Tag: wilcoxon

A graph-based genome and pan-genome variation of the model plant Setaria

Variation and evolution in Setaria We collected genome-wide resequencing data for 630 wild (S. viridis), 829 landrace and 385 modern cultivated accessions from the Setaria genus with an average sequencing depth of ~15×, of which 1,004 were newly generated and 840 were from previous studies16,21 (Supplementary Table 1). After aligning…

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Comparison of Oxford Nanopore Technologies and Illumina MiSeq sequencing with mock communities and agricultural soil

Study sites Soils were collected from two different sites (ARDEC: Colorado State University’s Agricultural Research, Development and Education Center in Fort Collins, CO; and CPCRC: USDA Columbia Plateau Conservation Research Center in Pendleton, OR). At each site, four replicate plots of no-till corn (ARDEC) or no-till annual wheat (CPCRC) were…

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Tox4 regulates transcriptional elongation and reinitiation during murine T cell development

Pan-hematopoietic Tox4 deletion reduces number of multipotential progenitors and impairs T cell development To understand the role of TOX4 in development, we generated Tox4 conditional knockout mice by the CRISPR-Cas9 methodology, and two loxP sites in the same orientation were inserted upstream and downstream of exons 4–6, respectively (Supplementary Fig. 1a). Considering…

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The Biostar Herald for Monday, June 05, 2023

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…

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Microbial diversity in the vaginal microbiota and its link to pregnancy outcomes

A prospective study of pregnant women We established a prospective cohort of 2313 pregnant women with the goal of studying the vaginal microbiota, its community composition and the presence of pathogenic bacteria in the peripartum period. Inclusions and data collection were performed in accordance with applicable laws and ethical standards. Ethical…

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Dissecting the impact of dietary fiber type on atherosclerosis in mice colonized with different gut microbial communities

Engraftment of donor communities prior to dietary treatment Germ-free (GF) female ApoE−/− mice were colonized with fecal samples from one of three human donors (Supplementary Fig. 1). These samples were selected from a repository of fecal specimens previously collected from adults in their mid-seventies36 and were chosen based on (i)…

Continue Reading Dissecting the impact of dietary fiber type on atherosclerosis in mice colonized with different gut microbial communities

Dissociation protocols used for sarcoma tissues bias the transcriptome observed in single-cell and single-nucleus RNA sequencing | BMC Cancer

Single-cell and single-nucleus RNA sequencing of sarcoma subtypes In this work, we studied sarcomas from varying tissue origins, including osteosarcoma (OS), Ewing sarcoma (ES), and desmoplastic small round cell tumor (DSRCT) (Fig. 1). We used different dissociation protocols: Miltenyi Tumor Dissociation Kit, cold-active protease derived from Bacillus licheniformis, and Nuclei EZ…

Continue Reading Dissociation protocols used for sarcoma tissues bias the transcriptome observed in single-cell and single-nucleus RNA sequencing | BMC Cancer

The menstrual cycle regularity and skin: irregular menstrual cycle affects skin physiological properties and skin bacterial microbiome in urban Chinese women | BMC Women’s Health

General characteristics of the participants The menstrual cycle regularity of the female participants and menstrual cycle-associated skin characteristics were obtained from the self-evaluation questionnaire. Nearly 9% of the participants reported an irregular menstrual cycle, and 66.5% reported a less regular menstrual cycle (Table 2). Thus, most of the women reported…

Continue Reading The menstrual cycle regularity and skin: irregular menstrual cycle affects skin physiological properties and skin bacterial microbiome in urban Chinese women | BMC Women’s Health

Generation of a mutator parasite to drive resistome discovery in Plasmodium falciparum

CRISPR editing of DNA polymerase δ To increase the genetic repertoire of P. falciparum parasites in culture, we aimed to generate parasites with impaired 3ʹ−5ʹ proof-reading activity from the catalytic subunit of DNA polymerase δ (PF3D7_1017000) in order to increase the level of basal spontaneous mutations, based on prior work…

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Weak phylogenetic and habitat effects on root trait variation of 218 Neotropical tree species

Introduction Tropical rainforests in the Amazon basin harbor the highest tree diversity on earth (Ter Steege et al., 2020). Most of this diversity is concentrated in a relatively small number of plant families, including Chrysobalanaceae, Fabaceae, Lauraceae, Lecythidaceae, Malvaceae (sensu lato), Myrtaceae, Rubiaceae, and Sapotaceae, that can comprise > 60%…

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IL5RA as an immunogenic cell death-related predictor in progression and therapeutic response of multiple myeloma

Differential expression analysis We downloaded GSE125361 (n = 48) microarray data from the Gene Expression Omnibus (GEO) database, which included 45 myeloma samples and 3 controls, for expression analysis of IL5RA in cancer16. Additionally, we analyzed the expression of IL5RA in smoldering myeloma (SMM) patients who progressed to active MM (n = 10) and…

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Gene expression in African Americans, Puerto Ricans and Mexican Americans reveals ancestry-specific patterns of genetic architecture

