]; for RVFV S, fwd, 5=-TGC CAC GAG TYA GAG CCA-3=, rev, 5=-GTG GGT CCG AGA GTY TGC-3=, probe, FAM-TCC TTC TCC CAG TCA GCC CCA C-BHQ-1 [89])."
sparser
"All rights reserved.) U VEITIS CAN BE OF INFECTIOUS OR NONINFECTIOUS
A(G/C)G G(G/C)G T(A/G)C GCA GGT A AGA A(G/C)G GTG T(A/G)C GCA GAT A Probe FAM-ACC ACG TCG AAA ACT TCG AA-MGBNFQ FAM-ACC ACG TCG AAA ACT TCA AA-MGBNFQ FAM-ACA CCG CGG CGT CA-MGBNFQ Coronavirus 229E Forward CAG TCA AAT GGG CTG ATG CA Reverse CAA AGG GCT ATA AAG AGA ATA AGG TAT TCT ND 53 Probe FAM-CCC TGA CGA CCA CGT TGT GGT TCA -TAMRA Coronavirus NL63 Forward AAG GGT TTT CCA CAG CTT GCT AAA GGT TTT CCA CAG CTT GCT ND 53 Reverse ATC ACC CAC TTC ATC AGT GCT AAC Probe FAM-TCA CTA TCA AAG AAT AAC GCA GCC TGA TTA GGA A -TAMRA Coronavirus OC43 Forward CGA TGA GGC TAT TCC GAC TAG GT Reverse CCT TCC TGA GCC TTC AAT ATA GTA ACC ND 53 Probe FAM-TCC GCC TGG CAC GGT ACT CCC T -TAMRA Enteroviruses Forward TCC TCC GGC CCC TGA Reverse AAT TGT CAC CAT AAG CAG CCA GAT TGT CAC CAT AAG CAG CCA ND 50 Probe FAM-CGG AAC CGA CTA CTT TGG GTG ACC GT -TAMRA FAM-CGG AAC CGA CTA CTT TGG GTG TCC GT -TAMRA Epstein-Barr virus Forward GGA ACC TGG TCA TCC TTT GC Reverse ACG TGC ATG GAC CGG TTA AT 50 copies/mL 42 Probe FAM-CGC AGG CAC TCG TAC TGC TCG CT -TAMRA Human herpesvirus 6 Forward GAA GCA GCA ATC GCA 160 copies/mL 42 Reverse ACA CA ATG TAA CTC Probe GGT GTA CGG TGT CTA FAM-AAC CCG TGC GCC GCT -TAMRA Human metapneumovirus Forward CAT ATA AGC ATG CTA TAT TAA AAG AGT CTC ND 49 Reverse CCT ATT TCT GCA GCA TAT TTG TAA TCA G Probe FAM-TG(C/T) AAT GAT GAG GGT GTC ACT GCG GTT G -TAMRA Influenza virus A Forward AAG ACC AAT CCT GTC ACC TCT GA Reverse CAA AGC GTC TAC GCT GCA GTC C ND 52 Probe FAM-TTT GTG TTC ACG CTC ACC GTG CC -TAMRA Influenza virus B Forward AAA TAC GGT GGA TTA AAC AAA AGC AA Reverse CCA GCA ATA GCT CCG AAG AAA ND 52 Probe FAM-CAC CCA TAT TGG GCA ATT TCC TAT GGC -TAMRA Parainfluenza virus 1 Forward TGA TTT AAA CCC GGT AAT TTC TCA T Reverse CCT TGT TCC TGC AGC TAT TAC AGA ND 51 Probe FAM-ACG ACA ACA GGA AAT C -TAMRA Parainfluenza virus 2 Forward AGG ACT ATG AAA ACC ATT TAC CTA AGT GA Reverse AAG CAA GTC TCA GTT CAG CTA GAT CA ND 51 Probe FAM-ATC AAT CGC AAA AGC TGT TCA GTC ACT GCT ATA C -TAMRA Parainfluenza virus 3 Forward TGA TGA AAG ATC AGA TTA TGC AT Reverse CCG GGA CAC CCA GTT GTG ND 51 Probe FAM-TGG ACC AGG GAT ATA CTA CAA AGG CAA AAT AAT ATT TCT C -TAMRA Continued on next page
FAM-GTA TCA TCA TCT GCC AAA TCG GCA ATT AAA CA -TAMRA Human parechovirus Forward TGC AAA CAC TAG TGG TA(A/T) GGC CC Reverse 1 TCA GAT CCA TAG TG(C/T) CAC TTG TTA CCT Reverse 2 TCA GAT CCA CAG TGT CTC TTG TTA CCT 1 TCID50/mL Forthcoming Probe FAM-CGA AGG ATG CCC AGA AGG TAC CCG -TAMRA Respiratory syncytial virus A Forward AGA TCA ACT TCT GTC ATC CAG CAA Reverse TTC TGA ACA TCA TAA TTA GGA GTA TCA AT ND 54 Probe FAM-CAC CAT CCA ACG GAG CAC AGG AGA T -TAMRA Respiratory syncytial virus B Forward AAG ATG CAA ATC ATA AAT TCA CAG GA Reverse TGA TAT CCA GCA TCT TTA AGT ATC TTT ATA GTG ND 54 Probe FAM-TCC CCT TCC TAA CCT GGA CAT AGC ATA TAA CAT ACC T -TAMRA Rubella virus Forward CAC GCC GCA CGG ACA Reverse 1 CAC CGG GAC TG(C/T) TG(A/G) TTG C 1.7 PFU/mL Forthcoming Reverse 2 CAC CGG GAC TGT TGG TTG C Probe FAM-AGG TCC CGC CCG AC-MGBNFQ Mycoplasma pneumoniae Forward GGT CAA TCT GGC GTG CAT CT Reverse TGG TAA CTG CCC CAC AAG C 50 CCU/mL 34 Probe FAM-TCC CCC GTT GAA AAA GTG AGT GGG T -TAMRA Chlamydia pneumoniae Forward TCC GCA TTG CTC AGC C Reverse AAA CAA TTT GCA TGA AGT CTG AGA A 4.9 IFU/mL 34 Probe FAM-TAA ACT TAA CTG CAT GGA ACC CTT CTT TAC TAG G -TAMRA CCU ϭ color-changing units; FAM ϭ 6-carboxyfluorescein fluorescent label; IFU ϭ inclusion-forming units; MGBNFQ ϭ minor groove binding nonfluorescent quencher; ND ϭ not determined; PFU ϭ plaque-forming units; TAMRA ϭ tetramethylrhodamine quencher; TCID50 ϭ tissue culture infectious dose 50."
sparser
"We recently reported that the acetylation status of ATG9A regulates its ability to interact with FAM134B (also referred to as RETREG1) and SEC62 ( xref ), two ER membrane-bound proteins that can act as receptors for LC3B through their LC3B-interacting region (LIR) ( xref ; xref ; xref ; xref )."
sparser
"In this study, we dissected the structural aspects of the ATG9A-FAM134B and ATG9A-SEC62 interaction, resolved the ATG9A interactome , and took advantage of AT-1 S113R/+ and AT-1 sTg mice to discover two ATG9A-interacting proteins—calreticulin (CALR) and heat shock protein beta 1 (HSPB1)—which engage from the lumenal and cytosolic sides of the ER membrane, respectively, to regulate the induction of reticulophagy."
NP affects USP9X
|
8
sparser
"In 2011, the groups of Frangioni and Nguyen reported the use of fluorescently tagged nerve tracers, namely, GE3082 and FAM-NP41, for the visualization of sciatic nerves. xref , xref In 2017, the group of Gibbs reported a dual fluorophore tissue staining method that reduced fluorescence background signals and aided in nerve-specific visualization. xref Parallel to this work, the Chin lab reported the use of [ 18 F]FTC-146 for the visualization of nerve injuries in a neuropathic pain model via targeting of the sigma-1 receptor. xref In 2013, Du Bois and colleagues reported the use of 18 F-labeled saxitoxin for the imaging of neuromas in a rat model of spared-nerve injury. xref While this represented the first small-molecule positron emission tomography (PET) imaging agent capable of targeting voltage-gated sodium channels, the reagent lacked specificity for a particular sodium channel subtype."
sparser
"To this end, 145-nucleosomes, 185-nucleosomes and oligonucleosomes were reconstituted using 5′-fluorescein (FAM)-labelled 145-dsDNA, 185-dsDNA and 2,450-dsDNA, respectively, and isolated HeLa nucleosomes were chemically labelled through the reaction of 5(6)-carboxyfluorescein N -hydroxysuccinimide ester (FAM-NHS) with Lys residues of histones."
| PMC
sparser
"Here, we detail
a protocol to label WWP2 at the N-terminus using Fluorescein NHS ester
(5/6-carboxyfluorescein succinimidyl ester, FAM-NHS ester) adopting a stepwise
labeling procedure (Basic Protocol 1 and 2), and then use the labeled FAM-WWP2 to
measure its binding affinity to its requisite E2 (UbcH5c) enzyme by performing MST
binding assays (Basic Protocol 3)."
sparser
"Bevacizumab-loaded tetra-PEG gel and 5-Carboxyfluorescein N-succinimidyl ester (FAM-NHS)-labeled IgG-loaded tetra-PEG gel were prepared by mixing tetra-PEG with thiol termini (tetra-PEG-SH) solution, maleimide termini (tetra-PEG-MA) solution, and bevacizumab or FAM-NHS labeled IgG."
sparser
"In the absence of GST–hPXR-LBD, these FAM-SRC1 peptides interacted with the Tb–anti-GST only very weakly, and these weak interactions correlated positively with the respective FAM-SRC1 peptide concentrations in a linear manner ( xref , lower curves with data points shown as closed triangles)."
sparser
"With the addition of the hPXR agonist T0901317 (10 μM), the total interactions (10 μM T0901317–mediated total bindings) between individual FAM-SRC1 peptides and the complex of Tb–anti-GST and GST–hPXR-LBD increased further, first in an exponential manner when the FAM-SRC1 peptide concentrations were low and then in a linear manner when the FAM-SRC1 peptide concentrations increased ( xref , upper curves with data points shown as closed squares)."
sparser
"These T0901317-induced specific interactions between FAM-SRC1 peptides and hPXR could be quantified by the relative areas ( xref , gray areas, calculated by using the GraphPad software Prism) between the respective T0901317 curves ( xref , upper curves) and DMSO curves ( xref , middle curve) in the presence of Tb–anti-GST and GST–hPXR-LBD, with areas of 7,764,875, 16,729,790, and 10,406,140 for FAM-SRC1-A, FAM-SRC1-B, and FAM-SRC1-C, respectively, with FAM-SRC1-B giving the largest induction among the three peptides tested."
sparser
"Binding of 125 I-labelled FAF to various fibrillin recombinant fragments was investigated in a slot binding assay, see Fig. xref A. This blot shows a concentration dependent binding of FAF to the N-terminal fragment of fibrillin-2 (rFBN2-N) and a slightly lower binding intensity to the N-terminal fragment of fibrillin-1 (rFBN1-N)."
reach
"Further investigations into the binding of FAF to fibrillin with surface plasmon resonance showed binding of FAF to both N-terminal fragments of fibrillin-1 and -2, with a slightly higher binding to rFBN2-N (K D : 3.7 nM) than rFBN1-N (K D : 22nM), _ FIG D. Protein FAF binds fibrillin both at the bacterial surface and in solution."
sparser
"Here, we detail
a protocol to label WWP2 at the N-terminus using Fluorescein NHS ester
(5/6-carboxyfluorescein succinimidyl ester, FAM-NHS ester) adopting a stepwise
labeling procedure (Basic Protocol 1 and 2), and then use the labeled FAM-WWP2 to
measure its binding affinity to its requisite E2 (UbcH5c) enzyme by performing MST
binding assays (Basic Protocol 3)."
sparser
"Binding of 125 I-labelled FAF to various fibrillin recombinant fragments was investigated in a slot binding assay, see Fig. xref A. This blot shows a concentration dependent binding of FAF to the N-terminal fragment of fibrillin-2 (rFBN2-N) and a slightly lower binding intensity to the N-terminal fragment of fibrillin-1 (rFBN1-N)."
reach
"Further investigations into the binding of FAF to fibrillin with surface plasmon resonance showed binding of FAF to both N-terminal fragments of fibrillin-1 and -2, with a slightly higher binding to rFBN2-N (K D : 3.7 nM) than rFBN1-N (K D : 22nM), _ FIG D. Protein FAF binds fibrillin both at the bacterial surface and in solution."
USP9X affects cell migration
|
1
5
USP9X inhibits cell migration.
|
3
USP9X inhibits cell migration. 3 / 4
|
3
reach
"The depletion and pharmacological inhibition of USP9X by WP1130, an inhibitor of USP9X, downregulate endogenous Snail1 protein, inhibit cell migration, invasion, metastasis, and increase cellular sensitivity to cisplatin and paclitaxel both in vitro and in vivo, whereas the reconstitution of Snail1 in cells with USP9X depletion at least partially reverses these phenotypes."
USP9X activates cell migration.
|
1
2
sparser
"Here, we detail
a protocol to label WWP2 at the N-terminus using Fluorescein NHS ester
(5/6-carboxyfluorescein succinimidyl ester, FAM-NHS ester) adopting a stepwise
labeling procedure (Basic Protocol 1 and 2), and then use the labeled FAM-WWP2 to
measure its binding affinity to its requisite E2 (UbcH5c) enzyme by performing MST
binding assays (Basic Protocol 3)."
sparser
"By systematically analyzing, Yu Zhao et al. demonstrated that the OTUD4 could complex with USP7-USP9X. They proved that the OTUD4-USP7-USP9X complex was required for alkylation damage resistance and repair via promoting stability of ALKBH3, a demethylases for alkylation damage repair [ xref ]."
sparser
"The SHH-FAM palmitoylation reaction rate was dependent on Pal-CoA, with titration generating V max = 0.081 pmol min –1 (95% CI 0.076–0.086 pmol min –1 ) and apparent K M = 170 nM (95% CI 110–230 nM, ESI, Fig. S1E xref ), in good agreement with previous studies of DDM-solubilised HHAT. xref , xref "
sparser
"Titration of DDM and TX-100 with Pal-SHH-FAM demonstrated close agreement between the detergent concentration required for half-maximal polarised signal (EC 50 ) and detergent CMC (DDM EC 50 = 150 μM (95% confidence interval (CI) 130–170 μM), CMC = 170 μM; TX-100 EC 50 = 180 μM (95% CI 140–220 μM), CMC = 200 μM; xref and S1A xref ). xref BSA titration broadly correlated polarisation EC 50 = 490 nM (95% CI 420–580) to the K d of BSA for palmitic acid (104 nM) ( xref ). xref No increase in polarised emission from non-palmitoylated SHH-FAM was observed at these concentrations."
sparser
"Residues 24–33 of SHH (the N-terminus of the mature SHH signalling protein) were synthesised with fluorescein labels as substrate (SHH-FAM) and palmitoylated product (Pal-SHH-FAM) peptides (ESI, Table S1 xref ), and prepared in mixtures with a range of detergents (2 mM) or the lipid-carrier protein bovine serum albumin (BSA, 0.15 mM)."
sparser
"The unlabelled SHH peptide or SHH(FL) substrates were employed as competitive inhibitors of SHH-FAM palmitoylation, affording IC 50 values of 370 nM (95% CI 300–470 nM) and 440 nM (95% CI 350–570 nM), respectively ( xref ), which corresponded to approximately 50% of the SHH-FAM concentration."
sparser
"CatG was adjusted to a final concentration of 80 µg/mL and incubated with the activity-based probe FAM-P1,5D-Suc-Val-Pro-PheP(OPh)2 (MARS116-FAM, final concentration 20 µM) [23] in DPBS pH 7.4 (no calcium, no magnesium, Gibco by Thermo Fisher Scientific, Karlsruhe, Germany, Cat."
sparser
"Purified CatG was preincubated with different concentrations of camostat and followed by adding the FAM-P1,5D-Suc-Val-Pro-PheP(OPh)2 (MARS116-FAM) activity-based probe (ABP), which is a directly 5(6)-carboxyfluorescein (FAM) conjugated peptidyl diphenyl phosphonate, to analyze whether camostat (Figure 1A) inhibits the proteolytic activity of CatG [23]."
sparser
"By systematically analyzing, Yu Zhao et al. demonstrated that the OTUD4 could complex with USP7-USP9X. They proved that the OTUD4-USP7-USP9X complex was required for alkylation damage resistance and repair via promoting stability of ALKBH3, a demethylases for alkylation damage repair [ xref ]."
sparser
"On the other hand inhibition of ERK and USP9x with pharmaceutical or genetic approach in breast cancer cells abolishes FFA promotion of TGF-β–induced SMAD4-USP9x interaction, SMAD4 nuclear retention, SMAD3/SMAD4 complex formation, and target gene expression, resulting in decrease in cancer cell invasion and metastasis ( xref )."
sparser
"We also found that FFA/ERK-induced SMAD4 T277 phosphorylation is indispensable in SMAD4-USP9x interaction and its deubiquitination as well as subsequent nuclear accumulation, which is required for TGF-β–induced breast cancer invasion and metastasis under the high FFA/obesity conditions."
sparser
"The SHH-FAM palmitoylation reaction rate was dependent on Pal-CoA, with titration generating V max = 0.081 pmol min –1 (95% CI 0.076–0.086 pmol min –1 ) and apparent K M = 170 nM (95% CI 110–230 nM, ESI, Fig. S1E xref ), in good agreement with previous studies of DDM-solubilised HHAT. xref , xref "
sparser
"Titration of DDM and TX-100 with Pal-SHH-FAM demonstrated close agreement between the detergent concentration required for half-maximal polarised signal (EC 50 ) and detergent CMC (DDM EC 50 = 150 μM (95% confidence interval (CI) 130–170 μM), CMC = 170 μM; TX-100 EC 50 = 180 μM (95% CI 140–220 μM), CMC = 200 μM; xref and S1A xref ). xref BSA titration broadly correlated polarisation EC 50 = 490 nM (95% CI 420–580) to the K d of BSA for palmitic acid (104 nM) ( xref ). xref No increase in polarised emission from non-palmitoylated SHH-FAM was observed at these concentrations."
sparser
"Residues 24–33 of SHH (the N-terminus of the mature SHH signalling protein) were synthesised with fluorescein labels as substrate (SHH-FAM) and palmitoylated product (Pal-SHH-FAM) peptides (ESI, Table S1 xref ), and prepared in mixtures with a range of detergents (2 mM) or the lipid-carrier protein bovine serum albumin (BSA, 0.15 mM)."
sparser
"The unlabelled SHH peptide or SHH(FL) substrates were employed as competitive inhibitors of SHH-FAM palmitoylation, affording IC 50 values of 370 nM (95% CI 300–470 nM) and 440 nM (95% CI 350–570 nM), respectively ( xref ), which corresponded to approximately 50% of the SHH-FAM concentration."
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6
USP9X affects cell adhesion
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6
reach
"From this screening, we have now thoroughly validated that depletion of the ubiquitin-specific protease 9X (USP9X) in HeLa and oropharyngeal squamous cell carcinoma (UMSCC74A) cells using small interfering RNA (siRNA), leads to significantly decreased survival of cells after high-LET radiation."
sparser
"On the contrary, practically identical EC 50 values were determined for the PARP2–XRCC1 complex by using either FAM-PARP2 or Cy3-XRCC1 as the labelled partner ( xref A and xref C; xref ), suggesting that the labelling of either partner with chemically different fluorophores did not disturb the protein–protein interaction."
sparser
"Typical curves obtained for FAM-PARP2 titration with unlabelled PARP2, PARP1, Polβ, and XRCC1 are shown in xref A. A substantial increase in fluorescence intensity of FAM-PARP2 (from 1.8- to 3.5-fold) in the presence of saturating concentrations of the most protein partners was detected, indicating that the local environment of the fluorophore changed upon protein–protein association."
sparser
"Then, the fluorophore was conjugated by amide bond formation following Dde deprotection (FAM-NPs (10)), and streptavidin was conjugated using glutaraldehyde as a cross-linker, following Fmoc deprotection, to achieve Strep-FAM-NPs (13). (1) FACS results were analysed using MFI (n = 3) in the APC channel, showing a strong MFI increase when the sandwich construct was complete ( Figure 4C) ."
| DOI
sparser
"Characterisation of Strep-FAM-NPs (13). (A) Size distribution determined by DLS; (B) Values of the zeta potential of amino-methyl PS-NPs (1) (blue), FAM-NPs (10) (dark green) and Strep-FAM-NPs (13) (green); (C) Scatter plot analysis representative of amino-methyl NPs (1) (blue) and Strep-FAM-NPs (13) (green); (D) Confocal laser microscopy analysis (63× magnification, 20 µm scale bar, FITC channel) and (E) Evaluation of morphology by transmission electron microscopy (TEM).
