Prediction and Experimental Verification of a Hierarchical Transcription Factor Regulatory Network of Porcine Myoglobin (Mb)

Myoglobin is a key chemical component that determines meat’s color and affects consumers’ purchase intentions. In this work, we firstly identified the promoter sequence of the Mb gene from the primary assembly of high-throughput genome sequencing in pigs, and predicted its potential transcription factors by LASAGNA. Through the data mining of the mRNA expression profile of longissimus dorsi muscle of different pig breeds, we constructed a hierarchical interplay network of Mb-TFs (Myoglobin-Transcription Factors), consisting of 16 adaptive transcription factors and 23 secondary transcription factors. The verification of gene expression in longissimus dorsi muscle showed that the Mb mRNA and encoded protein were significantly (p < 0.05) more abundant in Bama pigs than Yorkshire pigs. The qRT-PCR (Real-Time Quantitative Reverse Transcription PCR) validation on genes of the Mb-TFs network showed that FOS, STAT3, STAT1, NEFL21, NFE2L2 and MAFB were significant positive regulatory core transcription factors of Mb-TFs network in Bama pigs, whereas ATF3 was the secondary transcription factor most responsible for the activation of the above transcription factors. Our study provides a new strategy to unravel the mechanism of pork color formation, based on public transcriptome and genome data analysis.

High performance of a GPU-accelerated variant calling tool in genome data analysis

Rapid advances in next-generation sequencing (NGS) have facilitated ultralarge population and cohort studies that utilized whole-genome sequencing (WGS) to identify DNA variants that may impact gene function. Massive sequencing data require highly efficient bioinformatics tools to complete read alignment and variant calling as the fundamental analysis. Multiple software and hardware acceleration strategies have been developed to boost the analysis speed. This study comprehensively evaluated the germline variant calling of a GPU-based acceleration tool, BaseNumber, using WGS datasets from several sources, including gold-standard samples from the Genome in a Bottle (GIAB) project and the Golden Standard of China Genome (GSCG) project, resequenced GSCG samples, and 100 in-house samples from the China Deafness Genetics Consortium (CDGC) project. Sequencing data were analyzed on the GPU server using BaseNumber, the variant calling outputs of which were compared to the reference VCF or the results generated by the Burrows-Wheeler Aligner (BWA) + Genome Analysis Toolkit (GATK) pipeline on a generic CPU server. BaseNumber demonstrated high precision (99.32%) and recall (99.86%) rates in variant calls compared to the standard reference. The variant calling outputs of the BaseNumber and GATK pipelines were very similar, with a mean F1 of 99.69%. Additionally, BaseNumber took only 23 minutes on average to analyze a 48X WGS sample, which was 215.33 times shorter than the GATK workflow. The GPU-based BaseNumber provides a highly accurate and ultrafast variant calling capability, significantly improving the WGS analysis efficiency and facilitating time-sensitive tests, such as clinical WGS genetic diagnosis, and sheds light on the GPU-based acceleration of other omics data analyses.

SARS-CoV-2 genome variants epidemiology surveillance in Ethiopia and dynamic mutational changes of structural S Spike protein through computational analysis

Objective: This study aims to identify the variants of SARS-CoV-2 that were circulating in Ethiopia and spot dynamic mutational changes of spike antigenicity based on genome data analysis to put forward preventative measurement against pandemic. Results: The SARS-CoV-2 genomes from Ethiopia were confirmed to be evolutionary related to RaTG13 and SL- bat coronavirus and Spike receptor sites were conserved. The clade distribution of the genome was reflected as GH, GR and other O and intended for new variants. 3 female samples were detected as Variants of Interest VUI202012/01GRY B.1.1.7 which Pango linage B.1.1.7 was originated from the UK. Despite 21 notable mutations, 71% D614G, 28% D614X, 35% N501Y and 21% NSP5-S284G mutation occurred predominantly in our genome samples and could have antigenicity and infectivity effects. Mutation on N440K was perceived as antigenic-drift in a sample and potency resist SER-52 antibody neutralization and vaccine escape.

