Small variant benchmark from a complete assembly of X and Y chromosomes.

The sex chromosomes contain complex, important genes impacting medical phenotypes, but differ from the autosomes in their ploidy and large repetitive regions. To enable technology developers along with research and clinical laboratories to evaluate variant detection on male sex chromosomes X and Y, we create a small variant benchmark set with 111,725 variants for the Genome in a Bottle HG002 reference material. We develop an active evaluation approach to demonstrate the benchmark set reliably identifies errors in challenging genomic regions and across short and long read callsets.

Antihypertensive, Anti-Inflammatory, and Antiangiogenic In Silico Activity of Lactoferrin-Derived Peptides of Equine Milk Hydrolysate.

Background: Equine milk, including its whey proteins, is a source of nutrients and functional components in the human diet, and is especially beneficial for people with weakened immune systems, newborns, and athletes. Objectives Whey proteins in equine milk constitute approximately 20% of the total protein content and include various fractions such as albumin, globulin, and lactoferrin. Lactoferrin is one of the most extensively studied whey proteins in equine milk.

Genetic Polymorphism of Y-Chromosome in Turkmen Population from Turkmenistan.

This study investigates the Y-chromosome genetic diversity of the Turkmen population in Turkmenistan, analyzing 23 Y-STR loci for the first time in a sample of 100 individuals. Combined with comparative data from Turkmen populations in Afghanistan, Iran, Iraq, Russia, and Uzbekistan, this analysis offers insights into the genetic structure and relationships among Turkmen populations across regions across Central Asia and the Near East. High haplotype diversity in the Turkmen of Turkmenistan is shaped by founder effects (lineage expansions) from distinct haplogroups, with haplogroups Q and R1a predominating.

Proteins with alternative folds reveal blind spots in AlphaFold-based protein structure prediction.

In recent years, advances in artificial intelligence (AI) have transformed structural biology, particularly protein structure prediction. Though AI-based methods, such as AlphaFold (AF), often predict single conformations of proteins with high accuracy and confidence, predictions of alternative folds are often inaccurate, low-confidence, or simply not predicted at all. Here, we review three blind spots that alternative conformations reveal about AF-based protein structure prediction.

Standardization of Genomic Nomenclature across a Diverse Ecosystem of Stakeholders: Evolution and Challenges.

Background: Genetic testing has traditionally been divided into molecular genetics and cytogenetics, originally driven by the use of different assays and their associated limitations. Cytogenetic technologies such as karyotyping, fluorescent in situ hybridization or chromosomal microarrays are used to detect large "megabase level" copy number variants and other structural variants such as inversions or translocations. In contrast, molecular methodologies are heavily biased toward subgenic "small variants" such as single nucleotide variants, insertions/deletions, and targeted detection of intragenic, exon level deletions or duplications.

In Vitro conservation and genetic diversity analysis of rare species Ribes janczewskii.

Ribes janczewskii is a rare and valuable plant known for its resistance to spring frosts, pests, and diseases. It is used in hybridization to develop resistant currant varieties but is on the verge of extinction, listed in Kazakhstan Red Book. This study developed a micropropagation and slow-growth storage protocol for conservation.

Association of infection with colorectal cancer in Kazakhstani patients.

Objectives: is a gram-negative anaerobic bacillus associated with colorectal cancer (CRC). We aimed to determine the abundance of . and other CRC-associated bacteria using quantitative real-time polymerase chain reaction (qPCR) analysis to detect the possible correlations between tumor and normal tissues and the relationships between patients' clinical characteristics, diet, and CRC-associated bacteria.

An evaluation of the safety and efficacy of using decellularized bovine parietal peritoneum membranes as dural substitutes.

Purpose: The reconstruction of dura matter is a challenging problem for neurosurgeons. A number of materials for dural reconstruction have recently been developed, but some of them have poor biocompatibility, poor mechanical properties, and adverse effects. Bovine parietal peritoneum is a promising natural material for regenerative medicine and reconstructive surgery.

Leveraging Professional Radiologists' Expertise to Enhance LLMs' Evaluation for AI-generated Radiology Reports.

In radiology, Artificial Intelligence (AI) has significantly advanced report generation, but automatic evaluation of these AI-produced reports remains challenging. Current metrics, such as Conventional Natural Language Generation (NLG) and Clinical Efficacy (CE), often fall short in capturing the semantic intricacies of clinical contexts or overemphasize clinical details, undermining report clarity. To overcome these issues, our proposed method synergizes the expertise of professional radiologists with Large Language Models (LLMs), like GPT-3.