(13) to capture biotinylated PNA:DNA heteroduplex The capacity of Strep-FAM-NPs (13) to capture biotinylated PNA:DNA heteroduplex was evaluated using a sandwich-like assay, and the efficiency was evaluated by flow cytometry analysis."
| DOI
sparser
"Moreover, USP9X can increase MAPT phosphorylation via a second mechanism, by deubiquitinating the protein alpha-synuclein (SNCA) [ xref ], which functions as a connecting mediator between the glycogen synthase kinase 3β (GSK3B) and MAPT and has been shown to stimulate MAPT phosphorylation via GSK3B in vitro [ xref ]."
reach
"Moreover, USP9X can increase MAPT phosphorylation via a second mechanism, by deubiquitinating the protein alpha-synuclein (SNCA) [XREF_BIBR], which functions as a connecting mediator between the glycogen synthase kinase 3beta (GSK3B) and MAPT and has been shown to stimulate MAPT phosphorylation via GSK3B in vitro [XREF_BIBR]."
USP9X affects H3K9me3
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6
sparser
"As predicted from the structural studies, mutation of R298 (R298*: R298A) and the P-patch (P-patch*: P293A/P294A/P295A) resulted in significant gain of binding of mTTD-PHD V1 to the FAM-H3K9me3 peptide compared to the wild type protein as measured by FP (Figure xref ) and suggesting increased accessibility of the mTTD peptide-binding surface groove/R-pocket."
USP9X affects BP
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6
reach
"Importantly, USP9X depletion increased AMOTL2 mono-ubiquitination, an effect that was abolished by co-depletion of WWP1 using two independent small hairpin RNAs (shRNAs), confirming that the two enzymes indeed exhibit contrasting functions on the same AMOTL2 lysine residues (Fig S2B)."
"we report for the first time that USP9X is a deubiquitinase of Angiomotin-like 2 (AMOTL2) and that AMOTL2 mono-ubiquitination is required for YAP inhibition."
sparser
"Figure 5: Targeted delivery of DNA/RNA payloads to target cells using antibody functionalized RBCEVs. (A) Flow cytometry analysis reflecting the delivery of a FAM-conjugated non-targeting ASO (FAM-NC-ASO) to CA1a cells by EGFR-targeting or non-targeting RBCEVs. (B) Flow cytometry analysis demonstrating the delivery of FAM-ASO to H358 cells using EpCAM-mAb-conjugated RBCEVs or non-targeting RBCEVs. (C) Mean dGFP fluorescence of CA1a-dGFP cells determined using flow cytometry following incubation with EGFR-targeted or non-targeted RBCEVs loaded with GFP-siRNA. (D) Representative immunofluorescent images of CA1a-dGFP cells treated with dGFP-siRNA-loaded RBCEVs."
sparser
"On the contrary, practically identical EC 50 values were determined for the PARP2–XRCC1 complex by using either FAM-PARP2 or Cy3-XRCC1 as the labelled partner ( xref A and xref C; xref ), suggesting that the labelling of either partner with chemically different fluorophores did not disturb the protein–protein interaction."
sparser
"Typical curves obtained for FAM-PARP2 titration with unlabelled PARP2, PARP1, Polβ, and XRCC1 are shown in xref A. A substantial increase in fluorescence intensity of FAM-PARP2 (from 1.8- to 3.5-fold) in the presence of saturating concentrations of the most protein partners was detected, indicating that the local environment of the fluorophore changed upon protein–protein association."
sparser
"Then, the fluorophore was conjugated by amide bond formation following Dde deprotection (FAM-NPs (10)), and streptavidin was conjugated using glutaraldehyde as a cross-linker, following Fmoc deprotection, to achieve Strep-FAM-NPs (13). (1) FACS results were analysed using MFI (n = 3) in the APC channel, showing a strong MFI increase when the sandwich construct was complete ( Figure 4C) ."
| DOI
sparser
"Characterisation of Strep-FAM-NPs (13). (A) Size distribution determined by DLS; (B) Values of the zeta potential of amino-methyl PS-NPs (1) (blue), FAM-NPs (10) (dark green) and Strep-FAM-NPs (13) (green); (C) Scatter plot analysis representative of amino-methyl NPs (1) (blue) and Strep-FAM-NPs (13) (green); (D) Confocal laser microscopy analysis (63× magnification, 20 µm scale bar, FITC channel) and (E) Evaluation of morphology by transmission electron microscopy (TEM).
(13) to capture biotinylated PNA:DNA heteroduplex The capacity of Strep-FAM-NPs (13) to capture biotinylated PNA:DNA heteroduplex was evaluated using a sandwich-like assay, and the efficiency was evaluated by flow cytometry analysis."
| DOI
H3K9me3 affects USP9X
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6
sparser
"As predicted from the structural studies, mutation of R298 (R298*: R298A) and the P-patch (P-patch*: P293A/P294A/P295A) resulted in significant gain of binding of mTTD-PHD V1 to the FAM-H3K9me3 peptide compared to the wild type protein as measured by FP (Figure xref ) and suggesting increased accessibility of the mTTD peptide-binding surface groove/R-pocket."
BP affects USP9X
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6
sparser
"Figure 5: Targeted delivery of DNA/RNA payloads to target cells using antibody functionalized RBCEVs. (A) Flow cytometry analysis reflecting the delivery of a FAM-conjugated non-targeting ASO (FAM-NC-ASO) to CA1a cells by EGFR-targeting or non-targeting RBCEVs. (B) Flow cytometry analysis demonstrating the delivery of FAM-ASO to H358 cells using EpCAM-mAb-conjugated RBCEVs or non-targeting RBCEVs. (C) Mean dGFP fluorescence of CA1a-dGFP cells determined using flow cytometry following incubation with EGFR-targeted or non-targeted RBCEVs loaded with GFP-siRNA. (D) Representative immunofluorescent images of CA1a-dGFP cells treated with dGFP-siRNA-loaded RBCEVs."
USP9X affects degradation
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5
USP9X affects cell growth
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4
USP9X activates cell growth.
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2
USP9X inhibits cell growth.
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2
USP9X affects Subcutaneous Fat
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5
USP9X binds Subcutaneous Fat. 5 / 5
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5
sparser
"This study was conducted in three phases: (1) explicate the concept of stigma towards family caregivers of patients with mental illness, (2) develop and iteratively optimise a preliminary version of the SAT-FAM, and (3) test the psychometric properties of the final version of the SAT-FAM."
sparser
"Confocal immunofluorescence microscopy gave no signals in the absence of a fluorescence-labeled peptide (Fig. xref a,e), but detected the presence of specific signals on the surface of A10 cells and HAoSMCs onto which FAM-SBSN_HUMAN[225–237] (Fig. xref b,f) or FAM-SBSN_HUMAN[243–259] (Fig. xref c,g) were overlaid to bind to their cell surface."
USP9X affects RFP
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5
sparser
"Trans-autophosphorylation of exogenous kinase-dead Plk4 by endogenous wild-type Plk4 with which it is dimerized has been described xref , and the minor stabilization of Plk4 K41M observed in the presence of RFP-FAM46C may have reflected such homodimerization with endogenous Plk4, the latter being susceptible to regulation by FAM46C. The significant stabilizing effect of FAM46C on wild-type Plk4 protein level could also have potentially been due to an increase in Plk4 mRNA level mediated through FAM46C’s poly(A) RNA polymerase activity, but if this were the dominant mechanism, one might expect a corresponding increase in K41M protein stability, which was not observed."
sparser
"We conducted a cross-sectional study and investigated the association of serum OGN and FAM5C levels and muscle mass examined by whole-body dual-energy x-ray absorptiometry with bone mineral density (BMD), bone turnover markers, and the presence of vertebral fractures (VFs) in 156 postmenopausal women with type 2 diabetes mellitus (T2DM)."
sparser
"When the WriPdSf-2 primer set was applied to Chellaston ( S 7 S 23 ) × Lauranne ( S 3 S f ) F 1 progeny, HEX fluorescence was detected from the HEX-HEX genotype S 3 S 23 (half from each allele) and from the null-HEX genotype S 3 S 7 (all from S 3 ), FAM fluorescence was detected for the null-FAM genotype S 7 S f (all from S f ) and both HEX and FAM fluorescence were detected for the HEX-FAM genotype S 23 S f (HEX from S 23 and FAM from S f ) (Fig. xref )."
sparser
"FAM fluorescence for null-FAM heterozygotes ( S 7 S f for WriPdSf-2 and WriPdSf-5; S 8 S f for WriPdSf-2, WriPdSf-4 and WriPdSf-5), both HEX and FAM fluorescence for HEX-FAM heterozygotes ( S 1 S f and S 23 S f for WriPdSf-3 and S 5 S f for WriPdSf-4) and a low levels of HEX fluorescence for null-null heterozygotes ( S 1 S 7 for WriPdSf-2 and WriPdSf-6; S 1 S 8 for WriPdSf-2, WrPdSf-4 and WriPdSf-5)."
sparser
"TCA ATG TTT TCT CGC ATC GCA GCA CAA TAC 159 This work RP: Biotin-GCA ATC TCA AGG CAA CGG CTC AGA TCA AGG Probe: FAM-AAC TTG TTA AAA AAG CAT TCA ATC TGA TGG-THF-GTT CCT TGT ACA GCC
Comparison of RT-RPA-BP26, qPCR-IS711, cPCR-BP26 and Rose Bengal Plate test (RBPT) For the 45 vaginal ewe swabs collected; 28(62.2%), 28 (62.2%), and 27 (60.0%) were positive by RT-RPA-BP26, qPCR-IS711and cPCR-BP26respectively."
sparser
"All rights reserved.) U VEITIS CAN BE OF INFECTIOUS OR NONINFECTIOUS
A(G/C)G G(G/C)G T(A/G)C GCA GGT A AGA A(G/C)G GTG T(A/G)C GCA GAT A Probe FAM-ACC ACG TCG AAA ACT TCG AA-MGBNFQ FAM-ACC ACG TCG AAA ACT TCA AA-MGBNFQ FAM-ACA CCG CGG CGT CA-MGBNFQ Coronavirus 229E Forward CAG TCA AAT GGG CTG ATG CA Reverse CAA AGG GCT ATA AAG AGA ATA AGG TAT TCT ND 53 Probe FAM-CCC TGA CGA CCA CGT TGT GGT TCA -TAMRA Coronavirus NL63 Forward AAG GGT TTT CCA CAG CTT GCT AAA GGT TTT CCA CAG CTT GCT ND 53 Reverse ATC ACC CAC TTC ATC AGT GCT AAC Probe FAM-TCA CTA TCA AAG AAT AAC GCA GCC TGA TTA GGA A -TAMRA Coronavirus OC43 Forward CGA TGA GGC TAT TCC GAC TAG GT Reverse CCT TCC TGA GCC TTC AAT ATA GTA ACC ND 53 Probe FAM-TCC GCC TGG CAC GGT ACT CCC T -TAMRA Enteroviruses Forward TCC TCC GGC CCC TGA Reverse AAT TGT CAC CAT AAG CAG CCA GAT TGT CAC CAT AAG CAG CCA ND 50 Probe FAM-CGG AAC CGA CTA CTT TGG GTG ACC GT -TAMRA FAM-CGG AAC CGA CTA CTT TGG GTG TCC GT -TAMRA Epstein-Barr virus Forward GGA ACC TGG TCA TCC TTT GC Reverse ACG TGC ATG GAC CGG TTA AT 50 copies/mL 42 Probe FAM-CGC AGG CAC TCG TAC TGC TCG CT -TAMRA Human herpesvirus 6 Forward GAA GCA GCA ATC GCA 160 copies/mL 42 Reverse ACA CA ATG TAA CTC Probe GGT GTA CGG TGT CTA FAM-AAC CCG TGC GCC GCT -TAMRA Human metapneumovirus Forward CAT ATA AGC ATG CTA TAT TAA AAG AGT CTC ND 49 Reverse CCT ATT TCT GCA GCA TAT TTG TAA TCA G Probe FAM-TG(C/T) AAT GAT GAG GGT GTC ACT GCG GTT G -TAMRA Influenza virus A Forward AAG ACC AAT CCT GTC ACC TCT GA Reverse CAA AGC GTC TAC GCT GCA GTC C ND 52 Probe FAM-TTT GTG TTC ACG CTC ACC GTG CC -TAMRA Influenza virus B Forward AAA TAC GGT GGA TTA AAC AAA AGC AA Reverse CCA GCA ATA GCT CCG AAG AAA ND 52 Probe FAM-CAC CCA TAT TGG GCA ATT TCC TAT GGC -TAMRA Parainfluenza virus 1 Forward TGA TTT AAA CCC GGT AAT TTC TCA T Reverse CCT TGT TCC TGC AGC TAT TAC AGA ND 51 Probe FAM-ACG ACA ACA GGA AAT C -TAMRA Parainfluenza virus 2 Forward AGG ACT ATG AAA ACC ATT TAC CTA AGT GA Reverse AAG CAA GTC TCA GTT CAG CTA GAT CA ND 51 Probe FAM-ATC AAT CGC AAA AGC TGT TCA GTC ACT GCT ATA C -TAMRA Parainfluenza virus 3 Forward TGA TGA AAG ATC AGA TTA TGC AT Reverse CCG GGA CAC CCA GTT GTG ND 51 Probe FAM-TGG ACC AGG GAT ATA CTA CAA AGG CAA AAT AAT ATT TCT C -TAMRA Continued on next page
FAM-GTA TCA TCA TCT GCC AAA TCG GCA ATT AAA CA -TAMRA Human parechovirus Forward TGC AAA CAC TAG TGG TA(A/T) GGC CC Reverse 1 TCA GAT CCA TAG TG(C/T) CAC TTG TTA CCT Reverse 2 TCA GAT CCA CAG TGT CTC TTG TTA CCT 1 TCID50/mL Forthcoming Probe FAM-CGA AGG ATG CCC AGA AGG TAC CCG -TAMRA Respiratory syncytial virus A Forward AGA TCA ACT TCT GTC ATC CAG CAA Reverse TTC TGA ACA TCA TAA TTA GGA GTA TCA AT ND 54 Probe FAM-CAC CAT CCA ACG GAG CAC AGG AGA T -TAMRA Respiratory syncytial virus B Forward AAG ATG CAA ATC ATA AAT TCA CAG GA Reverse TGA TAT CCA GCA TCT TTA AGT ATC TTT ATA GTG ND 54 Probe FAM-TCC CCT TCC TAA CCT GGA CAT AGC ATA TAA CAT ACC T -TAMRA Rubella virus Forward CAC GCC GCA CGG ACA Reverse 1 CAC CGG GAC TG(C/T) TG(A/G) TTG C 1.7 PFU/mL Forthcoming Reverse 2 CAC CGG GAC TGT TGG TTG C Probe FAM-AGG TCC CGC CCG AC-MGBNFQ Mycoplasma pneumoniae Forward GGT CAA TCT GGC GTG CAT CT Reverse TGG TAA CTG CCC CAC AAG C 50 CCU/mL 34 Probe FAM-TCC CCC GTT GAA AAA GTG AGT GGG T -TAMRA Chlamydia pneumoniae Forward TCC GCA TTG CTC AGC C Reverse AAA CAA TTT GCA TGA AGT CTG AGA A 4.9 IFU/mL 34 Probe FAM-TAA ACT TAA CTG CAT GGA ACC CTT CTT TAC TAG G -TAMRA CCU ϭ color-changing units; FAM ϭ 6-carboxyfluorescein fluorescent label; IFU ϭ inclusion-forming units; MGBNFQ ϭ minor groove binding nonfluorescent quencher; ND ϭ not determined; PFU ϭ plaque-forming units; TAMRA ϭ tetramethylrhodamine quencher; TCID50 ϭ tissue culture infectious dose 50."
sparser
"The CD, fluorescence and colorimetric studies have consistently revealed that FAM-GOO showed strong capability of forming the triple helical structure, while FAM-GPP pronouncedly displayed the single stranded conformation at temperatures as low as 4 °C. The binding experiments have indicated that both peptide probes could recognize denatured collagen with high specificity, and FAM-GPP remarkably did not need the preheating treatment."
sparser
"It appears less likely that the endogenous inhibitor of caspase 8, c-FLIP [ xref ], which akin to Survivin and Mcl-1 is a molecule with a relatively short half-life and is stabilized by chaperones and potentially other deubiquitinases, is involved in TRAIL/WP1130-mediated cell death, because an interaction of Usp9X and c-FLIP has not been proven [ xref , xref ]."
reach
"It appears less likely that the endogenous inhibitor of caspase 8, c-FLIP [XREF_BIBR], which akin to Survivin and Mcl-1 is a molecule with a relatively short half-life and is stabilized by chaperones and potentially other deubiquitinases, is involved in TRAIL and WP1130 mediated cell death, because an interaction of Usp9X and c-FLIP has not been proven [XREF_BIBR, XREF_BIBR]."
Subcutaneous Fat affects USP9X
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5
USP9X binds Subcutaneous Fat. 5 / 5
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5
sparser
"This study was conducted in three phases: (1) explicate the concept of stigma towards family caregivers of patients with mental illness, (2) develop and iteratively optimise a preliminary version of the SAT-FAM, and (3) test the psychometric properties of the final version of the SAT-FAM."
sparser
"Confocal immunofluorescence microscopy gave no signals in the absence of a fluorescence-labeled peptide (Fig. xref a,e), but detected the presence of specific signals on the surface of A10 cells and HAoSMCs onto which FAM-SBSN_HUMAN[225–237] (Fig. xref b,f) or FAM-SBSN_HUMAN[243–259] (Fig. xref c,g) were overlaid to bind to their cell surface."
RFP affects USP9X
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5
sparser
"Trans-autophosphorylation of exogenous kinase-dead Plk4 by endogenous wild-type Plk4 with which it is dimerized has been described xref , and the minor stabilization of Plk4 K41M observed in the presence of RFP-FAM46C may have reflected such homodimerization with endogenous Plk4, the latter being susceptible to regulation by FAM46C. The significant stabilizing effect of FAM46C on wild-type Plk4 protein level could also have potentially been due to an increase in Plk4 mRNA level mediated through FAM46C’s poly(A) RNA polymerase activity, but if this were the dominant mechanism, one might expect a corresponding increase in K41M protein stability, which was not observed."
