Tag: dtu

Introduction Currently, the emergence of bacterial resistance poses a significant challenge to public health worldwide. With the widespread use of antimicrobial agents in recent years, the isolation of multidrug-resistant Escherichia coli has increased yearly, particularly among Extended Spectrum β-lactamases (ESBLs) producing strains, which can cause not only multi-site infections but…

On 5/25/23 15:23, Roger Mason wrote: > NodeName=node012 CoresPerSocket=2 > CPUAlloc=0 CPUTot=4 CPULoad=N/A > AvailableFeatures=(null) > ActiveFeatures=(null) > Gres=(null) > NodeAddr=node012 NodeHostName=node012 > RealMemory=10193 AllocMem=0 FreeMem=N/A Sockets=2 Boards=1 > State=UNKNOWN+DRAIN ThreadsPerCore=1 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A > Partitions=macpro > BootTime=None SlurmdStartTime=None > CfgTRES=cpu=4,mem=10193M,billing=4 > AllocTRES= > CapWatts=n/a > CurrentWatts=0 AveWatts=0 >…

Chenxing Wei,1,* Jian Chen,1,* Tanveer Muhammad Anwar,2,* Lingling Huang,1 Wenjie Yang,3 Xueyan Dong,1 Qiong Chen,1 Min Yue,2,4,5 Daojun Yu1,3 1Department of Medical Laboratory, Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, People’s Republic of China; 2Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University…

A new drug candidate targeting E. coli in the gut is in phase 1 clinical trials. According to a new paper published in Nature Biotechnology, it may improve the well-being of blood cancer patients and reduce their mortality rate from E. coli infections. Many people have experienced infections from E….

An overview of the SNIPR001 creation process. First, WT phages are screened against a panel of E. coli strains. Then, phages with broad activity against E. coli are tail fiber engineered and/or armed with CRISPR–Cas systems containing sequences specific to E. coli, creating CAPs. These CAPs are then tested for…

Introduction The worldwide dissemination of carbapenem-resistant Enterobacteriaceae (CRE), particularly carbapenem-resistant K. pneumoniae (CRKP), poses a significant risk to public health. CRKP can cause various infections, such as urinary tract infections, bloodstream infections, and pneumonia, leading to high morbidity and mortality.1 Prevention and control of K. pneumoniae infection are becoming more…

DOI: 10.18129/B9.bioc.pairedGSEA   Paired DGE and DGS analysis for gene set enrichment analysis Bioconductor version: Release (3.17) pairedGSEA makes it simple to run a paired Differential Gene Expression (DGE) and Differencital Gene Splicing (DGS) analysis. The package allows you to store intermediate results for further investiation, if desired. pairedGSEA comes…

On 4/24/23 08:09, Purvesh Parmar wrote: > thank you, however, because this is change in the data center, the names > of the servers contain datacenter names as well in its hostname and in > fqdn as well, hence i have to change both, hostnames as well as ip > addresses, compulsorily,…

The 16th European Conference on Fungal Genetics was held last month, and Vera Meyer and Arthur Ram, editors of Fungal Biology and Biotechnology, as well as students and postdocs from their labs, attended and selected their top 5 posters from the conference. We present a brief overview of these researchers…

COPENHAGEN – The Million Microbiomes from Humans Project (MMHP), an ambitious effort to sequence and analyze microbial DNA from a million human samples to construct a microbiome map of the human body and build the world’s largest human microbiome database, is back on track after being interrupted by the COVID-19…

DRIMseq error for paired sample analysis 0 @lucapiacentini-9597 Last seen 8 hours ago Italy Hello, I am doing a DTU with DRIMseq and I can get the results according to the following model: design_full <- model.matrix(~condition, data=DRIMSeq::samples(d)) where “condition” is my variable of interest (factor with 4 levels) and executing…

Hi, I am attempting to work through the workflow described in “Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification.” I am running into an error message when I try to make the counts dataframe for DRIMseq: Error in data.frame(gene_id = txdf$GENEID, feature_id = txdf$TXNAME, cts) : arguments…

The biotech industry across the world has been picking up its pace over the years. As many sectors plummeted during the pandemic, the biotechnology industry weathered the storm. Global biopharma companies are collaborating with biotechnology universities across the globe to improve research and development in various fields within the industry….

