Category: mRNA

Reproductive Medicine Associates of New York Presents Innovative Research at ASRM’s 77th Annual Meeting

RMA of New York leads the way with ground-breaking innovative genomics and artificial intelligence research to improve patient care and IVF success rates Published: Oct. 19, 2021 at 9:00 AM MDT|Updated: 4 hours ago BALTIMORE, Md., Oct. 19, 2021 /PRNewswire/ — Physicians and scientists at Reproductive Medicine Associates of New York…

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Codebase of deep learning models for inferring stability of mRNA molecules

Codebase of deep learning models for inferring stability of mRNA molecules, corresponding to the Kaggle Open Vaccine Challenge and accompanying manuscript “Predictive models of RNA degradation through dual crowdsourcing”, Wayment-Steele et al (2021) (full citation when available). Models contained here are: “Nullrecurrent”: A reconstruction of winning solution by Jiayang Gao….

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Postdoc In Bioinformatics Infection Immunology United Kingdom United Kingdom Jobs

Postdoc in Bioinformatics (Infection Immunology) United KingdomDirekt zum Inhalt springen Login Register MyTUM-Portal Technische Universität München 27.09.2021, Wissenschaftliches Personal Bioinformatician/Computational Biologist/Systems Immunologist (f/div/m) for two years initially with a possibility of extension to 5 and more years Requirements: o You have a PhD degree (or postgraduate degree MSc) in a…

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How to normalize Kallisto count matrix collapsed at gene-level with TMM/DESeq2?

Hi all, Sorry for the simple question but I’m new to Kallisto and could not reach a definitive conclusion based on other posts. I have two matrices of expression data (from a previous study) that I want to use for mRNA-miRNA correlation analysis. Based on the information provided by the…

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Prediction of single-cell miRNA-seq data in cancer

Context microRNAs (miRNAs) are small non-coding RNAs known to further regulate protein coding genes. They are important in many physiological and pathological processes. In cancer, in particular, they were demonstrated to be implicated to all the carcinogenesis: initiation, propagation and metastasis. Single cell mRNA-seq has revolutionized are vision of tumor…

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Gene Editing Facility | CRISPR | Cas9

The iPSC Derivation & Gene Editing Core is a facility established and managed by the MCRI Stem Cell Medicine Initiative and has been in operation since 2014. This facility brings together a team of highly experienced stem cell and molecular biologists with over 40 years combined experience to generate standard and gene-edited iPSC…

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Wondering what all the fuss about CRISPR is?

One major challenge faced in gene editing is the unavailability of a proper set of guidelines Gene editing is a method where a part of DNA is inserted, deleted, modified or even replaced. The ability to edit genes has helped study and understand their function better thus giving an insight…

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Medical College of Wisconsin hiring Bioinformatics Analyst I in Milwaukee, Wisconsin, United States

Position Description: Every great life-changing discovery begins the same way—with new knowledge. It can change everything, from a single life to the future of entire communities. That’s why academic medicine, and the continuous pursuit of knowledge, is at the center of everything we do at the Medical College of Wisconsin….

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Principal Scientist, Bioinformatics, Molecular Discovery on beHired.in

ROLE SUMMARY We are seeking a talented, experienced laboratory informatics scientist to join Pfizer’s BioMedicine Design organization located in Cambridge, Massachusetts.  The successful candidate will join a small team of computational biologists and software engineers to develop a broad array of fit for purpose computational and database tools in support…

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Computational methods for genomics data analysis: Cancer detection using circulating tumor DNA and miRNA expression inference in single cells

To join via Zoom: To join this seminar via Zoom, please request connection details from headsec [at] stat.ubc.ca To join in-person: To join this seminar in-person, online registration is required (limited seating) Title: Computational methods for genomics data analysis: Cancer detection using circulating tumor DNA and miRNA expression inference in…

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Regulatory Hurdles Block a Cancer Miracle

Scientific breakthroughs are sometimes a matter of serendipity. Eight years ago Meredith Halks-Miller, a pathologist at the genetic-screening company Illumina, stumbled on something unusual while running prenatal blood tests for fetal chromosomal abnormalities. In some blood samples, the fetal genes were normal but the maternal DNA wasn’t. Illumina alerted pregnant…

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Study supports efficacy and safety of lung-selective nanotherapy against SARS-CoV-2 infection