PRC2_complex affects USP9X
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1
4
reach
"These results suggest that BIX-01294 degrades the MCL1 through up-regulation of PMAIP1 and reduction of USP9X, which is consistent to our previous study that PMAIP1 upregulation reduces the availability of USP9X to MCL1, thereby promoting its ubiquitination and degradation, leading to the apoptosis of neoplastic cells [XREF_BIBR]."
sparser
"We conducted a cross-sectional study and investigated the association of serum OGN and FAM5C levels and muscle mass examined by whole-body dual-energy x-ray absorptiometry with bone mineral density (BMD), bone turnover markers, and the presence of vertebral fractures (VFs) in 156 postmenopausal women with type 2 diabetes mellitus (T2DM)."
sparser
"TCA ATG TTT TCT CGC ATC GCA GCA CAA TAC 159 This work RP: Biotin-GCA ATC TCA AGG CAA CGG CTC AGA TCA AGG Probe: FAM-AAC TTG TTA AAA AAG CAT TCA ATC TGA TGG-THF-GTT CCT TGT ACA GCC
Comparison of RT-RPA-BP26, qPCR-IS711, cPCR-BP26 and Rose Bengal Plate test (RBPT) For the 45 vaginal ewe swabs collected; 28(62.2%), 28 (62.2%), and 27 (60.0%) were positive by RT-RPA-BP26, qPCR-IS711and cPCR-BP26respectively."
sparser
"All rights reserved.) U VEITIS CAN BE OF INFECTIOUS OR NONINFECTIOUS
A(G/C)G G(G/C)G T(A/G)C GCA GGT A AGA A(G/C)G GTG T(A/G)C GCA GAT A Probe FAM-ACC ACG TCG AAA ACT TCG AA-MGBNFQ FAM-ACC ACG TCG AAA ACT TCA AA-MGBNFQ FAM-ACA CCG CGG CGT CA-MGBNFQ Coronavirus 229E Forward CAG TCA AAT GGG CTG ATG CA Reverse CAA AGG GCT ATA AAG AGA ATA AGG TAT TCT ND 53 Probe FAM-CCC TGA CGA CCA CGT TGT GGT TCA -TAMRA Coronavirus NL63 Forward AAG GGT TTT CCA CAG CTT GCT AAA GGT TTT CCA CAG CTT GCT ND 53 Reverse ATC ACC CAC TTC ATC AGT GCT AAC Probe FAM-TCA CTA TCA AAG AAT AAC GCA GCC TGA TTA GGA A -TAMRA Coronavirus OC43 Forward CGA TGA GGC TAT TCC GAC TAG GT Reverse CCT TCC TGA GCC TTC AAT ATA GTA ACC ND 53 Probe FAM-TCC GCC TGG CAC GGT ACT CCC T -TAMRA Enteroviruses Forward TCC TCC GGC CCC TGA Reverse AAT TGT CAC CAT AAG CAG CCA GAT TGT CAC CAT AAG CAG CCA ND 50 Probe FAM-CGG AAC CGA CTA CTT TGG GTG ACC GT -TAMRA FAM-CGG AAC CGA CTA CTT TGG GTG TCC GT -TAMRA Epstein-Barr virus Forward GGA ACC TGG TCA TCC TTT GC Reverse ACG TGC ATG GAC CGG TTA AT 50 copies/mL 42 Probe FAM-CGC AGG CAC TCG TAC TGC TCG CT -TAMRA Human herpesvirus 6 Forward GAA GCA GCA ATC GCA 160 copies/mL 42 Reverse ACA CA ATG TAA CTC Probe GGT GTA CGG TGT CTA FAM-AAC CCG TGC GCC GCT -TAMRA Human metapneumovirus Forward CAT ATA AGC ATG CTA TAT TAA AAG AGT CTC ND 49 Reverse CCT ATT TCT GCA GCA TAT TTG TAA TCA G Probe FAM-TG(C/T) AAT GAT GAG GGT GTC ACT GCG GTT G -TAMRA Influenza virus A Forward AAG ACC AAT CCT GTC ACC TCT GA Reverse CAA AGC GTC TAC GCT GCA GTC C ND 52 Probe FAM-TTT GTG TTC ACG CTC ACC GTG CC -TAMRA Influenza virus B Forward AAA TAC GGT GGA TTA AAC AAA AGC AA Reverse CCA GCA ATA GCT CCG AAG AAA ND 52 Probe FAM-CAC CCA TAT TGG GCA ATT TCC TAT GGC -TAMRA Parainfluenza virus 1 Forward TGA TTT AAA CCC GGT AAT TTC TCA T Reverse CCT TGT TCC TGC AGC TAT TAC AGA ND 51 Probe FAM-ACG ACA ACA GGA AAT C -TAMRA Parainfluenza virus 2 Forward AGG ACT ATG AAA ACC ATT TAC CTA AGT GA Reverse AAG CAA GTC TCA GTT CAG CTA GAT CA ND 51 Probe FAM-ATC AAT CGC AAA AGC TGT TCA GTC ACT GCT ATA C -TAMRA Parainfluenza virus 3 Forward TGA TGA AAG ATC AGA TTA TGC AT Reverse CCG GGA CAC CCA GTT GTG ND 51 Probe FAM-TGG ACC AGG GAT ATA CTA CAA AGG CAA AAT AAT ATT TCT C -TAMRA Continued on next page
FAM-GTA TCA TCA TCT GCC AAA TCG GCA ATT AAA CA -TAMRA Human parechovirus Forward TGC AAA CAC TAG TGG TA(A/T) GGC CC Reverse 1 TCA GAT CCA TAG TG(C/T) CAC TTG TTA CCT Reverse 2 TCA GAT CCA CAG TGT CTC TTG TTA CCT 1 TCID50/mL Forthcoming Probe FAM-CGA AGG ATG CCC AGA AGG TAC CCG -TAMRA Respiratory syncytial virus A Forward AGA TCA ACT TCT GTC ATC CAG CAA Reverse TTC TGA ACA TCA TAA TTA GGA GTA TCA AT ND 54 Probe FAM-CAC CAT CCA ACG GAG CAC AGG AGA T -TAMRA Respiratory syncytial virus B Forward AAG ATG CAA ATC ATA AAT TCA CAG GA Reverse TGA TAT CCA GCA TCT TTA AGT ATC TTT ATA GTG ND 54 Probe FAM-TCC CCT TCC TAA CCT GGA CAT AGC ATA TAA CAT ACC T -TAMRA Rubella virus Forward CAC GCC GCA CGG ACA Reverse 1 CAC CGG GAC TG(C/T) TG(A/G) TTG C 1.7 PFU/mL Forthcoming Reverse 2 CAC CGG GAC TGT TGG TTG C Probe FAM-AGG TCC CGC CCG AC-MGBNFQ Mycoplasma pneumoniae Forward GGT CAA TCT GGC GTG CAT CT Reverse TGG TAA CTG CCC CAC AAG C 50 CCU/mL 34 Probe FAM-TCC CCC GTT GAA AAA GTG AGT GGG T -TAMRA Chlamydia pneumoniae Forward TCC GCA TTG CTC AGC C Reverse AAA CAA TTT GCA TGA AGT CTG AGA A 4.9 IFU/mL 34 Probe FAM-TAA ACT TAA CTG CAT GGA ACC CTT CTT TAC TAG G -TAMRA CCU ϭ color-changing units; FAM ϭ 6-carboxyfluorescein fluorescent label; IFU ϭ inclusion-forming units; MGBNFQ ϭ minor groove binding nonfluorescent quencher; ND ϭ not determined; PFU ϭ plaque-forming units; TAMRA ϭ tetramethylrhodamine quencher; TCID50 ϭ tissue culture infectious dose 50."
sparser
"The CD, fluorescence and colorimetric studies have consistently revealed that FAM-GOO showed strong capability of forming the triple helical structure, while FAM-GPP pronouncedly displayed the single stranded conformation at temperatures as low as 4 °C. The binding experiments have indicated that both peptide probes could recognize denatured collagen with high specificity, and FAM-GPP remarkably did not need the preheating treatment."
Salusin-β affects USP9X
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4
sparser
"Confocal immunofluorescence microscopy with antibodies against the ATP synthase β-subunits revealed specific cell surface signals that were especially strong in the HeLa cells and the signals colocalized very well with those of cells onto which salusin-β-FAM was overlaid to bind to its cell surface receptors (Fig. xref , xref )."
sparser
"Overall, we confirmed that most samples were identified by multiplex RT-PCR
List of primer pairs and probe sets for target virus detection Forward ACA AGA CCA ATC CTG TCA CCT 63 Reverse TGG ACA AAG CGT CTA CGC T 64 Probe FAM-CTC ACC GTG CCC AGT GAG C-BHQ1 67 Influenza B NS & NEP Forward GGA TCC TCA ACT CAC TCT TCGA 63 Reverse CGG TGC TCT TGA CCA AAT TGG"
sparser
"For the detection of rhinoviruses, the following primers and probes were used: Forward-S1: WGC CVG CGT GGC KGC C, Forward-S2: AGC CYG CGT GGT GCC C, Reverse: GAA ACA CGG ACA CCC AAA GTA GT and probe FAM-CTC CGG CCC CTG AAT GYG GCT AA-TAMRA, at the rate of 300 nm per reaction for primers and 133 nm for the Pathogens 2021, 10, 516 9 of 12 probe."
sparser
"For the detection of rhinoviruses, the following primers and probes were used: Forward-S1: WGC CVG CGT GGC KGC C, Forward-S2: AGC CYG CGT GGT GCC C, Reverse: GAA ACA CGG ACA CCC AAA GTA GT and probe FAM-CTC CGG CCC CTG AAT GYG GCT AA-TAMRA, at the rate of 300 nm per reaction for primers and 133 nm for the probe."
Phenethyl isothiocyanate affects USP9X
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4
P4 affects USP9X
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4
N-ATF5-S1 affects USP9X
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4
sparser
"MRSA containing mecA target ssDNA interacts with carboxy fluorescein (FAM)-ssDNA-GO and removes FAM ssDNA to form double-stranded mecA-ssDNA FAM-SYBR Green I-ssDNA complex in the presence of intercalating fluorescent dye SYBR green I. SYBR green is further incorporated as the polymerase present in the solution extends target DNA using FAM ssDNA as template leading to increase in the fluorescence intensity [92]."
sparser
"MRSA containing mecA target ssDNA interacts with carboxy fluorescein (FAM)-ssDNA-GO and removes FAM ssDNA to form double-stranded mecA-ssDNA FAM-SYBR Green I-ssDNA complex in the presence of intercalating fluorescent dye SYBR green I. SYBR green is further incorporated as the polymerase present in the solution extends target DNA using FAM ssDNA as template leading to increase in the fluorescence intensity [ xref ]."
sparser
"MRSA containing mecA target ssDNA interacts with carboxy fluorescein (FAM)-ssDNA-GO and removes FAM ssDNA to form double-stranded mecA-ssDNA FAM-SYBR Green I-ssDNA complex in the presence of intercalating fluorescent dye SYBR green I. SYBR green is further incorporated as the polymerase present in the solution extends target DNA using FAM ssDNA as template leading to increase in the fluorescence intensity [ xref ]."
sparser
"MRSA containing mecA target ssDNA interacts with carboxy fluorescein (FAM)-ssDNA-GO and removes FAM ssDNA to form double-stranded mecA-ssDNA FAM-SYBR Green I-ssDNA complex in the presence of intercalating fluorescent dye SYBR green I. SYBR green is further incorporated as the polymerase present in the solution extends target DNA using FAM ssDNA as template leading to increase in the fluorescence intensity [92]."
EIF affects USP9X
|
4
sparser
"As shown in Figure xref , endogenous eIF4B was found to be coimmunoprecipitated with USP9X. Treatment with either MG132, a protease inhibitor, or N-ethylmaleimide (NEM), a deubiquitinase inhibitor, had no effect on the interaction between USP9X and eIF4B. Moreover, to rule out any RNA-mediated interactions, RNase A was added to the cell lysate during immunoprecipitation."
sparser
"This result makes PABP and eIF4E much less likely the direct substrate of USP9X. Of note, although eIF4B does not appear to be USP9X’s substrate, it may still play an important role in this process, most likely as a scaffolding protein connecting USP9X and eIF4A. This would be consistent with the interaction between eIF4B and USP9X."
USP9X affects ubiquitination
|
2
USP9X affects tumor growth
|
3
USP9X affects salusin-β
|
4
sparser
"Confocal immunofluorescence microscopy with antibodies against the ATP synthase β-subunits revealed specific cell surface signals that were especially strong in the HeLa cells and the signals colocalized very well with those of cells onto which salusin-β-FAM was overlaid to bind to its cell surface receptors (Fig. xref , xref )."
sparser
"Overall, we confirmed that most samples were identified by multiplex RT-PCR
List of primer pairs and probe sets for target virus detection Forward ACA AGA CCA ATC CTG TCA CCT 63 Reverse TGG ACA AAG CGT CTA CGC T 64 Probe FAM-CTC ACC GTG CCC AGT GAG C-BHQ1 67 Influenza B NS & NEP Forward GGA TCC TCA ACT CAC TCT TCGA 63 Reverse CGG TGC TCT TGA CCA AAT TGG"
sparser
"For the detection of rhinoviruses, the following primers and probes were used: Forward-S1: WGC CVG CGT GGC KGC C, Forward-S2: AGC CYG CGT GGT GCC C, Reverse: GAA ACA CGG ACA CCC AAA GTA GT and probe FAM-CTC CGG CCC CTG AAT GYG GCT AA-TAMRA, at the rate of 300 nm per reaction for primers and 133 nm for the Pathogens 2021, 10, 516 9 of 12 probe."
sparser
"For the detection of rhinoviruses, the following primers and probes were used: Forward-S1: WGC CVG CGT GGC KGC C, Forward-S2: AGC CYG CGT GGT GCC C, Reverse: GAA ACA CGG ACA CCC AAA GTA GT and probe FAM-CTC CGG CCC CTG AAT GYG GCT AA-TAMRA, at the rate of 300 nm per reaction for primers and 133 nm for the probe."
USP9X affects p4
|
4
sparser
"MRSA containing mecA target ssDNA interacts with carboxy fluorescein (FAM)-ssDNA-GO and removes FAM ssDNA to form double-stranded mecA-ssDNA FAM-SYBR Green I-ssDNA complex in the presence of intercalating fluorescent dye SYBR green I. SYBR green is further incorporated as the polymerase present in the solution extends target DNA using FAM ssDNA as template leading to increase in the fluorescence intensity [92]."
sparser
"MRSA containing mecA target ssDNA interacts with carboxy fluorescein (FAM)-ssDNA-GO and removes FAM ssDNA to form double-stranded mecA-ssDNA FAM-SYBR Green I-ssDNA complex in the presence of intercalating fluorescent dye SYBR green I. SYBR green is further incorporated as the polymerase present in the solution extends target DNA using FAM ssDNA as template leading to increase in the fluorescence intensity [ xref ]."
sparser
"MRSA containing mecA target ssDNA interacts with carboxy fluorescein (FAM)-ssDNA-GO and removes FAM ssDNA to form double-stranded mecA-ssDNA FAM-SYBR Green I-ssDNA complex in the presence of intercalating fluorescent dye SYBR green I. SYBR green is further incorporated as the polymerase present in the solution extends target DNA using FAM ssDNA as template leading to increase in the fluorescence intensity [ xref ]."
sparser
"MRSA containing mecA target ssDNA interacts with carboxy fluorescein (FAM)-ssDNA-GO and removes FAM ssDNA to form double-stranded mecA-ssDNA FAM-SYBR Green I-ssDNA complex in the presence of intercalating fluorescent dye SYBR green I. SYBR green is further incorporated as the polymerase present in the solution extends target DNA using FAM ssDNA as template leading to increase in the fluorescence intensity [92]."
USP9X affects homologous recombination
|
4
USP9X affects eIF
|
4
sparser
"As shown in Figure xref , endogenous eIF4B was found to be coimmunoprecipitated with USP9X. Treatment with either MG132, a protease inhibitor, or N-ethylmaleimide (NEM), a deubiquitinase inhibitor, had no effect on the interaction between USP9X and eIF4B. Moreover, to rule out any RNA-mediated interactions, RNase A was added to the cell lysate during immunoprecipitation."
sparser
"This result makes PABP and eIF4E much less likely the direct substrate of USP9X. Of note, although eIF4B does not appear to be USP9X’s substrate, it may still play an important role in this process, most likely as a scaffolding protein connecting USP9X and eIF4A. This would be consistent with the interaction between eIF4B and USP9X."
USP9X affects activity
|
4
sparser
"Regardless of this, our in vitro phosphatase assay demonstrated that FAM122A effectively inhibited the PP2A activity in the PP2A-Cα-pulled down precipitates with the same amounts of the PP2A-Cα complex, suggesting that the inhibitory activity of FAM122A involves its interaction with PP2A complex besides decreased PP2A-Cα."
sparser
"Human Coronavirus 229E (229E, ATCC VR-740) and Human Coronavirus OC43 (OC43, ATCC VR-1558)
NL63: 5′-GTG GTG TAC TTC TTG TTG ATGG, 3′-GGT ACT AGG CGT AGC AAC TATT, 56-FAM-AGG CAA CTG-ZEN-ACC CAC TTG AAC ACG-3IABkFQ; OC43: 5′-GGA CCT CAT TTG TGT GCA AAGTT, 3′-GCA GCC AAA GTG TAT CCA CTGA, JUN-TCA AAG TGT TGC CTC CAC TGC TCT CAGA-QSY; 229E: 5′-CAC TTT TGA CAA GAA AGC GTT TAC AC, 3′-CTG CGA CCA GCC ACT CTA CTAC, VIC-TAG CAG CGT CAT ACC TAG CTT GCC CACA-QSY; and HKU1: 5′-CTG GTT GGT GTT GGT GAA CATT, 3′-TGA TCC ATC CAA TAC ACC ACACT, FAM-TGC AGG GTT CGG TGTT-MGBNFQ.
and influenza viruses."
sparser
"After that, the detection of viral RNA was carried out using the followed sequence of primers (influenza A-Forward-5 GACCRATCCTGT-CACCTCTGA C 3 ; Reverse-5 AGGGCATTYTGGACAAAKCGTCTA3 ; influenza B-Forward-5 GGAGCAACCAATGCCAC 3 ; Reverse-5 GTKTAGGCGGTCTTGACCAG 3 ) and probes (influenza A-Probe1-5 FAM-TGC AGT CCT CGC TCA CTG GGC ACG-BHQ1-3 ; influenza B-Probe1 5'-(FAM)-ATAAACTTTGAAGCAGGAAT-(MGB)-3'), and also by using the AgPath-ID One-Step RT-PCR Kit (Applied Biosystems Inc., EUA) on an ABI 7500 SDS real-time PCR machine (Applied Biosystems, Weiterstadt, Germany)."
sparser
"Since we also had control data of diffusion times for FAM-SP and NK1R-NLPs alone, by comparing the average diffusion times of the mixture with the controls, we were able to infer the percentage of bound FAM-SP (Ligand bound %) versus the total amount of FAM-SP added and the concentration of free NK1R-NLPs at equilibrium ([NK1R-NLPs])."
sparser
"For example, we showed that two single nucleotide polymorphisms (SNPs) in the CAMP responsive element binding protein 1 gene ( CREB1 rs2253206 and rs2360969) were related to change in temperature during exercise, the SLIT2 SNP rs1379659 and the FAM5C SNP rs1935881 were associated with norepinephrine change during exercise, and a SNP in the μ–opioid receptor gene ( OPRM1 , rs1799971) was related to changes in norepinephrine and lactate [ xref ]."
sparser
"The AIapt/FAM/SH-3 W J was assembled by annealing three corresponding DNA strands at an equimolar ratio in TMS buffer (40 mM Tris−HCl, 10 mM MgCl 2 , 100 mM NaCl) by heating at 80 °C for 5 min, followed by slowly cooling down to 4 °C at a rate of 2 °C/min on a T100™ Thermal Cycler (Bio-rad)."
sparser
"LTM test indicated that exposure to a novel OF 2 h before retrieval-extinction significantly enhanced extinction (main group effects: F (2, 21) = 19.44; post hoc comparisons: nov-Ret, p < 0.001 vs . control), but exposure to a familiar OF had no effects (fam-Ret, p = 0.336 vs . control) (Fig. xref )."
sparser
"To map the PRICKLE1-USP9X interacting domain, recombinant vectors expressing full-length, N-terminal or C-terminal portions of PRICKLE1 (schematic diagrams in xref ) were transfected into HEK293T cells and immunoprecipitated via the Flag tag. xref showed that endogenous USP9X interacted specifically with the PRICKLE1 C-terminus."
USP9X affects PNA-GO
|
4
USP9X affects MARS116
|
4
USP9X affects LBVA3
|
4
USP9X affects GVF27
|
4
sparser
"MRSA containing mecA target ssDNA interacts with carboxy fluorescein (FAM)-ssDNA-GO and removes FAM ssDNA to form double-stranded mecA-ssDNA FAM-SYBR Green I-ssDNA complex in the presence of intercalating fluorescent dye SYBR green I. SYBR green is further incorporated as the polymerase present in the solution extends target DNA using FAM ssDNA as template leading to increase in the fluorescence intensity [92]."
sparser
"MRSA containing mecA target ssDNA interacts with carboxy fluorescein (FAM)-ssDNA-GO and removes FAM ssDNA to form double-stranded mecA-ssDNA FAM-SYBR Green I-ssDNA complex in the presence of intercalating fluorescent dye SYBR green I. SYBR green is further incorporated as the polymerase present in the solution extends target DNA using FAM ssDNA as template leading to increase in the fluorescence intensity [ xref ]."
sparser
"MRSA containing mecA target ssDNA interacts with carboxy fluorescein (FAM)-ssDNA-GO and removes FAM ssDNA to form double-stranded mecA-ssDNA FAM-SYBR Green I-ssDNA complex in the presence of intercalating fluorescent dye SYBR green I. SYBR green is further incorporated as the polymerase present in the solution extends target DNA using FAM ssDNA as template leading to increase in the fluorescence intensity [ xref ]."
sparser
"MRSA containing mecA target ssDNA interacts with carboxy fluorescein (FAM)-ssDNA-GO and removes FAM ssDNA to form double-stranded mecA-ssDNA FAM-SYBR Green I-ssDNA complex in the presence of intercalating fluorescent dye SYBR green I. SYBR green is further incorporated as the polymerase present in the solution extends target DNA using FAM ssDNA as template leading to increase in the fluorescence intensity [92]."
sparser
"Hence, all four mutants that reduced the perinuclear localization of filamin (Fig. xref ), either by disrupting filamin–FAM101B interaction (dnFLNA and dnFAM101B) or by disrupting the nuclear mechanotransduction (dnNesprin1 and dnLaminB1), also made cell competition more or less insensitive to ECM stiffness (Fig. xref )."
sparser
"The difference between the K 1/2max of eIF2B binding to the immobilized P-eIF2α-NTD in the BLI experiment and the IC 50 of P-eIF2α-NTD’s inhibitory effect on FAM-ISRIB binding to eIF2B ( xref B) might reflect the occupancy of both regulatory sites of eIF2B in the maximally inhibited state in the later assay and the limitation of occupancy to a single site on eIF2B in the BLI experiment ( xref B)."
reach
"The third ERP component commonly elicited by FAF, the P2, has been shown to increase linearly as the size of the feedback perturbations increases XREF_BIBR, leading to the suggestion that the amplitude of the P2 component reflects the size of the speech production error XREF_BIBR, XREF_BIBR."
