Bioinformatic identification of important roles of COL1A1 and TNFRSF12A in cartilage injury and osteoporosis.

Objective: The aim of this study was to identify the key regulatory mechanisms of cartilage injury and osteoporosis through bioinformatics methods, and to provide a new theoretical basis and molecular targets for the diagnosis and treatment of the disease.

Methods: Microarray data for cartilage injury (GSE129147) and osteoporosis (GSE230665) were first downloaded from the GEO database. Differential expression analysis was applied to identify genes that were significantly up-or down-regulated in the cartilage injury and osteoporosis samples.

Modeling Biases from Low-Pass Genome Sequencing to Enable Accurate Population Genetic Inferences.

Low-pass genome sequencing is cost-effective and enables analysis of large cohorts. However, it introduces biases by reducing heterozygous genotypes and low-frequency alleles, impacting subsequent analyses such as model-based demographic history inference. Several approaches exist for inferring an unbiased allele frequency spectrum (AFS) from low-pass data, but they can introduce spurious noise into the AFS.

Pharmacogenetics: Opportunities for the Research Program and Other Large Data Sets to Advance the Field.

Pharmacogenetic variation is common and an established driver of response for many drugs. There has been tremendous progress in pharmacogenetics knowledge over the last 30 years and in clinical implementation of that knowledge over the last 15 years. But there have also been many examples where translation has stalled because of the lack of available data sets for discovery or validation research.

Predicting transcriptional changes induced by molecules with MiTCP.

Studying the changes in cellular transcriptional profiles induced by small molecules can significantly advance our understanding of cellular state alterations and response mechanisms under chemical perturbations, which plays a crucial role in drug discovery and screening processes. Considering that experimental measurements need substantial time and cost, we developed a deep learning-based method called Molecule-induced Transcriptional Change Predictor (MiTCP) to predict changes in transcriptional profiles (CTPs) of 978 landmark genes induced by molecules. MiTCP utilizes graph neural network-based approaches to simultaneously model molecular structure representation and gene co-expression relationships, and integrates them for CTP prediction.

A meta-analysis of genome-wide association studies to identify candidate genes associated with feed efficiency traits in pigs.

Pig production is an agricultural sector of great economic and social relevance to Brazil and global markets. Feed efficiency traits directly influence the sustainability of pig production due to the economic impact of feed costs on the production system and the environmental footprint of the industry. Therefore, breeding for improved feed efficiency has been a target of worldwide pig breeding programs.

sp. nov., a bacterium isolated from the air of the Icelandic volcanic island Surtsey.

A novel bacterium, designated 19SA41, was isolated from the air of the Icelandic volcanic island Surtsey. Cells of strain 19SA41 are Gram-stain-negative, strictly aerobic, non-motile rods and form pale yellow-pigmented colonies. The strain grows at 4-30 °C (optimum, 22 °C), at pH 6-10 (optimum, pH 7.

Probing spin effects in phycocyanin using Janus-like ferromagnetic microparticles.

In an era of interdisciplinary scientific research, new methodologies are necessary to simultaneously advance several fields of study. One such case involves the measurement of electron spin effects on biological systems. While magnetic effects are well known in biology, recent years have shown a surge in published evidence isolating the dependence on spin, rather than magnetic field, in biological contexts.

Fully Atomistic Molecular Dynamics Simulation of Ice Nucleation Near an Antifreeze Protein.

Heterogeneous ice nucleation is a widespread phenomenon in nature. Despite extensive research on ice nucleation near biological antifreeze proteins, a probe for ice nucleation and growth processes at the atomic level is still lacking. Herein, we present simulation evidence of the heterogeneous ice nucleation process on the ice-binding surface (IBS) of the antifreeze protein (TmAFP).

Bayesian Inference of Phylogenetic Distances: Revisiting the Eigenvalue Approach.