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has proved to evade neutralization by antibodies elicited by vaccination and natural infection with the ancestral strains by the emergence of new variants. New therapeutic measures are essential to achieve better control of viral spread and disease severity. Study: Lung-selective Cas13d-based nanotherapy…

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Epigenetics Collide With Pharmacogenomics

The history of medicine is a never-ending work in progress. What is the next chapter in the psychiatry and genetics story? Let me begin with my conclusion: The current clinical use of pharmacogenomic testing in psychiatry to determine a metabolic enzyme’s activity to choose a medication to prescribe is not…

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The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests

Sequencing of Shorea leprosula genome Sample collection Leaf samples of S. leprosula were obtained from a reproductively mature (diameter at breast height, 50 cm) diploid tree B1_19 (DNA ID 214) grown in the Dipterocarp Arboretum, Forest Research Institute Malaysia (FRIM). DNA extraction Genomic DNA was extracted from leaf samples using the…

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CRISPR Gene Editing Reduces Disease-Causing Protein in Hered… : Neurology Today

By Thomas R. Collins October 7, 2021 The Science Explained Article In Brief CRISPR-Cas9 gene editing knocked out the production of misfolded transthyretin, which slowed the formation of amyloid, a contributor to transthyretin amyloidosis with polyneuropathy. The study was small and short-term, but experts said the…

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Linking Two Gene Activity via Transcription Factors similarities

Linking Two Gene Activity via Transcription Factors similarities 0 Let say I suspect Gene A and Gene B of mouse share similar Transcription Factor. What should I do to prove this? From my limited reading, I manage to obtain a list of TF from PROMO website for Gene A and…

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Comparative cellular analysis of motor cortex in human, marmoset and mouse

Statistics and reproducibility For multiplex fluorescent in situ hybridization (FISH) and immunofluorescence staining experiments, each ISH probe combination was repeated with similar results on at least two separate individuals per species, and on at least two sections per individual. The experiments were not randomized and the investigators were not blinded…

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Combining different data types into a single matrix for WGCNA using DESeq2 normalization

Combining different data types into a single matrix for WGCNA using DESeq2 normalization 0 Hi, I have two different RNA-seq datasets for the sample set of samples, generated using mRNA-seq and smallRNA-seq. The goal here is to identify a set of coding-genes and smallRNAs (no known function/targets) that act together….

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Duke Neuroscientist Co-Leads Massive Effort to Map Brain

DURHAM, N.C. — Every great exploration refines the map, and in the case of the massive BRAIN initiative funded by the National Institutes of Health, that new draft of the map has just been released. In a special collection of 17 new papers appearing Wednesday in the journal Nature, an…

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The 2021 Nobel prize in chemistry as it happens

12.01pm Holiday snap It turns out that Benjamin List was on holiday in Amsterdam when he got the call letting him know that his life was going to change forever (at least he was in a timezone amenable to getting the call, unlike David MacMillan, who’s based at Princeton University). …

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Generation of knock-in lampreys by CRISPR-Cas9-mediated genome engineering

Strategy for generating knock-in lampreys with the LcHsp70A promoter For CRISPR-Cas9-mediated knock-in via non-homologous end joining (NHEJ) in the lamprey, we used an experimental strategy previously established in zebrafish13 and medaka14 with minor modification: co-injection of sgRNA1 (for genome digestion), sgRNA2 (for plasmid digestion), donor plasmids, Cas9 mRNA, and fast…

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DeepMind AI ‘AlphaFold’ Gets Closer to Perfect Prediction of Protein Folding with Groundbreaking Accuracy

(Photo : Image from Unsplash Website) DeepMind AI ‘AlphaFold’ Gets Closer to Perfect Prediction of Protein Folding with Groundbreaking Accuracy A certain DeepMind AI known as AlphaFold has gotten closer to the perfect prediction of protein folding with groundbreaking accuracy. The DeepMind AI was able to predict the structure of…

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Sequencing, mRNA, nanocrystals: Field for Nobel Prize in chemistry wide open

Stockholm – Breakthroughs in DNA sequencing, innovative gas storage, nanocrystals or a second chance for mRNA COVID-19 vaccines? Speculators on the Nobel Prize in chemistry are spoiled for choice ahead of the announcement on Wednesday. The winner — or winners — of the prestigious prize will be unveiled at 11:45…

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Achieving high non-viral transfection performance for cell therapy processing

Cell therapies often involve introduction of genetically transformed cells into a patient. Recently there has been renewed interest in non-viral gene modification for this application as an alternative to lentiviral vectors. Non-viral electroporation utilizing CRISPR-Cas9 is continuing to show improved performance and safety benefits in the area of cell-based immunotherapy….

