Revisiting the electron transfer pathways between amicyanin and cytochrome from a theoretical perspective.

The phenomenon of electron transfer between cytochrome and amicyanin is a prevalent chemical process found in biological systems. In this study, we used MD simulation to explore the dynamic conformational changes and studied the possibilities of different electron transport pathways. Along with DFT computations, we employed the non-equilibrium green function for identifying electron transport channels within the system.

A genome-wide scan of non-coding RNAs and enhancers for refractive error and myopia.

Refractive error (RE) and myopia are complex polygenic conditions with the majority of genome-wide associated genetic variants in non-exonic regions. Given this, and the onset during childhood, gene-regulation is expected to play an important role in its pathogenesis. This prompted us to explore beyond traditional gene finding approaches.

Adipose-Derived Stromal Cell Conditioned Medium on Bone Remodeling: Insights from a 3D Osteoblast-Osteoclast Co-Culture Model.

This study describes the potential of the conditioned medium (CM) from adipose-derived mesenchymal stromal cells (ASCs) to affect the response of bone cells and support bone remodeling. This was in particular assessed by an in vitro model represented by a 3D human osteoblast-osteoclast co-culture. It has been reported that the effects of ASCs are predominantly attributable to the paracrine effects of their secreted factors, that are present as soluble factors or loaded into extracellular vesicles.

Topical review: sleep regulation as a novel target for treating preschool-aged children with attention-deficit/hyperactivity disorder symptoms.

Objective: Elevated attention-deficit/hyperactivity disorder (ADHD) symptoms in preschoolers are a risk factor for poorer psychiatric health, cognitive deficits, and social and academic impairment across the lifespan. The first-line treatment for these preschoolers, behavioral parent training (BPT), reduces children's disruptive behaviors and parenting stress, yet its impact on core ADHD symptoms is inconsistent. Early interventions targeting biological mechanisms linked to core ADHD pathophysiology are critically needed.

Customizing Tacrolimus Dosing in Kidney Transplantation: Focus on Pharmacogenetics.

Different polymorphisms in genes encoding metabolizing enzymes and drug transporters have been associated with tacrolimus pharmacokinetics. In particular, studies on CYP3A4 and CYP3A5, and their combined cluster have demonstrated their significance in adjusting tacrolimus dosing to minimize under- and overexposure thereby increasing the proportion of patients who achieve tacrolimus therapeutic target. Many factors influence the pharmacokinetics of tacrolimus, contributing to inter-patient variability affecting individual dosing requirements.

"They are not HIV treatments drugs; they are preventive drugs (PrEP)". Experiences of PrEP uptake among vulnerable adolescent girls and young women in Tanzania.

Introduction: HIV poses a significant global health concern, affecting adolescents among other populations. This is attributed to various vulnerabilities including biological factors, gender inequalities and limited access to comprehensive sexual and reproductive health services in sub-Saharan Africa. In Tanzania, adolescent girls, and young women (AGYW) face double the risk of HIV infection compared to their male counterparts.

Sex differences in mitochondrial free-carnitine levels in subjects at-risk and with Alzheimer's disease in two independent study cohorts.

A major challenge in the development of more effective therapeutic strategies for Alzheimer's disease (AD) is the identification of molecular mechanisms linked to specific pathophysiological features of the disease. Importantly AD has a two-fold higher incidence in women than men and a protracted prodromal phase characterized by amnestic mild-cognitive impairment (aMCI) suggesting that biological processes occurring early can initiate vulnerability to AD. Here, we used a sample of 125 subjects from two independent study cohorts to determine the levels in plasma (the most accessible specimen) of two essential mitochondrial markers acetyl-L-carnitine (LAC) and its derivative free-carnitine motivated by a mechanistic model in rodents in which targeting mitochondrial metabolism of LAC leads to the amelioration of cognitive function and boosts epigenetic mechanisms of gene expression.

QRFP43 modulates the activity of the hypothalamic-pituitary-thyroid axis in female sheep.

Since the early discovery of QRFP43, intensive research has been primarily focused on its role in the modulation of food intake. As is widely recognised, the regulation of the body's energy status is a highly complex process involving numerous systems, hormones and neurotransmitters. Among the most important regulators of energy status, alongside the satiety and hunger centre located in the hypothalamus, is the HPT axis, which directly and indirectly affects the regulation of metabolism in all cells of the body.

Eutrophication triggered changes in network structure and fluxes of the Comacchio Lagoon (Italy).

Coastal lagoons, which cover about 13% of coastline, are among the most productive ecosystems worldwide. However, they are subject to significant stressors, both natural and anthropogenic, which can alter ecosystem services and functioning and food web structure. In the Comacchio Lagoon (Northern Italy), eutrophication, among other minor factors, transformed the ecosystem in the early 1980s.

tomoseqr: A Bioconductor package for spatial reconstruction and visualization of 3D gene expression patterns based on RNA tomography.