We analyzed data from a total of 2,733 participants from the GALA II16 and SAGE17 asthma case–control studies who self-identified as African American (AA; n = 757), Puerto Rican (PR; n = 893), Mexican American (MX; n = 784) or other Latino American (LA; n = 299) (Table 1 and Supplementary Table 1). The median age of the…

Continue Reading Gene expression in African Americans, Puerto Ricans and Mexican Americans reveals ancestry-specific patterns of genetic architecture

Gut microbiome signatures of extreme environment adaption in Tibetan pig

1050 SGBs clustered from 8210 high-medium quality metagenome-assembled genomes (MAGs) Over 779 Gb metagenomic sequence data was generated by Illumina HiSeq × Ten platform from 65 TPs samples (Supplementary Table 1). We integrated the above sequencing raw reads with a published metagenomic sequence dataset of 287 captive pigs from Denmark, France…

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Comparative resistome, virulome and mobilome analysis of metagenomes from wild and farm animals

Resumo:  Although (in the context of bacterial infections) the goal of antibiotic use is to combat and eliminate pathogenic bacteria, hundreds of non-pathogenic bacterial species are also affected when antibiotics are administrated. This results in a selection of bacteria resistant to the class of antibiotic applied. Additionally, with the ability…

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Copy number alteration features in pan-cancer homologous recombination deficiency prediction and biology

Data collection for HRD prediction model training and validation For the development of the HRD prediction model, 1854 samples (WGS data) from the pan-cancer analysis of whole genomes9 (PCAWG) and 560 breast cancer samples (SNP array data)16 are collected. To obtain a high-confidence training dataset of HRD, samples with BRCA1/2…

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Downsampling of cells in scRNAseq DE analysis

Downsampling of cells in scRNAseq DE analysis 0 Hello, this is a general question with no specific example concerning differential gene expression analysis in scRNAseq data. We sometimes want to compare two conditions in our DE** analysis but we see the the sample size of these groups greatly differ. For…

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Basin-wide variation in tree hydraulic safety margins predicts the carbon balance of Amazon forests

Site description We assemble a pan-Amazon dataset of key HTs (\(\varPsi \)50, HSM50 and \(\varPsi \)dry), including 129 species distributed across 11 forest sites (Fig. 1 and Extended Data Fig. 1). The sites are old-growth lowland forests (less than 400 m of elevation), with no evidence of significant human disturbance, located…

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PAI-1 4G/5G polymorphism in patients with DM & hypertension

Introduction Diabetes mellitus (DM) is a group of metabolic syndromes characterized by disorders of glucose metabolism, including type 1 DM, type 2 DM, gestational DM, and specific types of DM due to other causes. DM is closely associated with abnormal cardiac electrophysiological signal conduction and arrhythmias, whereby it triggers sudden…

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Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data | Genome Biology

Overview of the study To uncover the contexts and biological processes that affect gene expression regulation, this study took advantage of both the resolution of single-cell data and the directionality captured by co-eQTLs. First, we constructed cell-type-specific co-expression networks using five scRNA-seq PBMC datasets from three recently generated PBMC scRNA-seq…

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r – Issues with my output. Did I mess up my RStudio settings?

When I first downloaded R, every time I ran a t.test or wilcox.test, the output would include not only the p-value but also the mean of the two groups being compared, class-interval etc. I have tried using the summary function but it doesn’t provide any extra detail. Now all I…

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Measuring antigen expression of cancer cell lines and circulating tumour cells

To quantify the expression of different antigens, cells were stained using monoclonal antibodies coupled to phycoerythrin (PE), after which the number of PE molecules per cell was determined using quantitative flow cytometry. Although the number of PE molecules will not be exactly equal to the number of antigens, in this…

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The evolution of non-small cell lung cancer metastases in TRACERx

The TRACERx 421 cohort The TRACERx study (clinicaltrials.gov/ct2/show/NCT01888601) is a prospective observational cohort study that aims to transform our understanding of NSCLC, the design of which has been approved by an independent research ethics committee (13/LO/1546). Informed consent for entry into the TRACERx study was mandatory and obtained from every…

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Optogenetic stimulation of mouse Hoxb8 microglia in specific regions of the brain induces anxiety, grooming, or both

Induction of grooming by optogenetic activation of Hoxb8 microglia in the DMS and mPFC The components that are critical for achieving Hoxb8 microglia dependent induction of anxiety and/or grooming in wildtype C57Bl/6 mice are: Hoxb8 microglia, Hoxb8IRESCre (a Cre driver specific to Hoxb8 microglia within the CNS), Ai32 (a Cre…

Continue Reading Optogenetic stimulation of mouse Hoxb8 microglia in specific regions of the brain induces anxiety, grooming, or both

PUREE: accurate pan-cancer tumor purity estimation from gene expression data

Genomics-based consensus tumor purity estimates For TCGA samples, genomic-based consensus tumor purities were computed as a mean of predictions from ABSOLUTE17, AbsCNSeq18, ASCAT15, and PurBayes16 following the approach reported in Ghoshdastider et al. 41. AbsCNSeq and PurBayes estimates are based on mutation variant allele frequency data, and ASCAT and ABSOLUTE…