Using genetic data to infer evolutionary distances between molecular sequence pairs based on a Markov substitution model is a common procedure in phylogenetics, in particular for selecting a good starting tree to improve upon. Many evolutionary patterns can be accurately modelled using substitution models that are available in closed form, including the popular general time reversible model (GTR) for DNA data. For more complex biological phenomena, such as variations in lineage-specific evolutionary rates over time (heterotachy), other approaches such as the GTR with rate variation (GTR ) are required, but do not admit analytical solutions and do not automatically allow for likelihood calculations crucial for Bayesian analysis.

Painful diabetic neuropathy is associated with accelerated epigenetic aging.

About one out of two diabetic patients develop diabetic neuropathy (DN), of these 20% experience neuropathic pain (NP) leading to individual, social, and health-economic burden. Risk factors for NP are largely unknown; however, premature aging was recently associated with several chronic pain disorders. DNA methylation-based biological age (DNAm) is associated with disease risk, morbidity, and mortality in different clinical settings.

Valorization of Cocoa and Peach-Palm Wastes for the Production of Amylases by Pleurotus pulmonarius CCB19 and Its Application as an Additive in Commercial Detergents.

In the context of agribusiness, the agricultural and livestock sectors generate a considerable quantity of waste on a daily basis. Solid-state fermentation (SSF) represents a potential alternative for mitigating the adverse effects of residue accumulation and for producing high-value products such as enzymes. Pleurotus pulmonarius is capable of producing a number of commercial enzymes, including amylases.

Unelongated Stems are an Active Nitrogen-Fixing Site in Rice Stems Supported by Both Sugar and Methane Under Low Nitrogen Conditions.

Enhancing nitrogen (N) fixation in rice plants can reduce N fertilizer application and contribute to sustainable rice production, particularly under low-N conditions. However, detailed microbial and metabolic characterization of N fixation in rice stems, unlike in the well-studied roots, has not been investigated. Therefore, the aim of this study was to determine the active N-fixing sites, their diazotroph communities, and the usability of possible carbon sources in stems compared with roots.

Modeling the Impact of Seasonality on Mosquito Population Dynamics: Insights for Vector Control Strategies.

Mosquitoes are important vectors for the transmission of some major infectious diseases of humans, i.e., malaria, dengue, West Nile Virus and Zika virus.

A Data-Informed Mathematical Model of Microglial Cell Dynamics During Ischemic Stroke in the Middle Cerebral Artery.

Neuroinflammation immediately follows the onset of ischemic stroke in the middle cerebral artery. During this process, microglial cells are activated in and recruited to the penumbra. Microglial cells can be activated into two different phenotypes: M1, which can worsen brain injury; or M2, which can aid in long-term recovery.

Potential prognostic and predictive biomarkers: METTL5, METTL7A, and METTL7B expression in gastrointestinal cancers.

Background: The methyltransferase gene family is known for its diverse biological functions and critical role in tumorigenesis. This study aimed to identify these family genes in common gastrointestinal (GI) cancers using comprehensive methodologies.

Methods: Gene identification involved analysis of scientific literature and insights from The Cancer Genome Atlas (TCGA) database.

Salivary proteomic analysis in patients with type 2 diabetes mellitus and periodontitis.

Objective: This study aimed to compare the salivary protein profile in individuals with Type 2 Diabetes Mellitus (DM2) and periodontitis and their respective controls.

Methods: Eighty participants were included in the study. The four groups were formed by individuals with DM2 and periodontitis (DM2 + P, n = 20), DM2 without periodontitis (DM2, n = 20), periodontitis without DM2 (P, n = 20) and individuals without periodontitis and without DM2 (H, n = 20).

Persistent prey species in the Lotka-Volterra apparent competition system with a single shared predator.

We analyze the Lotka-Volterra n prey-1 predator system with no direct interspecific interaction between prey species, in which every prey species undergoes the effect of apparent competition via a single shared predator with all other prey species. We prove that the considered system necessarily has a globally asymptotically stable equilibrium, and we find the necessary and sufficient condition to determine which of feasible equilibria becomes asymptotically stable. Such an asymptotically stable equilibrium shows which prey species goes extinct or persists, and we investigate the composition of persistent prey species at the equilibrium apparent competition system.

