Tag: GC

A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing

Introduction Short-read metagenomic sequencing is the technique most widely used to explore the natural habitat of millions of bacteria. In comparison with 16S rRNA sequencing, shotgun metagenomic sequencing (MGS) provides sequence information of the whole genomes, which can be used to identify different genes present in an individual bacterium and…

Continue Reading A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing

Use of CD32, CD44 and CD71 to differentiate follicular lymphoma and diffuse large B-cell lymphoma subtypes by flow cytometry

Many lymphomas can be immunophenotyped by flow cytometry (FCM), providing valuable diagnostic information.1 However, FCM cannot typically be used to distinguish follicular lymphoma (FL), diffuse large B-cell lymphoma, germinal centre type (DLBCL-GCB) and diffuse large B-cell lymphoma, non-germinal centre type (DLBCL-nGCB). To expand the utility of clinical FCM, we compared…

Continue Reading Use of CD32, CD44 and CD71 to differentiate follicular lymphoma and diffuse large B-cell lymphoma subtypes by flow cytometry

python – Reading files asynchronously hangs within Pytorch Dataset when DataLoader.num_workers > 1

I’m training a classifier on raw-bytes in binary files. Each file can be several megabytes long. I have a dataset with several millions of binaries in it. Loading all this data at once and keeping it all in memory is very expensive, so I wanted to write an IterableDataset to…

Continue Reading python – Reading files asynchronously hangs within Pytorch Dataset when DataLoader.num_workers > 1

Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species

Mitogenome organization, composition, and skewness The complete mitochondrial genome of B. dussumieri is (GenBank accession XX) 16,685 bp of length, which is similar to other mudskippers mitogenomes (16,470–17,243 bp) (Tables 1 and 2). The mitochondrial genome and the structure were also typical of the mudskipper species and with highly conservative sites, comprising…

Continue Reading Comparative mitochondrial genome brings insights to slight variation in gene proportion and large intergenic spacer and phylogenetic relationship of mudskipper species

Host Cell Proteins (HCPs) Enrichment in Monoclonal Antibody (mAb) Drug Product

To begin, remove the top and bottom caps from the spin column of the commercial protein enrichment kit and retain those for future use. Place the uncapped spin column in a two milliliter micro centrifuge tube. Centrifuge the setup at 1000 G and room temperature for 30 to 60 seconds…

Continue Reading Host Cell Proteins (HCPs) Enrichment in Monoclonal Antibody (mAb) Drug Product

N6-methyladenosine modification positively regulate Japanese encephalitis virus replication | Virology Journal

Burgess HM, Depledge DP, Thompson L, Srinivas KP, Grande RC, Vink EI, Abebe JS, Blackaby WP, Hendrick A, Albertella MR, Kouzarides T, Stapleford KA, Wilson AC, Mohr I. Targeting the m6A RNA modification pathway blocks SARS-CoV-2 and HCoV-OC43 replication. Genes Dev. 2021;35:1005–19. Article  CAS  PubMed  PubMed Central  Google Scholar  Chambers…

Continue Reading N6-methyladenosine modification positively regulate Japanese encephalitis virus replication | Virology Journal

Multiple Job openings at Gujarat Biotechnology Research Centre

Government of Gujarat has established Gujarat State Biotechnology Mission (GSBTM) as a nodal agency to develop overall development of biotechnology in the state in 2004. Major activities of GSBTM is promoting research and development in the field of biotechnology and supporting the development of biotechnology industries in the state. Besides…

Continue Reading Multiple Job openings at Gujarat Biotechnology Research Centre

Beyond recall: Evaluating Gemini with Vertex AI Auto SxS

Struggling to choose the best large language model (LLM) for your specific needs? Gemini, Google’s new powerhouse, shines in text generation, translation, and code, but how do you stack it up against others? Join Ivan Nardini, sales engineer, smart analytics, Google Cloud and Irina Sigler, product manager, Google Cloud deep…

Continue Reading Beyond recall: Evaluating Gemini with Vertex AI Auto SxS

European Mouse Mutant Cell Repository

The following list defines the different statuses that EUCOMM report on the constructs in their pipeline. Mice – Genotype confirmed (M-GC)The genotype of testcross offspring has been confirmed molecularly. Mice – Germline transmission (M-GLT)Test crosses of chimaeras indicate germline transmission of the ES cell mutation based on coat color. Mice…

Continue Reading European Mouse Mutant Cell Repository

Decent Uniquely mapped reads but no features

Decent Uniquely mapped reads but no features 0 Hi guys, I am analysing a mRNASeq dataset of extracellular vesicles. I get decent results for mapping using STAR Number of input reads | 32143093 Average input read length | 100 UNIQUE READS: Uniquely mapped reads number | 22862852 Uniquely mapped reads…

Continue Reading Decent Uniquely mapped reads but no features

Neutrophil extracellular trap-induced intermediate monocytes trigger macrophage activation syndrome in adult-onset Still’s disease | BMC Medicine

Wang MY, Jia JC, Yang CD, Hu QY. Pathogenesis, disease course, and prognosis of adult-onset Still’s disease: an update and review. Chin Med J (Engl). 2019;132(23):2856–64. Article  CAS  PubMed  Google Scholar  Feist E, Mitrovic S, Fautrel B. Mechanisms, biomarkers and targets for adult-onset Still’s disease. Nat Rev Rheumatol. 2018;14(10):603–18. Article …

Continue Reading Neutrophil extracellular trap-induced intermediate monocytes trigger macrophage activation syndrome in adult-onset Still’s disease | BMC Medicine

Trying to understand STAR fastqLog.final.out File

Trying to understand STAR fastqLog.final.out File 0 Hello, I am analyzing ribo-seq data and am trying to understand if my interpretation of star’s log file is correct. I do not have extensive bioinformatics/computational experience, so it’s been a bit difficult trying to understand how to proceed (the guides online are…

Continue Reading Trying to understand STAR fastqLog.final.out File

Enhancement and inactivation effect of CRISPR/Cas12a via extending hairpin activators for detection of transcription factors

Li Q, Song ZL, Zhang YX, Zhu LN, Yang Q, Liu XF, Sun XF, Chen XX, Kong RM, Fan GC, Luo XL (2023) Synergistic Incorporation of two ssDNA activators enhances the trans-cleavage of CRISPR/Cas12a. Anal Chem 95:8879–8888 Article  CAS  PubMed  Google Scholar  Ma JY, Wang SY, Du YC, Wang DX,…

Continue Reading Enhancement and inactivation effect of CRISPR/Cas12a via extending hairpin activators for detection of transcription factors

Seroprevalence and Molecular Characterization of B. abortus

Introduction Brucellosis is a zoonotic disease caused by Brucella spp., a gram-negative facultative intracellular coccobacillus.1 These microorganisms can infect livestock, wildlife, and humans, causing significant public concern and substantial agricultural economic loss. Currently, at least six novel Brucella species have been identified: Brucella pinnipedialis, Brucella ceti,2 Brucella papionis,3 Brucella microti,4…

