Tag: cDNA

genbank sequence format

HHS Vulnerability Disclosure, Help This document is an overview of the Entrez databases, with general information on If you are not sure that the “Save” option in your program will do this for you, use “Save As”, In Excel, select “Save As” from the File menu. optimizations to reduce memory…

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scRNA-seq for Microcephaly Research [I]: Single-Cell Droplet Encapsulation, mRNA Capture, and cDNA Synthesis

doi: 10.1007/978-1-0716-2752-5_8. Affiliations Expand Affiliations 1 Department of Medicine, Division of Immunology, Lowance Center for Human Immunology, Emory University School of Medicine, Atlanta, GA, USA. ben.babcock@emory.edu. 2 Department of Neurology, University of North Carolina Medical School, Chapel Hill, NC, USA. Item in Clipboard Benjamin Babcock et al. Methods Mol Biol. 2023….

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Independent Longitudinal Study Finds CareDx’s AlloSure Detects Early Signs of Rejection in Pediatric Kidney Transplant Patients

First Pediatric Study to Evaluate Use of AlloSure dd-cfDNA as Biomarker for Allograft BK Infection Findings Add to Growing Body of Evidence Showing Clinical Value of AlloSure for Surveillance in Pediatric Kidney Transplant Patients BRISBANE, Calif.–(BUSINESS WIRE)– CareDx, Inc. (Nasdaq: CDNA) – The Transplant Company™ focused on the discovery, development, and…

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Cellular glycan modification by B3GAT1 broadly restricts influenza virus infection

Ethics statement All procedures involving laboratory mice were approved by the Duke University IACUC under the protocol numbers A189-18-08 and A142-21-07. Mice were housed with up to five mice per cage and the ambient room conditions ranged from 70–74 °F and 30–70% humidity with a 12-hour dark/light cycle. Animals were assessed…

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Evasion of cGAS and TRIM5 defines pandemic HIV

Cells and reagents HEK293T and U87 cells were maintained in DMEM medium (Gibco) supplemented with 10% fetal bovine serum (FBS, Labtech) and 100 U ml−1 penicillin plus 100 μg ml−1 streptomycin (Pen/Strep; Gibco). THP-1-IFIT1 cells that had been modified to express Gaussia luciferase under the control of the IFIT1 promoter were described previously62. THP-1…

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Breadth of SARS-CoV-2 neutralization and protection induced by a nanoparticle vaccine

Animals and immunizations The study protocol and all veterinarian procedures were approved by the Bioqual IACUC per a memorandum of understanding with the Duke IACUC, and were performed based on standard operating procedures. Macaques studied were housed and maintained in an Association for Assessment and Accreditation of Laboratory Animal Care-accredited…

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Inferring and perturbing cell fate regulomes in human brain organoids

Experimental methods Stem cell and organoid culture We used six human iPS cell lines (Hoik1, Wibj2, Kucg2 from the HipSci resource47; 409B2 from the RIKEN BRC cell bank; 01F49i-N-B7 (B7) from Institute of Molecular and Clinical Ophthalmology Basel; and WTC from the Allen Institute) and three human ES cell lines (H1-PAX6YFP…

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How to read the AUGUSTUS results

Hi, everyone. I used AUGUSTUS to make a genetic prediction for a certain fish, but I don’t know how to read the results. I mainly do not understand the following three points. 1.What does “sequence number” mean? How is it different from scaffold number? 2.What does “none” mean? Does it…

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Isolation of Preadipocytes from Broiler Chick Embryos

The present protocol describes a simple method for isolating preadipocytes from adipose tissue in broiler embryos. This method enables isolation with high yield, primary culture, and adipogenic differentiation of preadipocytes. Oil Red O staining and lipid/DNA stain measured the adipogenic ability of isolated cells induced with differentiation media. Primary preadipocytes…

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All transcript variants in gene MAD1L1 – BIPMed SNP Array

Legend Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column’s header and hold it still. Below, a more detailed description is shown per column. Effect: The variant’s effect on the protein’s function, in the format ‘R/C’ where…

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Challenges of single-cell and single-nucleus RNA-sequencing from core needle biopsy specimens

Single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq) allow transcriptomic profiling of thousands of cells from a renal biopsy specimen at a single-cell resolution. Both methods are promising tools to unravel the underlying pathophysiology of glomerular diseases. KU Leuven researchers provide an overview of the technical challenges that should be…

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Bioinformatics Analysis of the Key Genes and Pathways in Multiple Myel

Introduction Multiple myeloma is a B-cell malignancy characterized by the malignant proliferation of clonal plasma cells in bone marrow,1 It is the second most common hematological malignancy after lymphoma.2 The age-standardised rate (ASR) of multiple myeloma incidence was 1·78 (95% UI 1·69-1·87) per 100 000 people globally and mortality was…

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Acute phase of ischemia-reperfusion in rats

Introduction Stroke is one of the leading causes of death and disability worldwide, which causes substantial economic and social burdens.1 Ischemic stroke is caused by insufficient blood and oxygen supply to the brain,2 accounting for about 85% of the casualties of stroke patients.3 The concept of treatment for ischemic injury…

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iPSCs derived from infertile men carrying complex genetic abnormalities can generate primordial germ-like cells