USP9X affects B55α
|
4
sparser
"Human Coronavirus 229E (229E, ATCC VR-740) and Human Coronavirus OC43 (OC43, ATCC VR-1558)
NL63: 5′-GTG GTG TAC TTC TTG TTG ATGG, 3′-GGT ACT AGG CGT AGC AAC TATT, 56-FAM-AGG CAA CTG-ZEN-ACC CAC TTG AAC ACG-3IABkFQ; OC43: 5′-GGA CCT CAT TTG TGT GCA AAGTT, 3′-GCA GCC AAA GTG TAT CCA CTGA, JUN-TCA AAG TGT TGC CTC CAC TGC TCT CAGA-QSY; 229E: 5′-CAC TTT TGA CAA GAA AGC GTT TAC AC, 3′-CTG CGA CCA GCC ACT CTA CTAC, VIC-TAG CAG CGT CAT ACC TAG CTT GCC CACA-QSY; and HKU1: 5′-CTG GTT GGT GTT GGT GAA CATT, 3′-TGA TCC ATC CAA TAC ACC ACACT, FAM-TGC AGG GTT CGG TGTT-MGBNFQ.
and influenza viruses."
sparser
"After that, the detection of viral RNA was carried out using the followed sequence of primers (influenza A-Forward-5 GACCRATCCTGT-CACCTCTGA C 3 ; Reverse-5 AGGGCATTYTGGACAAAKCGTCTA3 ; influenza B-Forward-5 GGAGCAACCAATGCCAC 3 ; Reverse-5 GTKTAGGCGGTCTTGACCAG 3 ) and probes (influenza A-Probe1-5 FAM-TGC AGT CCT CGC TCA CTG GGC ACG-BHQ1-3 ; influenza B-Probe1 5'-(FAM)-ATAAACTTTGAAGCAGGAAT-(MGB)-3'), and also by using the AgPath-ID One-Step RT-PCR Kit (Applied Biosystems Inc., EUA) on an ABI 7500 SDS real-time PCR machine (Applied Biosystems, Weiterstadt, Germany)."
sparser
"Since we also had control data of diffusion times for FAM-SP and NK1R-NLPs alone, by comparing the average diffusion times of the mixture with the controls, we were able to infer the percentage of bound FAM-SP (Ligand bound %) versus the total amount of FAM-SP added and the concentration of free NK1R-NLPs at equilibrium ([NK1R-NLPs])."
sparser
"For example, we showed that two single nucleotide polymorphisms (SNPs) in the CAMP responsive element binding protein 1 gene ( CREB1 rs2253206 and rs2360969) were related to change in temperature during exercise, the SLIT2 SNP rs1379659 and the FAM5C SNP rs1935881 were associated with norepinephrine change during exercise, and a SNP in the μ–opioid receptor gene ( OPRM1 , rs1799971) was related to changes in norepinephrine and lactate [ xref ]."
sparser
"The AIapt/FAM/SH-3 W J was assembled by annealing three corresponding DNA strands at an equimolar ratio in TMS buffer (40 mM Tris−HCl, 10 mM MgCl 2 , 100 mM NaCl) by heating at 80 °C for 5 min, followed by slowly cooling down to 4 °C at a rate of 2 °C/min on a T100™ Thermal Cycler (Bio-rad)."
sparser
"In this study, we dissected the structural aspects of the ATG9A-FAM134B and ATG9A-SEC62 interaction, resolved the ATG9A interactome , and took advantage of AT-1 S113R/+ and AT-1 sTg mice to discover two ATG9A-interacting proteins—calreticulin (CALR) and heat shock protein beta 1 (HSPB1)—which engage from the lumenal and cytosolic sides of the ER membrane, respectively, to regulate the induction of reticulophagy."
sparser
"LTM test indicated that exposure to a novel OF 2 h before retrieval-extinction significantly enhanced extinction (main group effects: F (2, 21) = 19.44; post hoc comparisons: nov-Ret, p < 0.001 vs . control), but exposure to a familiar OF had no effects (fam-Ret, p = 0.336 vs . control) (Fig. xref )."
sparser
"We also performed in vitro methylation assays using recombinant C2 domain of USP9X and PRMTs (PRMT1, PRMT3 and CARM1) and confirmed that USP9X is methylated by PRMT1 ( xref ), which is the predominant type I arginine methyltransferase in mammalian cells that accounts for 85% of cellular PRMT activity [ xref , xref ]."
reach
"We also performed in vitro methylation assays using recombinant C2 domain of USP9X and PRMTs (PRMT1, PRMT3 and CARM1) and confirmed that USP9X is methylated by PRMT1 (XREF_SUPPLEMENTARY), which is the predominant type I arginine methyltransferase in mammalian cells that accounts for 85% of cellular PRMT activity [XREF_BIBR, XREF_BIBR]."
sparser
"To map the PRICKLE1-USP9X interacting domain, recombinant vectors expressing full-length, N-terminal or C-terminal portions of PRICKLE1 (schematic diagrams in xref ) were transfected into HEK293T cells and immunoprecipitated via the Flag tag. xref showed that endogenous USP9X interacted specifically with the PRICKLE1 C-terminus."
sparser
"CatG was adjusted to a final concentration of 80 µg/mL and incubated with the activity-based probe FAM-P1,5D-Suc-Val-Pro-PheP(OPh)2 (MARS116-FAM, final concentration 20 µM) [23] in DPBS pH 7.4 (no calcium, no magnesium, Gibco by Thermo Fisher Scientific, Karlsruhe, Germany, Cat."
sparser
"Purified CatG was preincubated with different concentrations of camostat and followed by adding the FAM-P1,5D-Suc-Val-Pro-PheP(OPh)2 (MARS116-FAM) activity-based probe (ABP), which is a directly 5(6)-carboxyfluorescein (FAM) conjugated peptidyl diphenyl phosphonate, to analyze whether camostat (Figure 1A) inhibits the proteolytic activity of CatG [23]."
PNA-GO affects USP9X
|
4
MARS116 affects USP9X
|
4
LBVA3 affects USP9X
|
4
IITZ-01 affects USP9X
|
2
2
GVF27 affects USP9X
|
4
sparser
"MRSA containing mecA target ssDNA interacts with carboxy fluorescein (FAM)-ssDNA-GO and removes FAM ssDNA to form double-stranded mecA-ssDNA FAM-SYBR Green I-ssDNA complex in the presence of intercalating fluorescent dye SYBR green I. SYBR green is further incorporated as the polymerase present in the solution extends target DNA using FAM ssDNA as template leading to increase in the fluorescence intensity [92]."
sparser
"MRSA containing mecA target ssDNA interacts with carboxy fluorescein (FAM)-ssDNA-GO and removes FAM ssDNA to form double-stranded mecA-ssDNA FAM-SYBR Green I-ssDNA complex in the presence of intercalating fluorescent dye SYBR green I. SYBR green is further incorporated as the polymerase present in the solution extends target DNA using FAM ssDNA as template leading to increase in the fluorescence intensity [ xref ]."
sparser
"MRSA containing mecA target ssDNA interacts with carboxy fluorescein (FAM)-ssDNA-GO and removes FAM ssDNA to form double-stranded mecA-ssDNA FAM-SYBR Green I-ssDNA complex in the presence of intercalating fluorescent dye SYBR green I. SYBR green is further incorporated as the polymerase present in the solution extends target DNA using FAM ssDNA as template leading to increase in the fluorescence intensity [ xref ]."
sparser
"MRSA containing mecA target ssDNA interacts with carboxy fluorescein (FAM)-ssDNA-GO and removes FAM ssDNA to form double-stranded mecA-ssDNA FAM-SYBR Green I-ssDNA complex in the presence of intercalating fluorescent dye SYBR green I. SYBR green is further incorporated as the polymerase present in the solution extends target DNA using FAM ssDNA as template leading to increase in the fluorescence intensity [92]."
sparser
"Hence, all four mutants that reduced the perinuclear localization of filamin (Fig. xref ), either by disrupting filamin–FAM101B interaction (dnFLNA and dnFAM101B) or by disrupting the nuclear mechanotransduction (dnNesprin1 and dnLaminB1), also made cell competition more or less insensitive to ECM stiffness (Fig. xref )."
EOAI3402143 affects USP9X
|
1
3
sparser
"The difference between the K 1/2max of eIF2B binding to the immobilized P-eIF2α-NTD in the BLI experiment and the IC 50 of P-eIF2α-NTD’s inhibitory effect on FAM-ISRIB binding to eIF2B ( xref B) might reflect the occupancy of both regulatory sites of eIF2B in the maximally inhibited state in the later assay and the limitation of occupancy to a single site on eIF2B in the BLI experiment ( xref B)."
B55α affects USP9X
|
4
sparser
"In this study, we dissected the structural aspects of the ATG9A-FAM134B and ATG9A-SEC62 interaction, resolved the ATG9A interactome , and took advantage of AT-1 S113R/+ and AT-1 sTg mice to discover two ATG9A-interacting proteins—calreticulin (CALR) and heat shock protein beta 1 (HSPB1)—which engage from the lumenal and cytosolic sides of the ER membrane, respectively, to regulate the induction of reticulophagy."
reach
"The oligopeptide GPLGLAGC(PLG) was synthesized by Shanghai Sangon Biotech Co., Ltd. (Shanghai, China), and negative control (NC) siRNA, Cy3-siRNA (Cy3-conjugated NC siRNA at the 5′-end), fluorescein amidite (FAM)-siRNA (FAM-conjugated NC siRNA at the 5′-end), and PD-L1–siRNA (Sense: UUCUCCGAACGUGUCACGUTT; and antisense: ACGUGACACGUUCGGAGAATT) (Liu, Cao, et al., 2019) were synthesized by Shanghai GenePharma Co., Ltd. (Shanghai, China)."
TLyP-1 affects USP9X
|
3
SiRNA/Dox-TPGS-LPs affects USP9X
|
3
Nitric oxide affects USP9X
|
1
2
sparser
"This was due to the possibility of near-UV wavelengths generating toxic photo-products and radical oxygen among amino acid components of Dulbecco’s modified Eagle medium (DMEM).[ xref ]At 405 nm, hASCs transfected with either SNP-FAM or GNP-FAM were illuminated at 50 J of incident light energy, and 565 J at 530 nm."
sparser
"Further analyses revealed, (i) the canonical mTORC1 protein, RAPTOR, physically associates with Usp9x in embryonic brains, (ii) RAPTOR protein level is directly proportional to USP9X, in both loss- and gain-of-function experiments in cultured cells and, (iii) USP9X deubiquitlyating activity opposes the proteasomal degradation of RAPTOR."
reach
"Further analyses revealed, (i) the canonical mTORC1 protein, RAPTOR, physically associates with Usp9x in embryonic brains, (ii) RAPTOR protein level is directly proportional to USP9X, in both loss- and gain-of-function experiments in cultured cells and, (iii) USP9X deubiquitlyating activity opposes the proteasomal degradation of RAPTOR."
LifeAct affects USP9X
|
3
Hsa-miR-6895-3p affects USP9X
3
|
Hsa-miR-6849-3p affects USP9X
3
|
Hsa-miR-6818-3p affects USP9X
3
|
Hsa-miR-6732-3p affects USP9X
3
|
Hsa-miR-593-3p affects USP9X
3
|
Hsa-miR-5699-3p affects USP9X
3
|
Hsa-miR-548s affects USP9X
3
|
Hsa-miR-4684-5p affects USP9X
3
|
Hsa-miR-4421 affects USP9X
3
|
Hsa-miR-3926 affects USP9X
3
|
Hsa-miR-339-5p affects USP9X
3
|
Hsa-miR-3190-5p affects USP9X
3
|
Hsa-miR-10b-5p affects USP9X
3
|
Hsa-miR-10a-5p affects USP9X
3
|
eidos
"The depletion and pharmacological inhibition of USP9X by WP1130 , an inhibitor of USP9X , downregulate endogenous Snail1 protein , inhibit cell migration , invasion , metastasis , and increase cellular sensitivity to cisplatin and paclitaxel both in vitro and in vivo , whereas the reconstitution of Snail1 in cells with USP9X depletion at least partially reverses these phenotypes ."
sparser
"Family-based studies are robust against bias led from population stratification in genetic studies and helpful in understanding G × G. We proposed a new algorithm epistasis sparse factor analysis (EPISFA) and epistasis sparse factor analysis for linkage disequilibrium (EPISFA-LD) based on unsupervised machine learning to screen G × G. Extensive simulations were performed to compare EPISFA/EPISFA-LD with a classical family-based algorithm FAM-MDR (family-based multifactor dimensionality reduction)."
sparser
"Among the many different machine learning approaches for detecting GGIs, multifactor dimensionality reduction (MDR), proposed by Ritchie et al. [ xref ] has received much interest, and numerous extensions of MDR have been now developed, including quantitative MDR, for quantitative traits [ xref ]; generalized MDR (GMDR), for both quantitative and binary traits [ xref ]; MB-MDR, based on statistical testing [ xref ], Surv/Cox-MDR, for survival data [ xref , xref ]; FAM-MDR, for family data [ xref ], GEE/Multi-MDR, for multivariate traits [ xref , xref ], etc."
Benzyl isothiocyanate affects USP9X
|
3
Benzyl isothiocyanate inhibits USP9X. 3 / 3
|
3
sparser
"All rights reserved.) U VEITIS CAN BE OF INFECTIOUS OR NONINFECTIOUS
A(G/C)G G(G/C)G T(A/G)C GCA GGT A AGA A(G/C)G GTG T(A/G)C GCA GAT A Probe FAM-ACC ACG TCG AAA ACT TCG AA-MGBNFQ FAM-ACC ACG TCG AAA ACT TCA AA-MGBNFQ FAM-ACA CCG CGG CGT CA-MGBNFQ Coronavirus 229E Forward CAG TCA AAT GGG CTG ATG CA Reverse CAA AGG GCT ATA AAG AGA ATA AGG TAT TCT ND 53 Probe FAM-CCC TGA CGA CCA CGT TGT GGT TCA -TAMRA Coronavirus NL63 Forward AAG GGT TTT CCA CAG CTT GCT AAA GGT TTT CCA CAG CTT GCT ND 53 Reverse ATC ACC CAC TTC ATC AGT GCT AAC Probe FAM-TCA CTA TCA AAG AAT AAC GCA GCC TGA TTA GGA A -TAMRA Coronavirus OC43 Forward CGA TGA GGC TAT TCC GAC TAG GT Reverse CCT TCC TGA GCC TTC AAT ATA GTA ACC ND 53 Probe FAM-TCC GCC TGG CAC GGT ACT CCC T -TAMRA Enteroviruses Forward TCC TCC GGC CCC TGA Reverse AAT TGT CAC CAT AAG CAG CCA GAT TGT CAC CAT AAG CAG CCA ND 50 Probe FAM-CGG AAC CGA CTA CTT TGG GTG ACC GT -TAMRA FAM-CGG AAC CGA CTA CTT TGG GTG TCC GT -TAMRA Epstein-Barr virus Forward GGA ACC TGG TCA TCC TTT GC Reverse ACG TGC ATG GAC CGG TTA AT 50 copies/mL 42 Probe FAM-CGC AGG CAC TCG TAC TGC TCG CT -TAMRA Human herpesvirus 6 Forward GAA GCA GCA ATC GCA 160 copies/mL 42 Reverse ACA CA ATG TAA CTC Probe GGT GTA CGG TGT CTA FAM-AAC CCG TGC GCC GCT -TAMRA Human metapneumovirus Forward CAT ATA AGC ATG CTA TAT TAA AAG AGT CTC ND 49 Reverse CCT ATT TCT GCA GCA TAT TTG TAA TCA G Probe FAM-TG(C/T) AAT GAT GAG GGT GTC ACT GCG GTT G -TAMRA Influenza virus A Forward AAG ACC AAT CCT GTC ACC TCT GA Reverse CAA AGC GTC TAC GCT GCA GTC C ND 52 Probe FAM-TTT GTG TTC ACG CTC ACC GTG CC -TAMRA Influenza virus B Forward AAA TAC GGT GGA TTA AAC AAA AGC AA Reverse CCA GCA ATA GCT CCG AAG AAA ND 52 Probe FAM-CAC CCA TAT TGG GCA ATT TCC TAT GGC -TAMRA Parainfluenza virus 1 Forward TGA TTT AAA CCC GGT AAT TTC TCA T Reverse CCT TGT TCC TGC AGC TAT TAC AGA ND 51 Probe FAM-ACG ACA ACA GGA AAT C -TAMRA Parainfluenza virus 2 Forward AGG ACT ATG AAA ACC ATT TAC CTA AGT GA Reverse AAG CAA GTC TCA GTT CAG CTA GAT CA ND 51 Probe FAM-ATC AAT CGC AAA AGC TGT TCA GTC ACT GCT ATA C -TAMRA Parainfluenza virus 3 Forward TGA TGA AAG ATC AGA TTA TGC AT Reverse CCG GGA CAC CCA GTT GTG ND 51 Probe FAM-TGG ACC AGG GAT ATA CTA CAA AGG CAA AAT AAT ATT TCT C -TAMRA Continued on next page
FAM-GTA TCA TCA TCT GCC AAA TCG GCA ATT AAA CA -TAMRA Human parechovirus Forward TGC AAA CAC TAG TGG TA(A/T) GGC CC Reverse 1 TCA GAT CCA TAG TG(C/T) CAC TTG TTA CCT Reverse 2 TCA GAT CCA CAG TGT CTC TTG TTA CCT 1 TCID50/mL Forthcoming Probe FAM-CGA AGG ATG CCC AGA AGG TAC CCG -TAMRA Respiratory syncytial virus A Forward AGA TCA ACT TCT GTC ATC CAG CAA Reverse TTC TGA ACA TCA TAA TTA GGA GTA TCA AT ND 54 Probe FAM-CAC CAT CCA ACG GAG CAC AGG AGA T -TAMRA Respiratory syncytial virus B Forward AAG ATG CAA ATC ATA AAT TCA CAG GA Reverse TGA TAT CCA GCA TCT TTA AGT ATC TTT ATA GTG ND 54 Probe FAM-TCC CCT TCC TAA CCT GGA CAT AGC ATA TAA CAT ACC T -TAMRA Rubella virus Forward CAC GCC GCA CGG ACA Reverse 1 CAC CGG GAC TG(C/T) TG(A/G) TTG C 1.7 PFU/mL Forthcoming Reverse 2 CAC CGG GAC TGT TGG TTG C Probe FAM-AGG TCC CGC CCG AC-MGBNFQ Mycoplasma pneumoniae Forward GGT CAA TCT GGC GTG CAT CT Reverse TGG TAA CTG CCC CAC AAG C 50 CCU/mL 34 Probe FAM-TCC CCC GTT GAA AAA GTG AGT GGG T -TAMRA Chlamydia pneumoniae Forward TCC GCA TTG CTC AGC C Reverse AAA CAA TTT GCA TGA AGT CTG AGA A 4.9 IFU/mL 34 Probe FAM-TAA ACT TAA CTG CAT GGA ACC CTT CTT TAC TAG G -TAMRA CCU ϭ color-changing units; FAM ϭ 6-carboxyfluorescein fluorescent label; IFU ϭ inclusion-forming units; MGBNFQ ϭ minor groove binding nonfluorescent quencher; ND ϭ not determined; PFU ϭ plaque-forming units; TAMRA ϭ tetramethylrhodamine quencher; TCID50 ϭ tissue culture infectious dose 50."
sparser
"RSV-P0 a CAT CCT GAT ATA AGA TAT ATT TAC AGAAG[T(FAM-dT)][Y(THF)][T(BHQ-dT)]GAA AGA TTG CAA TGA[C3-spacer] 47 P-IC a GTA AGG TGC TAG ACT AAA ATT GTT GGGAC[T(HEX-dT)][T(THF)][T(BHQ-dT)]GAA TCT CTG AAG TAA AAG G[TTA TRG TGT CTT CYC TTC CTA ACC 30 qPCR-P FAM-TAA TAG GTA TGT TAT ATG CKATGTC-BHQ 25
The oligonucleotides used for RT-PCR, rtRAA, and RT-qPCR
The reproducibility of singleplex-rtRAA and duplex-rtRAA a Each dilution was tested in a total of 8 replicates"
Amiodarone affects USP9X
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3
USP9X affects tLyP-1
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3
USP9X affects signaling
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sparser
"Settleman and colleagues described that PDK4 downregulation changes pyruvate entry into the TCA cycle and is a critical regulator of EMT. xref KEGG pathway analysis of the microarray data demonstrated that the loss of FAM210B activates TGF- β signaling and subsequent EMT-associated gene expression, and we also confirmed the phenomenon in FAM210B or PDK4 knockdown cells ( xref )."
