Tag: ACTB

LncRNA/circRNA-mRNA networks in CARAS | JIR

Introduction Combined allergic rhinitis and asthma syndrome (CARAS), a new terminology introduced by the World Allergy Organization (WAO) in 2004, is an allergic reaction that occurs in the respiratory tract, including upper respiratory tract allergy (allergic rhinitis, AR) and lower respiratory tract allergy (asthma, AS).1,2 The incidence of AS in…

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Potent latency reversal by Tat RNA-containing nanoparticle enables multi-omic analysis of the HIV-1 reservoir

Participants and blood collection A total of n = 23 HIV-1 seropositive individuals on stably suppressive ART were included in this study (Supplementary Table 1). Participants were recruited at Ghent University Hospital. 2/23 individuals are female, 21/23 are male; the limited representation of female individuals in our study is a direct reflection of…

Continue Reading Potent latency reversal by Tat RNA-containing nanoparticle enables multi-omic analysis of the HIV-1 reservoir

Bioinformatics-based analysis of the relationship between disulfidptosis and prognosis and treatment response in pancreatic cancer

Identification of DRGs in PCa Figure 1a showed the flow chart of this study. To explore the role of DRGs in PCa, we analyzed the gene expression profiles of these 15 DRGs in PCa patients. As shown in Fig. 1b, for ACTN4, TLN1, IQGAP1, CD2AP, FLNA, MYH9, MYL6, and ACTB genes, the…

Continue Reading Bioinformatics-based analysis of the relationship between disulfidptosis and prognosis and treatment response in pancreatic cancer

Thyroid hormone-regulated chromatin landscape and transcriptional sensitivity of the pituitary gland

Mouse genetic models The ThrbHAB allele expresses TRβ proteins (TRβ1 and TRβ2) fused to a peptide with a hemagglutinin (HAx2) tag and a site for biotinylation by prokaryotic BirA ligase, modified from a published tag30. The tag was inserted at the endogenous Thrb gene by homologous recombination in W9.5 (129/Sv)…

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Electric Eels’ Shocking Ability To Alter The Genetics Of Nearby Animals

A new study has found that electric eels can alter the genetics of nearby animals through electrical discharges © Copyright by GrrlScientist | hosted by Forbes | LinkTr.ee The face of an electric eel. The massive electric organ in this species is made up of platelets of … [+] modified…

Continue Reading Electric Eels’ Shocking Ability To Alter The Genetics Of Nearby Animals

Electricity From Electric Eels May Transfer Genetic Material To Nearby Animals

EOD exposure from electric eel to zebrafish larvae. (A) This illustration depicts the experimental tank used to expose the recipient organism to the electric eel’s electric organ discharge (EOD). Within the tank, three carbon rod electrodes are placed: two inputs (colored black and red) and a ground electrode (colored green)….

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Characteristics of BMKS patient-, mother- and unrelated control-derived iPSCs.

For the analyses, data from two patient iPSC lines, two parent iPSC lines and two unrelated control iPSC lines were pooled. A) Relative TXNL4A mRNA expression levels for patient iPSCs compared to mother iPSCs and unrelated control iPSCs, determined using qPCR of cDNA from each cell line. Graphs were obtained…

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H101 for cervical cancer | DDDT

Introduction Patients with persistent, recurrent, or metastatic (P/R/M) cervical carcinoma respond poorly to treatment despite the best available therapeutic regimens, with a 5-year survival of 17%.1 Most of them are heavily pretreated with chemotherapy and/or radiotherapy, and many patients experience complications related to treatment or advanced disease, which exclude them…

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Mouse genome rewriting and tailoring of three important disease loci

BAC plasmids Human (CH17-203N23, CH17-449P15 and CH17-339H2) and mouse (RP23-51O13, RP23-75P20 and RP23-204E8) BACs were purchased from BACPAC Resources Center. Yeast–bacterium shuttle vector pLM1050 was modified by L. Mitchell based on a previous study28. pWZ699 was constructed by inserting a cassette containing pPGK-ΔTK-SV40pA transcription unit and the Actb gene into…

Continue Reading Mouse genome rewriting and tailoring of three important disease loci

Upregulation of WDR6 drives hepatic de novo lipogenesis in insulin resistance in mice

WDR6 is upregulated in response to insulin during insulin resistance We created an IR mouse model by feeding animals a HFD for 6 weeks20. Insulin injection was then performed (Fig. 1a). The phosphorylation of AKT, a key readout of the insulin signalling pathway21, showed decreased response to insulin, indicating resistance…

Continue Reading Upregulation of WDR6 drives hepatic de novo lipogenesis in insulin resistance in mice

Selective enrichment of plasma cell-free messenger RNA in cancer-associated extracellular vesicles