Patients and controls The patient 1 was 38 years old and consulted for infertility after he and his partner had been trying to conceive for 2 years. The patient was the first child of unrelated parents, and he had four brothers and five sisters whose fertility status could not be determined…

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Live-seq enables temporal transcriptomic recording of single cells

Biological materials RAW264.7, 293T and HeLa cells were obtained from ATCC. RAW264.7 cells with Tnf-mCherry reporter and relA-GFP fusion protein (RAW-G9 clone) were kindly provided by I.D.C. Fraser (National Institutes of Health). The IBA cell line derived from the stromal vascular fraction of interscapular brown adipose tissue of young male…

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Proscillaridin A induces mitochondrial damage and autophagy in pancreatic cancer and reduces the stability of SMAD4 in Panc-1 cells – Hou

Introduction Pancreatic cancer (PC) is one of the most aggressive and lethal cancers (1). Previous studies have shown that aging, environmental and behavioral changes are more closely related to the dramatic increase in the incidence of PC worldwide than genetic factors (2–5). A position paper published by the European Federation…

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Error in Create switchAnalyzeRlist

Error in Create switchAnalyzeRlist 0 Hello everyone., I am using isoformswitchinganalysisR to look at different transcript expression and quantification data generated using Kallisto. I have stuck in step of Create switchAnalyzeRlist. According to warning error it looks I have problem in gtf file. Really appreciate anybody can help me how…

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In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states

Animals and sample preparation Animal experiments were performed as previously described12. C57BL/6J WT mice or ob/ob mice at ten weeks of age were purchased from Japan SLC Inc. (Shizuoka, Japan). The phenotypic data of the mice are summarized in Table S1. Animal experiments were approved by the animal ethics committee…

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Home page The store will not work correctly in the case when cookies are disabled. JavaScript seems to be disabled in your browser. For the best experience on our site, be sure to turn on Javascript in your browser. Pioneer in Engineered Nucleases technologies from ZFNs and TALENs to CRISPRs…

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Interfering B cell receptor signaling via SHP-1/p-Lyn axis shows therapeutic potential in diffuse large B-cell lymphoma | Molecular Medicine

Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000;403(6769):503–11. CAS  PubMed  Article  Google Scholar  Camicia R, Winkler HC, Hassa PO. Novel drug targets for personalized precision medicine in relapsed/refractory diffuse large…

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Mapping reads using kallisto – rna seq analysis

Mapping reads using kallisto – rna seq analysis 0 Hi, I’m trying to map reads to a reference genome using kallisto for rna seq analysis with terminal on mac and the following command keeps loading for hours and won’t run. I’m not exactly sure where I’ve gone wrong. kallisto index…

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Lh3 Minimap2 Issues

Issue Title State Comments Created Date Updated Date Mapping reads against multi references. Any proposition? open 0 2022-06-28 2022-06-30 Inversion between tandem repeats yields misalignment closed 1 2022-06-21 2022-06-30 use minimap2 to extract mitochondrial reads from genome assembly open 0 2022-06-20 2022-06-30 Asking for #301 to be reopened closed 0…

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Terminator Upgrades Single-Cell RNA Sequencing Technology

Japanese scientists have developed a new method for DNA amplification and sequencing that improves the accuracy of single-cell RNA sequencing (scRNA-seq). The new method called TAS-Seq uses a terminal transferase enzyme that amplifies and sequences DNA complementary to mRNA (cDNA) in solid phase on a nanowell/magnetic bead-based cell isolation platform….

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Stabilizing and Anti-Repressor Elements Effectively Increases Transgene Expression in Transfected CHO Cells

doi: 10.3389/fbioe.2022.840600. eCollection 2022. Affiliations Expand Affiliations 1 School of Basic Medicine, Xinxiang Medical University, Xinxiang, China. 2 International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, China. Free PMC article Item in Clipboard Qin Li et al. Front Bioeng Biotechnol. 2022. Free PMC…

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An inducible system for expression and validation of the specificity of short hairpin RNA in mammalian cells – HKUST SPD

Bibliographic Details Author Ma, Hoi Tang On, Kin Fan Tsang, Yiu Huen Poon, Randy Yat Choi Issue Date 2007 Source Nucleic acids research, v. 35, (4), 2007, FEB, Article number e22 Abstract RNA interference (RNAi) by means of short hairpin RNA (shRNA) has developed into a powerful tool for loss-of-function…

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Alpelisib Plus Olaparib Phase 1b Clinical Trial for Patients With Advanced Triple-Negative Breast Cancer

For a study, researchers sought to present the breast cancer cohort. In a previous study, they reported on safety. They recommended a phase 2 dose (RP2D) of olaparib combined with the PI3Kα-specific inhibitor alpelisib in patients with high-grade serous ovarian cancer as studied in a phase 1b trial (NCT01623349). Investigators…

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MAGEA12 shRNA Plasmid Human) – Gentaur.com

Catalog number MBS8252845 Supplier Price 647 EUR Size 0,15 mg Other size please contact us to order other different size Properties Human proteins, cDNA and human recombinants are used in human reactive ELISA kits and to produce anti-human mono and polyclonal antibodies. Modern humans (Homo sapiens, primarily ssp. Homo sapiens sapiens). Depending on the…

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Frontiers | Serum and Serum Exosomal CircRNAs hsa_circ_0001492, hsa_circ_0001439, and hsa_circ_0000896 as Diagnostic Biomarkers for Lung Adenocarcinoma