USP9X affects siRNA/Dox-TPGS-LPs
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3
USP9X affects pathway
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3
sparser
"Since FAM134B activates the Akt/GSK‐3β/β‐catenin pathway, it was next determined whether this axis was involved in the increase in cell proliferation induced by FAM134B. Briefly, 7402 cells transfected with FAM134B were stably transfected with two siRNAs against β‐catenin, namely 7402 si β‐catenin#1 (FAM si β‐ca#1) and 7402 si β‐catenin#2 (FAM si β‐ca#2), respectively."
sparser
"This was due to the possibility of near-UV wavelengths generating toxic photo-products and radical oxygen among amino acid components of Dulbecco’s modified Eagle medium (DMEM).[ xref ]At 405 nm, hASCs transfected with either SNP-FAM or GNP-FAM were illuminated at 50 J of incident light energy, and 565 J at 530 nm."
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sparser
"Further analyses revealed, (i) the canonical mTORC1 protein, RAPTOR, physically associates with Usp9x in embryonic brains, (ii) RAPTOR protein level is directly proportional to USP9X, in both loss- and gain-of-function experiments in cultured cells and, (iii) USP9X deubiquitlyating activity opposes the proteasomal degradation of RAPTOR."
reach
"Further analyses revealed, (i) the canonical mTORC1 protein, RAPTOR, physically associates with Usp9x in embryonic brains, (ii) RAPTOR protein level is directly proportional to USP9X, in both loss- and gain-of-function experiments in cultured cells and, (iii) USP9X deubiquitlyating activity opposes the proteasomal degradation of RAPTOR."
USP9X affects lifeAct
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3
USP9X affects glycolytic process
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1
USP9X affects cell differentiation
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3
USP9X inhibits cell differentiation. 3 / 3
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3
reach
"As expected, Usp9x DeltaG colonic ulcers after acute colitis were marked by increased proliferation and decreased secretory differentiation, most likely because the normalization of c-Myc and NICD1 protein is delayed in the absence of Usp9x, and the damaged intestine was locked in a proliferative state (XREF_FIG)."
USP9X affects cell cycle
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3
sparser
"Family-based studies are robust against bias led from population stratification in genetic studies and helpful in understanding G × G. We proposed a new algorithm epistasis sparse factor analysis (EPISFA) and epistasis sparse factor analysis for linkage disequilibrium (EPISFA-LD) based on unsupervised machine learning to screen G × G. Extensive simulations were performed to compare EPISFA/EPISFA-LD with a classical family-based algorithm FAM-MDR (family-based multifactor dimensionality reduction)."
sparser
"Among the many different machine learning approaches for detecting GGIs, multifactor dimensionality reduction (MDR), proposed by Ritchie et al. [ xref ] has received much interest, and numerous extensions of MDR have been now developed, including quantitative MDR, for quantitative traits [ xref ]; generalized MDR (GMDR), for both quantitative and binary traits [ xref ]; MB-MDR, based on statistical testing [ xref ], Surv/Cox-MDR, for survival data [ xref , xref ]; FAM-MDR, for family data [ xref ], GEE/Multi-MDR, for multivariate traits [ xref , xref ], etc."
USP9X affects biosynthetic process
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3
USP9X inhibits biosynthetic process. 3 / 3
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3
reach
"In the absence of functional ZIKV NS5 RNA polymerase and informed by the observation that viral RNA polymerases present structural and functional similarities , we tested whether FAM E3 could inhibit the synthesis of ZIKV genomic RNA in vitro by purified bacteriophage SP6 RNA polymerase."
sparser
"All rights reserved.) U VEITIS CAN BE OF INFECTIOUS OR NONINFECTIOUS
A(G/C)G G(G/C)G T(A/G)C GCA GGT A AGA A(G/C)G GTG T(A/G)C GCA GAT A Probe FAM-ACC ACG TCG AAA ACT TCG AA-MGBNFQ FAM-ACC ACG TCG AAA ACT TCA AA-MGBNFQ FAM-ACA CCG CGG CGT CA-MGBNFQ Coronavirus 229E Forward CAG TCA AAT GGG CTG ATG CA Reverse CAA AGG GCT ATA AAG AGA ATA AGG TAT TCT ND 53 Probe FAM-CCC TGA CGA CCA CGT TGT GGT TCA -TAMRA Coronavirus NL63 Forward AAG GGT TTT CCA CAG CTT GCT AAA GGT TTT CCA CAG CTT GCT ND 53 Reverse ATC ACC CAC TTC ATC AGT GCT AAC Probe FAM-TCA CTA TCA AAG AAT AAC GCA GCC TGA TTA GGA A -TAMRA Coronavirus OC43 Forward CGA TGA GGC TAT TCC GAC TAG GT Reverse CCT TCC TGA GCC TTC AAT ATA GTA ACC ND 53 Probe FAM-TCC GCC TGG CAC GGT ACT CCC T -TAMRA Enteroviruses Forward TCC TCC GGC CCC TGA Reverse AAT TGT CAC CAT AAG CAG CCA GAT TGT CAC CAT AAG CAG CCA ND 50 Probe FAM-CGG AAC CGA CTA CTT TGG GTG ACC GT -TAMRA FAM-CGG AAC CGA CTA CTT TGG GTG TCC GT -TAMRA Epstein-Barr virus Forward GGA ACC TGG TCA TCC TTT GC Reverse ACG TGC ATG GAC CGG TTA AT 50 copies/mL 42 Probe FAM-CGC AGG CAC TCG TAC TGC TCG CT -TAMRA Human herpesvirus 6 Forward GAA GCA GCA ATC GCA 160 copies/mL 42 Reverse ACA CA ATG TAA CTC Probe GGT GTA CGG TGT CTA FAM-AAC CCG TGC GCC GCT -TAMRA Human metapneumovirus Forward CAT ATA AGC ATG CTA TAT TAA AAG AGT CTC ND 49 Reverse CCT ATT TCT GCA GCA TAT TTG TAA TCA G Probe FAM-TG(C/T) AAT GAT GAG GGT GTC ACT GCG GTT G -TAMRA Influenza virus A Forward AAG ACC AAT CCT GTC ACC TCT GA Reverse CAA AGC GTC TAC GCT GCA GTC C ND 52 Probe FAM-TTT GTG TTC ACG CTC ACC GTG CC -TAMRA Influenza virus B Forward AAA TAC GGT GGA TTA AAC AAA AGC AA Reverse CCA GCA ATA GCT CCG AAG AAA ND 52 Probe FAM-CAC CCA TAT TGG GCA ATT TCC TAT GGC -TAMRA Parainfluenza virus 1 Forward TGA TTT AAA CCC GGT AAT TTC TCA T Reverse CCT TGT TCC TGC AGC TAT TAC AGA ND 51 Probe FAM-ACG ACA ACA GGA AAT C -TAMRA Parainfluenza virus 2 Forward AGG ACT ATG AAA ACC ATT TAC CTA AGT GA Reverse AAG CAA GTC TCA GTT CAG CTA GAT CA ND 51 Probe FAM-ATC AAT CGC AAA AGC TGT TCA GTC ACT GCT ATA C -TAMRA Parainfluenza virus 3 Forward TGA TGA AAG ATC AGA TTA TGC AT Reverse CCG GGA CAC CCA GTT GTG ND 51 Probe FAM-TGG ACC AGG GAT ATA CTA CAA AGG CAA AAT AAT ATT TCT C -TAMRA Continued on next page
FAM-GTA TCA TCA TCT GCC AAA TCG GCA ATT AAA CA -TAMRA Human parechovirus Forward TGC AAA CAC TAG TGG TA(A/T) GGC CC Reverse 1 TCA GAT CCA TAG TG(C/T) CAC TTG TTA CCT Reverse 2 TCA GAT CCA CAG TGT CTC TTG TTA CCT 1 TCID50/mL Forthcoming Probe FAM-CGA AGG ATG CCC AGA AGG TAC CCG -TAMRA Respiratory syncytial virus A Forward AGA TCA ACT TCT GTC ATC CAG CAA Reverse TTC TGA ACA TCA TAA TTA GGA GTA TCA AT ND 54 Probe FAM-CAC CAT CCA ACG GAG CAC AGG AGA T -TAMRA Respiratory syncytial virus B Forward AAG ATG CAA ATC ATA AAT TCA CAG GA Reverse TGA TAT CCA GCA TCT TTA AGT ATC TTT ATA GTG ND 54 Probe FAM-TCC CCT TCC TAA CCT GGA CAT AGC ATA TAA CAT ACC T -TAMRA Rubella virus Forward CAC GCC GCA CGG ACA Reverse 1 CAC CGG GAC TG(C/T) TG(A/G) TTG C 1.7 PFU/mL Forthcoming Reverse 2 CAC CGG GAC TGT TGG TTG C Probe FAM-AGG TCC CGC CCG AC-MGBNFQ Mycoplasma pneumoniae Forward GGT CAA TCT GGC GTG CAT CT Reverse TGG TAA CTG CCC CAC AAG C 50 CCU/mL 34 Probe FAM-TCC CCC GTT GAA AAA GTG AGT GGG T -TAMRA Chlamydia pneumoniae Forward TCC GCA TTG CTC AGC C Reverse AAA CAA TTT GCA TGA AGT CTG AGA A 4.9 IFU/mL 34 Probe FAM-TAA ACT TAA CTG CAT GGA ACC CTT CTT TAC TAG G -TAMRA CCU ϭ color-changing units; FAM ϭ 6-carboxyfluorescein fluorescent label; IFU ϭ inclusion-forming units; MGBNFQ ϭ minor groove binding nonfluorescent quencher; ND ϭ not determined; PFU ϭ plaque-forming units; TAMRA ϭ tetramethylrhodamine quencher; TCID50 ϭ tissue culture infectious dose 50."
sparser
"RSV-P0 a CAT CCT GAT ATA AGA TAT ATT TAC AGAAG[T(FAM-dT)][Y(THF)][T(BHQ-dT)]GAA AGA TTG CAA TGA[C3-spacer] 47 P-IC a GTA AGG TGC TAG ACT AAA ATT GTT GGGAC[T(HEX-dT)][T(THF)][T(BHQ-dT)]GAA TCT CTG AAG TAA AAG G[TTA TRG TGT CTT CYC TTC CTA ACC 30 qPCR-P FAM-TAA TAG GTA TGT TAT ATG CKATGTC-BHQ 25
The oligonucleotides used for RT-PCR, rtRAA, and RT-qPCR
The reproducibility of singleplex-rtRAA and duplex-rtRAA a Each dilution was tested in a total of 8 replicates"
USP9X affects TD3
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3
sparser
"Confocal microscopic analysis of the intracellular accumulation of tONs/dONs duplexes was performed at the same time points as flow cytometry analysis (1, 2, 4, 8, 16, and 24 h after duplex addition to KB-8-5 cells) with the same tONs (FAM-TD3 and FAM-TD2, green channel) and dONs (By5.5-ON-PO and By5.5-ON-PX, red channel)."
USP9X affects TD2
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3
sparser
"Confocal microscopic analysis of the intracellular accumulation of tONs/dONs duplexes was performed at the same time points as flow cytometry analysis (1, 2, 4, 8, 16, and 24 h after duplex addition to KB-8-5 cells) with the same tONs (FAM-TD3 and FAM-TD2, green channel) and dONs (By5.5-ON-PO and By5.5-ON-PX, red channel)."
sparser
"The intensity of fluorescence of FAM-TD2 remained stably low (1 RFU) during the entire 24 h of incubation ( xref C, magenta and green lines), while intracellular accumulation of dONs mediated by TD2 gradually increased over 24 h, reaching MFI 10–20 RFU ( xref D, magenta and green lines)."
USP9X affects R1.3
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3
sparser
"Notably, the fluorescent tag – though clearly reducing the gel mobility of the oligonucleotides – neither affected the molecularity of R1.2 and R1.3 nor promoted the formation of aggregates, further corroborating the use of R1.2-FAM and R1.3-FAM as suitable models of R1.2 and R1.3 in studies with their molecular targets."
USP9X affects R1.2
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3
sparser
"Notably, the fluorescent tag – though clearly reducing the gel mobility of the oligonucleotides – neither affected the molecularity of R1.2 and R1.3 nor promoted the formation of aggregates, further corroborating the use of R1.2-FAM and R1.3-FAM as suitable models of R1.2 and R1.3 in studies with their molecular targets."
USP9X affects Parkinson Disease
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3
sparser
"1B R: GTG AGT AGG AGA GGT GAG AGAGG FAM-ACA CCA ATG CCC AAC TGC CTG CCT -TAMRA 109 F: GGG ATC TGA AAC AAC ATT CAT GTG IL-2 R: AGT CAG TGT TGA GAT GAT GCT TTG FAM -TGA TGA GAC AGC AACCA -TAMRA 88 F: TGC TGC CTC CAA GAA CAC AAC IL-4 R: GTC CTT CTC ATG GTG GCT GTAG FAM-CCG GAG CAC AGT CGC AGC CCT-TAMRA 160 F: ATG CAA TAA CCA CCC CTG ACC IL-6 R: CCA TGC TAC ATT TGC CGA AGAG FAM-ACC ACA AAT GCC AGC CTG CTG ACG -TAMRA 77 F: CGG AAG GAA CCA TCT CAC TGTG IL-8 R: AGA AAT CAG GAA GGC TGC CAAG FAM-TGA CTT CCA AGC TGG CCG TGG CTC -TAMRA 176 F: CAG CAA GAG ATC CTG GTC CTG IL-17 R: GGT CGG CTC TCC ATA GTC TAAC FAM-AGC CTC CAC ACT GCC CCA ACT CCT -TAMRA 96 F: GGC AAG GCT ATG TGA TTA CAAGG IFN-G R: CAT CAA GTG AAA TAA ACA CAC AAC CC FAM-AGG GGC CAA CTA GGC AGC CAA CCT -TAMRA 101 F: GCT CCA CGG AGA AGA ACT GC TGF-B R: GTT GGC ATG GTA GCC CTT GG FAM-CCA CTT CCA GCC GAG GTC CTT GCG -TAMRA 97 F: TCC ACC CAT GTG CTC CTC AC TNF-A R: TCT GGC AGG GGC TCT TGA TG FAM-CTA CCG AGT CCG TGT CTA CCA -TAMRA
depicts the relative expression levels of cytokine coding genes in COVID-19 patients and healthy subjects using box plot
Heatmap showing the correlation between expression amounts of cytokine coding genes and clinical/ demographic information among COVID-19 patients (red and blue colors indicate positive and negative correlations, respectively with dark colors showing stronger correlations)
ROC curves depicted by three machine learning models showing the power of cytokine coding genes in in distinguishing between COVID-19 patients and healthy controls (A) and between ICU-admitted patients and other patients (B) Fig. 4 ROC curves depicted by the linear discriminant analysis (LDA), showing the power of cytokine coding genes in in distinguishing between COVID-19 patients and healthy controls (A) and between ICU-admitted patients and other patients (B)
Correlation
Paraclinical parameters of the COVID-19 group Details of expression results of cytokine transcripts in study groups
Parameters obtained from ROC curve analysis for assessment of the diagnostic power of cytokine coding genes in COVID-19 AUC Sensitivity Specificity AUC Sensitivity Specificity AUC Sensitivity Specificity AUC Sensitivity Specificity AUC AUC Sensitivity Specificity AUC Sensitivity Specificity AUC Sensitivity Specificity AUC Sensitivity Specificity AUC"
sparser
"SARS-CoV(Drosten et al., 2003) 25-l reaction based on Superscript II RT/PlatinumTaqpolymerase one-step RT-PCR kit (Invitrogen): 5 l RNA, 1× buffer, 3.6 mM additional MgSO 4 , 0.6 l enzyme mixture, 240 nM probe BNITMSARP (FAM-TCG TGC GTG GAT TGG CTT TGA TGT-TAMRA), 200 nM primer BNITMSARS1 (TTA TCA CCC GCG AAG AAG CT), and 200 nM primer BNITMSARAs2 (CTC TAG TTG CAT GAC AGC CCT C) 7000 SDS machine (Applied Biosystems): 15 min at 45 • C; 3 min at 95 • C; 40 cycles with 15 s at 95 • C and 30 s at 58 • C with fluorescence measured at 58 • C (FAM detection channel without passive reference dye) Ebola virus (Gibb et al., 2001) 20-l reaction based on Brilliant single-step quantitative RT-PCR kit (Stratagene): 2 l RNA, 1× buffer, 2.5 mM MgCl 2 , 800 M dNTP, 1.25 U StrataScript RT, 1 U SureStart Taq polymerase, 250 nM probe EBOGP-1DZPrb (FAM-CTA CCA GCA GCG CCA GAC GG-TAMRA), 500 nM primer EBOGP-1D forward (TGG GCT GAA AAY TGC TAC AAT C), and 500 nM primer EBOGP-1D reverse (CTT TGT GMA CAT ASC GGC AC) 7000 SDS machine (Applied Biosystems): 30 min at 50 • C; 10 min at 95 • C; 45 cycles with 15 s at 95 • C and 30 s at 58 • C with fluorescence measured at 58 • C (FAM detection channel without passive reference dye) Abbreviations: FAM, 6-carboxyfluorescein; TAMRA, 6-carboxy-N,N,N ,N -tetramethylrhodamin; RT, reverse transcriptase."
sparser
"The results demonstrated that the centrosomal localization of PCM1 was mildly interrupted ( xref ), and the protein, but not mRNA, expression level of PCM1 decreased ( xref ), suggesting that PCM1 is a potential substrate of USP9X. However, we found that in USP9X-deficient cells, FLAG-tagged CEP131 could be effectively recruited to centrosome ( xref ), suggesting that mildly disrupted centrosomal localization of PCM1 associated with USP9X depletion has limited effect on CEP131 recruitment."
USP9X affects NCIT:C95943
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3
sparser
"To address the question of whether AAG interacts directly with the FAM or to a specific DNA sequence context or structure upstream of the εA site, we measured the anisotropy of AAG binding to undamaged DNA with an alternate sequence or with the FAM on the 5′-end of the complement strand ( xref )."
sparser
"HIV pol forward (mf299) GCA CTT TAA ATT TTC CCA TTA GTC CTA HIV pol reverse (mf302) CAA ATT TCT ACT AAT GCT TTT ATT TTT TCTTC HIV pol probe (mf348) FAM-AAG CCA GGA ATG GAT GG-MGB RPP30 forward GAT TTG GAC CTG CGA GCG RPP30 reverse GCG GCT GTC TCC ACA AGTC RPP30 probe VIC-CTG ACC TGA AGG CTC T-MGB 2.5."
USP9X affects LATS kinase
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3
reach
"Furthermore, the expression level of USP9X is positively related to LATS expression but negatively associated with the expression of YAP/TAZ in multiple tumor tissues, such as pancreatic cancer and breast cancer, demonstrating that USP9X potentiates LATS kinase in suppressing tumor growth (Toloczko et al., 2017)."
sparser
"To rule out the possibility that variations in the normalization procedure caused or contributed to these uptake differences, transport efficiency as indicated by the fluorescence intensity (RFU) of the FAM-CPP exposed cell layers was set in relation to the final peptide concentrations measured at the isosbestic point ( xref )."