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Sequencing, mRNA, or maybe nanocrystals? Wide-open field for Nobel Chemistry Prize

Issued on: 06/10/2021 – 07:28 Stockholm (AFP) Breakthroughs in DNA sequencing, innovative gas storage, nanocrystals or a second chance for mRNA Covid-19 vaccines? Speculators on the Nobel Prize in Chemistry are spoiled for choice ahead of the announcement on Wednesday. The winner — or winners — of the prestigious prize…

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Bionexus: Gene Synthesis Services

 GENE SYNTHESIS SERVICES Gene SynthesisBionexus will construct any gene the way you want it, from a few hundred base pairs to thousands of base pairs. The experts at Bionexus (over 9 years experience), will construct your gene and sequence both strands to ensure that you get no mutants.  Gene Synthesis…

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Cellectra

 · The hand-held Cellectra device administers a brief electrical pulse to reversibly open small pores in skin-area cells. Once inside the cell, the vaccine’s DNA plasmids instruct the cell to produce …Oct 25, 2016Dec 07, 2020Jun 23, 2020The CELLECTRA device uses a brief electrical pulse to reversibly open small pores…

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Cis-acting mutation affecting GJA5 transcription is underlying the Melanotic within-feather pigmentation pattern in chickens

Significance The molecular mechanisms underlying pigmentation patterns in animals is to a large extent an unresolved mystery in biology. For example, compared with mammals, birds show a stunning diversity in pigmentation patterns. This study advances the knowledge concerning the mechanisms creating periodic pigmentation patterns in individual feathers. We show that…

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40th Anniversary Recollections & Predictions

To help celebrate GEN’s 40th Anniversary with this special October issue, we asked scientists and business professionals in academia and industry to give us their reflections, impressions, and insights on the biotechnology industry and the life sciences. We also queried them on what they believe the future might look like…

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Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)

Hi all, I am a PhD student with biology background. I recently inherit a RNA Sequencing project from another PhD student in my lab. We already have paired-ended RNA-Seq data generated from Illumina HiSeq but haven’t started analysis yet. I have basic Linux command line training but have no idea about how…

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grep command to grep list of genes in one file (txt) present in other file(gff) but it did not work…?

grep command to grep list of genes in one file (txt) present in other file(gff) but it did not work…? 0 grep -w -f upregulated_genes_in_BEg GCA_900659725.1_ASM90065972v1_genomic.gff LOCUS10095 LOCUS10108 LOCUS10129 LOCUS10130 LOCUS10152 LOCUS10161 LOCUS10225 LOCUS10252 LOCUS10266 LOCUS10268 LOCUS10294 LOCUS10313 LOCUS10351 LOCUS10355 LOCUS10358 Gff file: CAACVG010000011.1 EMBL exon 112774 112954 . +…

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Adventures Leading to a Paradigm Shift in Healthcare

When I went to Caltech as a young assistant professor in 1970, I began thinking of all the possible research choices before me. Molecular immunology and technology development (initially protein sequencing) were no brainers, as I had been active in these areas during my graduate and NIH careers. But I…

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The top candidates for the Nobel battle

The award winners will be announced this week starting Monday when Karolinska Institutet reveals who will receive the award in medicine/physiology. Then the Academy of Sciences announces the winners in Physics (Tuesday) and Chemistry (Wednesday). People often sigh a little when they hear about prices, which is a normal reaction…

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blast protein alignment

28 set blast protein alignment Posted at 20:44h in Sem categoria by BLAST applied the standard genetic code for Query, translating GTG into valine (V). The BLAST is a set of algorithms that attempt to find a short fragment of a query sequence that aligns perfectly with a fragment of…

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Regulation of prefrontal patterning and connectivity by retinoic acid

Data reporting No statistical methods were used to predetermine sample size.  Data collection was performed by independent investigators. Prior to data analysis, all experiments were randomized and analysed by independent blinded observers. Analysis of human and macaque transcriptomic data Developing human and macaque brain RNA-seq data (counts file) with the…

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Single cell RNA sequencing (scRNA-seq) in cardiac tissue

