Preliminary Analysis of Placental DNA Methylation Profiles in Piglets with Extreme Birth Weight Variations.

Adequate birth weight is essential for animal survival and subsequent growth. However, the mechanism by which placental DNA methylation influences fetal growth remains incompletely understood. This study employed whole-genome bi-sulfite sequencing (WGBS) and RNA sequencing to analyze placental tissues from two weak piglets and two normal piglets born to the same sow.

Development of a multiplex recombinase amplification assay for the rapid and concurrent detection of human DNA and sex identification.

In forensic practice, it is essential to identify human DNA and determine the sex of individuals from biological samples collected at crime scenes. Currently, the common detection methods mainly focus on targeted DNA analysis based on PCR technology, which is time-consuming and relies on laboratory equipment. In recent years, recombinase polymerase amplification (RPA), as one of ubiquitous isothermal amplification technology, has gained popularity across various diagnostic fields due to its advantages of rapid processing and minimal temperature control requirements.

Explainable artificial intelligence in forensic DNA analysis: Alleles identification in challenging electropherograms using supervised machine learning methods.

Challenging samples in capillary electrophoresis (CE)-based short tandem repeat (STR) analysis often produce artefactual signals that cannot be completely filtered out by expert electropherogram (EPG) reading systems, complicating allele interpretation. Previous studies have demonstrated the potential of artificial intelligence (AI) to address this issue by accurately distinguishing allele signals from artefacts in EPGs. Traditional machine learning models offer significant advantages in enhancing the interpretability and transparency of AI models used in DNA analysis, particularly in criminal investigations and legal contexts.

Corrigendum: Set of 15 SNP-SNP markers for detection of unbalanced degraded DNA mixtures and noninvasive prenatal paternity testing.

[This corrects the article DOI: 10.3389/fgene.2021.

Effect of weight loss following Roux-en-Y gastric bypass on cancer risk: A Mendelian randomization study.

Cancer incidence and development are strongly correlated with obesity, however there is insufficient data to support a causal relationship between intentional weight loss and the prevention or promotion of cancer. We investigated the causal relationship between weight loss following Roux-en-Y gastric bypass (RYGB) and the incidence of 18 cancers using Mendelian randomization (MR). A genome-wide association studies (GWAS) data related to weight loss following RYGB from the GWAS catalog database were used as exposure, and GWAS data related to 18 cancers from the Medical Research Council integrative epidemiology unit open GWAS project were used as outcomes.

Association between solid cooking fuels exposure and metabolic syndrome: Evidence from China.

Epidemiological evidence connecting cooking fuel use to metabolic syndrome (MetS) is lacking. Solid cooking fuel usage and MetS prevalence were prospectively investigated in this study. We included participants in 2011 and 2015 from the China Health and Retirement Longitudinal Study (CHARLS) data.

The Research Progress of DNA Methylation in the Development and Function of the Porcine Placenta.

The pig is the most widely consumed domestic animal in China, providing over half of the meat supply in food markets. For livestock, a key economic trait is the reproductive performance, which is significantly influenced by placental development. The placenta, a temporary fetal organ, is crucial for establishing maternal-fetal communication and supporting fetal growth throughout pregnancy.

MHBase: A comprehensive database of short microhaplotypes for advancing forensic genetic analysis.

Microhaplotypes (MHs) were first recommended by Prof. Kidd for use in forensics because they can improve human identification, kinship analysis, mixture deconvolution, and ancestry prediction. Since their introduction, extensive research has demonstrated the advantages of MHs in forensic applications and provided useful data for different populations.

Development of a coding SNP panel for tracking the origin of whole-exome sequencing samples.

Whole-exome sequencing (WES) is widely used to diagnose complex genetic diseases and rare conditions. The implementation of a robust and effective quality control system for sample identification and tracking throughout the WES process is essential. We established a multiplex panel that included 22 coding single-nucleotide polymorphism (cSNP) loci.

Optimizing Analytical Thresholds for Low-Template DNA Analysis: Insights from Multi-Laboratory Negative Controls.

When analyzing challenging samples, such as low-template DNA, analysts aim to maximize information while minimizing noise, often by adjusting the analytical threshold (AT) for optimal results. A potential approach involves calculating the AT based on the baseline signal distribution in electrophoresis results. This study investigates the impact of reagent kits, testing quarters, environmental conditions, and amplification cycles on baseline signals using historical records and experimental data on low-template DNA.

Improving DNA mixtures analysis using compound markers composed of InDels and SNPs screened from the whole genome with next-generation sequencing.

Next-generation sequencing (NGS) allows for better identification of insertion and deletion polymorphisms (InDels) and their combination with adjacent single nucleotide polymorphisms (SNPs) to form compound markers. These markers can improve the polymorphism of microhaplotypes (MHs) within the same length range, and thus, boost the efficiency of DNA mixture analysis. In this study, we screened InDels and SNPs across the whole genome and selected highly polymorphic markers composed of InDels and/or SNPs within 300 bp.

HMGB1 released by mesothelial cells drives the development of asbestos-induced mesothelioma.

Asbestos is the main cause of malignant mesothelioma. Previous studies have linked asbestos-induced mesothelioma to the release of HMGB1 from the nucleus to the cytoplasm, and from the cytoplasm to the extracellular space. In the cytoplasm, HMGB1 induces autophagy impairing asbestos-induced cell death.