A Graphene-Based Bioactive Product with a Non-Immunological Impact on Mononuclear Cell Populations from Healthy Volunteers.

We previously described GMC, a graphene-based nanomaterial obtained from carbon nanofibers (CNFs), to be biologically compatible and functional for therapeutic purposes. GMC can reduce triglycerides' content in vitro and in vivo and has other potential bio-functional effects on systemic cells and the potential utility to be used in living systems. Here, immunoreactivity was evaluated by adding GMC in suspension at the biologically functional concentrations, ranging from 10 to 60 µg/mL, for one or several days, to cultured lymphocytes (T, B, NK), either in basal or under stimulating conditions, and monocytes that were derived under culture conditions to pro-inflammatory (GM-MØ) or anti-inflammatory (M-MØ) macrophages.

Novel lineage of anelloviruses with large genomes identified in dolphins.

Unlabelled: Anellovirus infections are ubiquitous in mammals but lack any clear disease association, suggesting a commensal virus-host relationship. Although anelloviruses have been identified in numerous mammalian hosts, their presence in members of the family Delphinidae has yet to be reported. Here, using a metagenomic approach, we characterize complete anellovirus genomes ( = 69) from four Delphinidae host species: short-finned pilot whale (, = 19), killer whale (, = 9), false killer whale (, = 6), and pantropical spotted dolphin (, = 1).

Kazakhstan tulips: comparative analysis of complete chloroplast genomes of four local and endangered species of the genus L.

Species of are important ornamental plants used for horticultural purposes in various countries, across Asia, Europe, and North Africa. The present study is the first report on typical features of the complete chloroplast genome sequence of four local and endangered species including , and from Kazakhstan using Illumina sequencing technology. The comparative analyses revealed that the complete genomes of four species were highly conserved in terms of total genome size (152.

Dynamic Cellular Proteome Remodeling during SARS-CoV-2 Infection. Identification of Plasma Protein Readouts.

The outbreak of COVID-19, led to an ongoing pandemic with devastating consequences for the global economy and human health. With the global spread of SARS-CoV-2, multidisciplinary initiatives were launched to explore new diagnostic, therapeutic, and vaccination strategies. From this perspective, proteomics could help to understand the mechanisms associated with SARS-CoV-2 infection and to identify new therapeutic options.

Identification of a depupylation regulator for an essential enzyme in .

In , proteins that are posttranslationally modified with a prokaryotic ubiquitin-like protein (Pup) can be degraded by bacterial proteasomes. A single Pup-ligase and depupylase shape the pupylome, but the mechanisms regulating their substrate specificity are incompletely understood. Here, we identified a depupylation regulator, a protein called CoaX, through its copurification with the depupylase Dop.

ClinVar: updates to support classifications of both germline and somatic variants.

ClinVar (www.ncbi.nlm.

ComFB, a new widespread family of c-di-NMP receptor proteins.

Cyclic dimeric GMP (c-di-GMP) is a widespread bacterial second messenger that controls a variety of cellular functions, including protein and polysaccharide secretion, motility, cell division, cell development, and biofilm formation, and contributes to the virulence of some important bacterial pathogens. While the genes for diguanylate cyclases and c-di-GMP hydrolases (active or mutated) can be easily identified in microbial genomes, the list of c-di-GMP receptor domains is quite limited, and only two of them, PliZ and MshEN, are found across multiple bacterial phyla. Recently, a new c-di-GMP receptor protein, named CdgR or ComFB, has been identified in cyanobacteria and shown to regulate their cell size and, more recently, natural competence.

How Much Force is Needed to Kill a Single Bacterium?

The interaction between bacteria and nanomaterials, particularly from a physical or mechanical perspective, has emerged as a topic of significant interest in both science and medicine. Mechanobactericidal nanomaterials, which exert antimicrobial effects through purely physical mechanisms, hold promise as alternative strategies to combat bacterial resistance to traditional antibiotics. High-aspect-ratio nanoparticles and surface topographies are being engineered to enhance their mechanobactericidal properties.

Genomic analysis of the early COVID-19 pandemic in Haiti reveals Caribbean-specific variant dynamics.

Pathogen sequencing during the COVID-19 pandemic has generated more whole genome sequencing data than for any other epidemic, allowing epidemiologists to monitor the transmission and evolution of SARS-CoV-2. However, large parts of the world are heavily underrepresented in sequencing efforts, including the Caribbean islands. We performed genome sequencing of SARS-CoV-2 from upper respiratory tract samples collected in Haiti during the spring of 2020.

InterPro: the protein sequence classification resource in 2025.

InterPro (https://www.ebi.ac.