Introduction Cardiovascular diseases (CVDs) are the leading cause of death globally, taking an estimated 17.9 million (32.1%) lives in 2015, up from 12.3 million (25.8%) in 1990.1,2 CVDs are highly heterogeneous diseases involving a group of disorders of the heart and blood vessels, which include cardiomyopathy, hypertensive heart disease, heart…

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Flagship Pioneering hiring Bioinformatics Scientist, Next Generation Sequencing (NGS) in Cambridge, Massachusetts, United States

Who We AreGenerate Biomedicines, Inc. is a Flagship backed, privately-held biotechnology company on a mission to reimagine the drug discovery process through the use of cutting-edge machine learning techniques. Core to Generate’s approach is the development and application of novel machine learning algorithms to solve foundational problems in molecular and…

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Mutational profile of the dystrophin gene

Introduction Duchenne Muscular Dystrophy (DMD-OMIM #310200) and Becker Muscular Dystrophy (BMD-OMIM #300376), are the most common hereditary muscular dystrophies around the world.1 DMD and BMD occur with a frequency of 1/3.300 and 1/6.000 newborn males, respectively.2 These dystrophinopathies are caused by alterations in the DMD gene and have an X-linked…

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Unraveling the hidden role of a uORF-encoded peptide as a kinase inhibitor of PKCs

Short open reading frames (ORF) upstream of the canonical ORF (uORFs) are found in about 40% of human protein-coding transcripts (1⇓–3). uORF-containing genes were shown to participate in heavily regulated processes, including differentiation, cell cycle control, and stress responses (4⇓–6). Ribosome profiling data revealed that many uORFs are translated (3,…

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All eyes on the Nobel Prizes for science next week. Here’s what to expect :: WRAL.com

By Katie Hunt, CNN CNN — The coronavirus pandemic has focused attention on the role of science in society like never before — and the pace of scientific discovery has been blistering. The greatest minds in physics, chemistry and medicine will be honored when the Nobel Prizes, the pinnacle of…

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All eyes on the Nobel Prizes for science next week. Here’s what to expect

While predicting who will win a Nobel Prize is famously difficult — the short list is secret, as are the nominators, and documents revealing the juicy details are sealed from public view for 50 years, here are some Nobel-worthy candidates and the life-changing discoveries they have made. The Lasker Awards…

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Which RNA type I should considered as long non-coding RNAs

Which RNA type I should considered as long non-coding RNAs 0 Hello We have exosome-sequensing (from plasma). In raw read counts file, I see 72650 gene names. This is how my read count file looks like I have created a percentage bar chart for categories of RNAs annotated in this…

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What a RefSeq does mean

What a RefSeq does mean 1 Hi We have exosome-seq (from plasma) results and in the chart I see panel RefSeq like WDR33 What RefSeq is here? Does it mean protein coding mRNAs? Because based on my understanding by exosome-seq we can not catch too much mRNA 🙁 This is…

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How to verify putative miRNA

How to verify putative miRNA 1 My PI gave me a list of some DNA sequences, each one around 25 nucleotides, that are suspected to code for Vitis Vitinesfera miRNA. To know if they are complementary to some mRNA for a known protein sequence, we do the following process: BLAST…

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Analysis and Applications for the Future Meeting

Presentation highlights a path forward to lead the development of the Company’s clinical-grade Next-Generation cf-mRNA Liquid Biopsy-Artificial Intelligence Technology Platform PALO ALTO, Calif., Sept. 29, 2021 /PRNewswire/ — Molecular Stethoscope, Inc., a Precision Medicine biotechnology company, announces a presentation at the 2021 16th annual Sequencing to Function: Analysis and Applications…

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Molecular Stethoscope, Inc. Announces Presentation at 16th Annual Sequencing to Function: Analysis and Applications for the Future Meeting | News

Presentation highlights a path forward to lead the development of the Company’s clinical-grade Next-Generation cf-mRNA Liquid Biopsy-Artificial Intelligence Technology Platform PALO ALTO, Calif., Sept. 29, 2021 /PRNewswire/ — Molecular Stethoscope, Inc., a Precision Medicine biotechnology company, announces a presentation at the 2021 16th annual Sequencing to Function: Analysis and Applications for…