Continue Reading Seroprevalence and Molecular Characterization of B. abortus

Molecular characterization of a tetra segmented ssDNA virus infecting Botrytis cinerea worldwide | Virology Journal

Analysis of the multisegmented nature of BcssDV1 genome B. cinerea field isolates were previously obtained from infected grapes of vineyards of Italy and Spain and their mycovirome was determined [8]. A new ssDNA virus (BcssDV1, Genbank accession no. MN625247) was discovered and characterized. The sequence previously characterized of BcssDV1 (from…

Continue Reading Molecular characterization of a tetra segmented ssDNA virus infecting Botrytis cinerea worldwide | Virology Journal

LncRNA/circRNA-mRNA networks in CARAS | JIR

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

Continue Reading LncRNA/circRNA-mRNA networks in CARAS | JIR

Understanding GPU Memory 2: Finding and Removing Reference Cycles

by Aaron Shi, Zachary DeVito This is part 2 of the Understanding GPU Memory blog series. Our first post Understanding GPU Memory 1: Visualizing All Allocations over Time shows how to use the memory snapshot tool. In this part, we will use the Memory Snapshot to visualize a GPU memory…

Continue Reading Understanding GPU Memory 2: Finding and Removing Reference Cycles

Frontiers Publishing Partnerships | Construction of recombinant adenovirus-5 vector to prevent replication-competent adenovirus occurrence

Introduction In recent years, recombinant adenoviral vectors have been used in different fields of biomedical sciences such as in vitro and in vivo gene transfer, vaccine development, and gene therapy (Russell, 2000; Mitani and Kubo, 2002). Multiple features of recombinant adenoviral vectors such as high packaging capacity for transgene insertion,…

Continue Reading Frontiers Publishing Partnerships | Construction of recombinant adenovirus-5 vector to prevent replication-competent adenovirus occurrence

Solved 33. The coding DNA sequence of a human gene contains

Transcribed image text: 33. The coding DNA sequence of a human gene contains 2001 base pairs. A CRISPR-Cas9 experiment is setting up to knock out this gene in the fibroblast cell lines. It is known that the GC content of the coding sequence of this gene is 60%. In CRISPR-Cas…

Continue Reading Solved 33. The coding DNA sequence of a human gene contains

machine learning – How to properly free GPU memory in Pytorch

I am using Pytorch with Pytorch-Lightning to train and validate a model. But during testing (test_step), I am faced with a CUDA memory error which I’m not sure how to resolve. The model trains and validates fine, and it is not an issue of batch size, data size or model…

Continue Reading machine learning – How to properly free GPU memory in Pytorch

MNCLCDA: predicting circRNA-drug sensitivity associations by using mixed neighbourhood information and contrastive learning | BMC Medical Informatics and Decision Making

circRNA-drug sensitivity associations We download the circRNA-drug sensitivity association dataset from reference [17], where Deng et al. [17] collected and organized the association data between circRNA and drug sensitivity from the circRic database [16]. Here, the drug sensitivity and circRNA data come from the GDSC database [19], which provides 80,076…

Continue Reading MNCLCDA: predicting circRNA-drug sensitivity associations by using mixed neighbourhood information and contrastive learning | BMC Medical Informatics and Decision Making

Alyglo Approved for Patients With Primary Humoral Immunodeficiency

The Food and Drug Administration (FDA) has approved GC Biopharma’s Alyglo™ (immune globulin intravenous, human-stwk) 10% liquid for the treatment of primary humoral immunodeficiency (PI) in adult patients 17 years of age and older. Manufactured from pooled human plasma from US donors, Alyglo supplies a broad spectrum of neutralizing IgG…

Continue Reading Alyglo Approved for Patients With Primary Humoral Immunodeficiency

FDA Approves Implant for Glaucoma

The US Food and Drug Administration (FDA) has approved an intracameral implant with 75 mcg of travoprost to reduce intraocular pressure (IOP) in patients with open-angle glaucoma (OAG) or ocular hypertension (OHT).  The iDose TR (Glaukos Corp) is inserted into a corneal incision on the temple side of the eye….

Continue Reading FDA Approves Implant for Glaucoma

Can DNA methylation disrupt the regulation of mitochondrial genes?

What is the role of methylation in the regulation of imprinted genes?4 answersDNA methylation plays a crucial role in the regulation of imprinted genes. Imprinted genes are genes that are expressed in a parent-of-origin-specific manner and are essential for normal embryonic development. Aberrant DNA methylation of imprinted genes has been…

Continue Reading Can DNA methylation disrupt the regulation of mitochondrial genes?

Importing Data In RStudio: A Step-By-Step Approach

Article Summary Box Recognizing various data types like numeric, integer, and logical in RStudio is essential for accurate data manipulation and import. Effective environment setup, including package installation and global option configuration, is pivotal for streamlined data import processes. Utilizing data.table’s fread function for handling large datasets enhances import efficiency,…

Continue Reading Importing Data In RStudio: A Step-By-Step Approach

haplotypecaller – NVIDIA Docs

Run a GPU-accelerated haplotypecaller. This tool applies an accelerated GATK CollectMultipleMetrics for assessing the metrics of a BAM file, such as including alignment success, quality score distributions, GC bias, and sequencing artifacts. This functions as a ‘meta-metrics’ tool, and can run any combination of the available metrics tools in GATK…

Continue Reading haplotypecaller – NVIDIA Docs

An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes

Background: The corona virus SARS-CoV-2 is the causative agent of recent most global pandemic. Its genome encodes various proteins categorized as non-structural, accessory, and structural proteins. The non-structural proteins, NSP1-16, are located within the ORF1ab. The NSP3, 4, and 6 together are involved in formation of double membrane vesicle (DMV)…

Continue Reading An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes

Google’s Next-gen Generative AI Hits the Enterprise

Google Cloud’s partners in retail, fashion, beauty and other segments are getting an artificial intelligence tool with the debut of Gemini Pro for enterprise, the tech giant revealed on Wednesday. The release builds on last week’s introduction of Gemini, Google’s next-generation generative AI models. The current iteration allows partners to…

Continue Reading Google’s Next-gen Generative AI Hits the Enterprise

How to run diamond blastp to get all vs all similarity score between proteins?

How to run diamond blastp to get all vs all similarity score between proteins? 0 Hi. I have a .fa file representing multiple predicted proteins. Example: >NC_001341.1_1 # 397 # 714 # 1 # ID=1_1;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.314 MCSSSIISEKHLKKNIFQKKAKVQYKIKKNRRGQINENKCSINPNKKRSKKIKKLAKQKD IQACINIGNRYVDVPIRPVSVADPDTPKETKEDKEKGCHFRNGIH* >NC_001341.1_2 # 788 # 1009 # 1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=GGAG/GAGG;rbs_spacer=5-10bp;gc_cont=0.306 MQCLISNEYHHNNNEHTSCINRINRNYRSNQRHHQGYNDLYDSINIIQGMLENLNASIVY FTKDGKYKLIMTL* Given this…

Continue Reading How to run diamond blastp to get all vs all similarity score between proteins?