USP9X affects K9me3
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3
USP9X affects JAK2-V617F
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3
reach
"The involvement of USP9X in deubiquitination of JAK2-V617F is further supported by the physical association between endogenous USP9X and JAK2-V617F observed in HEL cells (Figure 3G), which extends the previous study by Chou et al. [35] demonstrating this association in a transfection experiment in a nonhematopoietic cell line."
USP9X affects IRS-1/2
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3
USP9X affects HP1
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3
USP9X affects Genomic Instability
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3
reach
"The following findings were observed : (1) Expression of USP9X was down-regulated in the kidney tissue of db/db diabetic mice; (2) overexpression of USP9X suppressed high glucose (HG)-induced expressions of EMT markers and extra cellular matrix (ECM) in NRK-52E cells; (3) depletion of USP9X further aggravated EMT process and ECM production in NRK-52E cells; (4) USP9X deubiquitinated Cx43 and suppressed its degradation to regulate EMT process; (5) USP9X deubiquitinated Cx43 by directly binding to the C-terminal Tyr 286 of Cx43."
sparser
"To overcome limited access of in situ PLA analysis because of a small number of puncta, HA-ankyrin-G and Flag-Usp9X S3D were co-transfected in primary cultured cortical neurons to investigate the effect of phosphorylated-three serine sites in the peptidase domain of Usp9X (Usp9X S3D ) on ankyrin-G and spines."
USP9X affects FenA5
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3
USP9X affects FenA2
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3
USP9X affects FenA1
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3
USP9X affects Endoplasmic Reticulum Stress
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1
USP9X inhibits Endoplasmic Reticulum Stress. 3 / 3
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1
eidos
"Usp9X inhibition causes ER stress in MPNST cell lines Interestingly , both Usp9X pharmacological inhibition and silencing in MPNST cells elicited a significant increase in ATF3 , a typical marker of ER-stress ( Fig. 5a , b ) and in the pro-apoptotic BH3-only protein Noxa ( Fig. 5a , b ) ."
reach
"Direct and indirect ErbB2 effects may also explain our observation that siRNA knock down of the deubiquitylating enzyme, USP9x, significantly enhanced PS341 induced lysosomal decay of ErbB2, although the observed physical association between ErbB2 and USP9x and FAM in PS341 treated and untreated cells implicates direct mediation of this DUB in the ErbB2 internalization and ubiquitination induced by proteasome inhibition."
USP9X affects DNA/microRNA
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3
sparser
"Introduction of a farnesyl-deficient mutant of FAM83F in cells through CRISPR/Cas9 genome editing redirects the FAM83F–CK1α complex away from the plasma membrane and significantly attenuates Wnt signalling, indicating that FAM83F exerts its effects on Wnt signalling at the plasma membrane."
sparser
"This internally controlled quantitative real-time PCR assay targets the hexon gene of adenovirus, and is validated for detection Table 1 Nucleotide sequences of primers and probes used in this study
Sequence (5′ to 3′) Reference
CCA GGA CGC CTC GGA GTA [18] AdV2R AAA CTT GTT ATT CAG GCT GAA GTA CGT [18] AdV2pr FAM-AGT TTG CCC GCG CCA CCA CCG -BHQ1 * [18] AdV4F GGA CAG GAC GCT TCG GAG TA [18] AdV4R CTT GTT CCC CAG ACT GAA GTA GGT [18] AdV4pr FAM-CAG TTC GCC CGY GCM ACA G -BHQ1 * [ of types 1 to 52 [7] ."
sparser
"Ethical approval This article does not contain any studies with human participants or animals performed by any of the authors.
primer: 5'-TGA TCT GAG TCC AGG TGT T-3' hsa_circ_0002483 Forward primer: 5'-TGC CAA AAG GAT TTC TAA ACC AGT -3' Reverse primer: 5'-TTG GGG TCA AGG TAA GCA GC-3' hsa_circ_0002301 Forward primer: 5'-TAT ATG GTC AAC TGC AAC TTGGC-3' Reverse primer: 5'-TCA CAT GTC TCC ACC CTT GT-3' hsa_circ_0002141 Forward primer: 5'-TCA TTG TCA AGA GAG CAG ATACT-3' Reverse primer: 5'-TCC TTG TCT TTT CTG CAT CTTGA-3' GAPDH Forward primer: 5'-ATG AGG TCC ACC ACC CTG TT-3' Reverse primer: 5'-CTC AAG GGC ATC CTG GGC TA-3' CV-A16-VP1-1 (used for the construction of standard RNA) 5'-AAC ACT GAG GCT AGT AGT CAC-3' (sense) 5'-CGT GTT TGA TTC TCA TGT ACACC-3' (anti-sense) CV-A16-VP1-2 (used for qRT-PCR examination) 5'-GTT TGT GAA AAT GAC GGA CCC-3' (sense) 5'-GTC ATT TGC TTG AAG GTG CTC-3' (anti-sense) Probe: FAM-CAG CTC AAG TGT CAG TCC CCT-TAMRA was used for quantile normalization."
sparser
"Abbreviations: conc. =concentration Underlining and boldface indicate a locked nucleic acid (LNA) (Exiqon, Woburn, MA) ˟ Y=mix of C and T (pyrimidine) nucleosides, similar to "P" as listed in Harvey, JJ 27 (P is a universal base; (P)=dP-CE (pyrimidine derivative), designed to base pair with either A or G) FAM-CAG TCG GCC TTG CGT GAG TGG G-BHQ1 300nM Tatti, K. M. 39 , Kodani, M. 9
The Healthy Infant Nasal Transcriptome: A Benchmark Study OPEN."
USP9X affects CM
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3
sparser
"All rights reserved.) U VEITIS CAN BE OF INFECTIOUS OR NONINFECTIOUS
A(G/C)G G(G/C)G T(A/G)C GCA GGT A AGA A(G/C)G GTG T(A/G)C GCA GAT A Probe FAM-ACC ACG TCG AAA ACT TCG AA-MGBNFQ FAM-ACC ACG TCG AAA ACT TCA AA-MGBNFQ FAM-ACA CCG CGG CGT CA-MGBNFQ Coronavirus 229E Forward CAG TCA AAT GGG CTG ATG CA Reverse CAA AGG GCT ATA AAG AGA ATA AGG TAT TCT ND 53 Probe FAM-CCC TGA CGA CCA CGT TGT GGT TCA -TAMRA Coronavirus NL63 Forward AAG GGT TTT CCA CAG CTT GCT AAA GGT TTT CCA CAG CTT GCT ND 53 Reverse ATC ACC CAC TTC ATC AGT GCT AAC Probe FAM-TCA CTA TCA AAG AAT AAC GCA GCC TGA TTA GGA A -TAMRA Coronavirus OC43 Forward CGA TGA GGC TAT TCC GAC TAG GT Reverse CCT TCC TGA GCC TTC AAT ATA GTA ACC ND 53 Probe FAM-TCC GCC TGG CAC GGT ACT CCC T -TAMRA Enteroviruses Forward TCC TCC GGC CCC TGA Reverse AAT TGT CAC CAT AAG CAG CCA GAT TGT CAC CAT AAG CAG CCA ND 50 Probe FAM-CGG AAC CGA CTA CTT TGG GTG ACC GT -TAMRA FAM-CGG AAC CGA CTA CTT TGG GTG TCC GT -TAMRA Epstein-Barr virus Forward GGA ACC TGG TCA TCC TTT GC Reverse ACG TGC ATG GAC CGG TTA AT 50 copies/mL 42 Probe FAM-CGC AGG CAC TCG TAC TGC TCG CT -TAMRA Human herpesvirus 6 Forward GAA GCA GCA ATC GCA 160 copies/mL 42 Reverse ACA CA ATG TAA CTC Probe GGT GTA CGG TGT CTA FAM-AAC CCG TGC GCC GCT -TAMRA Human metapneumovirus Forward CAT ATA AGC ATG CTA TAT TAA AAG AGT CTC ND 49 Reverse CCT ATT TCT GCA GCA TAT TTG TAA TCA G Probe FAM-TG(C/T) AAT GAT GAG GGT GTC ACT GCG GTT G -TAMRA Influenza virus A Forward AAG ACC AAT CCT GTC ACC TCT GA Reverse CAA AGC GTC TAC GCT GCA GTC C ND 52 Probe FAM-TTT GTG TTC ACG CTC ACC GTG CC -TAMRA Influenza virus B Forward AAA TAC GGT GGA TTA AAC AAA AGC AA Reverse CCA GCA ATA GCT CCG AAG AAA ND 52 Probe FAM-CAC CCA TAT TGG GCA ATT TCC TAT GGC -TAMRA Parainfluenza virus 1 Forward TGA TTT AAA CCC GGT AAT TTC TCA T Reverse CCT TGT TCC TGC AGC TAT TAC AGA ND 51 Probe FAM-ACG ACA ACA GGA AAT C -TAMRA Parainfluenza virus 2 Forward AGG ACT ATG AAA ACC ATT TAC CTA AGT GA Reverse AAG CAA GTC TCA GTT CAG CTA GAT CA ND 51 Probe FAM-ATC AAT CGC AAA AGC TGT TCA GTC ACT GCT ATA C -TAMRA Parainfluenza virus 3 Forward TGA TGA AAG ATC AGA TTA TGC AT Reverse CCG GGA CAC CCA GTT GTG ND 51 Probe FAM-TGG ACC AGG GAT ATA CTA CAA AGG CAA AAT AAT ATT TCT C -TAMRA Continued on next page
FAM-GTA TCA TCA TCT GCC AAA TCG GCA ATT AAA CA -TAMRA Human parechovirus Forward TGC AAA CAC TAG TGG TA(A/T) GGC CC Reverse 1 TCA GAT CCA TAG TG(C/T) CAC TTG TTA CCT Reverse 2 TCA GAT CCA CAG TGT CTC TTG TTA CCT 1 TCID50/mL Forthcoming Probe FAM-CGA AGG ATG CCC AGA AGG TAC CCG -TAMRA Respiratory syncytial virus A Forward AGA TCA ACT TCT GTC ATC CAG CAA Reverse TTC TGA ACA TCA TAA TTA GGA GTA TCA AT ND 54 Probe FAM-CAC CAT CCA ACG GAG CAC AGG AGA T -TAMRA Respiratory syncytial virus B Forward AAG ATG CAA ATC ATA AAT TCA CAG GA Reverse TGA TAT CCA GCA TCT TTA AGT ATC TTT ATA GTG ND 54 Probe FAM-TCC CCT TCC TAA CCT GGA CAT AGC ATA TAA CAT ACC T -TAMRA Rubella virus Forward CAC GCC GCA CGG ACA Reverse 1 CAC CGG GAC TG(C/T) TG(A/G) TTG C 1.7 PFU/mL Forthcoming Reverse 2 CAC CGG GAC TGT TGG TTG C Probe FAM-AGG TCC CGC CCG AC-MGBNFQ Mycoplasma pneumoniae Forward GGT CAA TCT GGC GTG CAT CT Reverse TGG TAA CTG CCC CAC AAG C 50 CCU/mL 34 Probe FAM-TCC CCC GTT GAA AAA GTG AGT GGG T -TAMRA Chlamydia pneumoniae Forward TCC GCA TTG CTC AGC C Reverse AAA CAA TTT GCA TGA AGT CTG AGA A 4.9 IFU/mL 34 Probe FAM-TAA ACT TAA CTG CAT GGA ACC CTT CTT TAC TAG G -TAMRA CCU ϭ color-changing units; FAM ϭ 6-carboxyfluorescein fluorescent label; IFU ϭ inclusion-forming units; MGBNFQ ϭ minor groove binding nonfluorescent quencher; ND ϭ not determined; PFU ϭ plaque-forming units; TAMRA ϭ tetramethylrhodamine quencher; TCID50 ϭ tissue culture infectious dose 50."
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"NDR AAT AGG CGG ACC ACA TCT G 12.5 µL ND-FAM1 FAM-TCA TTC TTT ATA GAG GTA TCT TCA TCA TA-BHQ1 4 µL ND-FAM2 FAM-TCA TAC ACT ATT ATG GCG TCA TTC TT-
IBV-F2CAGTCC CDG ACG CGT GGT A 25 µL IBV-F3 GCT TTT GAG CCT AGC GTT 5 µL IBV-FAM1 FAM-ACT GGA ACA GGA CCD GCC GCT GAC CT-BHQ1 6 µL IBV-FAM2 FAM-CAC CAC CAG AAC CTG TCA CCT C-BHQ1 2 µL IBV-R1 CCT TWS CAG MAA CMC ACA CT 25 µL IBV-R2 GCC ATG TTG TCA CTG TCT ATT G 5 µL IC-2 EGFP-1-F GAC CAC TAC CAG CAG AAC AC 5 µL [25] EGFP-10-R CTT GTA CAG CTC GTC CAT GC 5 µL EGFP-HEX HEX-AGC ACC CAG TCC GCC CTG AGC A-BHQ1 3.75 µL 1 A stock mix of 200 µL was produced for each assay; the amount in µL of a 100 pmol µL −1 solution of each primer and probe for the stock mix is given here."
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"Reverse-transcribed MARV RNA, RVFV RNA and eukaryotic18S rRNA, was detected on the ABI 7500 Real-Time PCR System (Life Sciences, Grand Island, NY, USA) using the SuperScript III Platinum One-Step Q-RT-PCR Kit (Life Technologies) with amplification primers and reporter probes targeting the viral protein 40 (forward primer: GGA CCA CTG CTG GCC ATA TC, reverse primer: GAG AAC ATI TCG GCA GGA AG, probe 1: 56-FAM-ATC CTA AAC-ZEN-AGG CTT GTC TTC TCT GGG ACT T-3IABkFQ, probe 2: 56-FAM-ATC CTG AAT-ZEN-AAG CTC GTC TTC TCT GGG ACT T-3IABkFQ), large segment (forward primer: TGA AAA TTC CTG AGA CAC ATG G, reverse primer: ACT TCC TTG CAT CAT CTG ATG, probe: FAM-CAC AAG TCC ACA CAG GCC CCT TAC ATT G-BHQ1) and eukaryotic 18 S rRNA (Life Technologies) genes, respectively."
USP9X affects Bcr-Abl
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"This suggests that maintenance of CEP55 and CEP131 is the major factor contributing to reduced cell survival following relatively high-LET protons in the absence of USP9X.Our findings that USP9X does not affect cell cycle progression is in agreement with a previous study, which demonstrated that USP9X depletion was linked to an increased loss of anaphase-promoting complex/cyclosome (APC/C) substrates, in particular cyclin A, but also cyclin B and NEK2A, and that cells consequently failed to arrest mitosis after microtubule poisoning in HeLa cells and U2OS cells (35)."
USP9X affects 5-InsP
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"On the other hand inhibition of ERK and USP9x with pharmaceutical or genetic approach in breast cancer cells abolishes FFA promotion of TGF-β–induced SMAD4-USP9x interaction, SMAD4 nuclear retention, SMAD3/SMAD4 complex formation, and target gene expression, resulting in decrease in cancer cell invasion and metastasis ( xref )."
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"We also found that FFA/ERK-induced SMAD4 T277 phosphorylation is indispensable in SMAD4-USP9x interaction and its deubiquitination as well as subsequent nuclear accumulation, which is required for TGF-β–induced breast cancer invasion and metastasis under the high FFA/obesity conditions."
TD3 affects USP9X
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3
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"Confocal microscopic analysis of the intracellular accumulation of tONs/dONs duplexes was performed at the same time points as flow cytometry analysis (1, 2, 4, 8, 16, and 24 h after duplex addition to KB-8-5 cells) with the same tONs (FAM-TD3 and FAM-TD2, green channel) and dONs (By5.5-ON-PO and By5.5-ON-PX, red channel)."
TD2 affects USP9X
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3
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"Confocal microscopic analysis of the intracellular accumulation of tONs/dONs duplexes was performed at the same time points as flow cytometry analysis (1, 2, 4, 8, 16, and 24 h after duplex addition to KB-8-5 cells) with the same tONs (FAM-TD3 and FAM-TD2, green channel) and dONs (By5.5-ON-PO and By5.5-ON-PX, red channel)."
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"The intensity of fluorescence of FAM-TD2 remained stably low (1 RFU) during the entire 24 h of incubation ( xref C, magenta and green lines), while intracellular accumulation of dONs mediated by TD2 gradually increased over 24 h, reaching MFI 10–20 RFU ( xref D, magenta and green lines)."
sparser
"On the other hand inhibition of ERK and USP9x with pharmaceutical or genetic approach in breast cancer cells abolishes FFA promotion of TGF-β–induced SMAD4-USP9x interaction, SMAD4 nuclear retention, SMAD3/SMAD4 complex formation, and target gene expression, resulting in decrease in cancer cell invasion and metastasis ( xref )."
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"We also found that FFA/ERK-induced SMAD4 T277 phosphorylation is indispensable in SMAD4-USP9x interaction and its deubiquitination as well as subsequent nuclear accumulation, which is required for TGF-β–induced breast cancer invasion and metastasis under the high FFA/obesity conditions."
R1.3 affects USP9X
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3
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"Notably, the fluorescent tag – though clearly reducing the gel mobility of the oligonucleotides – neither affected the molecularity of R1.2 and R1.3 nor promoted the formation of aggregates, further corroborating the use of R1.2-FAM and R1.3-FAM as suitable models of R1.2 and R1.3 in studies with their molecular targets."
R1.2 affects USP9X
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"Notably, the fluorescent tag – though clearly reducing the gel mobility of the oligonucleotides – neither affected the molecularity of R1.2 and R1.3 nor promoted the formation of aggregates, further corroborating the use of R1.2-FAM and R1.3-FAM as suitable models of R1.2 and R1.3 in studies with their molecular targets."
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"1B R: GTG AGT AGG AGA GGT GAG AGAGG FAM-ACA CCA ATG CCC AAC TGC CTG CCT -TAMRA 109 F: GGG ATC TGA AAC AAC ATT CAT GTG IL-2 R: AGT CAG TGT TGA GAT GAT GCT TTG FAM -TGA TGA GAC AGC AACCA -TAMRA 88 F: TGC TGC CTC CAA GAA CAC AAC IL-4 R: GTC CTT CTC ATG GTG GCT GTAG FAM-CCG GAG CAC AGT CGC AGC CCT-TAMRA 160 F: ATG CAA TAA CCA CCC CTG ACC IL-6 R: CCA TGC TAC ATT TGC CGA AGAG FAM-ACC ACA AAT GCC AGC CTG CTG ACG -TAMRA 77 F: CGG AAG GAA CCA TCT CAC TGTG IL-8 R: AGA AAT CAG GAA GGC TGC CAAG FAM-TGA CTT CCA AGC TGG CCG TGG CTC -TAMRA 176 F: CAG CAA GAG ATC CTG GTC CTG IL-17 R: GGT CGG CTC TCC ATA GTC TAAC FAM-AGC CTC CAC ACT GCC CCA ACT CCT -TAMRA 96 F: GGC AAG GCT ATG TGA TTA CAAGG IFN-G R: CAT CAA GTG AAA TAA ACA CAC AAC CC FAM-AGG GGC CAA CTA GGC AGC CAA CCT -TAMRA 101 F: GCT CCA CGG AGA AGA ACT GC TGF-B R: GTT GGC ATG GTA GCC CTT GG FAM-CCA CTT CCA GCC GAG GTC CTT GCG -TAMRA 97 F: TCC ACC CAT GTG CTC CTC AC TNF-A R: TCT GGC AGG GGC TCT TGA TG FAM-CTA CCG AGT CCG TGT CTA CCA -TAMRA
depicts the relative expression levels of cytokine coding genes in COVID-19 patients and healthy subjects using box plot
Heatmap showing the correlation between expression amounts of cytokine coding genes and clinical/ demographic information among COVID-19 patients (red and blue colors indicate positive and negative correlations, respectively with dark colors showing stronger correlations)
ROC curves depicted by three machine learning models showing the power of cytokine coding genes in in distinguishing between COVID-19 patients and healthy controls (A) and between ICU-admitted patients and other patients (B) Fig. 4 ROC curves depicted by the linear discriminant analysis (LDA), showing the power of cytokine coding genes in in distinguishing between COVID-19 patients and healthy controls (A) and between ICU-admitted patients and other patients (B)
Correlation
Paraclinical parameters of the COVID-19 group Details of expression results of cytokine transcripts in study groups
Parameters obtained from ROC curve analysis for assessment of the diagnostic power of cytokine coding genes in COVID-19 AUC Sensitivity Specificity AUC Sensitivity Specificity AUC Sensitivity Specificity AUC Sensitivity Specificity AUC AUC Sensitivity Specificity AUC Sensitivity Specificity AUC Sensitivity Specificity AUC Sensitivity Specificity AUC"
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"SARS-CoV(Drosten et al., 2003) 25-l reaction based on Superscript II RT/PlatinumTaqpolymerase one-step RT-PCR kit (Invitrogen): 5 l RNA, 1× buffer, 3.6 mM additional MgSO 4 , 0.6 l enzyme mixture, 240 nM probe BNITMSARP (FAM-TCG TGC GTG GAT TGG CTT TGA TGT-TAMRA), 200 nM primer BNITMSARS1 (TTA TCA CCC GCG AAG AAG CT), and 200 nM primer BNITMSARAs2 (CTC TAG TTG CAT GAC AGC CCT C) 7000 SDS machine (Applied Biosystems): 15 min at 45 • C; 3 min at 95 • C; 40 cycles with 15 s at 95 • C and 30 s at 58 • C with fluorescence measured at 58 • C (FAM detection channel without passive reference dye) Ebola virus (Gibb et al., 2001) 20-l reaction based on Brilliant single-step quantitative RT-PCR kit (Stratagene): 2 l RNA, 1× buffer, 2.5 mM MgCl 2 , 800 M dNTP, 1.25 U StrataScript RT, 1 U SureStart Taq polymerase, 250 nM probe EBOGP-1DZPrb (FAM-CTA CCA GCA GCG CCA GAC GG-TAMRA), 500 nM primer EBOGP-1D forward (TGG GCT GAA AAY TGC TAC AAT C), and 500 nM primer EBOGP-1D reverse (CTT TGT GMA CAT ASC GGC AC) 7000 SDS machine (Applied Biosystems): 30 min at 50 • C; 10 min at 95 • C; 45 cycles with 15 s at 95 • C and 30 s at 58 • C with fluorescence measured at 58 • C (FAM detection channel without passive reference dye) Abbreviations: FAM, 6-carboxyfluorescein; TAMRA, 6-carboxy-N,N,N ,N -tetramethylrhodamin; RT, reverse transcriptase."