Clinical samples and plasma preparation Blood samples from control individuals and patients with multiple myeloma, liver cancer, and lung cancer were obtained from Oregon Health and Science University (OHSU) by Knight Cancer Institute Biolibrary and Oregon Clinical and Translational Research Institute (OCTRI). All samples were collected under OHSU institutional review…

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Identification and functional validation of SRC and RAPGEF1 as new direct targets of miR-203, involved in regulation of epidermal homeostasis

Keratinocyte and fibroblast cultures Normal human skin was obtained from surgical residues of breast reduction surgery, with the patients’ written informed consent in accordance with the Helsinki Declaration and with Article L. 1243-4 of the French Code of Public Health. Patients’ written informed consents were collected and kept by the…

Continue Reading Identification and functional validation of SRC and RAPGEF1 as new direct targets of miR-203, involved in regulation of epidermal homeostasis

Non-cell-autonomous cancer progression from chromosomal instability

Cell culture IMR90, 4T1, CT26, RAW264.7 and B16F10 cell lines were purchased from the American Type Culture Collection and cultured in MEM (IMR90), DMEM (B16F10, RAW264.7) or RPMI (4T1, IMR90, CT26) supplemented with 10% FBS in the presence of penicillin (50 U ml−1) and streptomycin (50 μg ml−1). All cells were found to be…

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LncRNA FENDRR suppresses melanoma growth

Introduction Cutaneous melanoma is a kind of highly aggressive and metastatic cancer.1 It only occurs in 5% of all skin cancers but causes more than 75% of deaths.2,3 Melanoma can be cured by surgical removal at an early stage.4 However, when the disease progresses to an advanced stage (stage IV),…

Continue Reading LncRNA FENDRR suppresses melanoma growth

How to automate a script using for?

How to automate a script using for? 0 Hey guys, All good? I use this simple script to generate roc curves: fit1=glm(Class ~ ACTB, data = mydata, family=’binomial’) pred1 = predict(fit1) roc1=roc(data$Class ~ pred1) plot(roc1, col=”black”, print.auc=TRUE, print.auc.cex = 0.8, print.auc.y=0.1, print.auc.x=0.2) My input table is as follows: Column 1…

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Landscape of mSWI/SNF chromatin remodeling complex perturbations in neurodevelopmental disorders

Bailey, M. H. et al. Comprehensive characterization of cancer driver genes and mutations. Cell 173, 371–385 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  Gabriele, M., Tobon, A. L., D’Agostino, G. & Testa, G. The chromatin basis of neurodevelopmental disorders: Rethinking dysfunction along the molecular and temporal axes. Prog. Neuropsychopharmacol….

Continue Reading Landscape of mSWI/SNF chromatin remodeling complex perturbations in neurodevelopmental disorders

T cell infiltration into the brain triggers pulmonary dysfunction in murine Cryptococcus-associated IRIS

Ethics statement C57BL6, Rag1−/− (002216), Tcra−/− (002116), CCR5−/− (005427), Slc17a7-IRES2-Cre-D knock-in mice (Vglut1-cre, 023527), Cd4-cre (022071), and floxed EYFP (7903) mice purchased from The Jackson Laboratory were used for the current work. Mice were group-housed with two to five in an individual cage and kept under specific pathogen-free conditions with…

Continue Reading T cell infiltration into the brain triggers pulmonary dysfunction in murine Cryptococcus-associated IRIS

Limma differential expression analysis across subtypes

I want to retrieve the ANOVA-based differential expression between KIRP1a, KIRP1b, KIRP1c, KIRP2a, KIRP2b, and KIRP2c groups to identify biomarkers for each group. My code below returned deg that are statistically significant but my heatmap (z-scaled) did not show any observable differences across the subtypes. Is there an issue with…

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Prioritization and functional validation of target genes from single-cell transcriptomics studies

List of congruent tip TEC markers The list of congruent tip TEC markers was extracted from a publicly available lung tumor study8. In brief, to identify congruent tip cell markers across freshly isolated human and murine TECs, as well as cultured human TECs, all genes that were most highly expressed…

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A viral pan-end RNA element and host complex define a SARS-CoV-2 regulon

Cell lines and culture A549-hACE2 [a gift from Dr. Ben tenOever3], 293 T, HEK293, A549, and 3T3-L1 pre-adipocyte cell lines (refer to Supplementary Table 1) were cultured in DMEM and 10% FBS. U937, Calu-3, and HCT116 cells were cultured in RPMI, EMEM, and McCoy’s 5 A media, respectively, with 10% FBS. Caco-2 cells…

Continue Reading A viral pan-end RNA element and host complex define a SARS-CoV-2 regulon

Lack of Cas13a inhibition by anti-CRISPR proteins from Leptotrichia prophages

Summary CRISPR systems are prokaryotic adaptive immune systems that use RNA-guided Cas nucleases to recognize and destroy foreign genetic elements. To overcome CRISPR immunity, bacteriophages have evolved diverse families of anti-CRISPR proteins (Acrs). Recently, Lin et al. (2020) described the discovery and characterization of 7 Acr families (AcrVIA1–7) that inhibit…