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Intermittent fasting modulates the intestinal microbiota and improves obesity and host energy metabolism

Weight loss and clinical improvements after IF intervention We performed a three-week intervention study on 72 adult Chinese volunteers subjected to a 5:2 program as detailed in Fig. 1a. The volunteers comprised individuals ranging from regular to obese (Supplementary Table 1). Seventeen clinical parameters were determined both before and after…

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High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of chemoresistance in leukemias

Nanopore reads coupled to a novel computational method extends analyses of differential methylation to sparse CpGs (outside CpG islands) We analyzed tumor samples at diagnosis (T) and relapse (R) from three AML patients (UD5, UD10 and AML2) who received standard chemotherapy and relapsed with chemoresistant disease (supplementary Table 1). DNA from…

Continue Reading High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of chemoresistance in leukemias

Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals

Diversity of within-host mutations in SARS-CoV-2 samples We analysed SARS-CoV-2 samples from 2,820 different individuals, alongside 29 other samples for quality control of the analysis (see Methods). The samples were collected from June-2020 to September-2022, covering the third to the fifth COVID-19 waves in HK. All samples had \(\ge\)90% genome…

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Clinical Efficacy and Diagnostic Value of Metagenomic Next-Generation

Introduction Infections are the major cause of human deaths worldwide and present a rising threat to public security.1 Antimicrobial resistance is a major concern that is threatening our ability to treat bacterial infections.2 Delayed administration of antibiotics significantly increases the in-hospital mortality rate.3 The tragic outcome of infection highlights the…

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The genomic landscape of reference genomes of cultivated human gut bacteria

The expanded repertoire of isolate genomes in CGR2 In continuation of our previous work on cultivation and sequencing gut-resident microbes, a total of ~20,000 bacterial isolates were cultivated. 4066 of these isolates were selected for whole-genome sequencing generating 3324 high-quality genomes with more than 90% completeness and less than 10%…

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Chronic Strongyloides stercoralis infection increases presence of the Ruminococcus torques group in the gut and alters the microbial proteome

Human ethics statement This study was approved by the Human Ethical Review Committee of Khon Kaen University, Thailand (HE641434) following the principles of the Declaration of Helsinki. Before stool samples were collected, participants were required to complete and sign written informed-consent forms. Participants and samples All samples came from residents…

Continue Reading Chronic Strongyloides stercoralis infection increases presence of the Ruminococcus torques group in the gut and alters the microbial proteome

Polycystic kidney disease 2-like 1 channel contributes to the bitter aftertaste perception of quinine

Chemicals Quinine hydrochloride and denatonium benzoate were obtained from Fujifilm Wako Pure Chemical (Osaka, Japan) and dissolved in a buffer or normal water. Collagenase A and dispase II were from Roche (Basel, Switzerland). Elastase was from Worthington Biochemical (Lakewood, NJ, USA). DNase I was from Merck (Darmstadt, Germany). Lipofectamine 2000…

Continue Reading Polycystic kidney disease 2-like 1 channel contributes to the bitter aftertaste perception of quinine

Abiotic selection of microbial genome size in the global ocean

Non-prokaryotic metagenomic sequences confound average genome size estimations In this work, we employed MicrobeCensus22 for de novo estimation of the average genome size (AGS) of microorganisms captured in shotgun metagenome sequences (Fig. 1a; Supplementary Data 1). Briefly, MicrobeCensus optimally aligns metagenomic reads to a set of 30 conserved single-copy gene (CSCG) families…

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Major cell-types in multiomic single-nucleus datasets impact statistical modeling of links between regulatory sequences and target genes

The number of cells in each cell-type biases the null distributions and statistics of the Z-scores method In this study, we refer to Z-score as the scaled Pearson R value of a cis-link between an ATACseq peak and a nearby gene against its matched trans-link null distribution (the Z-scores method,…

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The IPDGC/GP2 Hackathon – an open science event for training in data science, genomics, and collaboration using Parkinson’s disease data

GWAS-level and post-GWAS analyses GWAS of PD have nominated 90 independent risk signals in individuals of European ancestry, explaining ~16–36% of the heritable risk7, as well as two additional risk signals in Asian populations8. Typically, published GWAS are accompanied by various follow-up analyses, but performing these analyses is not always…

Continue Reading The IPDGC/GP2 Hackathon – an open science event for training in data science, genomics, and collaboration using Parkinson’s disease data

Population-level impacts of antibiotic usage on the human gut microbiome

A comprehensive catalogue of ARGs from the human microbiome We created a catalogue of ARGs across both the human microbiome and reference genomes by locating open reading frames (ORFs) on metagenomic assemblies from 8972 human microbiome samples spanning gut (7589), oral cavity (746), skin (380), airway (118), nasal cavity (55),…

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Technical assessment of different extraction methods and transcriptome profiling of RNA isolated from small volumes of blood

RNA quality and quantity Samples were divided into 6 groups, according to their (i) extraction method (manual vs automated); (ii) TURBO DNA Free treatment (treated vs untreated), and iii. starting volume of whole blood (16 μl, 33 μl, 50 μl and 66 μl). The elution volume was 50 μl for all the extractions performed. Thus,…

