BMC genomic data最新文献

Clinical trial number: Not applicable.

Aim: The purpose of this study was to discuss effects of exosome miRNA-369-3p on the biological behavior of trophoblast cells in gestational diabetes.

Materials and methods: Measuring miRNA-369-3p mRNA expression in Normal and GDM pregnant women by RT-qPCR assay; using high glucose to make GDM cell model; using CCK-8 and flow cytometry to evaluate cell proliferation andapoptosis; measuring cell invasion and migration by transwell and wound healing assay; IL-10 mRNA and protein expression by RT-qPCR and WB assay; correlation between miRNA-369-3p and IL-10 by Dual luciferase assay.

Results: Compared with normal pregnant women, miRNA-369-3p mRNA level significantly up-regulation in GDM pregnant women (P<0.001); with high glucose stimulating, compared with Normal group, the cell proliferation rate (78.30 ± 4.27%) significantly inhibited with cell apoptosis significantly increasing (24.55 ± 2.01%) (P<0.001), cell invasion (65.33 ± 3.65%) and migration (48.31 ± 4.18) activities significantly inhibited with IL-10 significantly down-regulation (P<0.001, respectively). With miRNA-369-3p inhibitor supplement, the cell activities were significantly improved with IL-10 increasing.

Conclusion: Exosome miRNA-369-3pknockdown had effects to improved high glucose induced HTR-8/Svneo cell biological activities by stimulating IL-10.

Coastal ecosystems along Nigeria's Gulf of Guinea face increasing pollution from industrial discharges and oil-related activities, posing serious threats to marine biodiversity. This study investigated detoxification gene expression cytochrome P450, aryl hydrocarbon receptor (AhR), and metallothionein (MT) in two sympatric croaker species, Pseudotolithus typus and Pseudotolithus elongatus, collected from Awoye, Ayetoro, and Idi-Ogba in Ondo State. Heavy metals and Polycyclic Aromatic Hydrocarbons (PAHs) were quantified in liver, gill, kidney, and muscle tissues, while gene expression was assessed using qPCR. Results revealed distinct spatial, seasonal, and tissue-specific bioaccumulation patterns, with higher contaminant loads during the dry season. The liver exhibited the highest total metal and PAH concentrations, followed by kidney, muscle, and gill tissues. P. elongatus accumulated higher contaminant levels than P. typus, particularly at Idi-Ogba, indicating greater anthropogenic influence. Gene expression analyses showed significant upregulation (p < 0.05) of AhR, cytochrome P450, and MT in liver and kidney tissues, correlating positively with contaminant concentrations. Regression models indicated strong associations between heavy metals and MT expression (R² = 0.999) and between PAHs and AhR/P450 expression (R² = 0.96-0.97). P. elongatus exhibited a stronger transcriptional response to organic pollutants, while P. typus responded more to metals, reflecting species-specific detoxification strategies. This study provides the first comparative molecular information into contaminant-induced stress in Pseudotolithus species, highlighting their potential as biomarkers for monitoring coastal pollution in the Gulf of Guinea.

Objectives: Thermophilic bacteria are valuable biotechnological resources. A thermophilic bacterium isolated from the Thai hot spring sediments was subjected to complete genome sequencing. Genome data will facilitate bacterial identification and comparative genomics within the Hydrogenophilus genus and provide insights into polyhydroxybutyrate biosynthesis pathways for industrial applications.

Data description: The H. thermoluteolus KS0102 genome comprises a single circular chromosome containing 2,136,028 bp and 61.70% GC. The genome was sequenced using Illumina and Oxford Nanopore technologies and assembled using Unicycler. It contained 1,848 CDS, 9 rRNAs, 49 tRNAs, and 1 CRISPR region. This dataset enables the investigation of polyhydroxybutyrate biosynthesis pathways and comparative genomic studies of thermophilic adaptation mechanisms in Hydrogenophilus species.

Background: The GenoPharm-GH project initiated in 2019, as a longitudinal, multi-site observational cohort study aimed at bridging gaps in understanding the influence of host genetics, pharmacokinetics and comorbidities on treatment outcome among persons living with HIV (PLWH) in Ghana.

Methods: The study is ongoing prospective, longitudinal, multi-site cohort associated with diverse projects being conducted throughout health facilities across Ghana. So far 2044 persons living with HIV (PLWH) aged ≥ 8 years have been registered. These participants are on treatment with antiretroviral therapies (ART). Viral suppression, treatment adherence (self-reported and pill count), clinical data, genetic variations, coinfections, and comorbidities are being studied among these participants. Samples from the studies have been stored in the biorepository in the PGMG laboratory.