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Discovery of two new isoforms of the human DUT gene

Overview of the isoform-specific determination of dUTPase gene expression Our aim was to determine the mRNA expression level of the dUTPase isoforms specifically. First, we investigated the Ensemble, the UniProt, and the NCBI Reference Sequences (RefSeq) databases and also took into account the Consensus CDS (CCDS) project. In the Ensemble…

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Targeted knock-ins with pseudovirus for the stable expression of large transgenes

Integrase-deficient lentivirus (IDLV) enables reverse transcription of an encoded payload from an RNA molecule into a DNA template, which creates a useful yet low-efficiency donor for HDR. We engineered the IDLV genome to include CRISPR ‘cut sites’ that match the intended genomic cut site (Fig. 1). Cas9 ribonucleoprotein electroporated into…

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Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk

Development and benchmarking of MEGAnE Accurate variant genotyping is required for statistical genetics. To enable both discovery and accurate MEV genotyping from genomes studied using short reads, we developed a new bioinformatic tool, mobile element genotype analysis environment (MEGAnE; Supplementary Note). Compared to SVs resolved by long reads, MEGAnE discovers…

Continue Reading Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk

Suppression of local inflammation via galectin-anchored indoleamine 2,3-dioxygenase

Recombinant protein expression and purification NanoLuc is the tradename of an engineered deep-sea shrimp luciferase variant developed by Promega Corporation36. Genes encoding fusion proteins were inserted into pET-21d(+) vectors between NcoI and XhoI sites. IDO-Gal3 genetic and protein sequences are provided in Supplementary Information. Plasmids confer ampicillin resistance and were…

Continue Reading Suppression of local inflammation via galectin-anchored indoleamine 2,3-dioxygenase

Stable expression of large transgenes via the knock-in of an integrase-deficient lentivirus

CLIP enables high-efficiency knock-in into an essential locus To create CLIP, we leverage integrase-deficient lentiviruses (IDLV) to deliver an HDR donor template as a viral RNA genome to cells25,26. IDLV consists of lentiviral components but with a D64V mutation in the integrase, maintaining this enzyme’s ability to package and nuclear…

Continue Reading Stable expression of large transgenes via the knock-in of an integrase-deficient lentivirus

A large portion of gene ID cannot be mapped when running the “bitr” command of the “clusterProfiler” package

A large portion of gene ID cannot be mapped when running the “bitr” command of the “clusterProfiler” package 0 Hello everyone, When I run the bitr command, I get warning message saying that 58.9% of input gene IDs are fail to map…, like the following: library(ggplot2) library(clusterProfiler) > gs.up =…

Continue Reading A large portion of gene ID cannot be mapped when running the “bitr” command of the “clusterProfiler” package

Topologically associating domain boundaries are required for normal genome function

ENCODE ChIP-seq data analysis and prioritization of TAD boundary deletion loci Previously published chromosome conformation capture data was used for combined analyses and selection of TAD boundary deletion loci in this study, wherein TAD boundary calls were based on the maximum enrichment of CTCF at the TAD borders and their…

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Comprehensive Analysis of circRNA-miRNA-mRNA Network in Cervical Squamous Cell Carcinoma by Integrated Analysis

Introduction Cervical cancer (CC) is one of the most widespread gynaecological cancers that threatens women’s health in developing countries.Citation1 CC progresses through a long stage of precancerous lesions, called cervical intraepithelial neoplasia (CIN), which is classified into three grades: CIN 1, CIN 2 and CIN 3.Citation2 Human papillomaviruses (HPVs) have…

Continue Reading Comprehensive Analysis of circRNA-miRNA-mRNA Network in Cervical Squamous Cell Carcinoma by Integrated Analysis

Acetylation of histone H2B marks active enhancers and predicts CBP/p300 target genes

Multiple H2BNTac sites occupy the same genomic regions H2BNTac sites are similarly regulated by CBP/p30018 (Supplementary Fig. 1a), yet the reported genome occupancy patterns of H2BNTac sites are dissimilar from each other22,23 (Supplementary Note 1). To resolve this conundrum, we systematically compared H3K27ac and H2BNTac genomic occupancy and regulation by…

Continue Reading Acetylation of histone H2B marks active enhancers and predicts CBP/p300 target genes

Collateral activity of the CRISPR/RfxCas13d system in human cells

Cell culture HEK293T, MEF-1, and U87 cell lines were used in this research. HEK293T was purchased from ATCC. MEF-1, and U87 cell lines were gifts from Muredach P. Reilly, Peter A. Sims, respectively. HEK293T, MEF-1, and U87 cells were cultured in DMEM with 4.5 g/L D-Glucose, supplemented with 10% fetal bovine…

Continue Reading Collateral activity of the CRISPR/RfxCas13d system in human cells

Establishing an RNA fusions panel in soft tissue sarcoma with clinical validation

Accuracy validation of the RNA fusion panel The method proposed in the study was validated using 48 synthetic DNA constructs and 31 samples with known fusions (17 PT samples from CAP, 14 samples tested by FISH assays), and the information for the 79 samples was referenced in Supplemental Table S2….