The Protective Mechanism of TFAM on Mitochondrial DNA and its Role in Neurodegenerative Diseases

Annesley SJ, Fisher PR (2019) Mitochondria in health and disease. Cells 8(7). doi.org/10.3390/cells8070680 Cannino G, Ferruggia E, Luparello C, Rinaldi AM (2009) Cadmium and mitochondria. Mitochondrion 9(6):377–384. doi.org/10.1016/j.mito.2009.08.009 Article  CAS  PubMed  Google Scholar  Bonora M, Missiroli S, Perrone M, Fiorica F, Pinton P, Giorgi C (2021) Mitochondrial control of genomic…

Continue Reading The Protective Mechanism of TFAM on Mitochondrial DNA and its Role in Neurodegenerative Diseases

[PyTorch] Delete Model And Free Memory (GPU / CPU)

Problem Last night I tried to improve some code about merge two models. Because my poor device, I cannot merge all layers totally, but need to merge them layer by layer for reducing my memory cost. I found how to free the memory of GPU is very easy, but CPU…

Continue Reading [PyTorch] Delete Model And Free Memory (GPU / CPU)

An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes | BMC Infectious Diseases

When compared to the genomes of other RNA viruses, coronaviruses have been found to possess largest genome sizes. They are capable of establishing reservoirs in both human and zoonotic populations, enabling their transmission and circulation among a range of animal hosts, including bats, pangolins, civets, cats, mice, pigs, whales, dogs,…

Continue Reading An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes | BMC Infectious Diseases

Widespread Bathyarchaeia encode a novel methy

image:  A. The relative abundance of microbial populations based on 16S rRNA gene-tag sequencing analysis before purification by adding antibiotics. B.Growth curves of Ca. B. ligniniphilus in anaerobic medium supplemented with lignin. The error bars were obtained from triplicate Q-PCR reactions. C.The relative abundance of microbial populations based on 16S…

Continue Reading Widespread Bathyarchaeia encode a novel methy

Human RAD52 stimulates the RAD51-mediated homology search

Introduction Homologous recombination (HR) is an evolutionarily conserved process that plays a pivotal role in genome stability, diversity, and plasticity. HR is indeed a key repair pathway able to faithfully repair DNA damages including double-strand breaks (DSBs) and DNA gaps by copying the error-free information from the template DNA normally…

Continue Reading Human RAD52 stimulates the RAD51-mediated homology search

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

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

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

Resin acids play key roles in shaping microbial communities during degradation of spruce bark

Bark preparation Spruce bark was obtained from the Iggesund pulp and paper mill (Iggesund, Holmen AB, Sweden), from a bark pile resulting from stripping of spruce logs at the mill after harvest, with the average age of trees at harvest being ~70 years. The bark was left to dry at…

Continue Reading Resin acids play key roles in shaping microbial communities during degradation of spruce bark

ncs v2.5.0 linker error when setting CONFIG_BOOTLOADER_MCUBOOT – Nordic Q&A – Nordic DevZone

Hello, I currently have an app using nRF Connect SDK v2.5.0. To enable FOTA I set CONFIG_NCS_SAMPLE_MCUMGR_BT_OTA_DFU and CONFIG_BOOTLOADER_MCUBOOT in my prj.conf (following the documentation instructions). After this building the app fails during linking for 3 different undefined references: [275/280] Linking C executable zephyr/zephyr_pre0.elf FAILED: zephyr/zephyr_pre0.elf zephyr/zephyr_pre0.map : && ccache /home/q/app/zephyr_workspace/toolchains/7795df4459/opt/zephyr-sdk/arm-zephyr-eabi/bin/arm-zephyr-eabi-gcc…

Continue Reading ncs v2.5.0 linker error when setting CONFIG_BOOTLOADER_MCUBOOT – Nordic Q&A – Nordic DevZone

Too many open files caused by persistent_workers and pin_memory – data

Having some trouble running PyTorch and Lightning with Optuna. After a few trials I run into the following error: OSError: [Errno 24] Too many open files I’ve assembled a script based on Optuna’s example of a PyTorch implementation that very consistently runs into this error on my machine. “”” Optuna…

Continue Reading Too many open files caused by persistent_workers and pin_memory – data

Effects of diabetes mellitus and glycemic traits on cardiovascular morpho-functional phenotypes | Cardiovascular Diabetology

American Diabetes A. Economic costs of Diabetes in the U.S. in 2017. Diabetes Care. 2018;41(5):917–28. Article  Google Scholar  Linssen PBC, Veugen MGJ, Henry RMA, van der Kallen CJH, Kroon AA, Schram MT, Brunner-La Rocca HP, Stehouwer CDA. Associations of (pre)Diabetes with right ventricular and atrial structure and function: the Maastricht…

Continue Reading Effects of diabetes mellitus and glycemic traits on cardiovascular morpho-functional phenotypes | Cardiovascular Diabetology

The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution

FAO, ITPS, GSBI, CBD & EC. State of knowledge of soil biodiversity – Status, challenges and potentialities, Report 2020. (FAO). doi.org/10.4060/cb1928en. 2020. Potapov, A. M. et al. Feeding habits and multifunctional classification of soil-associated consumers from protists to vertebrates. Biol. Rev. 97, 1057–1117 (2022). Article  PubMed  Google Scholar  García-Palacios, P.,…

Continue Reading The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution

Phenotypic profiling of solute carriers characterizes serine transport in cancer

Cell culture All cell lines used in this study were cultured at 37 °C in 5% CO2 in a humidified incubator. Human cell lines were authenticated by STR profiling using Promega GenePrint 10 and tested for Mycoplasma using Mycoalert (Lonza). Other than HCT116 p21−/− (a gift of B. Vogelstein60) all cell…

Continue Reading Phenotypic profiling of solute carriers characterizes serine transport in cancer

What are the factors that influence the bias of 16S rRNA gene ampicon sequencing?

What are the factors that contribute to coverage bias in amplicon sequencing?4 answersCoverage bias in amplicon sequencing can be influenced by several factors. These include differences in 3′-end stability, primer Tm, amplicon length, amplicon GC content, and GC content of amplicon flanking regions. The presence of a highly dominant taxon…

Continue Reading What are the factors that influence the bias of 16S rRNA gene ampicon sequencing?