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The Root Canal Microbiome Diversity and Function. A Whole- Metagenome Shotgun analysis

Aim: Evaluate the root canal microbiome composition and bacterial functional capability in cases of primary and secondary apical periodontitis utilizing whole-metagenome shotgun sequencing. Methodology: Twenty-two samples from patients with primary root canal infections, and eighteen samples obtained from previously treated teeth currently diagnosed with apical periodontitis were analyzed with whole…

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Add Pairwise Comparisons P-values to a GGPlot

stat_pwc {ggpubr} R Documentation Add Pairwise Comparisons P-values to a GGPlot Description add pairwise comparison p-values to a ggplot such as box plots, dot plots and stripcharts. Usage stat_pwc( mapping = NULL, data = NULL, method = “wilcox_test”, method.args = list(), ref.group = NULL, label = “p.format”, y.position = NULL,…

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ancombc documentation

excluded in the analysis. Solve optimization problems using an R interface to NLopt. The overall false discovery rate is controlled by the mdFDR methodology we In this formula, other covariates could potentially be included to adjust for confounding. depends on our research goals. W, a data.frame of test statistics. enter…

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RNA editing analysis using REDItools

RNA editing analysis using REDItools 0 Hi I am doing RNA editing analysis using REDItools. I have two data sets one is mRNAseq reads of 150bp and other is total RNAseq reads of 101 bps. Sample size is below 5 in each dataset and would like to combine them. Since…

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Network expansion of genetic associations defines a pleiotropy map of human cell biology

Systematic augmentation of GWAS with network propagation Recent studies have shown that a comprehensive protein interaction network is critical for network propagation efforts9. Here, we combined the International Molecular Exchange physical protein interaction dataset19 from IntAct (protein–protein interactions)20, Reactome (pathways)21 and SIGNOR (directed signaling pathways)22. To facilitate re-use of these…

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Brain expression quantitative trait locus and network analyses reveal downstream effects and putative drivers for brain-related diseases

Harmonizing datasets for eQTL and co-regulation analysis We combined 14 eQTL datasets into the ‘MetaBrain’ resource to maximize statistical power to detect eQTLs and create a brain-specific gene co-regulation network (Fig. 2, Supplementary Figs. 1–7 and Supplementary Table 1). Previous to quality control (QC), MetaBrain includes 7,604 RNA-seq samples and…

Continue Reading Brain expression quantitative trait locus and network analyses reveal downstream effects and putative drivers for brain-related diseases

ASGARD is A Single-cell Guided Pipeline to Aid Repurposing of Drugs

Summary of a Single-cell Guided Pipeline to Aid Repurposing of Drugs Using scRNA-seq data, ASGARD repurposes drugs for disease by fully accounting for the cellular heterogeneity of patients (Fig. 1, Formula 1 in “Methods” section). In ASGARD, every cell cluster in the diseased sample is paired to that in the normal…

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Neuronal APOE4 removal protects against tau-mediated gliosis, neurodegeneration and myelin deficits

Neuron-specific removal of the APOE gene in tauopathy mice Our laboratory previously generated mouse lines expressing a floxed human APOE3 or APOE4 gene45 and a Cre recombinase gene under the control of a neuron-specific synapsin-1 promoter (Syn1-Cre)46. These floxed APOE-KI (fE) mice express homozygous human APOE3 or APOE4 in place…

Continue Reading Neuronal APOE4 removal protects against tau-mediated gliosis, neurodegeneration and myelin deficits

SJW SJW Group Common Stock (DE)

Outlook: SJW Group Common Stock (DE) is assigned short-term Ba1 & long-term Ba1 estimated rating.Dominant Strategy : SellTime series to forecast n: 19 Feb 2023 for (n+8 weeks)Methodology : Modular Neural Network (Emotional Trigger/Responses Analysis) Abstract SJW Group Common Stock (DE) prediction model is evaluated with Modular Neural Network (Emotional…

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Metagenomic next-generation sequencing of plasma

Introduction Metagenomic next-generation sequencing (mNGS), a new pathogen detection technology, does not rely on sequence amplification of specific gene primers. It is increasingly used in clinical pathogen detection due to its short sequencing time1 and high sensitivity, and the approximate detection sensitivity range is 68%-88%.2,3 We found that the overall…

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Comparing Sets of Correlations

Comparing Sets of Correlations 0 I have a single cell expression matrix and a set of transcription factor-target interactions. I want to test if the expression correlations between actual transcription factor-target interactions are greater than 10000 random off target links (so a transcription factor to a non-target). My gut says…

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Active predation, phylogenetic diversity, and global prevalence of myxobacteria in wastewater treatment plants

Myxococcota and Bdellovibrionota were active constituents of activated sludge microbiota To explore the predating activity and diversity of predatory bacteria in activated sludge, 13C-labeled Escherichia coli and Pseudomonas putida cells (determined as 97.09 and 97.30 atom% 13C, respectively) were added to the sludge microcosms for maximumly eight days of incubation,…

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Enolase-1 & prognosis & immune infiltration in breast cancer

