Novel biallelic MCMDC2 variants were associated with meiotic arrest and nonobstructive azoospermia.

Nonobstructive azoospermia (NOA), one of the most severe types of male infertility, etiology often remains unclear in most cases. Therefore, this study aimed to detect four biallelic detrimental variants (0.5%) in the minichromosome maintenance domain containing 2 (MCMDC2) genes in 768 NOA patients by whole-exome sequencing (WES).

Mir-615-5p inhibits cervical cancer progression by targeting TMIGD2.

Background: Cervical cancer (CC) is a prevalent gynecological malignancy, contributing to a substantial number of fatalities among women. MicroRNAs (miRNAs) have emerged as promising biomarkers with significant potential for the early detection and prognosis of CC.

Objective: This study aimed to explore the clinical significance and biological role of miR-615-5p in CC, with the goal of identifying novel biomarkers for this disease.

Interplay of swine acute diarrhoea syndrome coronavirus and the host intrinsic and innate immunity.

Swine acute diarrhoea syndrome coronavirus (SADS-CoV), a novel HKU2-related coronavirus of bat origin, is a newly emerged swine enteropathogenic coronavirus that causes severe diarrhoea in piglets. SADS-CoV has a broad cell tropism with the capability to infect a wide variety of cells from human and diverse animals, which implicates its ability to hold high risks of cross-species transmission. The intracellular antiviral immunity, comprised of the intrinsic and innate immunity, represents the first line of host defence against viral infection prior to the onset of adaptive immunity.

miR-9-5p/HMMR regulates the tumorigenesis and progression of clear cell renal cell carcinoma through EMT and JAK1/STAT1 signaling pathway.

Background: The most common malignant type of kidney cancer is clear cell renal cell carcinoma (ccRCC). The expression levels of hyaluronan-mediated motility receptor (HMMR) in many tumor types are significantly elevated. HMMR is closely associated with tumor-related progression, treatment resistance, and poor prognosis, and has yet to be fully investigated in terms of its expression patterns and molecular mechanisms of action in ccRCC.

Pre-processing of paleogenomes: mitigating reference bias and postmortem damage in ancient genome data.

We investigate alternative strategies against reference bias and postmortem damage in low coverage paleogenomes. Compared to alignment to the linear reference genome, we show that masking known polymorphic sites and graph alignment effectively remove reference bias, but only starting from raw read files. We next study approaches to overcome postmortem damage: trimming, rescaling, and our newly developed algorithm, bamRefine (github.

A novel homozygous intronic variant in CDT1 that alters splicing causes Meier-Gorlin syndrome, and a review of published mutations and growth hormone treatments.

Background: Meier-Gorlin syndrome (MGORS) is a rare autosomal inherited form of primordial dwarfism. Pathogenic variants in 13 genes involved in DNA replication initiation have been identified in this disease, but homozygous intronic variants have never been reported. Additionally, whether growth hormone (GH) treatment can increase the height of children with MGORS is unclear.

Integrated bioinformatics analysis and experimental validation of exosome-related gene signature in steroid-induced osteonecrosis of the femoral head.

Background: Steroid-induced osteonecrosis of the femoral head (SIONFH) is a universal hip articular disease and is very hard to perceive at an early stage. The understanding of the pathogenesis of SIONFH is still limited, and the identification of efficient diagnostic biomarkers is insufficient. This research aims to recognize and validate the latent exosome-related molecular signature in SIONFH diagnosis by employing bioinformatics to investigate exosome-related mechanisms in SIONFH.

Hypoxic BMSC-derived exosomal miR-210-3p promotes progression of triple-negative breast cancer cells via NFIX-Wnt/β-catenin signaling axis.

Background: Bone marrow mesenchymal stem cells (BMSCs) are a crucial component of the tumor microenvironment (TME), with hypoxic conditions promoting their migration to tumors. Exosomes play a vital role in cell-to-cell communication within the TME. Hypoxic TME have a great impact on the release, uptake and biofunctions of exosomes.

Metabolic profiling of Perilla leaves of different colors: insights into metabolite variation and bioactive compound distribution.