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genbank submission bankit

Submission of sequence data to NCBI archives . Learn more. This post will show you how to… Careers, General: your contact details, authors, publication, data release date, Original or third-party assembly/annotation, Set designation (if applicable) for multiple sequences of the same locus, Nucleotide sequences in FASTA or alignment format, Source…

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mRNA Could Fight Diseases Such as Alzheimer’s and Cancer, With Help of UVA Scientist

This year, the public was introduced to messenger ribonucleic acid, or mRNA, when it became a hero in the worldwide race to develop COVID-19 vaccines. Scientists lab-engineered mRNA to instruct human cells how to recognize, and then destroy, the spike protein that is the entryway for the virus. Highly effective…

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Molecular profiles and urinary biomarkers of upper tract urothelial carcinomas associated with aristolochic acid exposure

This article was originally published here Int J Cancer. 2021 Sep 27. doi: 10.1002/ijc.33827. Online ahead of print. ABSTRACT Recurrent upper urinary tract carcinomas (UTUC) arise in the context of nephropathy linked to exposure to the herbal carcinogen aristolochic acid (AA). Here we delineated the molecular programs underlying UTUC tumorigenesis…

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rs2507799 was found to be linked with increased risk for IS

Introduction Ischemic stroke (IS) is caused by the sudden loss of blood circulation to an area of the brain that causes injury to neurological function and represents a major cause of global disability and mortality.1 IS is known to be a heterogeneous and multifactorial disease. Genetic factors, particularly those involving…

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PM Modi at UNGA 2021

Prime Minister Narendra Modi marked another milestone in India’s fight against COVID-19 during the 76th United Nations General Assembly session. PM Modi talked about the development of the DNA vaccine in India, which can be administered to those above the age of 12. During his address in the UNGA session…

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Creative Biolabs Announces Personalized Solutions for Oligonucleotide Synthesis

(ProNewsReport Editorial):- New York City, New York Sep 26, 2021 (Issuewire.com) – Oligonucleotide synthesis, the chemical synthesis of relatively short fragments of nucleic acids with defined chemical structure, plays an important role in creating biomolecules for biological, medical, and clinical applications. Up to August 2021, more than 14 oligonucleotide drugs have been approved by FDA (the…

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Modi spotlights India’s role as a ‘reliable, democratic global partner’

NEW YORK — In his address to the high-level debate at the UN General Assembly on Saturday, Narendra Modi reaffirmed India’s commitment to democracy, highlighted its great strides in developing and manufacturing COVID-19 vaccines, and warned against “countries with regressive thinking.” In a pre-recorded address, Prime Minister Modi highlighted that…

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The complicated truth about “junk DNA”

Imagine human The genome is a string as long as a football field, and all the genes encoding proteins are gathered near the end of the foot. Take two big steps forward; all protein information is now behind you. There are 3 billion base pairs in the DNA of the…

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India logs 28,326 new cases, 260 deaths in last 24 hrs

India has reported a surge in its active Covid-19 cases and deaths on Sunday, as per the latest data by the Union ministry of health. India saw a rise of 2,034 active cases in a day. At present, India’s active case count stands at 3,03,476, which is 0.90% of the…

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Modi at UNGA: Terror also threatens countries trying to use it as political tool

Prime Minister Narendra Modi on Saturday addressed the United Nations General Assembly in New York. This was his first in-person address to the UNGA since 2019, with 2020’s session held virtually. Modi used his address to hail his government’s achievements, including arranging affordable housing for the poor, deploying vaccinations at…

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Nations using terror as ‘political tool’ must understand it is big threat for them: PM

Prime Minister Narendra Modi addresses the 76th Session of the UN General Assembly in New York City on Saturday. ‘Essential to ensure Afghan territory not used for terrorism’*Modi concludes 3-day productive visit to US UNITED NATIONS, Sept 25: Prime Minister Narendra Modi said today that countries with “regressive thinking” that…

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No weak links: A W&M-based collaborative advances understanding of neural control of respiration

(Most of) the team:  Team members that successfully completed a Patch-Seq analysis of respiratory-control neurons are (from left) Greg Smith, Margaret Saha, Prajkta Kallurkar and Christopher Del Negro. Not pictured are team members Tina Picardo and Yae Sugimura.  Courtesy photo by Joseph McClain |  September 24, 2021 Patch-Seq is shorthand…

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Extracting The Features From Genbank File

Hi I have a set of the genes (mouse) for which i would like to get the function, tissue specificity and other features. I have obtained a file (.dat) from uniprot which has all such information. but it also has unwanted information. The data seems to be in genbank format….