A physiologically based pharmacokinetic (PBPK) model describing the kinetics of a commercial mixture α-, β-, and γ-hexabromocyclododecane exposure in mice.

Hexabromocyclododecane (HBCD) is a brominated flame retardant, that is added, but not chemically bonded, to consumer products. HBCD is sold as a commercial-grade HBCD mixture containing three major stereoisomers: alpha (α), beta (β), and gamma (γ), with relative amounts of 12% for α-HBCD, 6% for β-HBCD, and 82% for γ-HBCD. HBCDs are widely measured in the environment and in biological matrices.

Dietary and competition effects on life history attributes of Chrysomya megacephala and Lucilia sericata (Diptera: Calliphoridae) in south-west Europe.

The range of the oriental latrine fly (Chrysomya megacephala) is currently expanding. It coexists with another blowfly with a similar ecology, the green bottle fly (Lucilia sericata), one of the most abundant species in carrion during warm months. It is essential to understand the influence of temperature, larval substrate type, and larval competition on the development rates of these necrophagous calliphorids to evaluate the role and the adaptation of C.

"Methyl jasmonate: bridging plant defense mechanisms and human therapeutics".

A volatile organic substance produced from jasmonic acid, methyl jasmonate (MJ/MeJA), is an important plant hormone involved in stress responses and plant defense. Apart from its role in plants, MJ has garnered significant attention because of its pharmacological effects and possible therapeutic use in human health. This thorough analysis looks into the many biological actions of MJ, such as its antioxidant, anti-inflammatory, and anti-cancer effects.

Highly Sensitive Digital and Analog Immunoassay Based on Submicron Magnetic Beads and Fluorescent Microspheres.

The detection of disease-related protein biomarkers plays a crucial role in the early diagnosis, treatment, and monitoring of diseases. The concentrations of protein biomarkers can vary significantly in different diseases or stages of the same disease. However, most of the existing analytical methods cannot simultaneously meet the requirements of high sensitivity and a wide dynamic range.

Rectification of planar orientation angle switches behavior and replenishes contractile junctions.

In the early Drosophila embryo, germband elongation is driven by oriented cell intercalation through t1 transitions, where vertical (dorsal-ventral aligned) interfaces contract and then resolve into new horizontal (anterior-posterior aligned) interfaces. Here, we show that contractile events produce a continuous "rectification" of cell interfaces, in which interfaces systematically rotate toward more vertical orientations. As interfaces rotate, their behavior transitions from elongating to contractile regimes, indicating that the planar polarized identities of cell-cell interfaces are continuously re-interpreted in time depending on their orientation angle.

Associations of Short-Term Ozone Exposure With Hypoxia and Arterial Stiffness.

Background: Epidemiological studies reported associations between ozone (O) exposure and cardiovascular diseases, yet the biological mechanisms remain underexplored. Hypoxia is a shared pathogenesis of O-associated diseases; therefore, we hypothesized that O exposure may induce changes in hypoxia-related markers, leading to adverse cardiovascular effects.

Objectives: This study aimed to investigate associations of short-term O exposure with hypoxic biomarkers and arterial stiffness.

Human keratinocytes grown at a gas-permeable interface in vitro stratify correctly to generate engineered human epidermis.

Background: One of the key functions of human skin is to provide a barrier, protecting the body from the surrounding environment and maintaining homeostasis of the internal environment. A mature, stratified epidermis is critical to achieve skin barrier function and is particularly important when producing skin grafts in vitro for wound treatment. For decades epidermal stratification has been achieved in vitro by culturing keratinocytes at an air-liquid interface, triggering proliferating basal keratinocytes to differentiate and form all epidermal layers.

Host range of the oothecal parasitoid Aprostocetus hagenowii (Hymenoptera: Eulophidae).

Aprostocetus hagenowii (Ratzburg) is a generalist parasitoid of cockroach (Blattodea) oothecae. Previous studies examining the host range of A. hagenowii have largely focused on cockroaches of economic and medical importance, which represent a minority of species in an order filled with species of diverse morphology, behavior, and ecology.