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"The results demonstrated that the centrosomal localization of PCM1 was mildly interrupted ( xref ), and the protein, but not mRNA, expression level of PCM1 decreased ( xref ), suggesting that PCM1 is a potential substrate of USP9X. However, we found that in USP9X-deficient cells, FLAG-tagged CEP131 could be effectively recruited to centrosome ( xref ), suggesting that mildly disrupted centrosomal localization of PCM1 associated with USP9X depletion has limited effect on CEP131 recruitment."
NCIT:C95943 affects USP9X
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"To address the question of whether AAG interacts directly with the FAM or to a specific DNA sequence context or structure upstream of the εA site, we measured the anisotropy of AAG binding to undamaged DNA with an alternate sequence or with the FAM on the 5′-end of the complement strand ( xref )."
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"HIV pol forward (mf299) GCA CTT TAA ATT TTC CCA TTA GTC CTA HIV pol reverse (mf302) CAA ATT TCT ACT AAT GCT TTT ATT TTT TCTTC HIV pol probe (mf348) FAM-AAG CCA GGA ATG GAT GG-MGB RPP30 forward GAT TTG GAC CTG CGA GCG RPP30 reverse GCG GCT GTC TCC ACA AGTC RPP30 probe VIC-CTG ACC TGA AGG CTC T-MGB 2.5."
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"To rule out the possibility that variations in the normalization procedure caused or contributed to these uptake differences, transport efficiency as indicated by the fluorescence intensity (RFU) of the FAM-CPP exposed cell layers was set in relation to the final peptide concentrations measured at the isosbestic point ( xref )."
K9me3 affects USP9X
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3
JAK2-V617F affects USP9X
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"The involvement of USP9X in deubiquitination of JAK2-V617F is further supported by the physical association between endogenous USP9X and JAK2-V617F observed in HEL cells (Figure 3G), which extends the previous study by Chou et al. [35] demonstrating this association in a transfection experiment in a nonhematopoietic cell line."
IRS-1/2 affects USP9X
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3
HP1 affects USP9X
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3
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"When the WriPdSf-2 primer set was applied to Chellaston ( S 7 S 23 ) × Lauranne ( S 3 S f ) F 1 progeny, HEX fluorescence was detected from the HEX-HEX genotype S 3 S 23 (half from each allele) and from the null-HEX genotype S 3 S 7 (all from S 3 ), FAM fluorescence was detected for the null-FAM genotype S 7 S f (all from S f ) and both HEX and FAM fluorescence were detected for the HEX-FAM genotype S 23 S f (HEX from S 23 and FAM from S f ) (Fig. xref )."
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"FAM fluorescence for null-FAM heterozygotes ( S 7 S f for WriPdSf-2 and WriPdSf-5; S 8 S f for WriPdSf-2, WriPdSf-4 and WriPdSf-5), both HEX and FAM fluorescence for HEX-FAM heterozygotes ( S 1 S f and S 23 S f for WriPdSf-3 and S 5 S f for WriPdSf-4) and a low levels of HEX fluorescence for null-null heterozygotes ( S 1 S 7 for WriPdSf-2 and WriPdSf-6; S 1 S 8 for WriPdSf-2, WrPdSf-4 and WriPdSf-5)."
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"To overcome limited access of in situ PLA analysis because of a small number of puncta, HA-ankyrin-G and Flag-Usp9X S3D were co-transfected in primary cultured cortical neurons to investigate the effect of phosphorylated-three serine sites in the peptidase domain of Usp9X (Usp9X S3D ) on ankyrin-G and spines."
FenA5 affects USP9X
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3
FenA2 affects USP9X
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3
FenA1 affects USP9X
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3
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"Direct and indirect ErbB2 effects may also explain our observation that siRNA knock down of the deubiquitylating enzyme, USP9x, significantly enhanced PS341 induced lysosomal decay of ErbB2, although the observed physical association between ErbB2 and USP9x and FAM in PS341 treated and untreated cells implicates direct mediation of this DUB in the ErbB2 internalization and ubiquitination induced by proteasome inhibition."
DNA/microRNA affects USP9X
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"Introduction of a farnesyl-deficient mutant of FAM83F in cells through CRISPR/Cas9 genome editing redirects the FAM83F–CK1α complex away from the plasma membrane and significantly attenuates Wnt signalling, indicating that FAM83F exerts its effects on Wnt signalling at the plasma membrane."
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"This internally controlled quantitative real-time PCR assay targets the hexon gene of adenovirus, and is validated for detection Table 1 Nucleotide sequences of primers and probes used in this study
Sequence (5′ to 3′) Reference
CCA GGA CGC CTC GGA GTA [18] AdV2R AAA CTT GTT ATT CAG GCT GAA GTA CGT [18] AdV2pr FAM-AGT TTG CCC GCG CCA CCA CCG -BHQ1 * [18] AdV4F GGA CAG GAC GCT TCG GAG TA [18] AdV4R CTT GTT CCC CAG ACT GAA GTA GGT [18] AdV4pr FAM-CAG TTC GCC CGY GCM ACA G -BHQ1 * [ of types 1 to 52 [7] ."
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"Ethical approval This article does not contain any studies with human participants or animals performed by any of the authors.
primer: 5'-TGA TCT GAG TCC AGG TGT T-3' hsa_circ_0002483 Forward primer: 5'-TGC CAA AAG GAT TTC TAA ACC AGT -3' Reverse primer: 5'-TTG GGG TCA AGG TAA GCA GC-3' hsa_circ_0002301 Forward primer: 5'-TAT ATG GTC AAC TGC AAC TTGGC-3' Reverse primer: 5'-TCA CAT GTC TCC ACC CTT GT-3' hsa_circ_0002141 Forward primer: 5'-TCA TTG TCA AGA GAG CAG ATACT-3' Reverse primer: 5'-TCC TTG TCT TTT CTG CAT CTTGA-3' GAPDH Forward primer: 5'-ATG AGG TCC ACC ACC CTG TT-3' Reverse primer: 5'-CTC AAG GGC ATC CTG GGC TA-3' CV-A16-VP1-1 (used for the construction of standard RNA) 5'-AAC ACT GAG GCT AGT AGT CAC-3' (sense) 5'-CGT GTT TGA TTC TCA TGT ACACC-3' (anti-sense) CV-A16-VP1-2 (used for qRT-PCR examination) 5'-GTT TGT GAA AAT GAC GGA CCC-3' (sense) 5'-GTC ATT TGC TTG AAG GTG CTC-3' (anti-sense) Probe: FAM-CAG CTC AAG TGT CAG TCC CCT-TAMRA was used for quantile normalization."
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"Abbreviations: conc. =concentration Underlining and boldface indicate a locked nucleic acid (LNA) (Exiqon, Woburn, MA) ˟ Y=mix of C and T (pyrimidine) nucleosides, similar to "P" as listed in Harvey, JJ 27 (P is a universal base; (P)=dP-CE (pyrimidine derivative), designed to base pair with either A or G) FAM-CAG TCG GCC TTG CGT GAG TGG G-BHQ1 300nM Tatti, K. M. 39 , Kodani, M. 9
The Healthy Infant Nasal Transcriptome: A Benchmark Study OPEN."
CM affects USP9X
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"Of particular notice, we observed identical effects of the USP9X-WT1-IL-8 axis on mitotic survival in A549 cells, an epithelial lung adenocarcinoma cell line (Supplementary Fig. 5h, i), suggesting a general mechanism of this regulatory nexus on mitotic survival.Finally, we investigated the effect of CDC14B silencing, which results in hyper-phosphorylation of USP9X at serine 2563."
sparser
"All rights reserved.) U VEITIS CAN BE OF INFECTIOUS OR NONINFECTIOUS
A(G/C)G G(G/C)G T(A/G)C GCA GGT A AGA A(G/C)G GTG T(A/G)C GCA GAT A Probe FAM-ACC ACG TCG AAA ACT TCG AA-MGBNFQ FAM-ACC ACG TCG AAA ACT TCA AA-MGBNFQ FAM-ACA CCG CGG CGT CA-MGBNFQ Coronavirus 229E Forward CAG TCA AAT GGG CTG ATG CA Reverse CAA AGG GCT ATA AAG AGA ATA AGG TAT TCT ND 53 Probe FAM-CCC TGA CGA CCA CGT TGT GGT TCA -TAMRA Coronavirus NL63 Forward AAG GGT TTT CCA CAG CTT GCT AAA GGT TTT CCA CAG CTT GCT ND 53 Reverse ATC ACC CAC TTC ATC AGT GCT AAC Probe FAM-TCA CTA TCA AAG AAT AAC GCA GCC TGA TTA GGA A -TAMRA Coronavirus OC43 Forward CGA TGA GGC TAT TCC GAC TAG GT Reverse CCT TCC TGA GCC TTC AAT ATA GTA ACC ND 53 Probe FAM-TCC GCC TGG CAC GGT ACT CCC T -TAMRA Enteroviruses Forward TCC TCC GGC CCC TGA Reverse AAT TGT CAC CAT AAG CAG CCA GAT TGT CAC CAT AAG CAG CCA ND 50 Probe FAM-CGG AAC CGA CTA CTT TGG GTG ACC GT -TAMRA FAM-CGG AAC CGA CTA CTT TGG GTG TCC GT -TAMRA Epstein-Barr virus Forward GGA ACC TGG TCA TCC TTT GC Reverse ACG TGC ATG GAC CGG TTA AT 50 copies/mL 42 Probe FAM-CGC AGG CAC TCG TAC TGC TCG CT -TAMRA Human herpesvirus 6 Forward GAA GCA GCA ATC GCA 160 copies/mL 42 Reverse ACA CA ATG TAA CTC Probe GGT GTA CGG TGT CTA FAM-AAC CCG TGC GCC GCT -TAMRA Human metapneumovirus Forward CAT ATA AGC ATG CTA TAT TAA AAG AGT CTC ND 49 Reverse CCT ATT TCT GCA GCA TAT TTG TAA TCA G Probe FAM-TG(C/T) AAT GAT GAG GGT GTC ACT GCG GTT G -TAMRA Influenza virus A Forward AAG ACC AAT CCT GTC ACC TCT GA Reverse CAA AGC GTC TAC GCT GCA GTC C ND 52 Probe FAM-TTT GTG TTC ACG CTC ACC GTG CC -TAMRA Influenza virus B Forward AAA TAC GGT GGA TTA AAC AAA AGC AA Reverse CCA GCA ATA GCT CCG AAG AAA ND 52 Probe FAM-CAC CCA TAT TGG GCA ATT TCC TAT GGC -TAMRA Parainfluenza virus 1 Forward TGA TTT AAA CCC GGT AAT TTC TCA T Reverse CCT TGT TCC TGC AGC TAT TAC AGA ND 51 Probe FAM-ACG ACA ACA GGA AAT C -TAMRA Parainfluenza virus 2 Forward AGG ACT ATG AAA ACC ATT TAC CTA AGT GA Reverse AAG CAA GTC TCA GTT CAG CTA GAT CA ND 51 Probe FAM-ATC AAT CGC AAA AGC TGT TCA GTC ACT GCT ATA C -TAMRA Parainfluenza virus 3 Forward TGA TGA AAG ATC AGA TTA TGC AT Reverse CCG GGA CAC CCA GTT GTG ND 51 Probe FAM-TGG ACC AGG GAT ATA CTA CAA AGG CAA AAT AAT ATT TCT C -TAMRA Continued on next page
FAM-GTA TCA TCA TCT GCC AAA TCG GCA ATT AAA CA -TAMRA Human parechovirus Forward TGC AAA CAC TAG TGG TA(A/T) GGC CC Reverse 1 TCA GAT CCA TAG TG(C/T) CAC TTG TTA CCT Reverse 2 TCA GAT CCA CAG TGT CTC TTG TTA CCT 1 TCID50/mL Forthcoming Probe FAM-CGA AGG ATG CCC AGA AGG TAC CCG -TAMRA Respiratory syncytial virus A Forward AGA TCA ACT TCT GTC ATC CAG CAA Reverse TTC TGA ACA TCA TAA TTA GGA GTA TCA AT ND 54 Probe FAM-CAC CAT CCA ACG GAG CAC AGG AGA T -TAMRA Respiratory syncytial virus B Forward AAG ATG CAA ATC ATA AAT TCA CAG GA Reverse TGA TAT CCA GCA TCT TTA AGT ATC TTT ATA GTG ND 54 Probe FAM-TCC CCT TCC TAA CCT GGA CAT AGC ATA TAA CAT ACC T -TAMRA Rubella virus Forward CAC GCC GCA CGG ACA Reverse 1 CAC CGG GAC TG(C/T) TG(A/G) TTG C 1.7 PFU/mL Forthcoming Reverse 2 CAC CGG GAC TGT TGG TTG C Probe FAM-AGG TCC CGC CCG AC-MGBNFQ Mycoplasma pneumoniae Forward GGT CAA TCT GGC GTG CAT CT Reverse TGG TAA CTG CCC CAC AAG C 50 CCU/mL 34 Probe FAM-TCC CCC GTT GAA AAA GTG AGT GGG T -TAMRA Chlamydia pneumoniae Forward TCC GCA TTG CTC AGC C Reverse AAA CAA TTT GCA TGA AGT CTG AGA A 4.9 IFU/mL 34 Probe FAM-TAA ACT TAA CTG CAT GGA ACC CTT CTT TAC TAG G -TAMRA CCU ϭ color-changing units; FAM ϭ 6-carboxyfluorescein fluorescent label; IFU ϭ inclusion-forming units; MGBNFQ ϭ minor groove binding nonfluorescent quencher; ND ϭ not determined; PFU ϭ plaque-forming units; TAMRA ϭ tetramethylrhodamine quencher; TCID50 ϭ tissue culture infectious dose 50."
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"NDR AAT AGG CGG ACC ACA TCT G 12.5 µL ND-FAM1 FAM-TCA TTC TTT ATA GAG GTA TCT TCA TCA TA-BHQ1 4 µL ND-FAM2 FAM-TCA TAC ACT ATT ATG GCG TCA TTC TT-
IBV-F2CAGTCC CDG ACG CGT GGT A 25 µL IBV-F3 GCT TTT GAG CCT AGC GTT 5 µL IBV-FAM1 FAM-ACT GGA ACA GGA CCD GCC GCT GAC CT-BHQ1 6 µL IBV-FAM2 FAM-CAC CAC CAG AAC CTG TCA CCT C-BHQ1 2 µL IBV-R1 CCT TWS CAG MAA CMC ACA CT 25 µL IBV-R2 GCC ATG TTG TCA CTG TCT ATT G 5 µL IC-2 EGFP-1-F GAC CAC TAC CAG CAG AAC AC 5 µL [25] EGFP-10-R CTT GTA CAG CTC GTC CAT GC 5 µL EGFP-HEX HEX-AGC ACC CAG TCC GCC CTG AGC A-BHQ1 3.75 µL 1 A stock mix of 200 µL was produced for each assay; the amount in µL of a 100 pmol µL −1 solution of each primer and probe for the stock mix is given here."
sparser
"Reverse-transcribed MARV RNA, RVFV RNA and eukaryotic18S rRNA, was detected on the ABI 7500 Real-Time PCR System (Life Sciences, Grand Island, NY, USA) using the SuperScript III Platinum One-Step Q-RT-PCR Kit (Life Technologies) with amplification primers and reporter probes targeting the viral protein 40 (forward primer: GGA CCA CTG CTG GCC ATA TC, reverse primer: GAG AAC ATI TCG GCA GGA AG, probe 1: 56-FAM-ATC CTA AAC-ZEN-AGG CTT GTC TTC TCT GGG ACT T-3IABkFQ, probe 2: 56-FAM-ATC CTG AAT-ZEN-AAG CTC GTC TTC TCT GGG ACT T-3IABkFQ), large segment (forward primer: TGA AAA TTC CTG AGA CAC ATG G, reverse primer: ACT TCC TTG CAT CAT CTG ATG, probe: FAM-CAC AAG TCC ACA CAG GCC CCT TAC ATT G-BHQ1) and eukaryotic 18 S rRNA (Life Technologies) genes, respectively."
6,7-dimethoxy-2-(4-methyl-1,4-diazepan-1-yl)-N-[1-(phenylmethyl)-4-piperidinyl]-4-quinazolinamine affects USP9X
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3
6,7-dimethoxy-2-(4-methyl-1,4-diazepan-1-yl)-N-[1-(phenylmethyl)-4-piperidinyl]-4-quinazolinamine decreases the amount of USP9X. 3 / 3
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3
5-InsP affects USP9X
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3
Valproic acid affects USP9X
2
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Tumour suppressor affects USP9X
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2
Streptavidin affects USP9X
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2
RpsN1 affects oleic acid
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2
Potassium chromate affects USP9X
2
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P130-AMOT affects USP9X
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2
Oleic acid affects rpsN1
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2
Kinase domain affects USP9X
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2
USP9X binds kinase domain. 2 / 2
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2
sparser
"A total of six conserved protein domains were identified in GhWAKs, including GUB_WAK_bind (wall-associated receptor kinase galacturonan-binding, PF13947), WAK (wall-associated kinase, PF08488), WAK assoc. (wall-associated receptor kinase C-terminal, PF14380), EGF (EGF, PF00008; cEGF, PF12662; hEGF, PF12661; EGF_CA, PF07645; EGF_3, PF12947), DUF1199 (domain of unknown function, PF06712) and protein kinase domain (pkinase, PF00069; pkinase_Tyr, PF07714; kinase-like, PF14531; protein-kinase domain of FAM69, PF12260) (Fig. xref a)."
| PMC
HMPV N gene sequences affects USP9X
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2
sparser
"To confirm the positive UpE samples, RT-PCR was carried out for orf1a with the identical protocol using EMC-Orf1a-Fwd primer 5'-CCA CTA CTC CCA TTT CGT CAG-3'EMC-Orf1a-Rev primer CAG TAT G TGT AGT GCG CAT ATA AGC A and EMC-Orf1a-Prb: FAM-TTG CAA ATT GGC TT GCC CCC ACT-BHQ1 probe."
sparser
"The corresponding sequences for N were 5 GGGGAACTTCTCCTGCTAGAAT3 (F), 5 CAGACATTTTGCTCTCAAGCTG3 (R) and 5 FAM-TTG CTGCTGCTTGACAGATTTAMRA3 (probe) and for ORF1ab were 5 CCCTGTGGGTTTTACACTTAA3 (F), 5 ACGATTGTGCATCAGCTGA3 (R), and 5 -CY3 CCGTCTGCGGTATGTGGAAAGGTTATGGBH Q1-3 (probe)."