Introduction Breast cancer is the most prevalent malignancy and the leading cause of cancer death in women worldwide.1 After its diagnosis, the most immediate challenge is to tailor treatment strategies and predict the prognosis; traditional clinicopathologic features, including estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2…

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Issue with VCF format while using Pharmcat

Hello everybody, I am using pharmcat tool’s prerprocessor feature to preprocessmy vcf file using the command > python3 pharmcat_vcf_preprocessor.py -vcf sample.vcf But I think there is some issue with my vcf file as this command outputs an error > Reading samples from sample.vcf … Saving output to . > >…

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WSM Williams-Sonoma Inc. Common Stock (DE)

Outlook: Williams-Sonoma Inc. Common Stock (DE) is assigned short-term Ba1 & long-term Ba1 estimated rating.Dominant Strategy : BuyTime series to forecast n: 27 Jan 2023 for (n+16 weeks)Methodology : Reinforcement Machine Learning (ML) Abstract Williams-Sonoma Inc. Common Stock (DE) prediction model is evaluated with Reinforcement Machine Learning (ML) and Wilcoxon…

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Sodium bicarbonate for kidney transplant recipients with metabolic acidosis in Switzerland: a multicentre, randomised, single-blind, placebo-controlled, phase 3 trial

Background Metabolic acidosis is common in kidney transplant recipients and is associated with declining graft function. Sodium bicarbonate treatment effectively corrects metabolic acidosis, but no prospective studies have examined its effect on graft function. Therefore, we aimed to test whether sodium bicarbonate treatment would preserve graft function and slow the…

Continue Reading Sodium bicarbonate for kidney transplant recipients with metabolic acidosis in Switzerland: a multicentre, randomised, single-blind, placebo-controlled, phase 3 trial

FinnGen provides genetic insights from a well-phenotyped isolated population

To benchmark our register-based phenotyping and to explore the value of the isolated setting of Finland, we selected 15 diseases with more than 1,000 cases in FinnGen and for which well-powered GWAS data have been published. We evaluated the accuracy of our phenotyping by comparing the genetic correlations and effect…

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Journal Of Pakistan Medical Association

Manzar Abbas  ( 5th Year MBBS Student. )Hareem Rauf  ( 4th Year MBBS Student. )Javeria Bilal Qamar  ( 3rd Year MBBS Student. )Syeda Ramlah Tul Sania  ( 5th Year MBBS Student. )Russell Seth Martins  ( Department of Pediatrics and Child Health. )Zahra Hasan  ( Aga Khan University, Karachi, Pakistan, ) …

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Alternative splicing and genetic variation of mhc-e: implications for rhesus cytomegalovirus-based vaccines

The gene expression of Mamu-E is regulated by extensive alternative splicing that is conserved among HLA-E isoforms To accurately define Mamu-E transcript structures, we aimed to use high-quality, full-length transcript sequences obtained by long-read transcriptome sequencing41. Since the sequences of MHC genes are very similar, it was critical that we…

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Integrative cross-species analysis of GABAergic neuron cell types and their functions in Alzheimer’s disease

The heterogeneity of GABAergic neurons in human, macaque, mouse, and pig To perform a cross-species comparative study of the GABAergic neurons, we collected the snRNA-seq datasets of the cerebral cortex for human10,11, macaque12,13, mouse14,15, and pig16. After cell-type annotation and filtering out the excitatory neurons and non-neurons, the GABAergic neurons…

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Simulated global warming affects endophytic bacterial and fungal communities of Antarctic pearlwort leaves and some bacterial isolates support plant growth at low temperatures

Sample collection Colobanthus quitensis samples were collected at King George Island near the Henryk Arctowski Polish Antarctic Station, Maritime Antarctica (62°14’ S, 58°48’ W) during the summer season (February 2018). Samples were collected inside the Antarctic Specially Protected Area (ASPA) 128 using permits provided by The Chilean Antarctic Institute (INACH)…

Continue Reading Simulated global warming affects endophytic bacterial and fungal communities of Antarctic pearlwort leaves and some bacterial isolates support plant growth at low temperatures

Multi-level cellular and functional annotation of single-cell transcriptomes using scPipeline

Software Figure preparation: CorelDRAW x8 (Corel); Bioinformatic analyses: R v 4.0.3 (R Foundation for Statistical Computing). Computational resources Analyses were run on a desktop computer with an Intel Core i9-10900L CPU (3.70 GHz, 10 cores, 20 threads) with 120 GB RAM running Windows 10 Pro (v21H2). Data preprocessing scRNA-seq data sets…

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Genomic signatures associated with maintenance of genome stability and venom turnover in two parasitoid wasps

Genomic features of two Anastatus wasps, A. japonicus and A. fulloi We employed PacBio high-fidelity (HiFi) long-read sequencing and Illumina short-read sequencing technologies to generate high-quality contigs for two Anastatus wasps, A. japonicus and A. fulloi (Supplementary Tables 1 and 2). These contigs were further scaffolded using Hi-C libraries to…

Continue Reading Genomic signatures associated with maintenance of genome stability and venom turnover in two parasitoid wasps