Introduction Lung cancer is associated with high morbidity and mortality and continues to be a major public health problem worldwide (1). Lung adenocarcinoma (LUAD) is the most common histological type of lung cancer. While the 5-year survival rates of patients with lung cancer are still <15%, rates are closer to…

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b30_m7_l06_assign.docx.pdf – Biology 30: Module 7: Lesson 6 1 Assignment MODULE 7: LESSON 6 ASSIGNMENT This Module 7: Lesson 6 Assignment is worth 14

Unformatted text preview: Biology 30: Module 7: Lesson 6 1 Assignment MODULE 7: LESSON 6 ASSIGNMENT This Module 7: Lesson 6 Assignment is worth 14 marks. The value of each assignment and each question is stated in the left margin. Review the lesson online in ‘content’. In your eText, review…

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LncRNA Sequencing Helps to Find Deep Links to Disease

Long non-coding RNAs (lncRNAs) are a class of RNAs that do not code for proteins and are typically greater than 200 nucleotides in length. Studies have shown that lncRNAs are quite complex in function and play an important role in various biological processes such as development, differentiation, proliferation, metastasis, apoptosis,…

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In vivo hypermutation and continuous evolution

Arnold, F. H. Design by directed evolution. Acc. Chem. Res. 31, 125–131 (1998). Google Scholar  Packer, M. S. & Liu, D. R. Methods for the directed evolution of proteins. Nat. Rev. Genet. 16, 379–394 (2015). Google Scholar  Drake, J. W., Charlesworth, B., Charlesworth, D. & Crow, J. F. Rates of…

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il15 related Antibodies, Proteins, cDNA and ELISA Kits- Cusabio

Interleukin-15 is a protein in humans that is encoded by IL15 gene. Cytokine that stimulates the proliferation of T-lymphocytes. Stimulation by IL-15 requires interaction of IL-15 with components of IL-2R, including IL-2R beta and probably IL-2R gamma but not IL-2R alpha. il15 Proteins il15 Proteins for Mus musculus (Mouse) il15…

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Variant #0000255165 (NC_000010.10:g.123278248A>G, FGFR2(NM_000141.4):c.939+1245T>C) – Global Variome shared LOVD

Variant #0000255165 (NC_000010.10:g.123278248A>G, FGFR2(NM_000141.4):c.939+1245T>C) Chromosome 10 Allele Unknown Affects function (as reported) Probably does not affect function Affects function (by curator) Not classified Classification method – Clinical classification likely benign DNA change (genomic) (Relative to hg19 / GRCh37) g.123278248A>G DNA change (hg38) g.121518734A>G Published as FGFR2(NM_022970.3):c.1035T>C (p.Y345=) ISCN – DB-ID FGFR2_000119 Variant remarks VKGL data sharing initiative Nederland Reference – ClinVar ID – dbSNP ID – Origin CLASSIFICATION record Segregation –…

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Biogenesis, biology and characterization of circular RNAs

Biogenesis, biology and characterization of circular RNAs Kristensen LS et al. The biogenesis, biology and characterization of circular RNAs. Nat Rev Genet. (2019) Summary text Biogenesis and properties of circRNAs Biogenesis of cirRNA Characteristics of circRNAs Discover and analyze circRNAs circRNA genome-wide analysis CircRNA site-specific analysis circRNA visualization Biological functions…

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Normal With Genetic Disorder +ddTTP tetranucleotide

Transcribed image text: Normal With Genetic Disorder +ddTTP tetranucleotide tetranucleotide pentanucleotide pentanucleotide heptanucleotide heptanucleotide +ddATP mononucleotide mononucleotide trinucleotide trinucleotide hexanucleotide +ddCTP dinucleotide dinucleotide nonanucleotide hexanucleotide nonanucleotide +ddGTP octanucleotide octanucleotide decanucleotide decanucleotide (a) What base was altered and to which was it altered? Answer: From C V to A (b) What…

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Frontiers | COMMD2 Upregulation Mediated by an ncRNA Axis Correlates With an Unfavorable Prognosis and Tumor Immune Infiltration in Liver Hepatocellular Carcinoma

Introduction Liver hepatocellular carcinoma (LIHC) is the most common type of primary cancer in the liver and third leading cause of cancer-related mortality worldwide (1). Although substantial improvements have been made in LIHC therapy, particularly in molecular targeted therapy and immunotherapy (2, 3), the 5-year survival rate of LIHC is…

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Competent Cells Market is poised to reach US$ 2,100 Million value by the end of 2022.

