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Postdoctoral positions in Sustainability, Genomics, Microbiology, and Bioinformatics/Data Science… job with Technical University of Denmark (DTU)
DTU Biosustain is actively seeking candidates for postdoctoral roles in fields such as sustainability, genomics, microbiology, and bioinformatics/data science. We welcome applications from researchers in these or related fields, especially those focusing on large-scale data integration using advanced technologies (e.g., long-read, single-cell, microscopy, metabolic) for sustainable food and agricultural production….
ST23 Klebsiella pneumoniae in China
Introduction Klebsiella pneumoniae (KP), a member of the Enterobacteriaceae family, inhabits aquatic environments and can colonise respiratory and gastrointestinal tracts in humans, making it a significant opportunistic pathogen. It may result in pneumonia, meningitis, urinary tract infections, and bloodstream infections. Hypervirulent Kp (HvKp) is believed to cause severe community-acquired invasive…
When is RESUME an invalid node state?
Hi Xaver, Your version of Slurm may matter for your power saving experience. Do you run an updated version? /Ole On 12/6/23 10:54, Xaver Stiensmeier wrote: > Hi Ole, > > I will double check, but I am very sure that giving a reason is possible > as it has been done at…
[slurm-users] Usage of particular GPU out of 4 GPUs while submitting
Hi Daniel Letai Thanks for the quick response and guidance. I have done the changes as mentioned in gres.conf and slurm.conf and now I am able to submit the jobs to a particular GPU. Regarding MIG, it was just a thought came in m mind, in case studentA wants to…
all(rownames(cts) %in% txdf$TXNAME) is FALSE in DTU Analysis in R
Good afternoon, I am trying to do a DTU analysis for my research, but I am kinda new to this stuff and I have some problems. In particular on point 5). I am following the workflow of Bioconductor vignette rnaseqDTU and my pipeline is this: 1) read salmon quants ##…
Catalytically inactive long prokaryotic Argonaute systems employ distinct effectors to confer immunity via abortive infection
Bacterial strains and phages Escherichia coli DH5a was routinely grown in Lysogeny broth (LB) medium and used for plasmid cloning, while E. coli BL21 (DE3) was used for protein production and the in vivo assays. E. coli phages T5, T7 and Lambda-vir are gifts from Shi Chen lab (Wuhan University,…
World’s First Pan-Genome Analysis Unveils New Food, Health Avenues
A team of international researchers has published the first comprehensive comparative pan-genome analysis of lactic acid bacteria (LAB), a family of microorganisms essential to natural ecosystems and the food industry. The study was carried out by scientists from the Novo Nordisk Foundation Center for Biosustainability (DTU Biosustain) and the University…
Molecular characterization and functional implications on mouse peripheral blood mononuclear cells of annexin proteins from Echinococcus granulosus sensu lato | Parasites & Vectors
Parasites and animals PSCs were collected from hydatid cysts isolated from the liver of sheep infected with E. granulosus s.l. from a slaughterhouse in Sichuan province, China. The PSCs and cyst walls were separated and treated as described in previous reports [22]. The viability and molecular genotyping of PSCs were…
[slurm-users] Slurm powersave
I’m experimenting with slurm powersave and I have several questions. I’m following the guidance from slurm.schedmd.com/power_save.html and the great presentation from our own slurm.schedmd.com/SLUG23/DTU-SLUG23.pdf I am running slurm 23.02.3 1) I’m not sure I fully understand ReconfigFlags=KeepPowerSaveSettings The documentations ways that if set, an “scontrol reconfig” command will preserve the current state of…
Genomic Analysis of CR-hvKP in a Chinese Tertiary Hospital
Introduction Klebsiella pneumoniae (KP) is a common opportunistic pathogen in clinical practice, capable of causing infectious diseases in the urinary tract, respiratory tract, blood, and soft tissues.1 Hypervirulent Klebsiella pneumoniae (hvKp) has a higher virulence than KP2 and can cause severe infectious diseases, including pyogenic liver abscess, endophthalmitis, and meningitis.3,4…
Whole genomes from bacteria collected at diagnostic units around the world 2020
Preparation of partners to collect samples Partners registered for participation by contributing isolates or DNA samples to the study. Material was sent to partners according to their registered participation format. This included material for sample collection, metadata registration, DNA extraction and sample shipment to Denmark. Specific protocols were provided, according…
RStudio Server: Connection refused when rendering Quarto Document – RStudio IDE
Hi all, I’m preparing materials for my “R for Bio Data Science” and I am facing issues, when redering Quarto docs. I am simply trying to render the template document, which results in the html-file: teaching.healthtech.dtu.dk/22100/rstudio2/files/projects/r_for_bio_data_science/lab_01_exercises.html Which I can see by clicking and selecting “View in web browser”. Note that:…
(18 August – “Enzyme Stability Prediction”) A free webinar on on-going CAFA5 (Critical Assessment of Functional Annotation of proteins) challenge