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Biotechnology timeline: Humans have manipulated genes since the ‘dawn of civilization’

Historically, biotech has been primarily associated with food, addressing such issues as malnutrition and famine. Today, biotechnology is most often associated with the development of drugs. But drugs are hardly the future of biotech. We’ve entered the Fourth Industrial Revolution, and genetics are on a new level. Biotech is paving…

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Exactly what is and is not included in the jab

Vaccine conspiracy theories are nothing new. Prior to the coronavirus pandemic, and Operation Warp Speed, the most well-known conspiracy theory about vaccines was that the MMR (Measles Mumps Rubella) vaccine causes autism (this has been repeatedly debunked). But as early as 1903, the mark from the smallpox vaccine was considered…

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Dna Research Using Biopython | Free eBooks Download

Category: Tutorial Posted on 2021-09-21, by raymanhero. Description DNA Research using BiopythonMP4 | Video: AVC 1280×720 | Audio: AAC 44KHz 2ch | Duration: 1 Hours | Lec: 9 | 400 MBGenre: eLearning | Language: English =============== An Introduction To Bioinformatics DNA Research using Biopython, An Introduction To Bioinformatics, is a…

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Functional succinate dehydrogenase deficiency is a common adverse feature of clear cell renal cancer

Clear cell renal cell carcinoma (ccRCC) is by far the most common type of kidney cancer, accounting for ∼80% of all kidney cancers (1). Despite recent advances, metastatic ccRCC is a generally incurable malignancy, with a 5-y survival rate <20%, highlighting the need for further biologic and therapeutic insights in…

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Download mRNA fasta sequence for all proteins in the escherichia coli mg1655 genome

Download mRNA fasta sequence for all proteins in the escherichia coli mg1655 genome 2 Hi, I am looking for a way to download the fasta sequence of all protein coding mRNA in the escherichia coli genome. Does anyone know a simple way to do this. I would be most comfortable…

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BioChain announces expanded line of NGS characterized bio-samples for oncology researchers

NEWARK, Calif., Sept. 22, 2021 /PRNewswire/ — BioChain Institute, (“BioChain”), a leader in high quality processed bio-sample products, announced an expanded line of Next Generation Sequencing (NGS) characterized bio-samples encompassing a variety of cancer-related mutations available for preclinical drug development and as reference samples for CLIA labs.  “Scientists are looking for…

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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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Is it possible to isolate and merge overlapping hits from a BLAST search Aligned Fasta file?

Hello all, Hope you’re well. I started a PhD in Jan this year and frankly I am struggling. I’m coming into the second week of trying to figure out how to attempt this problem and it’s honestly starting to get to me a bit – the current task I’m working…

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Ttc30a affects tubulin modifications in a model for ciliary chondrodysplasia with polycystic kidney disease

Significance Cilia are tubulin-based cellular appendages, and their dysfunction has been linked to a variety of genetic diseases. Ciliary chondrodysplasia is one such condition that can co-occur with cystic kidney disease and other organ manifestations. We modeled skeletal ciliopathies by mutating two established disease genes in Xenopus tropicalis frogs. Bioinformatic…

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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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Bioconductor – GeneGA

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see GeneGA. Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm Bioconductor version: 2.9 R based Genetic algorithm for gene expression optimization by considering both mRNA secondary structure…

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Can you BLAST on specific sequences? : bioinformatics

Hi all, noob MSc here. I want to confirm the knockdown targets of my siRNAs (i.e. check an siRNA knocks down more than one transcript variant) I’d like to find an efficient method. Method #1: CTRL+F my siRNA sequence on the FASTA mRNA sequence Con: this only allows for 100%…

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CVC Files Opposition to ToolGen Substantive Motion No. 1 | McDonnell Boehnen Hulbert & Berghoff LLP

On July 15th, Junior Party the University of California/Berkeley, the University of Vienna, and Emmanuelle Charpentier (collectively, “CVC”) filed its Opposition to Senior Party ToolGen’s Substantive Motion No. 1 for benefit of priority to U.S. Provisional Application No. 61/837,481, filed June 20, 2013 (“P3” or “ToolGen P3”), or alternatively, International…