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NAD+ precursor supplementation prevents mtRNA/RIG-I-dependent inflammation during kidney injury

Altered NAD+ metabolism is prominent in diseased human kidneys We collected human kidney samples from healthy controls (n = 25) and patients with diabetic or hypertensive KD, defined as estimated glomerular filtration rate (eGFR) less than 60 ml min−1 per 1.73 m2 and kidney fibrosis (n = 25) (Fig. 1a). The mean eGFR values were 95 ml min−1 per 1.73 m2 (healthy…

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Using the blast api from Python (3)

Hi all, I’m trying to use the blast api (blast.ncbi.nlm.nih.gov/Blast.cgi) from Python using the requests module. My goal is to send a sequence and get genomic (Ensembl GRCh38) coordinates back. request=”https://blast.ncbi.nlm.nih.gov/Blast.cgi?QUERY=gagtctcctttggaactctgcaggttctatttgctttttcccagatgagctctttttctggtgtttgtct&DATABASE=nt&PROGRAM=blastn&CMD=Put&FORMAT_TYPE=JSON2′ (This sequence is part of the ACTB gene) I sent it to the server like this: response = requests.get(request)…

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Extract Interactions using paxtoolsr from Pathway Commons

Extract Interactions using paxtoolsr from Pathway Commons 1 I am looking for interactions between a protein (ACTB) and calcium and I want to use the paxtoolsr package. Is this possible? What code is necessary? r pathway • 50 views • link updated 1 hour ago by cannin ▴ 350 •…

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Barrier-to-autointegration factor 1 promotes gammaherpesvirus reactivation from latency

Biosafety statement All experiments with cell lines and viral infections were carried out in a Biosafety Level 2 facility under the approval of the Biosafety Office in the Department of Environment, Health and Safety and the Institutional Biosafety Committee at the University of North Carolina at Chapel Hill. The laboratory…

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Identification of key genes related to immune infiltration in cirrhosis via bioinformatics analysis

Lozano, R. et al. Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet 380(9859), 2095–2128 (2012). Google Scholar  Blachier, M., Leleu, H., Peck-Radosavljevic, M., Valla, D. C. & Roudot-Thoraval, F….

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Dual roles of mTORC1-dependent activation of the ubiquitin-proteasome system in muscle proteostasis

Sustained skeletal muscle mTORC1 activity upregulates the ubiquitin proteasome system To understand the molecular mechanisms causing atrophy in muscles with high mTORC1 activation, we first analyzed the transcriptome of the fast-type extensor digitorum longus (EDL) muscle in 3-month-old TSCmKO mice6. A short-term (3 day) treatment with rapamycin was used to…

Continue Reading Dual roles of mTORC1-dependent activation of the ubiquitin-proteasome system in muscle proteostasis

Transcription-independent regulation of STING activation and innate immune responses by IRF8 in monocytes

Reagents, antibodies, viruses and cells LMW-Poly(I:C), LPS, 2′3′-cGAMP and DMXAA (InvivoGen); hydroxyurea, camptothecin and mitomycin C (MCE); GM-CSF, Flt3L (peproTech); lipofectamine 2000 (Invitrogen); polybrene (Millipore); RNAiso Plus (Takara); HT-DNA (Sigma); SYBR (BIO-RAD); dual-specific luciferase assay kit (Promega); ELISA kit for murine Ifn-β (PBL); ELISA kits for murine IP-10 (Biolegend) were…

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Transcriptional profiling of macrophages reveals distinct parasite stage-driven signatures during early infection by Leishmania donovani

Infection with L. donovani amastigotes or promastigotes promotes early changes in the mRNA pool of the host cell To compare the early effects of the two life stages L. donovani in the mature mRNA pool of the host cell, total cytosolic mRNA extracts from bone marrow-derived macrophage (BMDM) cultures infected…

Continue Reading Transcriptional profiling of macrophages reveals distinct parasite stage-driven signatures during early infection by Leishmania donovani

Validation of hub genes in acute pancreatitis

Introduction Acute pancreatitis (AP) is a common disease found in clinics, and requires urgent Hospital admission. The incidence of AP is increasing in recent years worldwide.1 The patients with AP increased from 1,727,789.3 to 2,814,972.3 between 1990 and 2019 in 204 countries and territories.2 Meanwhile, nearly 20% of AP patients…

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