Categories
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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 …
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…
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,…
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…
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…
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…
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…
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,…
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…
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…
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…
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…
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….
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…
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,…
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…
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)…
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…
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…
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…
[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…
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,…
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…
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…
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)…
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…
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…
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…
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…
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.,…
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…
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…
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…
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)….
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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…
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,…
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…
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…
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…
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…
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…
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…
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,…
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…
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…
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…
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…
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…
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…
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;+…
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…
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….
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…
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…
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…
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…
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…
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…
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,…
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…
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…
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…
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…
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…
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…
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…
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…
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 …
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…
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…
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 …
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…
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…
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….