Ciguatoxin CTX1B affects USP9X
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2
Arginine affects USP9X
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2
Apt affects GO
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2
VAD affects USP9X
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2
USP9X affects tumour suppressor
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2
USP9X affects translation
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2
USP9X affects streptavidin
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2
USP9X affects signal transduction
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2
USP9X affects oleic acid, and rpsN1
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2
USP9X affects lipopolysaccharide
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2
USP9X activates lipopolysaccharide. 2 / 2
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2
USP9X affects kinase domain
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2
USP9X binds kinase domain. 2 / 2
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2
sparser
"A total of six conserved protein domains were identified in GhWAKs, including GUB_WAK_bind (wall-associated receptor kinase galacturonan-binding, PF13947), WAK (wall-associated kinase, PF08488), WAK assoc. (wall-associated receptor kinase C-terminal, PF14380), EGF (EGF, PF00008; cEGF, PF12662; hEGF, PF12661; EGF_CA, PF07645; EGF_3, PF12947), DUF1199 (domain of unknown function, PF06712) and protein kinase domain (pkinase, PF00069; pkinase_Tyr, PF07714; kinase-like, PF14531; protein-kinase domain of FAM69, PF12260) (Fig. xref a)."
| PMC
USP9X affects growth
|
1
reach
"The following findings were observed : (1) Expression of USP9X was down-regulated in the kidney tissue of db/db diabetic mice; (2) overexpression of USP9X suppressed high glucose (HG)-induced expressions of EMT markers and extra cellular matrix (ECM) in NRK-52E cells; (3) depletion of USP9X further aggravated EMT process and ECM production in NRK-52E cells; (4) USP9X deubiquitinated Cx43 and suppressed its degradation to regulate EMT process; (5) USP9X deubiquitinated Cx43 by directly binding to the C-terminal Tyr 286 of Cx43."
reach
"The following findings were observed : (1) Expression of USP9X was down-regulated in the kidney tissue of db/db diabetic mice; (2) overexpression of USP9X suppressed high glucose (HG)-induced expressions of EMT markers and extra cellular matrix (ECM) in NRK-52E cells; (3) depletion of USP9X further aggravated EMT process and ECM production in NRK-52E cells; (4) USP9X deubiquitinated Cx43 and suppressed its degradation to regulate EMT process; (5) USP9X deubiquitinated Cx43 by directly binding to the C-terminal Tyr 286 of Cx43."
USP9X affects fluorescein
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2
USP9X activates fluorescein. 2 / 2
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2
reach
"Fluorescein labelled peptides were synthesized for VIP-82, ATSP-7041 and sMTIDE-02, by addition of FAM to their N-terminus via a beta-alanine linker, and then tested in the T22 p53 reporter assay to ensure that they retained comparable biological activity to their unlabeled analogs, respectively."
USP9X affects development
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2
sparser
"To confirm the positive UpE samples, RT-PCR was carried out for orf1a with the identical protocol using EMC-Orf1a-Fwd primer 5'-CCA CTA CTC CCA TTT CGT CAG-3'EMC-Orf1a-Rev primer CAG TAT G TGT AGT GCG CAT ATA AGC A and EMC-Orf1a-Prb: FAM-TTG CAA ATT GGC TT GCC CCC ACT-BHQ1 probe."
sparser
"The corresponding sequences for N were 5 GGGGAACTTCTCCTGCTAGAAT3 (F), 5 CAGACATTTTGCTCTCAAGCTG3 (R) and 5 FAM-TTG CTGCTGCTTGACAGATTTAMRA3 (probe) and for ORF1ab were 5 CCCTGTGGGTTTTACACTTAA3 (F), 5 ACGATTGTGCATCAGCTGA3 (R), and 5 -CY3 CCGTCTGCGGTATGTGGAAAGGTTATGGBH Q1-3 (probe)."
USP9X affects arginine
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2
USP9X affects WP1130
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2
USP9X affects VAD
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2
sparser
"To determine the efficiency of the decoy peptides on competing AGO2 interaction with endogenous MSI1, FAM was used to label the HIV-TAT-conjugated (TAT-FAM) peptides that were then utilized to assess the uptake rate by measuring concentration of decoy peptide at half-maximal response (EC50) in GBM cells."
sparser
"Among them, high expression of 12 lncRNAs (SH3TC2-DT, LINC00982, LINC00899, GRM7-AS1, MIR155HG, AC005392.2, LINC01132, AL133353.1, AF064858.1, LINC01979, AC103702.1, and DLGAP1-AS3) and 31 mRNAs (TMEM273, PRDM16, SH3TC2, LCT, ENPP2, CCDC113, ATRNL1, TRIM16, LDLRAD2, MPZL2, HOXB6, SCHIP1, ARHGEF5, CAMK2A, NLRP2, CCL1, H2AFY2, GLI2, APOL4, HOXA7, PBX3, PDGFD, HOXB2, HOXB5, LCN8, TRIM15, GOLGA8B, CACNG4, FAM47E-STBD1, REN, and FAM47E) were associated with poor OS ( xref , xref )."
sparser
"For example, we showed that two single nucleotide polymorphisms (SNPs) in the CAMP responsive element binding protein 1 gene ( CREB1 rs2253206 and rs2360969) were related to change in temperature during exercise, the SLIT2 SNP rs1379659 and the FAM5C SNP rs1935881 were associated with norepinephrine change during exercise, and a SNP in the μ–opioid receptor gene ( OPRM1 , rs1799971) was related to changes in norepinephrine and lactate [ xref ]."
USP9X affects Radiation, Ionizing
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2
reach
"From this screening, we have now thoroughly validated that depletion of the ubiquitin-specific protease 9X (USP9X) in HeLa and oropharyngeal squamous cell carcinoma (UMSCC74A) cells using small interfering RNA (siRNA), leads to significantly decreased survival of cells after high-LET radiation."
USP9X affects Procollagen
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2
USP9X affects Mlp37
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2
sparser
"1B R: GTG AGT AGG AGA GGT GAG AGAGG FAM-ACA CCA ATG CCC AAC TGC CTG CCT -TAMRA 109 F: GGG ATC TGA AAC AAC ATT CAT GTG IL-2 R: AGT CAG TGT TGA GAT GAT GCT TTG FAM -TGA TGA GAC AGC AACCA -TAMRA 88 F: TGC TGC CTC CAA GAA CAC AAC IL-4 R: GTC CTT CTC ATG GTG GCT GTAG FAM-CCG GAG CAC AGT CGC AGC CCT-TAMRA 160 F: ATG CAA TAA CCA CCC CTG ACC IL-6 R: CCA TGC TAC ATT TGC CGA AGAG FAM-ACC ACA AAT GCC AGC CTG CTG ACG -TAMRA 77 F: CGG AAG GAA CCA TCT CAC TGTG IL-8 R: AGA AAT CAG GAA GGC TGC CAAG FAM-TGA CTT CCA AGC TGG CCG TGG CTC -TAMRA 176 F: CAG CAA GAG ATC CTG GTC CTG IL-17 R: GGT CGG CTC TCC ATA GTC TAAC FAM-AGC CTC CAC ACT GCC CCA ACT CCT -TAMRA 96 F: GGC AAG GCT ATG TGA TTA CAAGG IFN-G R: CAT CAA GTG AAA TAA ACA CAC AAC CC FAM-AGG GGC CAA CTA GGC AGC CAA CCT -TAMRA 101 F: GCT CCA CGG AGA AGA ACT GC TGF-B R: GTT GGC ATG GTA GCC CTT GG FAM-CCA CTT CCA GCC GAG GTC CTT GCG -TAMRA 97 F: TCC ACC CAT GTG CTC CTC AC TNF-A R: TCT GGC AGG GGC TCT TGA TG FAM-CTA CCG AGT CCG TGT CTA CCA -TAMRA
depicts the relative expression levels of cytokine coding genes in COVID-19 patients and healthy subjects using box plot
Heatmap showing the correlation between expression amounts of cytokine coding genes and clinical/ demographic information among COVID-19 patients (red and blue colors indicate positive and negative correlations, respectively with dark colors showing stronger correlations)
ROC curves depicted by three machine learning models showing the power of cytokine coding genes in in distinguishing between COVID-19 patients and healthy controls (A) and between ICU-admitted patients and other patients (B) Fig. 4 ROC curves depicted by the linear discriminant analysis (LDA), showing the power of cytokine coding genes in in distinguishing between COVID-19 patients and healthy controls (A) and between ICU-admitted patients and other patients (B)
Correlation
Paraclinical parameters of the COVID-19 group Details of expression results of cytokine transcripts in study groups
Parameters obtained from ROC curve analysis for assessment of the diagnostic power of cytokine coding genes in COVID-19 AUC Sensitivity Specificity AUC Sensitivity Specificity AUC Sensitivity Specificity AUC Sensitivity Specificity AUC AUC Sensitivity Specificity AUC Sensitivity Specificity AUC Sensitivity Specificity AUC Sensitivity Specificity AUC"
USP9X affects MD3 domain
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2
USP9X affects LPNP-siRNA
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2
USP9X affects IGF-IR protein
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2
USP9X affects Hydrogen-Ion Concentration
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2
USP9X activates Hydrogen-Ion Concentration. 2 / 2
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2
reach
"Quantitatively analyzing such single particle regions where both FAM and ATTO647N signal spots were present, and altering the pH of the imaging buffer the immobilized aC’ dots were immersed in (Figure S5), we found that the FAM/ATTO647N intensity ratio still increased with pH, albeit with large deviations across different spots."
USP9X affects Hfq65.D16
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2
USP9X affects GO
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2
sparser
"In order to verify whether USP9X truly interacts with the Hippo pathway, we expressed HA-tagged version of different Hippo pathway components in HEK293 and checked if endogenous USP9X is indeed associated with each of them. xref , right panel, shows that among the 13 Hippo components tested, LATS2 and WW45 interact with USP9X strongly."
sparser
"For example, FNDC3A can bind FAM46C to inhibit multiple myeloma progression by regulating autophagy [ xref ], and FNDC5 regulates the conversion of white fat to brown fat [ xref , xref ] and improves insulin resistance by regulating the macrophage polarization, thereby reducing the validation response of adipose tissue [ xref ]."
USP9X affects FMK
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2
USP9X affects FAP
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2
sparser
"Samples were considered positive for SARS-CoV-2 only if all 3 transcripts — N1, N2, and RP — were detected. (See Supplemental Methods for details.)
We measured the expression levels of fibroblast activation markers FAP and POSTN, along with housekeeping genes GAPDH and ribosomal protein S13 (RPS13), in total RNA extracted from FFPE COVID-19 ventricular tissue, using the Reliance One-Step Multiplex Supermix (Bio-Rad), customized PrimePCR Probe Assays (FAP-FAM, POSTN-HEX, GAPDH-Cy5.5, RPS13-Cy5; Bio-Rad), and the CFX96 Touch Real Time PCR Detection System (Bio-Rad)."
USP9X affects Doublecortin
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2
USP9X affects DNA/GO
|
2
reach
"In order to confirm this interaction using another method, recombinant collagen V was radiolabelled with iodine and its interaction with different strains of F. magna was examined, _ FIG C. Again, F. magna strains expressing FAF bound collagen V, while strain 505, which does not express FAF, bound almost no collagen V."
USP9X affects Carcinogenesis
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2
sparser
"They bitch on how the Fam-Med guys don’t know what they’re doing, or they’ve lost touch or not sufficiently skilled … It seems like they sometimes think of them as incompetent and unable to manage patients appropriately … So, I have a fear that that might happen if I go into Family Medicine."
sparser
"As we found that CELF2 directly binds to FAM198B, we next investigated the coregulation of ovarian cancer cell proliferation and migration by CELF2 and FAM198B. CELF2-overexpressing CAOV-3 and SK-OV-3 cells were transfected with siRNAs targeting FAM198B (siFAM198B#1 and siFAM198B#2), and then qRT-PCR and western blots were performed to assess the knockdown efficiency ( xref A and 7B)."
USP9X affects AβOs
|
2
TDRD3 affects arginine
|
2
sparser
"To determine the efficiency of the decoy peptides on competing AGO2 interaction with endogenous MSI1, FAM was used to label the HIV-TAT-conjugated (TAT-FAM) peptides that were then utilized to assess the uptake rate by measuring concentration of decoy peptide at half-maximal response (EC50) in GBM cells."
STIL affects MD3 domain
|
2
sparser
"Among them, high expression of 12 lncRNAs (SH3TC2-DT, LINC00982, LINC00899, GRM7-AS1, MIR155HG, AC005392.2, LINC01132, AL133353.1, AF064858.1, LINC01979, AC103702.1, and DLGAP1-AS3) and 31 mRNAs (TMEM273, PRDM16, SH3TC2, LCT, ENPP2, CCDC113, ATRNL1, TRIM16, LDLRAD2, MPZL2, HOXB6, SCHIP1, ARHGEF5, CAMK2A, NLRP2, CCL1, H2AFY2, GLI2, APOL4, HOXA7, PBX3, PDGFD, HOXB2, HOXB5, LCN8, TRIM15, GOLGA8B, CACNG4, FAM47E-STBD1, REN, and FAM47E) were associated with poor OS ( xref , xref )."
sparser
"For example, we showed that two single nucleotide polymorphisms (SNPs) in the CAMP responsive element binding protein 1 gene ( CREB1 rs2253206 and rs2360969) were related to change in temperature during exercise, the SLIT2 SNP rs1379659 and the FAM5C SNP rs1935881 were associated with norepinephrine change during exercise, and a SNP in the μ–opioid receptor gene ( OPRM1 , rs1799971) was related to changes in norepinephrine and lactate [ xref ]."
sparser
"For example, we showed that two single nucleotide polymorphisms (SNPs) in the CAMP responsive element binding protein 1 gene ( CREB1 rs2253206 and rs2360969) were related to change in temperature during exercise, the SLIT2 SNP rs1379659 and the FAM5C SNP rs1935881 were associated with norepinephrine change during exercise, and a SNP in the μ–opioid receptor gene ( OPRM1 , rs1799971) was related to changes in norepinephrine and lactate [ xref ]."
RNAi affects USP9X
|
2
Procollagen affects USP9X
|
2
Mlp37 affects USP9X
|
2
sparser
"1B R: GTG AGT AGG AGA GGT GAG AGAGG FAM-ACA CCA ATG CCC AAC TGC CTG CCT -TAMRA 109 F: GGG ATC TGA AAC AAC ATT CAT GTG IL-2 R: AGT CAG TGT TGA GAT GAT GCT TTG FAM -TGA TGA GAC AGC AACCA -TAMRA 88 F: TGC TGC CTC CAA GAA CAC AAC IL-4 R: GTC CTT CTC ATG GTG GCT GTAG FAM-CCG GAG CAC AGT CGC AGC CCT-TAMRA 160 F: ATG CAA TAA CCA CCC CTG ACC IL-6 R: CCA TGC TAC ATT TGC CGA AGAG FAM-ACC ACA AAT GCC AGC CTG CTG ACG -TAMRA 77 F: CGG AAG GAA CCA TCT CAC TGTG IL-8 R: AGA AAT CAG GAA GGC TGC CAAG FAM-TGA CTT CCA AGC TGG CCG TGG CTC -TAMRA 176 F: CAG CAA GAG ATC CTG GTC CTG IL-17 R: GGT CGG CTC TCC ATA GTC TAAC FAM-AGC CTC CAC ACT GCC CCA ACT CCT -TAMRA 96 F: GGC AAG GCT ATG TGA TTA CAAGG IFN-G R: CAT CAA GTG AAA TAA ACA CAC AAC CC FAM-AGG GGC CAA CTA GGC AGC CAA CCT -TAMRA 101 F: GCT CCA CGG AGA AGA ACT GC TGF-B R: GTT GGC ATG GTA GCC CTT GG FAM-CCA CTT CCA GCC GAG GTC CTT GCG -TAMRA 97 F: TCC ACC CAT GTG CTC CTC AC TNF-A R: TCT GGC AGG GGC TCT TGA TG FAM-CTA CCG AGT CCG TGT CTA CCA -TAMRA
depicts the relative expression levels of cytokine coding genes in COVID-19 patients and healthy subjects using box plot
Heatmap showing the correlation between expression amounts of cytokine coding genes and clinical/ demographic information among COVID-19 patients (red and blue colors indicate positive and negative correlations, respectively with dark colors showing stronger correlations)
ROC curves depicted by three machine learning models showing the power of cytokine coding genes in in distinguishing between COVID-19 patients and healthy controls (A) and between ICU-admitted patients and other patients (B) Fig. 4 ROC curves depicted by the linear discriminant analysis (LDA), showing the power of cytokine coding genes in in distinguishing between COVID-19 patients and healthy controls (A) and between ICU-admitted patients and other patients (B)
Correlation
Paraclinical parameters of the COVID-19 group Details of expression results of cytokine transcripts in study groups
Parameters obtained from ROC curve analysis for assessment of the diagnostic power of cytokine coding genes in COVID-19 AUC Sensitivity Specificity AUC Sensitivity Specificity AUC Sensitivity Specificity AUC Sensitivity Specificity AUC AUC Sensitivity Specificity AUC Sensitivity Specificity AUC Sensitivity Specificity AUC Sensitivity Specificity AUC"
MD3 domain affects USP9X
|
2
MB affects USP9X
|
2
LPNP-siRNA affects USP9X
|
2
Hfq65.D16 affects USP9X
|
2
GO affects apt
|
2
sparser
"In order to verify whether USP9X truly interacts with the Hippo pathway, we expressed HA-tagged version of different Hippo pathway components in HEK293 and checked if endogenous USP9X is indeed associated with each of them. xref , right panel, shows that among the 13 Hippo components tested, LATS2 and WW45 interact with USP9X strongly."
sparser
"For example, FNDC3A can bind FAM46C to inhibit multiple myeloma progression by regulating autophagy [ xref ], and FNDC5 regulates the conversion of white fat to brown fat [ xref , xref ] and improves insulin resistance by regulating the macrophage polarization, thereby reducing the validation response of adipose tissue [ xref ]."
FMK affects VAD
|
2
FAP affects USP9X
|
2
sparser
"Samples were considered positive for SARS-CoV-2 only if all 3 transcripts — N1, N2, and RP — were detected. (See Supplemental Methods for details.)
We measured the expression levels of fibroblast activation markers FAP and POSTN, along with housekeeping genes GAPDH and ribosomal protein S13 (RPS13), in total RNA extracted from FFPE COVID-19 ventricular tissue, using the Reliance One-Step Multiplex Supermix (Bio-Rad), customized PrimePCR Probe Assays (FAP-FAM, POSTN-HEX, GAPDH-Cy5.5, RPS13-Cy5; Bio-Rad), and the CFX96 Touch Real Time PCR Detection System (Bio-Rad)."
Drosophila fat facets deubiquitinating enzyme affects USP9X
|
2
Doublecortin affects USP9X
|
2
DNA/GO affects USP9X
|
2
reach
"In order to confirm this interaction using another method, recombinant collagen V was radiolabelled with iodine and its interaction with different strains of F. magna was examined, _ FIG C. Again, F. magna strains expressing FAF bound collagen V, while strain 505, which does not express FAF, bound almost no collagen V."
CP2005 affects USP9X
|
2
sparser
"They bitch on how the Fam-Med guys don’t know what they’re doing, or they’ve lost touch or not sufficiently skilled … It seems like they sometimes think of them as incompetent and unable to manage patients appropriately … So, I have a fear that that might happen if I go into Family Medicine."
sparser
"It appears less likely that the endogenous inhibitor of caspase 8, c-FLIP [ xref ], which akin to Survivin and Mcl-1 is a molecule with a relatively short half-life and is stabilized by chaperones and potentially other deubiquitinases, is involved in TRAIL/WP1130-mediated cell death, because an interaction of Usp9X and c-FLIP has not been proven [ xref , xref ]."
reach
"It appears less likely that the endogenous inhibitor of caspase 8, c-FLIP [XREF_BIBR], which akin to Survivin and Mcl-1 is a molecule with a relatively short half-life and is stabilized by chaperones and potentially other deubiquitinases, is involved in TRAIL and WP1130 mediated cell death, because an interaction of Usp9X and c-FLIP has not been proven [XREF_BIBR, XREF_BIBR]."
sparser
"As we found that CELF2 directly binds to FAM198B, we next investigated the coregulation of ovarian cancer cell proliferation and migration by CELF2 and FAM198B. CELF2-overexpressing CAOV-3 and SK-OV-3 cells were transfected with siRNAs targeting FAM198B (siFAM198B#1 and siFAM198B#2), and then qRT-PCR and western blots were performed to assess the knockdown efficiency ( xref A and 7B)."
AβOs affects USP9X
|
2