Human hg38 chr6:31,165,200-31,165,800 UCSC Genome Browser v457

     Custom Tracks ac4C-RIP-seq peaks, hESC CTL-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC CTL-2hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-2hidedensesquishpackfull    Mapping and Sequencing Base Positionhidedensefull p14 Fix Patcheshidedensesquishpackfull p14 Alt Haplotypeshidedensesquishpackfull Assemblyhidedensesquishpackfull Centromereshidedensesquishpackfull Chromosome Bandhidedensesquishpackfull Clone Endshidedensesquishpackfull Exome Probesetshidedensesquishpackfull FISH Cloneshidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Contigshidedensefull GRC Incidenthidedensesquishpackfull Hg19…

Continue Reading Human hg38 chr6:31,165,200-31,165,800 UCSC Genome Browser v457

A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes

Friedman-Einat, M. & Seroussi, E. Avian leptin: bird’s-eye view of the evolution of vertebrate energy-balance control. Trends Endocrinol. Metab. 30, 819–832 (2019). Article  CAS  PubMed  Google Scholar  International Chicken Genome Sequencing C. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432, 695–716 (2004)….

Continue Reading A chromosome-level genome assembly for the Silkie chicken resolves complete sequences for key chicken metabolic, reproductive, and immunity genes

Innovent Announces the Phase 3 ORIENT-16 Study Results Published in JAMA Evaluating Sintilimab in Combination with Chemotherapy for the First-Line Treatment of Gastric or Gastroesophageal Junction (G/GEJ) Adenocarcinoma, Business News

ROCKVILLE, Md. and SUZHOU, China, Dec. 6, 2023 /PRNewswire/ — Innovent Biologics, Inc. (“Innovent”) (HKEX: 01801), a world-class biopharmaceutical company that develops, manufactures and commercializes high quality medicines for the treatment of oncology, autoimmune, metabolic, ophthalmology and other major diseases, announced the interim analysis results of ORIENT-16, the Phase 3 study evaluating…

Continue Reading Innovent Announces the Phase 3 ORIENT-16 Study Results Published in JAMA Evaluating Sintilimab in Combination with Chemotherapy for the First-Line Treatment of Gastric or Gastroesophageal Junction (G/GEJ) Adenocarcinoma, Business News

Innovent Announces the Phase 3 ORIENT-16 Study Results Published in JAMA Evaluating Sintilimab in Combination with Chemotherapy for the First-Line Treatment of Gastric or Gastroesophageal Junction (G/GEJ) Adenocarcinoma USA – English APAC – Traditional Chinese APAC – English

ROCKVILLE, Md. and SUZHOU, China, Dec. 5, 2023 /PRNewswire/ — Innovent Biologics, Inc. (“Innovent”) (HKEX: 01801), a world-class biopharmaceutical company that develops, manufactures and commercializes high quality medicines for the treatment of oncology, autoimmune, metabolic, ophthalmology and other major diseases, announced the interim analysis results of ORIENT-16, the Phase 3 study evaluating…

Continue Reading Innovent Announces the Phase 3 ORIENT-16 Study Results Published in JAMA Evaluating Sintilimab in Combination with Chemotherapy for the First-Line Treatment of Gastric or Gastroesophageal Junction (G/GEJ) Adenocarcinoma USA – English APAC – Traditional Chinese APAC – English

Calculate GC content for entire chromosome

If you’re comfortable using Python, I’ve created a script that calculates the GC content and GC-skew for each contig, scaffold, or chromosome in a fasta file. This is specifically designed for generating data for a circos plot. To use the script, make sure you have Biopython installed in your conda…

Continue Reading Calculate GC content for entire chromosome

Noncoding mutations cause super-enhancer retargeting resulting in protein synthesis dysregulation during B cell lymphoma progression

B cells undergo a series of programmed genomic alterations that enable the immunoglobulin light and heavy chain loci to generate high-affinity antibodies against invading pathogens. First, B cells undergo variability, diversity and joining (VDJ) recombination in the bone marrow with subsequent somatic hypermutation (SHM) and class switch recombination (CSR) occurring…

Continue Reading Noncoding mutations cause super-enhancer retargeting resulting in protein synthesis dysregulation during B cell lymphoma progression

Targeting the epigenome to reinvigorate T cells for cancer immunotherapy | Military Medical Research

Tsui C, Kretschmer L, Rapelius S, Gabriel SS, Chisanga D, Knöpper K, et al. MYB orchestrates T cell exhaustion and response to checkpoint inhibition. Nature. 2022;609(7926):354–60. Article  CAS  PubMed  PubMed Central  Google Scholar  Zhu L, Zhou X, Gu M, Kim J, Li Y, Ko CJ, et al. Dapl1 controls NFATc2…

Continue Reading Targeting the epigenome to reinvigorate T cells for cancer immunotherapy | Military Medical Research

Cadonilimab/Chemotherapy Meets Primary End Point in Phase 3 AK104-303 Trial

Cadonilimab/Chemotherapy Meets Primary End Point in Phase 3 AK104-303 Trial Findings from the phase 3 AK104-303 trial (NCT04982237) suggest that patients with recurrent or metastatic cervical cancer may derive a progression-free survival (PFS) benefit with frontline cadonilimab (AK104) plus platinum-based chemotherapy—with or without bevacizumab (Avastin). Data from the prespecified interim…

Continue Reading Cadonilimab/Chemotherapy Meets Primary End Point in Phase 3 AK104-303 Trial

The Frequency of CYP2D6 and CYP3A4/5 Genotypes and The Impact of Their Allele Translation and Phenoconversion-Predicted Enzyme Activity on Risperidone Pharmacokinetics in Saudi Children with Autism

Al-Dosari MS, Al-Jenoobi FI, Alkharfy KM, Alghamdi AM, Bagulb KM, Parvez MK, Al-Mohizea AM, Al-Muhsen S, Halwani R (2013) High prevalence of CYP2D6*41 (G2988A) allele in Saudi Arabians. Environ Toxicol Pharmacol 36:1063–1067. doi.org/10.1016/j.etap.2013.09.008 Article  PubMed  CAS  Google Scholar  Almandil NB, Alkuroud DN, AbdulAzeez S, AlSulaiman A, Elaissari A, Borgio JF…

Continue Reading The Frequency of CYP2D6 and CYP3A4/5 Genotypes and The Impact of Their Allele Translation and Phenoconversion-Predicted Enzyme Activity on Risperidone Pharmacokinetics in Saudi Children with Autism

140releng-powerpc64le-quarterly][biology/cytoscape] Failed for cytoscape-3.6.1 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/foul2/data/140releng-powerpc64le-quarterly/84b4661ec108/logs/cytoscape-3.6.1.log Build URL: pkg-status.freebsd.org/foul2/build.html?mastername=140releng-powerpc64le-quarterly&build=84b4661ec108 Log: =>> Building biology/cytoscape build started at Sat Dec 2…

Continue Reading 140releng-powerpc64le-quarterly][biology/cytoscape] Failed for cytoscape-3.6.1 in build

pytorch – CUDA out of memory when using Optuna

Half month ago, I can use Optuna without a problem to do a 48-Hour study, with around 150+ trials. Yesterday I tried Optuna again on the same model, same dataset, same batch size and same device (A100 40GB or V100 32GB), but I always got torch.cuda.OutOfMemoryError: CUDA out of memory…

Continue Reading pytorch – CUDA out of memory when using Optuna

Genomic analysis of Coccomyxa viridis, a common low-abundance alga associated with lichen symbioses