Welcome to a webinar: John Mitchell “Kaggle Competition Review: Novozymes Enzyme Stability Prediction” Friday 18 August, 18.00 (CET time, e.g. Paris time) Full announcement: www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/418295 Welcome to the webinar on Friday: John Mitchell who is expert both in bioinformatics and machine learning, and also experienced Kaggler and one of the…
(27 July – “DeepLoc”) A free webinar on on-going CAFA5 (Critical Assessment of Functional Annotation of proteins) challenge
Henrik Nielsen,Vineet Thumuluri , José Juan Almagro Armenteros “DeepLoc 2.0: multi-label subcellular localization prediction using protein language models” Thursday 27 July, 19.00 (CET time) Add to Google Calendar The talk will be based on the recent paper with the same title (Nucleic Acids Res. 2022 (www.ncbi.nlm.nih.gov/pmc/articles/PMC9252801/) ). The prediction of…
IsoformSwitchAnalyserR lmportR data warning.
I am trying to run IsoformSwitchAnalyzeR using R version 4.3.0 using following command: aSwitchList2 <- importRdata( isoformCountMatrix = salmonQuant$counts, isoformRepExpression = salmonQuant$abundance, designMatrix = myDesign, isoformExonAnnoation = “gencode.v40.annotation.gtf.gz”, isoformNtFasta = “gencode.v40.transcripts.fa”, addAnnotatedORFs = TRUE, showProgress = TRUE, ignoreAfterBar =FALSE) This is the Output : Step 1 of 10: Checking data…Step…
Bioconductor – makecdfenv
DOI: 10.18129/B9.bioc.makecdfenv This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see makecdfenv. CDF Environment Maker Bioconductor version: 3.15 This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership…
Syllabus, Entrance Exams, Top Colleges, Admission, Jobs, and Salary 2023-24
Bioinformatics is essentially information science that combines informatics and biology. This field of study is multidisciplinary and focuses on genetics and molecular biology. The structure and composition of biological molecules are analyzed through the use of computational techniques. The field can assist researchers in developing more potent medical treatments and…
Genomic characteristics of ESBL-producing E. coli in China
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…
[slurm-users] Nodes stuck in drain state
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 >…
Resistance of Nosocomial Acinetobacter baumannii
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…
Scientists create first CRISPR-based drug targeting the microbiome
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….
Scientists create the first CRISPR-based drug candidate targeting the microbiome
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…
Phenotypic and Genetic Analysis of KPC-49
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…
Bioconductor – pairedGSEA
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…
[slurm-users] Migration of slurm communication network / Steps / how to
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,…
On Biology Highlighting five posters from the 16th European Conference on Fungal Genetics
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…
Powered by MGI Tech, ‘Million Microbiomes’ Project Back on Track After COVID Slowdown
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
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…
Error generating counts df for use with DRIMSeq/DEXseq
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…
10 universities to study biotechnology around the world
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….
Leveling the Field in Ancient DNA Research
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…
Antioxidant enzymes that target hydrogen peroxide are conserved across the animal kingdom, from sponges to mammals
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,…
A 10-year microbiological study of Pseudomonas aeruginosa strains revealed the circulation of populations resistant to both carbapenems and quaternary ammonium compounds
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…
Acquisition of new function through gene duplication in the metallocarboxypeptidase family
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…
Bioconductor – rnaseqDTU
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…
Human mtDNA Haplogroup Classification Using a Pangenomic Reference Graph
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…
Whole genome sequence analysis of the first reported isolate of Salmonella Agona carrying blaCTX-M-55 gene in Brazil
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…
Rapid emergence of extensively drug-resistant Shigella sonnei in France
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…
[slurm-users] How to launch slurm services after installation
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…
AIM brings innovations from labs to hospitals and masses
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…
Separate exogenous from endogenous transcripts using Salmon RNAseq DTU
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…
Extensively drug resistant E. coli LZ00114
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…
Two PhD scholarships in Transporter Protein Engineering at DTU Biosustain
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
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)…
Plasmid-Encoded VIM-2-pProducing Pseudomonas stutzeri | IDR
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…