A latest research study published by Future Market Insights (FMI) projects the global competent cells market to register an impressive 8.1% CAGR throughout the forecast period 2017 to 2022. The global market for competent cells is estimated to exceed US$ 2,000 Mn in revenues by 2022-end. Competent Cells Available in the Market…

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TF differentiation of hiPSCs at Wellcome Sanger Institute

Salary per annum: c.£33,900 Contract Length: 2 years Here at the world-famous and internationally respected Wellcome Sanger Institute, we have an exciting opportunity for a postdoctoral researcher to perform high throughput screening for transcription factor-driven differentiation in human pluripotent stem cells (hiPSCs) in order to create better in vitro differentiated cells that more faithfully…

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CareDx Showcases Leadership with Over 25 Oral Presentations and Posters at the International Society for Heart and Lung Transplantation Meeting

CareDx, Inc. Data Highlights Clinical Utility of CareDx Solutions, Including Findings from Surveillance HeartCare Outcomes Registry (SHORE) Demonstrating Power of Multimodality Assessment for More Precise Interventions CareDx Symposia Feature Latest Advancements Including XenoSure and XenoMap SOUTH SAN FRANCISCO, Calif., April 20, 2022 (GLOBE NEWSWIRE) — CareDx, Inc. (Nasdaq: CDNA) –…

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Whole-genome analysis of coxsackievirus B3 reflects its genetic diversity in China and worldwide | Virology Journal

Song Y, Zhang Y, Han Z, Xu W, Xiao J, Wang X, et al. Genetic recombination in fast-spreading coxsackievirus A6 variants: a potential role in evolution and pathogenicity. Virus Evol. 2020;6:2. doi.org/10.1093/ve/veaa048. Article  Google Scholar  Chen J, Han Z, Wu H, Xu W, Yu D, Zhang Y. A large-scale outbreak…

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Shrna Lentiviral Particles Recipes

Lentiviral Clone&Lentivirus packaging services – GeneCopoeia Recipes Details: Advantages of lentiviral ORF cDNA, promoters, shRNA, and microRNA clones High efficiency of gene delivery to virtually all cell types and whole model organisms. A lentiviral system is very effective at delivering genetic material to whole model organisms and almost all mammalian…

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how to build index for cdna?

Hello, I can build index for Mus_musculus.GRCm38.dna_sm.toplevel.fa, but when build for Mus_musculus.GRCm38.cdna.all.fa, there is a bug: “rsem-extract-reference-transcripts Mus_musculus.GRCm38.cdna.all.fa 0 Mus_musculus.GRCm38.cdna.all.fa.gtf None 0 Mus_musculus.GRCm38.cdna.all” failed! Plase check if you provide correct parameters/options for the pipeline! Traceback (most recent call last): File “../indrops.py”, line 1770, in project.build_transcriptome(args.genome_fasta_gz, args.ensembl_gtf_gz, mode=args.mode) File “../indrops.py”, line…

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Using salmon in Galaxy

Hi everyone. I am executing Salmon in Galaxy in order to carry out gene quantification from mouse RNA-Seq data (6 samples). To do so, I am providing a reference genome (cDNA, in fasta format), the processed reads (in fastqsanger.gz format) of one of these samples (after executing Trim-Galore) and a…

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Low transcript quantification with Salmon using GRCm39 annotations

Hi everyone, first time working with mouse samples and unfortunately, there are fewer resources available for the latest mouse Ensembl genome than I was expecting. What I’ve done: I performed rRNA depletion on total RNA extracted from mouse tissue and created Illumina libraries using a cDNA synthesis kit with random…

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Minimap2 options for Nanopore cDNA direct seq

Minimap2 options for Nanopore cDNA direct seq 0 Hello, I’m working with ONT RNA seq data and I used the cDNA direct seq to do the seq. I want to look for long deletions in mRNAs that are not spliced, for this, I want to use the splice option of…

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CircRNA circFADS2 is under-expressed in sepsis and protects lung cells from LPS-induced apoptosis by downregulating miR-133a | Journal of Inflammation

Sepsis patients and healthy controls A total of 62 sepsis patients (male/female: 32/30; mean age, 52.3±4.9 years) who were admitted to Minhang Hospital, Fudan University between March 2018 and March 2020 were enrolled in the study. In addition, 62 healthy controls (male/female: 32/30; mean age, 52.4±4.8 years) who were at…

Continue Reading CircRNA circFADS2 is under-expressed in sepsis and protects lung cells from LPS-induced apoptosis by downregulating miR-133a | Journal of Inflammation

Transcriptional kinetics and molecular functions of long noncoding RNAs

Ethical compliance The research carried out in this study has been approved by the Swedish Board of Agriculture, Jordbruksverket: N343/12. Cell culture Mouse primary fibroblasts were derived from adult (>10 weeks old) CAST/EiJ × C57BL/6J or C57BL/6J × CAST/EiJ mice by skinning, mincing and culturing tail explants (for at least 10 d) in DMEM high…

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Highlight points on a plot

R: Highlight points on a plot maText {marray} R Documentation Highlight points on a plot Description This function may be used to highlight a subset of points on an existing plot, such as a plot produced by plot, maPlot, or maPlot.func. Usage maText(subset=NULL, labels=as.character(1:length(subset)), …) Arguments subset A “logical” or…

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Drosophila carrying epilepsy-associated variants in the vitamin B6 metabolism gene PNPO display allele- and diet-dependent phenotypes

Pyridox(am)ine 5′-phosphate oxidase (PNPO; Enzyme Commission Number 1.4.3.5) is a rate-limiting enzyme in the synthesis of vitamin B6 (VB6) (1). Mutations in PNPO can cause neonatal epileptic encephalopathy, a devastating disease that usually leads to death if untreated (2). Recently, PNPO mutations have also been reported in patients with infantile…

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Extracellular circulating miRNAs as stress-related signature to search and rescue dogs

Study approval was provided by the Research Ethics Committee of the University of Perugia (report n.2018-21 of 11/12/2018) according to Italian Ministry of Health legislation18. All methods were carried out following relevant guidelines and regulations and the study was carried out in compliance with the ARRIVE guidelines. Informed consent is…