Honegger, R. The lichen symbiosis: What is so spectacular about it?. Lichenologist 30, 193–212 (1998). Article  Google Scholar  Grube, M. & Berg, G. Microbial consortia of bacteria and fungi with focus on the lichen symbiosis. Fung. Biol. Rev. 23, 72–85 (2009). Article  Google Scholar  Spribille, T. et al. Basidiomycete yeasts…

Continue Reading Genomic analysis of Coccomyxa viridis, a common low-abundance alga associated with lichen symbioses

Dissemination feature based on PET/CT is a risk factor for diffuse large B cell lymphoma patients outcome | BMC Cancer

Sehn LH, Salles G. Diffuse large B-Cell lymphoma. N Engl J Med. 2021;384(9):842–58. Article  CAS  PubMed  PubMed Central  Google Scholar  Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and Mortality Worldwide for 36 cancers in 185…

Continue Reading Dissemination feature based on PET/CT is a risk factor for diffuse large B cell lymphoma patients outcome | BMC Cancer

Identification of intergenerational epigenetic inheritance by whole genome DNA methylation analysis in trios

Epigenetic changes are typically thought to be markers of cell differentiation or somatic changes caused by interactions with the environment16. However, recent studies have shown that some of these environmentally induced changes can be passed down from one generation to the next, demonstrating their heritability19,21,42,43. Though this mechanism has long…

Continue Reading Identification of intergenerational epigenetic inheritance by whole genome DNA methylation analysis in trios

Using metagenome assembly and binning to identify and mitigate contamination in a genome

Hi everyone, This may be a silly question, but I am interested if using metagenome assembly and binning is a valid method of determining if a sample contains a mixture of species. Similarly, can metagenomics be used to identify and remove contamination from a single genome? For some background, I…

Continue Reading Using metagenome assembly and binning to identify and mitigate contamination in a genome

Salpa genome and developmental transcriptome analyses reveal molecular flexibility enabling reproductive success in a rapidly changing environment

Loeb, V. et al. Effects of sea-ice extent and krill or salp dominance on the Antarctic food web. Nature 387, 897–900 (1997). Article  ADS  CAS  Google Scholar  Atkinson, A., Siegel, V., Pakhomov, E. & Rothery, P. Long-term decline in krill stock and increase in salps within the Southern Ocean. Nature…

Continue Reading Salpa genome and developmental transcriptome analyses reveal molecular flexibility enabling reproductive success in a rapidly changing environment

nrfConnect 2.5.0: mbedTLS fails to compile (calloc()) – Nordic Q&A – Nordic DevZone

Hi there: we’ve just updated from nrfConnect 2.3.0 to nrfConnect 2.5.0 and mbedTLS (which seems to have been modified in nrfConnect 2.5.0) now fails to link (in platform.c) because it needs and is unable to find calloc(): /home/arm_embedded_gcc-10-2020-q4-major/bin/ld.bfd: modules/mbedtls/libmbedTLSBase.a(platform.c.obj):/home/nrfconnectsdk-v2.5.0/modules/crypto/mbedtls/library/platform.c:56: undefined reference to `calloc’ As you can see, we are just compiling…

Continue Reading nrfConnect 2.5.0: mbedTLS fails to compile (calloc()) – Nordic Q&A – Nordic DevZone

Genome characteristics of atypical porcine pestivirus from abortion cases in Shandong Province, China | Virology Journal

Viral metagenomic analysis The number of clean reads was 21,157,543 for the RNA sample and 26,789,502 for the DNA sample. For RNA, the data were assembled to a total sequence length of 2,337,534, with 60.92% GC content. The length of the largest contig was 11,556 nt, which was identified as…

Continue Reading Genome characteristics of atypical porcine pestivirus from abortion cases in Shandong Province, China | Virology Journal

Two mitochondrial HMG-box proteins, Cim1 and Abf2, antagonistically regulate mtDNA copy number in Saccharomyces cerevisiae | Nucleic Acids Research

Abstract The mitochondrial genome, mtDNA, is present in multiple copies in cells and encodes essential subunits of oxidative phosphorylation complexes. mtDNA levels have to change in response to metabolic demands and copy number alterations are implicated in various diseases. The mitochondrial HMG-box proteins Abf2 in yeast and TFAM in mammals…

Continue Reading Two mitochondrial HMG-box proteins, Cim1 and Abf2, antagonistically regulate mtDNA copy number in Saccharomyces cerevisiae | Nucleic Acids Research

Phylogenomic assessment of 23 equid alphaherpesvirus 1 isolates obtained from USA-based equids | Virology Journal

Damiani AM, de Vries M, Reimers G, Winkler S, Osterrieder N. A severe equine herpesvirus type 1 (EHV-1) abortion outbreak caused by a neuropathogenic strain at a breeding farm in northern Germany. Vet Microbiol. 2014;172(3–4):555–62. Article  PubMed  Google Scholar  Negussie H, Gizaw D, Tessema TS, Nauwynck HJ. Equine herpesvirus-1 myeloencephalopathy,…

Continue Reading Phylogenomic assessment of 23 equid alphaherpesvirus 1 isolates obtained from USA-based equids | Virology Journal

East Asian-specific and cross-ancestry genome-wide meta-analyses provide mechanistic insights into peptic ulcer disease

We conducted a three-stage genome-wide analysis of PUD and its subtypes. An overview of the workflow is provided in Fig. 1 and Supplementary Fig. 1. PUD cases in the east Asian populations were obtained by combining individuals with any of the two major PUD subtypes (DU and GU), which were…

Continue Reading East Asian-specific and cross-ancestry genome-wide meta-analyses provide mechanistic insights into peptic ulcer disease

Sanger sequencing & Fragment analysis

When designing custom primers, please remember that properly designed primer is crucial for DNA sequencing. Keep in mind the following rules: Primers should have a melting temperature (Tm) of 55-60 °C. Primers should not form dimers or hairpins (> 3 bp). Make sure that there is no potential non-specific binding…

Continue Reading Sanger sequencing & Fragment analysis

Chromosome-scale genome of the human blood fluke Schistosoma mekongi and its implications for public health | Infectious Diseases of Poverty

Barnett R. Schistosomiasis. (1474–547X (Electronic)). Steinmann P, Keiser J, Bos R, Tanner M, Utzinger J. Schistosomiasis and water resources development: systematic review, meta-analysis, and estimates of people at risk. Lancet Infect Dis. 2006;6(7):411–25. Article  PubMed  Google Scholar  Uthailak N, Adisakwattana P, Thiangtrongjit T, Limpanont Y, Chusongsang P, Chusongsang Y, et…

Continue Reading Chromosome-scale genome of the human blood fluke Schistosoma mekongi and its implications for public health | Infectious Diseases of Poverty

Exploring the promising potential of induced pluripotent stem cells in cancer research and therapy | Molecular Cancer