Results: Among the cohort, ≥ 95% are on dolutegravir-based ART; 58% have viral loads less than 50 copies/mL at the latest visit with approximately 10-15% in virologic failure (> 1000cp/mL). Drug metabolite profiling has been undertaken for dolutegravir in mono infections and coinfections with malaria. Pharmacogenetics data for CYP3A4, CYP3A5, UGT1A1 and ApoE have been determined in sub-studies. Coinfections and other non-communicable diseases observed include hepatitis B and C, tuberculosis, pneumonia, diabetes and hypertension indicating the need for integrated care strategies for PLWH. A biorepository has been created for sub-studies and future analysis.

Conclusions: The project provides a strong avenue for translational HIV research, guiding policy and enhancing long-term results. Expanding biobanking and ongoing follow-up should help to improve knowledge of treatment outcomes, support individualised HIV treatment, and direct further therapeutic interventions. Participants are followed up and data updated at regular intervals to understand the dynamics of treatment outcome.

Background: Pachystachys lutea Nees is a typical species of the family Acanthaceae, native to tropical South America. As an evergreen shrub, it has found extensive application in landscape greening due to its unique ornamental value. However, there are currently no phylogenetic and genetic studies on the chloroplast (cp.) genome of P. lutea.

Results: This study characterized the cp. genome of P. lutea using high-throughput sequencing technology and analyzed its structural features and phylogenetic position using bioinformatics methods. The results indicated that the cp. genome had a high degree of conservation in gene structure and gene content, with a typical quadripartite structure. Its total length is 151,574 bp and the total GC content is 38.18%. A total of 132 genes were annotated, including 87 protein-coding genes (PCGs), 37 tRNAs and eight rRNA genes. Through the comparative analysis, the diversity and variation of large single-copy (LSC) and small single-copy (SSC) regions were significantly higher than those of inverted repeat (IR) regions. Genes with high nucleotide polymorphism, such as rps19, ycf1, and ndhF provided potential reference loci for molecular identification within the P. lutea. The phylogenetic analysis showed that the P. lutea and Clinacanthus nutans forms a sister group with 100% bootstrap value, which proves that P. lutea develops conservatively in the course of evolution.

Conclusion: This paper for the first time reports the phylogenetic study of the complete cp. genome within the genus Pachystachys. The study provides a theoretical basis for the research on genetic diversity, molecular markers, and species identification of plants in the Acanthaceae family. It enriches the genetic information and supports the evolutionary relationships among plants in this family.

Objectives: This dataset was generated as part of a study investigating the impact of crude and encapsulated Acacia mearnsii tannin extracts on the rumen microbiota of South African Mutton Merino sheep. The aim was to provide high-quality metagenomic data to support methane mitigation strategies through dietary interventions targeting rumen microbial communities.

Data description: Rumen fluid was collected from 24 rams (six per treatment) fed a total mixed ration (TMR) supplemented with either distilled water (control), monensin (positive control), crude tannin, or microencapsulated tannin. However, one sample did not yield sufficient sequencing depth, resulting in 23 usable datasets. DNA was extracted and subjected to shotgun metagenomic sequencing on the Illumina NovaSeq 6000 platform. The dataset comprises paired-end reads deposited in the NCBI SRA under accession SRP480487. Taxonomic profiling reveals dominant phyla such as Bacteroidetes and Firmicutes, and the presence of archaeal genera such as Methanobrevibacter. This dataset provides insights into the structural and functional composition of the rumen microbiome and may be useful for comparative studies and biotechnology applications.

Objectives: Megasphaera elsdenii is a commensal bacterium and a promising probiotic candidate that is frequently given as a supplement directly to ruminant animals. Animals that are fed grain, benefit greatly from the organism's ability to convert lactic acid into volatile fatty acids, particularly butyrate, valerate, isobutyrate, and propionate, which are important sources of energy for animals. This conversion helps modulate rumen acidity and prevent ruminal acidosis (SARA), a prevalent condition in the feedlot cattle. The objective of this work was to generate a high-quality draft genome assembly of M. elsdenii which will contribute to enhancing animal feed supplementation, by improving our understanding of its interactions with the host.

Data description: Here, we describe the genome sequence of M. elsdenii isolate CH4, one of the most promising probiotic candidates, commonly administered as a direct-fed microbe supplement to ruminant animals. Sequencing reads from M. elsdenii produced approximately 5.6 Mb. The assembly generated a draft genome size of 2.5 Mb, consisting of 27 contigs, with an N50 of 102.8 KB. Examination of the genome completeness and contamination was assessed using CheckM v1.0.18 and reported as 93.57 and 4.34%, respectively. The draft genome sequence will allow improved genomic comparisons among the probiotic strains of the genus Megasphaera, particularly with the aim of improving our knowledge of their animal-probiotic interactions as well as their population biology.