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17 Experts Share Technologies Making A Positive Impact On Society

getty In the realm of science fiction, there are plenty of stories focused on technology that ends up having a sinister effect on humankind. And as technology continues to play a greater role in our work and personal lives, cautionary tales have arisen that remind us that even tools created…

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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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CRISPR/Cas9 and mRNA-Based Technology Allows for Gene Editing and Expression in CLL Cells

“Overall, our results describe a workflow to elaborate robust protocols for gene editing and expression in primary tumor cells,” lead study author Federica Nardi, of the University of Siena and Fondazione Toscana Life Sciences, in Siena, Italy, and coauthors wrote in the poster. Patient-derived cancer cells can be used to…

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Haplotype divergence supports long-term asexuality in the oribatid mite Oppiella nova

Significance Putatively ancient asexual species pose a challenge to theory because they appear to escape the predicted negative long-term consequences of asexuality. Although long-term asexuality is difficult to demonstrate, specific signatures of haplotype divergence, called the “Meselson effect,” are regarded as strong support for long-term asexuality. Here, we provide evidence…

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The 13 health care leaders on the list

Time this week released its “100 Most Influential People” list, which includes a number of individuals who have made major contributions to health care. The 10 ‘most influential’ health care companies, according to TIME The list This year, TIME recognized several health care providers, scientists, public health officials, and advocates for their…

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Omics data collection and merging of datasets from different studies

Omics data collection and merging of datasets from different studies 0 Hi! I’m going to do omics analysis on skin basal cell carcinoma. I’m currently trying to find publicly available data to use to make a data collection. I have looked after RNA-seq(high throughput) in GEO and found some studies…

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Shen Bin/Lou Xin team achieves efficient and accurate editing of zebrafish mitochondrial DNA

Mitochondrial diseases are a major genetic disease. The prevalence rate among newborns in the United States is about 1 in 5000. China currently lacks complete epidemiological data on mitochondrial diseases. At present, nearly 300 genes that cause mitochondrial diseases are known, including both mitochondrial DNA (mtDNA) coding and nuclear DNA…

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How should an expression matrix look?

How should an expression matrix look? 0 Hello everybody. I am new to doing data analysis. So I have this problem. I have to download mRNA and miRNA data from TCGABiolinks, this is one of my two queries. and then I’m supposed to apply some functions to discretize it and…

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FDA approves first trial investigating CRISPR gene editing as HIV cure

The US Food and Drug Administration (FDA) has given the nod for Excision BioTherapeutics to begin trials testing CRISPR gene editing as a treatment for HIV. EBT-101 will be a first-in-human, CRISPR-based one-time gene therapy to be evaluated in individuals with HIV. On 15 September Excision announced that the FDA…

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Climate Change Likely To Abruptly Impact Algae in the Global Ocean

Scientists sample a brown mat of aggregated phytoplankton. Credit: Katrin Schmidt Global warming is likely to cause abrupt changes to important algal communities because of shifting biodiversity ‘break point’ boundaries in the oceans – according to research from the University of East Anglia and the Earlham Institute. A new study,…

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How climate change could impact algae in the global ocean

Scientists sample a brown mat of aggregated phytoplankton. Credit: Katrin Schmidt Global warming is likely to cause abrupt changes to important algal communities because of shifting biodiversity ‘break point’ boundaries in the oceans—according to research from the University of East Anglia and the Earlham Institute. A new study, published today…

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SNP of the SREK1 gene is associated with COPD in Kashi

Introduction Chronic obstructive pulmonary disease (COPD) is a chronic respiratory disorder that progresses slowly and is characterized by an obstructive ventilatory pattern, which is rarely reversible. The main risk factors are active smoking, genetic factors, and air pollution. In particular, COPD has been a major public health problem and will…

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Identification of Prognosis-Associated Biomarkers in Thyroid Carcinoma

Introduction Thyroid cancer (TC) is a common endocrine malignancy with a rapidly increasing incidence worldwide, and the estimated new cases and deaths are notably higher in women than in men.1 Papillary thyroid carcinoma (PTC) is identified as the most common pathological type of TC, and accounts for approximately 80–85% of…

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Researchers Engineer a Mini CRISPR Genetic Editing System That Could Be Easier To Deliver Into Cells

CRISPR illustration. Credit: National Institutes of Health A compact and efficient CRISPR-Cas system, named CasMINI, could be broadly useful for cell-engineering and gene-therapy applications because it is easier to deliver into cells. The findings appear in a study that was published on September 3, 2021, in the journal Molecular Cell….