Metagenomic Next-Generation Sequencing in the Diagnosis of Infectious

Introduction Infection due to myelosuppression after chemotherapy for malignancies is a common complication and cause of treatment-related death.1,2 In clinical practice, the traditional identification of pathogens relies heavily on laboratory capacity to detect common pathogenic microorganisms with discrete methods, such as assays for pathogen-specific antibodies, nucleic acids and antigens, and…

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Subtype and cell type specific expression of lncRNAs provide insight into breast cancer

lncRNA expression according to breast cancer clinicopathological subtypes To identify lncRNAs expressed by specific breast cancer subtypes or associated with clinicopathological features, we analyzed RNA-sequencing data from two large independent breast cancer cohorts: SCAN-B (n = 3455)17 and TCGA-BRCA (n = 1095). We focused on lncRNAs annotated in the Ensembl18 v93 non-coding reference transcriptome…

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Bronchoalveolar Lavage Fluid for Metagenomic Sequencing

Introduction Severe pneumonia is one of the most common causes of infectious diseases among patients in the intensive care unit (ICU), and this can lead to various complications and high mortality.1–3 Timely and accurate pathogen diagnoses are crucial for appropriate antimicrobial therapy and improved clinical outcomes. However, the low detection…

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Nitrogen cycling and microbial cooperation in the terrestrial subsurface

Distribution of nitrogen-cycling pathways in groundwater Differences in nitrogen-cycling processes based on oxygen and nitrate concentrations Sixteen metagenomes (Table S4) were obtained from duplicate wells at four sites (A–D) from two unconfined alluvial aquifers (Canterbury, Fig. S1). These sites encompassed varied nitrate (0.45–12.6 g/m3), DO (0.37–7.5 mg/L), and dissolved organic carbon (DOC) (0–26 g/m3)…

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Dietary selection of metabolically distinct microorganisms drives hydrogen metabolism in ruminants

Volatile fatty acid production and absorption is modulated by diet Animals were adapted to a starch-rich diet by gradually increasing dietary concentrate content from 50 to 90% over the three 100-d experimental periods (Fig. 1A). With both diets, rumen structure and epithelial morphology were robust and rumen pH remained above 6.0…

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Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

Mapping molecular changes across malignant transformation We generated single-cell data for 81 samples collected from eight FAP and seven non-FAP donors (Fig. 1a and Supplementary Tables 1 and 2). For each tissue, we performed matched scATAC-seq and snRNA-seq (10x Genomics). We obtained high-quality single-cell chromatin accessibility profiles for 447,829 cells…

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Subsetting DESEQ2 VST Microbiome Data

Subsetting DESEQ2 VST Microbiome Data 1 @f8d5630d Last seen 16 hours ago Germany Hello there, the question is a bit off topic I am currently using DESEQ2 to normalize 16S microbiome data as advised several times in the recent literature. Currently I am facing the problem that I have 16S…

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Effects of terfenadine and diphenhydramine on the CYP2D6 activity in healthy volunteers.

The aim of this study was to investigate the effects of two antihistaminic drugs, terfenadine and diphenhydramine on CYP2D6 activity by using debrisoquine as a model substrate. The study was carried out as an in vivo single-dose study in 12 young, healthy men. All volunteers had previously been identified as…

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Vertical stratification of the air microbiome in the lower troposphere

Significance Large-scale meteorological and biological data demonstrate the vertical stratification of airborne biomass. The previously described diel cycle of airborne microorganisms is shown to disappear at height. Atmospheric turbulence and stratification are shown to be defining factors for the scale and boundaries, dynamics, and natural variability of airborne biomass, resulting…

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Identification of a four-gene signature & PTC.

Introduction Thyroid carcinoma (THCA) is the most common type of endocrine malignancy and its incidence is increasing.1 Based on its histopathological characteristics, thyroid carcinoma can be classified into multiple subtypes, such as papillary thyroid carcinoma (PTC), follicular thyroid carcinoma, and anaplastic thyroid carcinoma.2 PTC is the most common subtype of…

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The Identification of Prognostic and Metastatic Alternative Splicing in Skin Cutaneous Melanoma

Skin cutaneous melanoma (SKCM) is a type of highly invasive cancer originated from melanocytes. It is reported that aberrant alternative splicing (AS) plays an important role in the neoplasia and metastasis of many types of cancer. Therefore, we investigated whether ASEs of pre-RNA have such an influence on the prognosis…

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Bioinformation Analysis Reveals IFIT1 as Potential Biomarkers in Centr

Introduction Tuberculosis (TB) is considered to be one of the top ten causes of death in the world, about a quarter of the world’s population is infected with M. tuberculosis.1 The World Health Organization (WHO) divides tuberculosis into pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB). Although breakthroughs have been made…

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Pan-AMPK activator O304 prevents gene expression changes and remobilisation of histone marks in islets of diet-induced obese mice

O304 treatment prevents islet gene expression signature changes induced by HFD We have previously demonstrated that the AMPK activator O304 improves blood glucose homeostasis in both human T2D subjects as well as in high-fat diet induced obese and diabetic mouse models. In the present study, we have now analysed the…