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Exosomal microRNA-618 derived from mesenchymal stem cells attenuate the progression of hepatic fibrosis by targeting Smad4

Introduction Hepatic fibrosis (HF) is a pathological phenomenon produced in the process of long-term damage and repair in the liver [1,2]. During the formation of HF, hepatocytes are damaged by various factors, such as chronic liver disease, and excessive intake of alcohol, and secrete a variety of cytokines [3]. Subsequently,…

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Kallisto mapping paired end

Kallisto mapping paired end 0 Hello everyone, I am new to bioinformatics and i am trying to use kallisto to map paired end data. However, I got an error by running the command. So does anyone know what did I do wrong here? Thank you! Here is my command: kallisto…

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Requirement of Xk and Vps13a for the P2X7-mediated phospholipid scrambling and cell lysis in mouse T cells

Significance The extracellular concentration of adenosine triphosphate (ATP) reaches several hundred micromoles in the inflamed tissues or tumor environment. A high concentration of ATP activates P2X7, a purinergic receptor, and induces the formation of a nonselective cation channel, accompanied by reversible phosphatidylserine (PtdSer) exposure, leading to cell lysis. Here, we…

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Cell Strain-Derived Induced Pluripotent Stem Cells as an Isogenic Approach To Investigate Age-Related Host Response to Flaviviral Infection

INTRODUCTION Dengue is the most common mosquito-borne viral disease globally (1). This acute disease, which can be life-threatening, is caused by four different dengue viruses (DENVs) (DENV-1, DENV-2, DENV-3, and DENV-4). An estimated 390 million people are infected with these DENVs annually (2), and populations throughout the tropics face frequent…

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Comprehensive circRNA Analyses in Human Vertebrae of GIOP and Its Molecular Mechanism

Circular RNAs (circRNAs) are a novel class of noncoding RNAs that play important roles in human diseases. However, the regulation of circRNAs in glucocorticoid-induced osteoporosis (GIOP) has not been reported. In this study, we performed high-throughput sequencing to identify altered circRNAs in the vertebrae from GIOP patients. A total of…

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Variant #0000726648 (NC_000017.10:g.7100169G>A, ACADVL(NM_000018.3):c.-23135G>A) – Global Variome shared LOVD

Variant #0000726648 (NC_000017.10:g.7100169G>A, ACADVL(NM_000018.3):c.-23135G>A) Chromosome 17 Allele Unknown Affects function (as reported) Effect unknown Affects function (by curator) Not classified Classification method – Clinical classification VUS DNA change (genomic) (Relative to hg19 / GRCh37) g.7100169G>A DNA change (hg38) – Published as DLG4(NM_001321075.2):c.990C>T (p.G330=) ISCN – DB-ID DLG4_000038 Variant remarks VKGL data sharing initiative Nederland Reference – ClinVar ID – dbSNP ID – Origin CLASSIFICATION record Segregation – Frequency – Re-site –…

Continue Reading Variant #0000726648 (NC_000017.10:g.7100169G>A, ACADVL(NM_000018.3):c.-23135G>A) – Global Variome shared LOVD

Variant #0000803285 (NC_000007.13:g.92730753A>G, SAMD9(NM_017654.3):c.4658T>C) – Global Variome shared LOVD

Variant #0000803285 (NC_000007.13:g.92730753A>G, SAMD9(NM_017654.3):c.4658T>C) Chromosome 7 Allele Unknown Affects function (as reported) Effect unknown Affects function (by curator) Not classified Classification method – Clinical classification VUS DNA change (genomic) (Relative to hg19 / GRCh37) g.92730753A>G DNA change (hg38) – Published as SAMD9(NM_017654.3):c.4658T>C (p.I1553T), SAMD9(NM_017654.4):c.4658T>C (p.I1553T) ISCN – DB-ID SAMD9_000024 See all 3 reported entries Variant remarks VKGL data sharing initiative Nederland Reference – ClinVar ID – dbSNP ID – Origin CLASSIFICATION…

Continue Reading Variant #0000803285 (NC_000007.13:g.92730753A>G, SAMD9(NM_017654.3):c.4658T>C) – Global Variome shared LOVD

Profiling and functional characterization of maternal mRNA translation during mouse maternal-to-zygotic transition

INTRODUCTION Mammalian life starts with the fusion of two terminally differentiated gametes, sperm and oocyte, resulting in a totipotent zygote. After going through preimplantation development, the zygote reaches blastocyst before implantation. The two most important events taking place during preimplantation development are zygotic genome activation (ZGA) and the first cell…

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Ensembl VEP gnomAD annotated allele frequencies different from gnomAD browser

I’ve annotated some variants using VEP, and was looking at the minor allele frequencies. Some of the variants had very different MAFs in the annotation than I expected (I expected MAF < 1%, whereas some annotated MAFs were >50%). I looked up the same variants on the gnomAD v3 browser,…

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Novel diagnostic biomarkers for keloid based on GEO database

Introduction Keloid is excessive fibrosis of the skin that extends beyond the area of injury and does not regress.1 Keloid can occur in the joints and mouth after several years of severe injury, including burns, chemical injury, wound, and surgical incision.2 Keloids on the joints affect the quality of life,…