Background: Perilla frutescens (L.) Britt. (Lamiaceae) leaves are essential culinary and medicinal herbs, native to East Asian countries.

A sweeping view of avian mycoplasmas biology drawn from comparative genomic analyses.

Background: Avian mycoplasmas are small bacteria associated with several pathogenic conditions in many wild and poultry bird species. Extensive genomic data are available for many avian mycoplasmas, yet no comparative studies focusing on this group of mycoplasmas have been undertaken so far.

Results: Here, based on the comparison of forty avian mycoplasma genomes belonging to ten different species, we provide insightful information on the phylogeny, pan/core genome, energetic metabolism, and virulence of these avian pathogens.

Mining functional gene modules by multi-view NMF of phenome-genome association.

Background: Mining functional gene modules from genomic data is an important step to detect gene members of pathways or other relations such as protein-protein interactions. This work explores the plausibility of detecting functional gene modules by factorizing gene-phenotype association matrix from the phenotype ontology data rather than the conventionally used gene expression data. Recently, the hierarchical structure of phenotype ontologies has not been sufficiently utilized in gene clustering while functionally related genes are consistently associated with phenotypes on the same path in phenotype ontologies.

Genome-wide identification of CAMTA gene family in teak (Tectona grandis) and functional characterization of TgCAMTA1 and TgCAMTA3 in cold tolerance.

Background: Calmodulin-binding transcription activator (CAMTA) proteins play significant roles in signal transduction, growth and development, as well as abiotic stress responses, in plants. Understanding their involvement in the low-temperature stress response of teak is vital for revealing cold resistance mechanisms.

Results: Through bioinformatics analysis, the CAMTA gene family in teak was examined, and six CAMTA genes were identified in teak.

Genetic Commonalities Between Metabolic Syndrome and Rheumatic Diseases Through Disease Interactome Modules.

This study aims to elucidate the potential genetic commonalities between metabolic syndrome (MetS) and rheumatic diseases through a disease interactome network, according to publicly available large-scale genome-wide association studies (GWAS). The analysis included linkage disequilibrium score regression analysis, cross trait meta-analysis and colocalisation analysis to identify common genetic overlap. Using modular partitioning, the network-based association between the two disease proteins in the protein-protein interaction set was divided and quantified.

IRE1α-XBP1 safeguards hematopoietic stem and progenitor cells by restricting pro-leukemogenic gene programs.

Hematopoietic stem cells must mitigate myriad stressors throughout their lifetime to ensure normal blood cell generation. Here, we uncover unfolded protein response stress sensor inositol-requiring enzyme-1α (IRE1α) signaling in hematopoietic stem and progenitor cells (HSPCs) as a safeguard against myeloid leukemogenesis. Activated in part by an NADPH oxidase-2 mechanism, IRE1α-induced X-box binding protein-1 (XBP1) mediated repression of pro-leukemogenic programs exemplified by the Wnt-β-catenin pathway.

Alterations in the uterine echotexture, hemodynamics, and histological findings in relation to metabolomic profiles in goats with different ovarian activities (active versus inactive ovaries).

This study investigated, for the first time, the alterations in the uterine echotexture and blood flow in cyclic and acyclic (inactive ovary) goats using ultrasonography. The study aimed also to evaluate the metabolomic changes in the plasma of cyclic and acyclic goats. Furthermore, the histopathological approach was applied to the specimens of the uterus to validate the findings of this study.

Bioinformatics analysis of mitochondrial metabolism-related genes demonstrates their importance in renal cell carcinoma.

Purpose: Clear cell renal cell carcinoma (ccRCC) is resistant to radiotherapy and chemotherapy. Thus, it is necessary to find new diagnostic markers and therapeutic targets to increase the overall outcomes of ccRCC. Recent studies have shown that therapeutic methods that interfere with the energy transfer system can also positively affect the treatment process.

Prognosis of aggressive adult T-cell leukemia/lymphoma with central nervous system infiltration and utility of CD7 versus CADM1 flowcytometric plots of cerebrospinal fluid.