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Crosstalk between Venous Thromboembolism and Periodontal Diseases: A Bioinformatics Analysis

This article was originally published here Dis Markers. 2021 Dec 10;2021:1776567. doi: 10.1155/2021/1776567. eCollection 2021. ABSTRACT BACKGROUND: This current study applied bioinformatics analysis to reveal the crosstalk between venous thromboembolism (VTE) and periodontitis, as well as the potential role of immune-related genes in this context. METHODS: Expression data were downloaded…

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Adrenal aldosterone-producing adenoma | IJGM

Background Primary hyperaldosteronism (PA) is characterized by spontaneous secretion of excessive aldosterone and inhibition of plasma renin activity.1 The pathogenesis of adrenal aldosterone-producing adenoma (APA) involves the abnormal proliferation of adrenal cortex cells and the excessive secretion of aldosterone, accounting for nearly 30% of PA. Excessive secretion of aldosterone can…

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The ENmix DNA methylation analysis pipeline for Illumina BeadChip and comparisons with seven other preprocessing pipelines | Clinical Epigenetics

Methylation analysis pipelines The ENmix pipeline performs data preprocessing in a stepwise way, including ENmix background correction [1], RELIC dye bias correction [3], optional inter-array normalization, RCP probe-type bias correction [2], quality control, filtering of low-quality data points, and imputation. ENmix background correction employs a mixture of exponential and truncated…

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Parallel genomic responses to historical climate change and high elevation in East Asian songbirds

Extreme environments present profound physiological stress. The adaptation of closely related species to these environments is likely to invoke congruent genetic responses resulting in similar physiological and/or morphological adaptations, a process termed “parallel evolution” (1). Existing evidence shows that parallel evolution is more common at the phenotypic level than at…

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Analysis of Community Composition of Bacterioplankton in Changle Seawater in China by Illumina Sequencing Combined with Bacteria Culture

Orthop Surg. 2021 Nov 24. doi: 10.1111/os.13060. Online ahead of print. ABSTRACT OBJECTIVES: To characterize the abundance and relative composition of seawater bacterioplankton communities in Changle city using Illumina MiSeq sequencing and bacterial culture techniques. METHODS: Seawater samples and physicochemical factors were collected from the coastal zone of Changle city…

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Diagnostic markers of AIDS combined with TM infection

Introduction The prevalence of Human immunodeficiency virus/Acquired Immune Deficiency Syndrome (HIV/AIDS) is still a public health problem that threatens the health of all human beings. According to the latest report of the World Health Organization, in the end of 2019, there were 38 million patients with human immunodeficiency virus/acquired immunodeficiency…

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An evolutionary functional genomics approach identifies novel candidate regions involved in isoniazid resistance in Mycobacterium tuberculosis

Functional genomics allows for detection of resistance-associated genomic regions We generated a highly saturated M. tuberculosis H37Rv pool with over 100,000 different transposon-insertion mutants following the protocol by Long et al.8. Using TnSeq, we found 58,389 out of 74,603 possible insertion sites had at least one read, meaning a saturation…

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Asc-Seurat: analytical single-cell Seurat-based web application | BMC Bioinformatics

To demonstrate Asc-Seurat’s functionalities, we analyzed the publicly available 10× Genomics’ 3k Peripheral Blood Mononuclear Cells (PBMC) dataset [26], showcasing the analysis of an individual sample. In addition, we used a second PBMC dataset to demonstrate the analysis integrating multiple samples in Asc-Seurat. The second PBMC dataset was generated by Hang…

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Frontiers | Metagenomic Analysis Reveals New Microbiota Related to Fiber Digestion in Pigs

Introduction Corn and soybean meal are the main components of high energy and high protein diets for pigs and are also the main raw materials of food products for human consumption, fermentation, and bioenergy industry (Sevillano et al., 2018). As the arable land of food crops was limited whereas the…

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Chapter 9 Differential abundance analysis

Here, we analyse abundances with three different methods: Wilcoxon test (CLR), DESeq2, and ANCOM-BC. All of these test statistical differences between groups. We will analyse Genus level abundances. We might want to first perform prevalence filtering to reduce the amount of multiple tests. In this particular dataset, all genera pass…

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best practice for applying FDR to highly similar group DEG analysis

hi, i am grad student who is mid of master’s degree. one of my project is revealing some genes that differentially expressed between cancer that has small size and do not lymph node metastasis and cancer that has small size and do lymph node metastasis. i’d done sampling from 10…

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Factors influencing multidrug-resistant tuberculosis | IDR

Introduction Pediatric tuberculosis (TB) is a significant global health threat and is one of the top ten causes of death in children.1 Globally, in 2019, an estimated 10.0 million people fell ill with TB, with children (aged under 15 years old) accounting for 12%, causing 1.4 million deaths.2 With the…

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PER1 as a Tumor Suppressor Attenuates Breast Cancer

Introduction Breast cancer is one of the most common malignancies in women, with a high mortality rate around the world.1,2 Although multidisciplinary therapeutic strategies, including surgical resection, chemoradiotherapy, endocrine and anti-HER2 therapy, have made substantial progress over the past decade, there are still a considerable proportion of breast cancer patients…