Rowe RG, Daley GQ. Induced pluripotent stem cells in disease modelling and drug discovery. Nat Rev Genet. 2019;20:377–88. Article  CAS  PubMed  PubMed Central  Google Scholar  Li L, Papadopoulos V. Advances in stem cell research for the treatment of primary hypogonadism. Nat Rev Urol. 2021;18:487–507. Article  CAS  PubMed  Google Scholar  Lawrence…

Continue Reading Exploring the promising potential of induced pluripotent stem cells in cancer research and therapy | Molecular Cancer

Whole genome sequencing provides evidence for Bacillus velezensis SH-1471 as a beneficial rhizosphere bacterium in plants

Inhibition effect of strain SH-1471 on plant pathogenic fungi The results of the plate confrontation experiment showed that B. velezensis SH-1471 had good inhibitory effects on various pathogenic microorganisms (Fig. 1). Specifically, our experiment showed that its inhibition rates on Sclerotinia scrotiorum, Phoma mateuciicola, and Fusarium oxysporum were 93.5%, 90.3%, and…

Continue Reading Whole genome sequencing provides evidence for Bacillus velezensis SH-1471 as a beneficial rhizosphere bacterium in plants

Plants | Free Full-Text | The Development of Plant Genome Sequencing Technology and Its Conservation and Application in Endangered Gymnosperms

The PacBio RS II sequencer has been effectively utilized to generate a 1.27 Gb genome assembly of Dendrobium officinale [70]. By utilizing advanced sequencing technologies such as Illumina HiSeq, Nanopore, PacBio, and Hi-C, the results have revealed remarkable N50 values of 44 Mb and 65.35 Mb for Gardenia jasminoides and…

Continue Reading Plants | Free Full-Text | The Development of Plant Genome Sequencing Technology and Its Conservation and Application in Endangered Gymnosperms

Sequence-Based Classification and Identification | SpringerLink

Adékambi T, Drancourt M, Raoult D (2009) The rpoB gene as a tool for clinical microbiologists. Trends Microbiol 17:37–45 CrossRef  PubMed  Google Scholar  Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410 CrossRef  CAS  PubMed  Google Scholar  Arahal DR,…

Continue Reading Sequence-Based Classification and Identification | SpringerLink

Depletion of tRNA CCA-adding enzyme in Mycobacterium tuberculosis leads to polyadenylation of transcripts and precursor tRNAs

Rv3907c is the CCA-adding enzyme in Mycobacterium It remains unclear whether the rv3907c gene product, originally annotated as poly(A) polymerase, is in fact the CCA-adding enzyme in Mtb. Rv3907c is composed of three domains, an N-terminal class II polymerase β superfamily domain, a central RNA-binding domain and a C-terminal HD…

Continue Reading Depletion of tRNA CCA-adding enzyme in Mycobacterium tuberculosis leads to polyadenylation of transcripts and precursor tRNAs

Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster | Microbiome

Diversity of the RCA cluster and genome characteristics The phylogenomic analysis yielded three major clades within the RCA cluster (Fig. 1) Genomes of the three clades were relatively distinct with appr. < 70% average nucleotide identity (ANI), resulting in the proposal of three genera, the known genus Planktomarina, and two new genera without…

Continue Reading Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster | Microbiome

CRISPR-Cas9 Gene Editing Is On The Cusp Of Something Big

Natali_Mis Gene editing, also known as genome editing, is a method where the DNA of an organism is modified using biotechnological techniques. It allows scientists to add, remove, or alter genetic material at particular locations in the genome. This 2-part series will cover the basics of CRISPR-Cas9 (see below) in…

Continue Reading CRISPR-Cas9 Gene Editing Is On The Cusp Of Something Big

The Rauvolfia tetraphylla genome suggests multiple distinct biosynthetic routes for yohimbane monoterpene indole alkaloids

Genome sequencing and assembly of R. tetraphylla After DNA extraction from young leaves and sequencing, the R. tetraphylla genome was first assembled into 1008 contigs with an N50 of 3.7 Mb. After haplotigs removal and a final pilon polishing, the 364,945,498 bp final assembly was distributed across 76 scaffolds with an N50…

Continue Reading The Rauvolfia tetraphylla genome suggests multiple distinct biosynthetic routes for yohimbane monoterpene indole alkaloids

Akeso’s Phase 3 Trial for Cervical Cancer Attains Progression-Free Survival -November 22, 2023 at 08:51 pm EST

Market Closed – Hong Kong Stock Exchange 03:08:04 2023-11-23 am EST 5-day change 1st Jan Change 47.45 HKD +2.26% +4.29% +10.35% This article is reserved for members Not a member ? Free registration Akeso’s Phase 3 Trial for Cervical Cancer Attains Progression-Free Survival 08:51pm MT Akeso, Inc. Announces AK104-303, A…

Continue Reading Akeso’s Phase 3 Trial for Cervical Cancer Attains Progression-Free Survival -November 22, 2023 at 08:51 pm EST

Fermentation | Free Full-Text | Whole-Genome Sequencing of Lactiplantibacillus plantarum YY-112 and Investigation of Its Immune-Modulating Abilities In Vivo

Author Contributions Conceptualization, Y.Y. and Y.G.; Data curation, M.L. and W.Z.; Formal analysis, M.L., W.Z., W.T. and J.L.; Funding acquisition, Y.Y. and Y.G.; Investigation, J.X., Y.Y. and Y.G.; Methodology, M.L., J.L. and Y.Y.; Project administration, Y.Y.; Resources, J.X., Y.Y. and Y.G.; Software, M.L., W.Z. and W.T.; Supervision, J.X., Y.Y. and…

Continue Reading Fermentation | Free Full-Text | Whole-Genome Sequencing of Lactiplantibacillus plantarum YY-112 and Investigation of Its Immune-Modulating Abilities In Vivo

merge .pdata and .xdata sections from host object files

diff –git a/src/cmd/cgo/internal/test/callback_windows.go b/src/cmd/cgo/internal/test/callback_windows.gonew file mode 100644index 0000000..95e97c9— /dev/null+++ b/src/cmd/cgo/internal/test/callback_windows.go@@ -0,0 +1,133 @@+// Copyright 2023 The Go Authors. All rights reserved.+// Use of this source code is governed by a BSD-style+// license that can be found in the LICENSE file.++package cgotest++/*+#include <windows.h>+USHORT backtrace(ULONG FramesToCapture, PVOID *BackTrace) {+#ifdef _AMD64_+ CONTEXT context;+…

Continue Reading merge .pdata and .xdata sections from host object files

Phenotypic drug-susceptibility profiles and genetic analysis based on whole-genome sequencing of Mycobacterium avium complex isolates in Thailand

Abstract Mycobacterium avium complex (MAC) infections are a significant clinical challenge. Determining drug-susceptibility profiles and the genetic basis of drug resistance is crucial for guiding effective treatment strategies. This study aimed to determine the drug-susceptibility profiles of MAC clinical isolates and to investigate the genetic basis conferring drug resistance using…

Continue Reading Phenotypic drug-susceptibility profiles and genetic analysis based on whole-genome sequencing of Mycobacterium avium complex isolates in Thailand

Molecular epidemiology and characteristics of respiratory syncytial virus among hospitalized children in Guangzhou, China | Virology Journal

Falsey AR, Walsh EE. Respiratory syncytial virus infection in adults. Clin Microbiol Rev. 2000;13(3):371–84. Article  CAS  PubMed  PubMed Central  Google Scholar  Walker CLF, Rudan I, Liu L, Nair H, Theodoratou E, Bhutta ZA, O’Brien KL, Campbell H, Black RE. Global burden of childhood pneumonia and diarrhoea. Lancet (London, England). 2013;381(9875):1405–16….