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A cell-based phenotypic library selection and screening approach for the de novo discovery of novel functional chimeric antigen receptors

Cell lines and culture Unless stated otherwise, all tumor target cell lines were sourced from the ATCC via LGC Standards. Human endogenous mesothelin (MSLN)-positive target cell lines H-226 (lung carcinoma, MSLN+, ATCC® CRL-5826™) and AsPC-1 (ATCC CRL-1682), and MSLN-negative Raji control cells (ATCC CCL-86) were cultured in RPMI-1640 Glutamax (Life Technologies,…

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Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor | BMC Genomics

1. Sharma VK. Adaptive significance of circadian clocks. Chronobiol Int. 2003;20(6):901–19. PubMed  Google Scholar  2. Paranjpe DA, Sharma VK. Evolution of temporal order in living organisms. J Circadian Rhythms. 2005;3(1):7. PubMed  PubMed Central  Google Scholar  3. Yerushalmi S, Green RM. Evidence for the adaptive significance of circadian rhythms. Ecol Lett….

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DESeq2 analysis for targeted RNA-seq

Dear all, I am attempting to perform DESeq2 analysis (using the Geneious plugin) for targeted RNA-seq of several hundred genes. Only the target set of genes is sequenced, as the primer that I use for first strand cDNA synthesis is specific to the target set of genes. I have three…

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NIH Study Shows Using CareDx’s AlloSure Lung for Transplant Surveillance is More Effective than Diagnostic Bronchoscopy at Identifying Rejection

SOUTH SAN FRANCISCO, Calif., Jan. 07, 2022 (GLOBE NEWSWIRE) — CareDx, Inc.,  (Nasdaq: CDNA) – The Transplant Company™ focused on the discovery, development, and commercialization of clinically differentiated, high-value healthcare solutions for transplant patients and caregivers – today announced the results of a study led by the National Institutes of…

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Identification of differentially expressed genes in AF

Defeng Pan,1,&ast; Yufei Zhou,2,&ast; Shengjue Xiao,1,&ast; Yue Hu,3,&ast; Chunyan Huan,1 Qi Wu,1 Xiaotong Wang,1 Qinyuan Pan,1 Jie Liu,1 Hong Zhu1 1Department of Cardiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People’s Republic of China; 2Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of…

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SAMD9

cite web | title = Entrez Gene: SAMD9 sterile alpha motif domain containing 9| url = www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=54809| accessdate = ] PBB_Summarysection_title = summary_text = References Further reading PBB_Further_reading citations = *cite journal | author=Maruyama K, Sugano S |title=Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with…

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Phospholipase A2 inhibitor and LY6/PLAUR domain-containing protein PINLYP regulates type I interferon innate immunity

Significance Interferon (IFN)-mediated antiviral responses serve as the first line of the host innate immune defense against viral infection. Here we identify a previously uncharacterized protein designated phospholipase A2 inhibitor and LY6/PLAUR domain-containing protein (PINLYP), which is essential for embryonic development and plays an important role in type I IFN…

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China Paper Sharing | SEU/TJU: circRNA is a gene therapy target for RCC Manufacturer and Supplier

  Basic information Title: ciRS-7 is a prognostic biomarker and potential gene therapy target for renal cell carcinoma   Journal: Molecular Cancer     Impact factor: 27.401   Vazyme products:   HiScript® III 1st Strand cDNA Synthesis Kit (+gDNA wiper)(number: Vazyme #R312, for 1st Strand cDNA Synthesis) AceQ® qPCR SYBR Green Master Mix (High ROX Premixed)(number: Vazyme…

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A TaqI polymorphism detected by a genomic clone at the locus D5S39 (5q11-13).

.=/ 1991 Oxford University Press 1720 Nucleic Acids Research, Vol. 19, No. 7 A Taql polymorphism detected by a genomic clone at the locus D5S39 (5q11 -13) Kpnl RFLP at the human muscletype phosphofructokinase (PFKM) gene locus B.S.Mankoo, G.Melmer, G.Kalsi, R.Sherrington and H.M.D.Gurling Department of Academic Psychiatry, University College and…

Continue Reading A TaqI polymorphism detected by a genomic clone at the locus D5S39 (5q11-13).

Omics advanced 07 | transcriptome mRNA | miRNA | lncrna

A brief introduction mRNA,miRNA,lncRNA And circRNA Principle of genome sequencing 、 Routine analysis of Shengxin . Catalog Introduction to transcriptome sequencing mRNA|miRNA|lncRNA|circRNA Introduction to analysis mRNA Group miRNA Group lncRNA Group circRNA Group mRNA|miRNA|lncRNA|circRNA Correlation analysis Reference Introduction to transcriptome sequencing Transcriptome (Transcriptome) Is a single or group of cells…

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Human EpCAM/TROP1 (NP_002345) VersaClone cDNA RDC1470: R&D Systems

Long Name Epithelial Cell Adhesion Molecule Entrez Gene IDs 4072 (Human); 17075 (Mouse); 171577 (Rat); 102123042 (Cynomolgus Monkey) Alternate Names 17-1A; 323/A3; ACSTD1; antigen identified by monoclonal AUA1; CD326 antigen; CD326; Cell surface glycoprotein Trop-1; chromosome 4, surface marker (35kD glycoprotein); DIAR5; EGP; EGP-2; EGP314; EGP40; EpCAM; epithelial cell adhesion…