The prognosis of adult T-cell leukemia/lymphoma (ATL) with primary central nervous system (CNS) involvement has been unclear since the advent of new therapies. Recently, we have shown that flow cytometric CD7/CADM1 analysis of CD4 + cells (HAS-Flow) is useful to detect ATL cells that are not morphologically diagnosed as ATL cells. We investigated the role of CNS involvement in ATL using cytology and HAS-Flow by analyzing cerebrospinal fluid (CSF) from 73 aggressive ATL cases.

Identification of a distal enhancer of Ucp1 essential for thermogenesis and mitochondrial function in brown fat.

Uncoupling protein 1 (UCP1) is a crucial protein located in the mitochondrial inner membrane that mediates nonshivering thermogenesis. However, the molecular mechanisms by which enhancer-promoter chromatin interactions control Ucp1 transcriptional regulation in brown adipose tissue (BAT) are unclear. Here, we employed circularized chromosome conformation capture coupled with next-generation sequencing (4C-seq) to generate high-resolution chromatin interaction profiles of Ucp1 in interscapular brown adipose tissue (iBAT) and epididymal white adipose tissue (eWAT) and revealed marked changes in Ucp1 chromatin interaction between iBAT and eWAT.

Prospective validation of ORACLE, a clonal expression biomarker associated with survival of patients with lung adenocarcinoma.

Human tumors are diverse in their natural history and response to treatment, which in part results from genetic and transcriptomic heterogeneity. In clinical practice, single-site needle biopsies are used to sample this diversity, but cancer biomarkers may be confounded by spatiogenomic heterogeneity within individual tumors. Here we investigate clonally expressed genes as a solution to the sampling bias problem by analyzing multiregion whole-exome and RNA sequencing data for 450 tumor regions from 184 patients with lung adenocarcinoma in the TRACERx study.

Uncovering genetic determinants of antioxidant properties in Thai landrace rice through genome-wide association analysis.

Pigmented rice (Oryza sativa L.) is recognized as a source of natural antioxidant compounds, such as flavonoids, oryzanol, tocopherol, and anthocyanin. Because of their nutritional benefits, anthocyanin-enriched or pigmented rice varieties are feasible alternatives for promoting human health.

Tyrosine phosphatase SHP2 accelerated ovarian cancer via modulating integrin/ E-Cadherin/ ZEB1 induced EMT.

This article focusing on examining the function and further, molecular function of SHP2 in ovarian cancer (OC). For the molecular mechanism, bioinformatics was applied to study the specifically expressed genes in ovarian cancer ; the western blotting was applied to identify the EGF, p-SHP2, ZEB1, and E-Cadherin expressions in ovarian cancer tissue and pair adjacent tissue; then SKOV3 cells were treated with EGF and infected with E-Cadherin overexpression lentivirus, and then cells were treated with benzyl butyl phthalate and IRS-1 respectively. Detection of expression of p-SHP2, ZEB1, E-Cadherin, α3-integrin, p-Src, p-SMAD2, Snail, Slug and SKOV3 cells of migration and invasion abilities were detected using Western blot method and cell scratch assay and Transwell assay; Progression of ovarian cancer was detected using subcutaneous tumor transplantation assay in nude mice and HE staining method and immunocyto.

A collaborative network analysis for the interpretation of transcriptomics data in Huntington's disease.

Rare diseases may affect the quality of life of patients and be life-threatening. Therapeutic opportunities are often limited, in part because of the lack of understanding of the molecular mechanisms underlying these diseases. This can be ascribed to the low prevalence of rare diseases and therefore the lower sample sizes available for research.

Proteomic analysis reveals the difference between the spermatozoa of young and old Sus scrofa.

The Wannan black pig is a superior local breed in Anhui province, renowned for its exceptional meat quality and remarkable adaptability to various environmental conditions. Semen, being a crucial indicator of male sexual maturity and fertility, significantly influences the performance of breeding boars. The molecular basis for comprehending the fecundity of boars in practical production lies in understanding the disparities in sperm proteins among boars of varying ages.