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Mutational Analysis of Mitochondrial tRNA Genes

Introduction Diabetes is a very complex disease characterized by the presence of chronic hyperglycemia. Clinically, insulin-dependent type 1 and non-insulin-dependent type 2 are the main types of diabetes. Among them, type 2 diabetes mellitus (T2DM, [MIM125853]) is a common endocrine disorder affecting approximately 10% of adult population.1 In most cases,…

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Classifiers for predicting coronary artery disease

Introduction Coronary artery disease (CAD) is a complex pathology associated with behavioral and environmental factors.1–3 CAD shows high prevalence and is associated with a high fatality rate among cardiovascular diseases. The main manifestations of CAD are stable or unstable angina pectoris and identifiable or unrecognized myocardial infarction.4 The main risk…

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Sickle Cell Disease: Could CRISPR’s Gene Therapy Editing Tech be the First Cure for It?

The notorious Sickle Cell disease may soon have a potential cure to the illness that it brings to humans, and it is through gene therapy that researchers are looking into now. CRISPR’s Gene Editing technology with the Cas9 method has been applied to try and fight against sickle cell, something…

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Batch correction for DE analysis

Batch correction for DE analysis 0 Hi, I have tried DE analysis using total and mRNA seq data (5 total RNA data and 5 mRNA data) and making the MDS plot in which 5 total RNA data are included in 2 groups (A, B). In the MDS plot, the samples…

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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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Bioconductor – GEOexplorer (development version)

DOI: 10.18129/B9.bioc.GEOexplorer     This is the development version of GEOexplorer; to use it, please install the devel version of Bioconductor. GEOexplorer: an R/Bioconductor package for gene expression analysis and visualisation Bioconductor version: Development (3.14) GEOexplorer is a Shiny app that enables exploratory data analysis and differential gene expression of…

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Get gene names from rs SNP ids

Gene to rs id library(biomaRt) ## It might take long time to process if many genes (>50) in the list. ## hgnc_gene_symbols.txt is the file that has the list of gene symbols one per line. genes <- read.table(“~/hgnc_gene_symbols.txt”) ensembl = useMart(“ensembl”, dataset=”hsapiens_gene_ensembl”) dbsnp = useMart(“snp”, dataset = “hsapiens_snp”) getHGNC2ENSG =…

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All Aboard for the BioRevolution!

By Jamie Metzl & Jeremy Schwartz, WisdomTree Discussing the investing opportunity of one of the 21st century’s defining megatrends  WisdomTree has collaborated with Dr. Jamie Metzl to help create the WisdomTree BioRevolution Index (WTDNA), the underlying Index that the WisdomTree BioRevolution Fund (WDNA) seeks to track. Dr. Metzl is the author of Hacking Darwin: Genetic…

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CRISPR Convenience: Cas7-11 Redefines RNA Editing

Scientists, typically, are on their own after their post-doc ends. Sometimes, albeit rarely, they team up, blending their ideas, money, and people. Connie Cepko, PhD, and Cliff Tabin, PhD, pioneered the idea of a lab partnership, spending the last few decades working together in their shared lab at Harvard Medical…

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Searching for mRNA ending with a specific 3′ pattern in NON-poly-A RNASeq data.

Searching for mRNA ending with a specific 3′ pattern in NON-poly-A RNASeq data. 0 Hi all, asking for a colleague, I’m looking for human non-poly-A mRNA that would end with a specific pattern ( say CCGCAT ). is it possible to find this in a RNA-SEQ data ? (e.g: www.ncbi.nlm.nih.gov//sra?term=SRR059132…

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Embrace WDNA as BioRevolution Gains Momentum

Investors looking for innovative companies and disruptive growth opportunities without excessive exposure to the technology sector would do well to check out healthcare. Arguably, healthcare is the most innovative sector aside from tech and the one with the next largest arena of disruptive growth opportunities. However, many traditional healthcare exchange…

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CRISPR: The health revolution that will define the 21st Century

Scientists are a cautious bunch, fond of a caveat even when describing their own research. “Our favourite expressions are ‘Yes, but…’ and ‘On the other hand…’ and ‘It remains unclear…’” says gene editor Dr Fyodor Urnov. “So please add all of that to what I’m about to say. “If CRISPR…

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