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Very important pharmacogene variants in the Blang population

Introduction The use of drugs should be different among diverse ethnic groups because of differences in ethnicity, age, sex, environmental factors and genetic factors. If these differences are ignored, then drug sensitivity, metabolic rate, and adverse reactions are affected, which influences the curative effect of drugs and aggravates the illness…

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Single-cell delineation of lineage and genetic identity in the mouse brain

STICR lentiviral library preparation and validation We synthesized a high-complexity lentivirus barcode library that encodes approximately 60–70 million distinct oligonucleotide RNA sequences (STICR barcodes). STICR barcodes comprised three distinct oligonucleotide fragments cloned sequentially into a multicloning site within the 3′ UTR of an enhanced green fluorescent protein (eGFP) transgene under…

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Large-scale genome-wide study reveals climate adaptive variability in a cosmopolitan pest

Genomic data The foundational resource for this study was a dataset of 40,107,925 nuclear SNPs sequenced from a worldwide sample of 532 DBM individuals collected in 114 different sites based on our previous project15. DNA was extracted from each of the 532 individuals using DNeasy Blood and Tissue Kit (Qiagen,…

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Prognosis Biomarkers via WGCNA in HCC

Introduction According to the cancer statistics reported in 2020, hepatocellular carcinoma (HCC) is the main type of Primary Carcinoma of the Liver and the second leading causes of cancer-related death globally, with a five-year survival rate < 20%.1 Currently, surgical resection, a standard therapy for HCC, contributes to the prognosis…

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Twin Prime Editing Promises More Precise DNA Changes Without Double-Strand Breaks

NEW YORK – Researchers at the Broad Institute have developed a new prime editing method that allows for more precise replacement or excision of DNA sequences at endogenous human genomic sites, without the need for double-strand DNA breaks (DSBs). In a paper published on Thursday in Nature Biotechnology, researchers led…

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Tau and PQBP1: Protein Interaction Induces In

image: PQBP1 functions in brain microglia, which corresponds to dendritic cells or a part of macrophage regulating innate immune system, as an intracellular receptor for HIV cDNA and Tau proteins similarly. view more  Credit: Department of Neuropathology, TMDU Researchers from Tokyo Medical and Dental University clarify the role of cell receptor…

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Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model | BMC Biology

Organoid culture of small intestinal cells and lentiviral transduction C57BL/6J mice and BALB/cAnu/nu immune-deficient nude mice were purchased from CLEA Japan (Tokyo, Japan). The small intestine was harvested from wild-type male C57BL/6J mice at 3–5 weeks of age (Additional file 1: Figure S9A). Crypts were purified and dissociated into single cells,…

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Transposition and duplication of MADS-domain transcription factor genes in annual and perennial Arabis species modulates flowering

Annual and perennial species occur in many plant families. Annual plants and some perennials are monocarpic (flowering once in their life cycle), characterized by a massive flowering and typically produce many seeds before the whole plant senesces. By contrast, most perennials live for many years, show delayed reproduction, and are…

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miRNAs and mRNAs in intestinal ischemia-reperfusion injury

Introduction Intestinal ischemia-reperfusion (II/R) injury is a severe clinical complication common in the Intensive Care Unit (ICU). It is associated with high morbidity and mortality.1 Usually, this problem is followed by various causes, including sepsis, shock, trauma, and so on.2 Intestinal ischemia-reperfusion injury destroys intestinal tissue and impairs the function…

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Selection of DNA Aptamers Recognizing EpCAM-Positive Prostate Cancer b

Introduction Prostate cancer (PCa) is one of the most common genitourinary system malignant tumor in men worldwide. In Asian countries, many patients with PCa are often diagnosed at an advanced stage maybe mostly because of a large population base with relatively backward economic development and imperfect cancer screening system of…

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Submit sequence data to NCBI

Data provision and standards. GEO sequence submission procedures are designed to encourage provision of MINSEQE elements: Thorough descriptions of the biological samples under investigation, and procedures to which they were subjected. Thorough descriptions of the protocols used to generate and process the data. Request updates to accessioned records per the…

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Getting exon sequences for all human genes

Getting exon sequences for all human genes 2 Hi everyone, I would be very grateful if you could help me. I want to download the sequences of all the exons for each human gene. I went to ensembl biomart and tried to do it for BRCA2 first (this was a…

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How to Create Loop for all fastq file

How to Create Loop for all fastq file 0 Dear All, hope you are doing well. I am trying to write a loop for my all fastq and doing preprocessing using bash. I am taking an error, Can you help me to write bash loops? for file in *.fastq; do…

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The sardine run in southeastern Africa is a mass migration into an ecological trap

INTRODUCTION Large-scale annual migrations occur in an extraordinary range of animals, from insects to the great whales. While the driving mechanisms of these migrations are varied and sometimes poorly understood, they often represent a way of optimizing conditions for breeding and adult fitness when these are in conflict. Often, populations…

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MYO10 drives genomic instability and inflammation in cancer

INTRODUCTION Genomic instability often refers to the existence of a variety of DNA alterations, ranging from single nucleotide changes (such as base substitution, deletion, and insertion) to chromosomal rearrangements (e.g., gain or loss of a segment or the whole chromosome) (1). Loss of genome stability can lead to early onset…