CircMAPK9 promotes adipogenesis through modulating hsa-miR-1322/FTO axis in obesity.

Circular RNA (circRNA) is a special category of non-coding RNA that has garnered increasing attention in the exploration of lipid metabolism. However, the functional regulation mechanisms of circRNAs in obesity diseases remain unclear. By whole transcriptome sequencing, a total of 164 circular RNAs were found to exhibit differential expression between lean and obese individuals.

(-)-Epigallocatechin-3-gallate promotes intestinal epithelial proliferation and barrier function after ischemia/reperfusion injury via activation of Nurr1.

Context: (-)-Epigallocatechin-3-gallate (EGCG) is involved in cell proliferation and ischemia/reperfusion (I/R) injury of several organs.

Objective: To identify the role of EGCG in intestinal epithelial proliferation and barrier exposed to I/R injury.

Material And Methods: Fifty Sprague-Dawley rats were divided into sham, I/R, I/R + EGCG (12.

Development of specific and rapid detection of human DNA by recombinase polymerase amplification assay for forensic analysis.

The determination of human-derived samples is very important in forensic investigations and case investigation in order to determine vital information on the suspect and the case. In this study, we established a recombinase polymerase amplification (RPA) assay for rapid identification of human-derived components. The sensitivity of the assay was 0.

Evaluation of microhaplotype panels for complex kinship analysis using massively parallel sequencing.

In recent years, microhaplotypes (MHs) have become a research hotspot within the field of forensic genetics. Traditional MHs contain only SNPs that are closely linked within short fragments. Herein, we broaden the concept of general MHs to include short InDels.

An MPS-Based 50plex Microhaplotype Assay for Forensic DNA Analysis.

Microhaplotypes (MHs) are widely accepted as powerful markers in forensic studies. They have the advantage of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), with no stutter and amplification bias, short fragments and amplicons, low mutation and recombination rates, and high polymorphisms. In this study, we constructed a panel of 50 MHs that are distributed on 21 chromosomes and analyzed them using the Multiseq multiple polymerase chain reaction (multi-PCR) targeted capture sequencing protocol based on the massively parallel sequencing (MPS) platform.

Establishment of a co-analysis system for personal identification and body fluid identification: a preliminary report.

Analysis of genetic markers can provide clues for case investigation. Short tandem repeat (STR) detection and analysis are widely used for both personal identification and parentage testing. However, DNA analysis currently cannot provide sufficient information for body fluid identification.

An overview of SNP-SNP microhaplotypes in the 26 populations of the 1000 Genomes Project.

Microhaplotypes (MHs) are a promising new type of forensic markers that are defined by the combinations of two- or more single-nucleotide polymorphisms (SNPs) within 200 bp. Their advantages, such as low mutation rates, lack of stutter artifacts, and short amplicons, have improved human identification, kinship analysis, ancestry prediction, and mixture deconvolution capabilities. Information on published MHs, e.

Set of 15 SNP-SNP Markers for Detection of Unbalanced Degraded DNA Mixtures and Noninvasive Prenatal Paternity Testing.

Unbalanced and degraded mixtures (UDM) are very common in forensic DNA analysis. For example, DNA signals from criminal suspects are masked by a large amount of DNA from victims, or cell-free fetal DNA (cffDNA) in maternal plasma is masked by a high background of maternal DNA. Currently, detecting minor DNA in these mixtures is complex and challenging.

Asbestos-induced chronic inflammation in malignant pleural mesothelioma and related therapeutic approaches-a narrative review.

Objective: The aim of this review is addressing the mechanisms of asbestos carcinogenesis, including chronic inflammation and autophagy-mediated cell survival, and propose potential innovative therapeutic targets to prevent mesothelioma development or improve drug efficacy by reducing inflammation and autophagy.

Background: Diffuse malignant pleural mesothelioma is an aggressive cancer predominantly related to chronic inflammation caused by asbestos exposure. Millions of individuals have been exposed to asbestos or to other carcinogenic mineral fibers occupationally or environmentally, resulting in an increased risk of developing mesothelioma.

Validation of the Microreader 28A ID System: A 6-dye multiplex amplification assay for forensic application.

The Microreader 28A ID System is a new 28-plex genotyping system with 6-dye multiplex amplification, which allows the simultaneous amplification of all 20 Combined DNA Index System (CODIS) core loci (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, vWA, D1S1656, D2S441, D2S1338, D10S1248, D12S391, D19S433, D22S1045), plus five extended STRs loci (D6S1043, Penta D, Penta E, DYS391, SE33), 2 Y-Indels (Rs2032678, Rs771783753), and the amelogenin loci. This system can be used for forensic analyses, such as personal identification, kinship testing, scientific research, database applications, and other aspects of human genetic identification. The validation of the Microreader 28A ID System followed the "Validation Guidelines for DNA Analysis Methods (2016)" described by the Scientific Working Group on DNA Analysis Methods and the regulations published by the China Ministry of Public Security.

Association of Clinical Parameters and Prognosis with the Pretreatment Systemic Immune-inflammation Index (SII) in Patients with Gastric Cancer.

This study explored the relationship between the pretreatment systemic immune-inflammation index (SII) and overall survival (OS) in gastric cancer (GC) patients. A systemic literature search was performed to find out the articles that estimated the relationship of SII with specific clinical parameters and OS in GC patients. Nine articles (including 10 studies) were included.