Continue Reading Molecular epidemiology and characteristics of respiratory syncytial virus among hospitalized children in Guangzhou, China | Virology Journal

Exome and genome sequencing to unravel the precise breakpoints of partial trisomy 6q and partial Monosomy 2q | BMC Pediatrics

Here, we report a proband with characteristic features of the clinical syndrome, including downward-slanting palpebral fissures; delayed development of bilateral optic nerve hypoplasia; facial deformity with a small mouth, thin lips, micrognathia, and blepharophimosis; short neck; abnormal deciduous teeth; and malformations of the thorax and short ribs. The proband showed…

Continue Reading Exome and genome sequencing to unravel the precise breakpoints of partial trisomy 6q and partial Monosomy 2q | BMC Pediatrics

STAR alignment speed

STAR alignment speed 1 Hello, I am trying to align RNA sequencing data from the NCBI SRA database to the Apis mellifera genome with STAR. The alignment worked fine. However, the mapping step of the alignment seems to be a bit slow. Furthermore, increasing the number of available threads does…

Continue Reading STAR alignment speed

Complete mitochondrial genome analyses confirm that bat Polychromophilus and ungulate Plasmodium constitute a distinct clade independent of other Plasmodium species

Blood samples, DNA extraction, mitochondrial genome amplification and sequencing Following established procedures, bat blood samples were collected from designated sampling sites in Kanchanaburi, located in western Thailand, during the years 2019 and 202123,33,34. For this study, four bat samples (2 Myotis siligoensis and 2 Hipposideros gentilis) were utilized. These samples…

Continue Reading Complete mitochondrial genome analyses confirm that bat Polychromophilus and ungulate Plasmodium constitute a distinct clade independent of other Plasmodium species

De novo genome assembly of the invasive mosquito species Aedes japonicus and Aedes koreicus | Parasites & Vectors

Genome length and GC content Using a hybrid approach that combines Oxford Nanopore long reads and Illumina short reads data, we assembled a scaffold-level version of Ae. koreicus and Ae. japonicus genomes whose size was assessed as 1.24 and 1.39 gigabase (Gb) pairs, respectively. These dimensions resemble those of other…

Continue Reading De novo genome assembly of the invasive mosquito species Aedes japonicus and Aedes koreicus | Parasites & Vectors

Should I remove Kmers identified in FastQC?

Should I remove Kmers identified in FastQC? 2 Hi, apologies for this basic questions, I new in NGS quality control. I have been check my NGS data (Illumina – HiSeq 2500 2*100pb) using FastQC after trimming Nextera Adaptater with bbduck (BBTool package) using trimming overlap (ktrim=r k=25 mink=11 hdist=1 tpe…

Continue Reading Should I remove Kmers identified in FastQC?

Accuracy and depth evaluation of clinical low pass genome sequencing in the detection of mosaic aneuploidies and CNVs | BMC Medical Genomics

Study design and sample collection To evaluate the accuracy and benchmark the optimal DP of LP GS in the detection of mosaicism, evaluation strategies were designed using simulated data and virtual samples, respectively (Fig. 1). The DNA of a total of 28 clinical samples (S1 ~ S28) (aborted fetal tissue, whole blood, chorionic…

Continue Reading Accuracy and depth evaluation of clinical low pass genome sequencing in the detection of mosaic aneuploidies and CNVs | BMC Medical Genomics

Advancing personalized medicine in brain cancer: exploring the role of mRNA vaccines | Journal of Translational Medicine

Personalized medicine aims to revolutionize healthcare by providing tailored treatments based on an individual’s unique characteristics. Genetic information of the host and target plays a crucial role in determining disease susceptibility and treatment response [1, 2]. By utilizing genomic analysis, biomarker identification, risk assessment, tailored treatment strategies, and continuous monitoring,…

Continue Reading Advancing personalized medicine in brain cancer: exploring the role of mRNA vaccines | Journal of Translational Medicine

featureCount Error “No paired-end reads were detected in paired-end read library”

I created a combined mm39 and MHV-A59 (Viral) reference genome and aligned my paired end reads using STAR with the following input commands: STAR –runMode alignReads –runThreadN 16 –genomeDir /genomeDir –readFilesIn /FastqDir/1.fq.gz, /FastqDir/2.fq.gz –readFilesCommand gunzip -c –outReadsUnmapped Fastx –outSAMtype BAM SortedByCoordinate It seems that everything went fine. Here is a…

Continue Reading featureCount Error “No paired-end reads were detected in paired-end read library”

Wheat Sequencing: The Pan-Genome and Opportunities for Accelerating Breeding

Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, Costa de Oliveira A, Cseke LJ, Dempewolf H, De Pace C, Edwards D, Gepts P, Greenland A, Hall AE, Henry R, Hori K, Howe GT, Hughes S, Humphreys M, Lightfoot D, Marshall A, Mayes S, Nguyen HT, Ogbonnaya…

Continue Reading Wheat Sequencing: The Pan-Genome and Opportunities for Accelerating Breeding

CG Oncology Announces Presentation of the First Phase 3 Monotherapy Data for Cretostimogene Grenadenorepvec in BCG-Unresponsive NMIBC Patients at SUO 2023 | DNA RNA and Cells

CG Oncology Announces Presentation of the First Phase 3 Monotherapy Data for Cretostimogene Grenadenorepvec in BCG-Unresponsive NMIBC Patients at SUO 2023 Details Category: DNA RNA and Cells Published on Wednesday, 15 November 2023 12:31 Hits: 91 IRVINE, CA, USA I November 14, 2023 ICG Oncology, Inc. announced today that interim…

Continue Reading CG Oncology Announces Presentation of the First Phase 3 Monotherapy Data for Cretostimogene Grenadenorepvec in BCG-Unresponsive NMIBC Patients at SUO 2023 | DNA RNA and Cells

Comparative genomics and genome-wide SNPs of endangered Eld’s deer provide breeder selection for inbreeding avoidance

De novo genome assemblies and genome annotation We assembled a de novo genome of a seven-year-old male SED from Ubon Ratchathani Zoo using a combination of Illumina short-reads (92.94 × coverage) and PacBio long-reads (61.6 × coverage) (GenBank accession number: JACCHN000000000). Additionally, we used MGI short-reads (52.15 × coverage) to assemble a de novo genome of…