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Disabling de novo DNA methylation in embryonic stem cells allows an illegitimate fate trajectory

The mammalian genome is characterized by widespread methylation of cytosine residues. After fertilization, however, both maternal and paternal genomes undergo extensive demethylation, reaching a low point in the blastocyst (1⇓⇓–4). The embryo genome is then remethylated by the activity of de novo DNA methylation enzymes (5). Mouse embryonic stem (ES)…

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Next Generation Sequencing in tissues: Fully in situ methods

Here, Synthetic Biology Platform Lead at the Wyss Institute for Biologically Inspired Engineering, Richie Kohman, continues exploring the breakthroughs of Next Generation Sequencing (NGS) Exploring the locations and identities of RNA within biological tissues can uncover important information about cell types and states as well as give insight into cellular…

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Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India

COVID-19 laboratory screening Nasopharyngeal/Nasal/Oropharyngeal swabs in viral transport medium (VTM) received from acute phase patients with defined symptoms, asymptomatic cases with contact history with positive patients/ travel history were processed for laboratory confirmation of SARS-CoV-2 at Defence Research and Development Establishment, (DRDE) Gwalior, M.P., India. These samples were referred for…

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Ancestral polymorphisms shape the adaptive radiation of Metrosideros across the Hawaiian Islands

Significance Some of the most spectacular adaptive radiations of plants and animals occur on remote oceanic islands, yet such radiations are preceded by founding events that severely limit genetic variation. How genetically depauperate founder populations give rise to the spectacular phenotypic and ecological diversity characteristic of island adaptive radiations is…

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Getting cDNA sequence from NCBI

Getting cDNA sequence from NCBI 1 I am looking at NCBI’s api page and I cannot seem to find any endpoint that returns the cDNA by transcript id. In fact NCBI nuccore has a webpage for this. and if I want to i can scrape the part coming after ORIGIN….

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nanopore sequencing stock

It holds a 15% stake in the company and has valued its holding at £340m, giving a valuation of more than £2bn for the company. . While the company’s current shareholders have recorded its value at just over £2bn, analysts . Essay from the year 2011 in the subject Business…

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Gene expression profiling of contralateral dorsal root gangl

Introduction Mirror-image pain (MIP) is a mysterious pain phenomenon which is accompanied with many clinical pain conditions.1 MIP develops from the healthy body region which is contralateral to the actual injured site.1–3 MIP is typically characterized by increased mechanical hypersensitivity on the uninjured mirror-image body side.4 It can be triggered…

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ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIF–containing protein that controls root growth angle in barley and wheat

    Significance To date, the potential of utilizing root traits in plant breeding remains largely untapped. In this study, we cloned and characterized the ENHANCED GRAVITROPISM2 (EGT2) gene of barley that encodes a STERILE ALPHA MOTIF domain–containing protein. We demonstrated that EGT2 is a key gene of root growth…

Continue Reading ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIF–containing protein that controls root growth angle in barley and wheat

PROPER-Seq Uses NGS to ID Undiscovered Protein-Protein Interactions

NEW YORK – A new method for profiling protein-protein interactions (PPIs) using next-generation sequencing as a readout has the potential to reveal thousands of previously undiscovered combinations in human cells. The method, called PROPER-seq (protein-protein interaction sequencing), tags proteins with RNA barcodes that form chimeric sequences when brought into proximity with…

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A systematic method for DNA fragment amplification and sequencing based on DNA indexing technology. Protocol and technical considerations

DNA indexing is based on a presynthesized library of oligonucleotide adaptors (256 in total), named indexers, and type-IIS restriction endonucleases. It enables amplification and direct analysis of large DNA fragments with low overall redundancy and without subcloning. Here, we describe a detailed protocol for PCR-based amplification of DNA fragments followed…

Continue Reading A systematic method for DNA fragment amplification and sequencing based on DNA indexing technology. Protocol and technical considerations

High-purity production and precise editing of DNA base editing ribonucleoproteins

Abstract Ribonucleoprotein (RNP) complex–mediated base editing is expected to be greatly beneficial because of its reduced off-target effects compared to plasmid- or viral vector–mediated gene editing, especially in therapeutic applications. However, production of recombinant cytosine base editors (CBEs) or adenine base editors (ABEs) with ample yield and high purity in…

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An epigenetic basis of inbreeding depression in maize

INTRODUCTION Charles R. Darwin documented inbreeding depression as growth disadvantages from self-fertilization compared to outcrossing in many plants (1). Prevailing hypotheses suggest that inbreeding depression results from the exposure of deleterious recessive alleles and/or loss of overdominant alleles due to increased homozygosity (2, 3) or reduced recombination frequency in some…

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Multiform antimicrobial resistance from a metabolic mutation

Abstract A critical challenge for microbiology and medicine is how to cure infections by bacteria that survive antibiotic treatment by persistence or tolerance. Seeking mechanisms behind such high survival, we developed a forward-genetic method for efficient isolation of high-survival mutants in any culturable bacterial species. We found that perturbation of…

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Nuclear protein in testis carcinoma

Introduction Nuclear protein in testis (NUT) carcinoma (NC) is defined by the rearrangement of the chromosomal region 15q14 harboring the NUTM1 gene. As a clinically aggressive neoplasm with poor differentiation, NC was previously believed to occur primarily in children and young adolescents. However, with an increasing number of reports, middle-aged…

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