SARS-CoV-2 Genome Variants Epidemiology Surveillance in Ethiopia and Targeted Mutational Changes of Structural S Spike Proteins Through Computational Analysis

Objective: This study aims to identify the variants of SARS CoV 2 that were circulating in Ethiopia and spot dynamic mutational changes of spike antigenicity based on genome data analysis to put forward preventative measurement against pandemic. Results: The genomes from Ethiopia were confirmed to be evolutionary related to RaTG13 and SL- bat coronavirus and Spike receptor sites were conserved. The clade distribution of the genome was reflected as GH, GR and other O and intended for new variants. 3 female samples were detected as variants of concern VUI202012/01GRY B.1.1.7 which Pango linage B.1.1.7 was originated from the UK. Despite 21 notable mutations, 71% D614G, 28% D614X, 35% N501Y and 21% NSP5 S284G mutation were occurred predominantly in our genome samples. and could be antigenicity and infectivity. Mutation on N440K was perceived in a sample and potency resist SER-52 antibody neutralization and vaccine escape.

An insight into the evolutionary history of Indonesian cattle assessed by whole genome data analysis

The domestication of Indonesian cattle was investigated through a study of their genetic diversity, up to the genome level. Little documentation exists regarding the history of domestication of Indonesian cattle and questions remain despite a growing body of molecular evidence. In this study, we genotyped seven Indonesian cattle breeds using an Illumina BovineSNP50 Bead Chip to provide insight into their domestication and demographic history in a worldwide population context. Our analyses indicated the presence of hybrid cattle, with Bos javanicus and Bos indicus ancestries being most prevalent, as well as purebred cattle. We revealed that all the breeds were interconnected through several migration events. However, their demographic status varied widely. Although almost all the Indonesian cattle had an effective population size higher than the minimum level required to ensure breed fitness, efforts are still needed to maintain their genetic variability and purity.

Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically relevant bacteria

Carbapenemases inactivate most β-lactam antibiotics, including carbapenems, and have frequently been reported among Enterobacteriaceae , Acinetobacter spp. and Pseudomonas spp. Traditionally, the horizontal gene transfer of carbapenemase-encoding genes (CEGs) has been linked to plasmids. However, given that integrative and conjugative elements (ICEs) are possibly the most abundant conjugative elements among prokaryotes, we conducted an in silico analysis to ascertain the likely role of ICEs in the spread of CEGs among all bacterial genomes (n=182 663). We detected 17 520 CEGs, of which 66 were located within putative ICEs among several bacterial species (including clinically relevant bacteria, such as Pseudomonas aeruginosa , Klebsiella pneumoniae and Escherichia coli ). Most CEGs detected within ICEs belong to the IMP, NDM and SPM metallo-beta-lactamase families, and the serine beta-lactamase KPC and GES families. Different mechanisms were likely responsible for acquisition of these genes. The majority of CEG-bearing ICEs belong to the MPFG, MPFT and MPFF classes and often encode resistance to other antibiotics (e.g. aminoglycosides and fluoroquinolones). This study provides a snapshot of the different CEGs associated with ICEs among available bacterial genomes and sheds light on the underappreciated contribution of ICEs to the spread of carbapenem resistance globally.

BART3D: Inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data

ABSTRACTSummaryIdentification of functional transcriptional regulators associated with chromatin interactions is an important problem in studies of 3-dimensional genome organization and gene regulation. Direct inference of TR binding has been limited by the resolution of Hi-C data. Here, we present BART3D, a computational method for inferring TRs associated with genome-wide differential chromatin interactions by comparing Hi-C maps from two states, leveraging public ChIP-seq data for human and mouse. We demonstrate that BART3D can detect relevant TRs from dynamic Hi-C profiles with TR perturbation or cell differentiation. BART3D can be a useful tool in 3D genome data analysis and functional genomics research.Availability and ImplementationImplemented in Python, source code freely available at https://github.com/zanglab/[email protected] InformationSupplementary data are available.

L-cysteine transporter-PCR to detect hydrogen sulfide-producing Campylobacter fetus

Phenotypic differences between Campylobacter fetus fetus and C. fetus venerealis subspecies allow the differential diagnosis of bovine genital campylobacteriosis. The hydrogen sulfide production, for example, is a trait exclusive to C. fetus fetus and C. fetus venerealis biovar intermedius. This gas that can be biochemically tested can be produced from L-cysteine (L-Cys). Herein, we report a novel multiplex-PCR to differentiate C. fetus based on the evaluation of a deletion of an ATP-binding cassette-type L-Cys transporter that could be involved in hydrogen sulfide production, as previously described. A wet lab approach combined with an in silico whole genome data analysis showed complete agreement between this L-Cys transporter-PCR and the hydrogen sulfide production biochemical test. This multiplex-PCR may complement the tests currently employed for the differential diagnosis of C. fetus.