Some stories of history are written in ink, and others are written in nucleotide bases. Ancient DNA (aDNA) analysis – the study of DNA from archaeological or paleontological specimens – is perhaps the closest scientists will ever come to a time machine – a window into the past. In this…

Our metazoan-wide survey has provided the most comprehensive analysis to date of gene number and phylogenetic distribution of three key antioxidant gene families across the animal kingdom. Genes encoding all three families were observed in 18 metazoan species; the exception is the ctenophore Mnemiopsis leidyi that has PRX and GPX,…

P. aeruginosa bacterial strains Reference strains Four well-described and genome-available reference strains were used in the present study, ATCC27853 and ATCC15442, obtained from the American Type Culture Collection (ATCC), and PAO1 and PA14, from the collection of Institut Pasteur (Paris, France). Strain ATCC15442 is recommended for disinfectant susceptibility testing44, strain…

Recent gene duplication in the MCP gene family The MCP family of enzymes presents evidence of common ancestry, both in terms of sequence and structural homology and the chromosomal arrangement of genes. We were interested to know if any of these MCP genes continued to be duplicated more recently, and…

DOI: 10.18129/B9.bioc.rnaseqDTU     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see rnaseqDTU. RNA-seq workflow for differential transcript usage following Salmon quantification Bioconductor version: 3.14 RNA-seq workflow for differential transcript usage (DTU) following Salmon quantification. This workflow uses Bioconductor packages tximport, DRIMSeq, and…

Tool:HaploCart: Human mtDNA Haplogroup Classification Using a Pangenomic Reference Graph 0 Current mitochondrial DNA (mtDNA) haplogroup classification tools map reads to a single reference genome and perform inference based on the detected mutations to this reference. This approach biases haplogroup assignments towards the reference and prohibits accurate calculations of the…

Bacterial isolate Adolfo Lutz Institute is a regional reference laboratory for Salmonella isolates from São Paulo, Brazil. Thus, all isolates received are submitted to classical serotyping, antimicrobial susceptibility testing, and molecular-typing by PFGE and next-generation sequencing. Isolate 288_18 was recovered from a blood sample from a patient with clinical symptoms…

Antimicrobial susceptibility data of S. sonnei in France Our review of S. sonnei antimicrobial susceptibility data obtained between 2005 and 2021 (based on 7121 isolates received and confirmed at the French National Reference Center for E. coli, Shigella and Salmonella, FNRC-ESS, Institut Pasteur) revealed a sharp increase in the percentage…

Hello, all supported build flags are available with “./configure –help” command. On of them is “–with-systemdsystemunitdir=DIR”, which will allow you to specify the directory for the systemd service files for all Slurm daemons. The most important of the flags is imho the “–prefix”, which sets the installation directory. I’ll describe my build setup shortly…

Human body like the Space is an endless frontier made even more complex by the irreversibility of life by the arrow of time. Similar to the mystery of origin of the Universe some problems in the human body are so complex, for example, the problem of qualia or the Hard…

Dear friends, We are trying to use Salmon for DTU analysis. We want to separate exogenous from endogenous transcripts by following this post www.biostars.org/p/443701/ and this paper f1000research.com/articles/7-952 We are focusing on a gene called ASCL1 (endo-ASCL1). We transduced cells with lentiviral vector containing ASCL1 ORF only (Lenti-ASCL1). There should…

Introduction Escherichia coli is a common Gram-negative opportunistic pathogen that causes invasive host infections through virulence factors such as flagella, toxin secretion, and adhesins. According to the source of the infection, pathogenic E. coli can be classified as intestinal (diarrheagenic) and extraintestinal (ExPEC). Uropathogenic E. coli (UPEC) is the most…

The Yeast Metabolic Engineering group develops novel yeast cell factories to produce sustainable chemicals and natural products. We apply advanced genome editing, metabolic modeling, transporter engineering, and ‘omic data analyses for data-guided strain design. We are looking for two motivated, talented PhD students to join our team to study small…

Transcriptional noise detection and Salmon TPMs 1 Hello, I’m analysing RNA-seq data from two datasets (from healthy samples) and created a unique GTF file to identify new isoforms by using StringTie. Then I used Salmon to estimate their TPMs, but I have some questions hoping anyone can help me: 1)…

Introduction Pseudomonas stutzeri is an aerobic, nonfermenting, active, Gram-negative oxidase-positive bacterium with unique colony morphology.1,2 Burri and Stutzer first described it in 1985,3 and the specific metabolic properties, such as denitrification, degradation of aromatic compounds, and nitrogen fixation, distinguish it from other pseudomonads species.2,4 Historically, P. stutzeri was not commonly…