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LncRNA MIAT services as a noninvasive biomarker

Introduction BC is the most common cancer among women that is responsible for the most of the cancer-related death in worldwide.1 The occurrence of BC accounts for 7–8% of the entire number of malignant tumors.2 Accumulating evidence have shown that immunoreaction plays an important role in oncogenesis and progression.3,4 However,…

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The translatome of neuronal cell bodies, dendrites, and axons

Significance Proteins are the key drivers of neuronal synaptic function. The regulation of gene expression is important for the formation and modification of synapses throughout the lifespan. The complexity of dendrites and axons imposes unique challenges for protein supply at remote locations. The discovery of messenger RNAs (mRNAs) and ribosomes…

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Population structure, biogeography and transmissibility of Mycobacterium tuberculosis

Detailed population structure of L1–4 and a hierarchical sub-lineage naming system We assembled a high-quality data set of whole genomes, antibiotic resistance phenotypes, and geographic sites of isolation for 9584 clinical Mtb samples (“Methods” section and Supplementary Data 1). Of the total, 4939 (52%) were pan-susceptible, i.e., susceptible to at least…

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Probiotic consumption influences universal adaptive mutations in indigenous human and mouse gut microbiota

Probiotic intake commonly altered the genetic composition of gut microbial residents To comprehensively understand the adaptive mutations in the resident gut microbiota due to probiotic intake, we first collected and curated publicly available metagenomic studies related to probiotics with the following criteria. (1) The study has a longitudinal design, which…

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Comparison of sequencing data processing pipelines and application to underrepresented African human populations | BMC Bioinformatics

Literature survey We reviewed the processing pipelines of 29 HTS studies, 23 of which focus on human populations and six on other mammals (listed in Table 1). Table 1 List of studies included in the literature survey We summarized the information for some processing steps in Table 2 (see Additional…

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

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

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Comparing two RNA-seq data sets mouse and human

Comparing two RNA-seq data sets mouse and human 0 Hi I have a question. We have two RNA-Seq data sets one from mouse and one from human for our gene modification, and we wanted to know how similar they are from each other. I know i can convert the mouse…

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Microsatellites bioinformatics analysis for population genetics – Freelance Job in Physical Sciences – Less than 30 hrs/week – Less than 1 month

Looking for a bioinformatician biologist for data analysis as soon as possible with Expertise in using the below software 1. FSTAT v2.9.3.2 (Goudet, 1995): For allelic richness (AR) (with the rarefaction method to correct for differences in sample size) 2. BOTTLENECK v1.2.02 (Cornuet & Luikart, 1996; Piry et al., 1999)…

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Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model | BMC Biology

Organoid culture of small intestinal cells and lentiviral transduction C57BL/6J mice and BALB/cAnu/nu immune-deficient nude mice were purchased from CLEA Japan (Tokyo, Japan). The small intestine was harvested from wild-type male C57BL/6J mice at 3–5 weeks of age (Additional file 1: Figure S9A). Crypts were purified and dissociated into single cells,…

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Bioconductor – ALDEx2

DOI: 10.18129/B9.bioc.ALDEx2     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ALDEx2. Analysis Of Differential Abundance Taking Sample Variation Into Account Bioconductor version: 3.9 A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard…

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Disabling de novo DNA methylation in embryonic stem cells allows an illegitimate fate trajectory

The mammalian genome is characterized by widespread methylation of cytosine residues. After fertilization, however, both maternal and paternal genomes undergo extensive demethylation, reaching a low point in the blastocyst (1⇓⇓–4). The embryo genome is then remethylated by the activity of de novo DNA methylation enzymes (5). Mouse embryonic stem (ES)…

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An epigenetic basis of inbreeding depression in maize

INTRODUCTION Charles R. Darwin documented inbreeding depression as growth disadvantages from self-fertilization compared to outcrossing in many plants (1). Prevailing hypotheses suggest that inbreeding depression results from the exposure of deleterious recessive alleles and/or loss of overdominant alleles due to increased homozygosity (2, 3) or reduced recombination frequency in some…

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Bioconductor – unifiedWMWqPCR

DOI: 10.18129/B9.bioc.unifiedWMWqPCR     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see unifiedWMWqPCR. Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data Bioconductor version: 3.11 This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing…

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Integrated bioinformatics analysis to identify abnormal CC

Introduction In recent years, the morbidity and mortality of colon cancer have increased rapidly, both being ranked fourth worldwide. Although surgery-based comprehensive treatments improve the prognosis of colon cancer, because of the lack of available means for early diagnosis, the mortality level remains high for patients with advanced-stage cancer. The…

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Pericentromeric noncoding RNA changes DNA binding of CTCF and inflammatory gene expression in senescence and cancer

Significance During the aging process, senescent cells secrete inflammatory factors, causing various age-related pathologies. Thus, controlling the senescence-associated secretory phenotype (SASP) can tremendously benefit human health. Although SASP seems to be induced by the alteration of chromosomal organization, its underlying mechanism remains unclear. Here, it has been revealed that noncoding…

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