Continue Reading Comparative genomics and genome-wide SNPs of endangered Eld’s deer provide breeder selection for inbreeding avoidance

Predicting cancer subtypes from nucleosome profiling of cell-free DNA

Abstract Modern cancer treatments take advantage of genomic differences between tumors to kill cancer cells using targeted approaches. Typically, this requires a tumor biopsy in order to get tissue for phenotypic and genotypic analysis. However, in late-stage cancer, surgical biopsies of metastases may not be part of the standard of…

Continue Reading Predicting cancer subtypes from nucleosome profiling of cell-free DNA

CRISPR-broad: combined design of multi-targeting gRNAs and broad, multiplex target finding

CRISPR-broad framework We developed a procedural pipeline for detecting gRNAs and implemented this in Python as a standalone application (Fig. 1a). For speeding up gRNA selection, we employed multithreading and used big data Python module Pandas. This allowed splitting millions of short sequences for mapping and processing large numbers of uncompressed…

Continue Reading CRISPR-broad: combined design of multi-targeting gRNAs and broad, multiplex target finding

Ginsenoside Rg3 enriches SCFA-producing commensal bacteria to confer protection against enteric viral infection via the cGAS-STING-type I IFN axis

Rg3 elicits protection against local and systemic enteric virus infection by regulating the intestinal microbiome To assess the antiviral effects of Rg3 in vivo, groups of C57BL/6J mice (referred to as WT B6 hereafter) were orally administered Rg3 for 3 consecutive days, inoculated with MNV-1 by the peroral route, and…

Continue Reading Ginsenoside Rg3 enriches SCFA-producing commensal bacteria to confer protection against enteric viral infection via the cGAS-STING-type I IFN axis

Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae

Sheridan, P. O. et al. Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nat. Commun. 11, 1–12 (2020). Article  Google Scholar  Sheridan, P. O., Meng, Y., Williams, T. A. & Gubry-Rangin, C. Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota. Nat. Commun. 13, 1–13…

Continue Reading Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae

In silico prospecting of the mtDNA of Macrobrachium amazonicum from transcriptome data | BMC Genomics

Bentes B, Martinelli J, Souza L, Cavalcante D, Almeida M, Isaac V. Spatial distribution of the amazon river prawn Macrobrachium Amazonicum (Heller, 1862) (Decapoda, Caridea, Palaemonidae) in two perennial creeks of an estuary on the northern coast of Brazil (Guajará Bay, Belém, Pará). Brazilian J Biol. 2011;71:925–35. Article  Google Scholar …

Continue Reading In silico prospecting of the mtDNA of Macrobrachium amazonicum from transcriptome data | BMC Genomics

Identification of metabolites via spectral library search?

Identification of metabolites via spectral library search? 0 Hi everyone, I am very new to single-cell metabolomics and today I want to jump in this area. I have been reading many review papers related to identification of metabolites at single-cell resolution from spectral data through spectral library search and I…

Continue Reading Identification of metabolites via spectral library search?

HDAC3 deacetylates H3K27ac and H3K9ac on the TrkC promoter to exacerbate sevoflurane-induced neurotoxicity

Apai C, Shah R, Tran K, Pandya Shah S (2021) Anesthesia and the developing brain: a review of sevoflurane-induced neurotoxicity in pediatric populations. Clin Ther 43:762–778 Article  CAS  PubMed  Google Scholar  Chai G et al (2022) Sevoflurane inhibits histone acetylation and contributes to cognitive dysfunction by enhancing the expression of…

Continue Reading HDAC3 deacetylates H3K27ac and H3K9ac on the TrkC promoter to exacerbate sevoflurane-induced neurotoxicity

Zebrafish danRer11 chr6:43,426,661-43,433,266 UCSC Genome Browser v456

     DANIO-CODE Track Hub 3P-seq trackshidedensesquishpackfull CAGE-seq trackshidedensesquishpackfull ChIP-seq trackshidedensesquishpackfull RNA-seq trackshidedensefull Cell Typeshidedensesquishpackfull Consensus promotershidedensesquishpackfull Conservation and CRISPR targetshideshow COPEs and pooled DOPEshideshow Enhancer validationhideshow HiC trackshidedensefull Stages_Typeshidedensesquishpackfull    Mapping and Sequencing Base Positionhidedensefull Assemblyhidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Incidenthidedensesquishpackfull INSDChidedensesquishpackfull RefSeq Acchidedensesquishpackfull Restr Enzymeshidedensesquishpackfull Short Matchhidedensesquishpackfull   …

Continue Reading Zebrafish danRer11 chr6:43,426,661-43,433,266 UCSC Genome Browser v456

Insights gained from single-cell analysis of chimeric antigen receptor T-cell immunotherapy in cancer | Military Medical Research

Zhu J, Ke Y, Liu Q, Yang J, Liu F, Xu R, et al. Engineered Lactococcus lactis secreting Flt3L and OX40 ligand for in situ vaccination-based cancer immunotherapy. Nat Commun. 2022;13(1):7466. Article  CAS  PubMed  PubMed Central  Google Scholar  Evans ER, Bugga P, Asthana V, Drezek R. Metallic nanoparticles for cancer…

Continue Reading Insights gained from single-cell analysis of chimeric antigen receptor T-cell immunotherapy in cancer | Military Medical Research

Nascent ribosomal RNA act as surfactant that suppresses growth of fibrillar centers in nucleolus

Transcription and RNA processing The occupancy \({n}_{{{{{{\rm{ps}}}}}}}\) of the TSS of the active rDNA by Pol I follows the kinetic equation $$\frac{d}{{dt}}{n}_{{{{{{\rm{ps}}}}}}}={k}_{{{{{{\rm{on}}}}}}}\rho \left(1-{n}_{{{{{{\rm{ps}}}}}}}\right)-{k}_{{{{{{\rm{off}}}}}}}{n}_{{{{{{\rm{ps}}}}}}}-{k}_{{{{{{\rm{e}}}}}}}{n}_{{{{{{\rm{ps}}}}}}}.$$ (5) Equation (5) suggests that the occupancy \({n}_{{{{{{\rm{ps}}}}}}}\) changes due to the binding of Pol I from the FC (the first term), the unbinding of Pol I…

Continue Reading Nascent ribosomal RNA act as surfactant that suppresses growth of fibrillar centers in nucleolus

The correlation between gut microbiome and atrial fibrillation: pathophysiology and therapeutic perspectives | Military Medical Research

Kim JE, Li B, Fei L, Horne R, Lee D, Loe AK, et al. Gut microbiota promotes stem cell differentiation through macrophage and mesenchymal niches in early postnatal development. Immunity. 2022;55(12):2300-17.e6. Article  CAS  PubMed  Google Scholar  Xiao W, Su J, Gao X, Yang H, Weng R, Ni W, et al….

Continue Reading The correlation between gut microbiome and atrial fibrillation: pathophysiology and therapeutic perspectives | Military Medical Research