RNA tomography computationally reconstructs 3D spatial gene expression patterns genome-widely from 1D tomo-seq data, generated by RNA sequencing of cryosection samples along three orthogonal axes. We developed tomoseqr, an R package designed for RNA tomography analysis of tomo-seq data, to reconstruct and visualize 3D gene expression patterns through user-friendly graphical interfaces. We show the effectiveness of tomoseqr using simulated and real tomo-seq data, validating its utility for researchers.

Comparing subsampling strategies for metagenomic analysis in microbial studies using amplicon sequence variants versus operational taxonomic units.

The microbiome is increasingly regarded as a key component of human health, and analysis of microbiome data can aid in the development of precision medicine. Due to the high cost of shotgun metagenomic sequencing (SM-seq), microbiome analyses can be done cost-effectively in two phases: Phase 1-sequencing of 16S ribosomal RNA, and Phase 2-SM-seq of an informative subsample. Existing research suggests strategies to select the subsample based on biological diversity and dissimilarity metrics calculated using operational taxonomic units (OTUs).

Genomic evidence of improved fertility and adaptation in Iranian domestic sheep attributed to introgression from Asiatic Mouflon and urial.

Due to the diverse climate in Iran, there has been an opportunity for the emergence of different domestic sheep breeds. On the other hand, two of the seven wild sheep species have settled in the broad areas of Iran. This study investigated the introgression between wild and domestic Iranian sheep using the whole genome sequencing data for 55 domestic and 19 wild sheep.

Exploring lipidome mediated inflammatory pathways in acute pancreatitis using mendelian randomization.

Acute pancreatitis (AP) is a severe gastrointestinal condition with an increasing incidence of hyperlipidemic etiology. The investigation employed a two-sample, bidirectional Mendelian randomization method to investigate potential causal relationship between lipidome profiles, inflammatory mediators, and AP. Exploration of genetic variants across the genome in a study population of 10,630 AP cases and 844,679 non-AP individuals revealed multiple lipidome entities significantly associated with AP risk.

Identifying representative sequences of protein families using submodular optimization.

Identifying representative sequences for groups of functionally similar proteins and enzymes poses significant computational challenges. In this study, we applied submodular optimization, a method effective in data summarization, to select representative sequences for thioesterase enzyme families. We introduced and validated two algorithms, Greedy and Bidirectional Greedy, using curated protein sequence data from the ThYme (Thioester-active enzYmes) database.

The pathomechanism of bone marrow edema in the femoral head necrosis with pericollapse stage.

Bone marrow edema (BME), a notable manifestation during the progression of osteonecrosis of the femoral head (ONFH), exhibits significant associations with femoral head collapse, pain, and prognosis, howeverits' pathogenesis remains underexplored. In this study, specimens from patients undergoing total hip arthroplasty (THA) were analyzed. The results revealed significantly higher Visual Analog Scale (VAS) scores and CT low-density area ratio in the BME group compared to the control group.

Activity of the mammalian DNA transposon piggyBat from Myotis lucifugus is restricted by its own transposon ends.

Members of the piggyBac superfamily of DNA transposons are widely distributed in host genomes ranging from insects to mammals. The human genome has retained five piggyBac-derived genes as domesticated elements although they are no longer mobile. Here, we have investigated the transposition properties of piggyBat from Myotis lucifugus, the only known active mammalian DNA transposon, and show that its low activity in human cells is due to subterminal inhibitory DNA sequences.

Speciation and historical invasions of the Asian black-spined toad (Duttaphrynus melanostictus).

Animal translocations provide striking examples of the human footprint on biodiversity. Combining continental-wide genomic and DNA-barcoding analyses, we reconstructed the historical biogeography of the Asian black-spined toad (Duttaphrynus melanostictus), a toxic commensal amphibian that currently threatens two biodiversity hotspots through biological invasions (Wallacea and Madagascar). The results emphasize a complex diversification shaped by speciation and mitochondrial introgression that comprises two distinct species.

Mitochondria- and ER-associated actin are required for mitochondrial fusion.

Mitochondria are crucial for cellular metabolism and signalling. Mitochondrial activity is modulated by mitochondrial fission and fusion, which are required to properly balance metabolic functions, transfer material between mitochondria, and remove defective mitochondria. Mitochondrial fission occurs at mitochondria-endoplasmic reticulum (ER) contact sites, and requires the formation of actin filaments that drive mitochondrial constriction and the recruitment of the fission protein DRP1.

Comprehensive analysis of LMNB2 in pan-cancer and identification of its biological role in sarcoma.

Backgrounds: Sarcoma (SARC) is a mesenchymal tumor which often responds poorly to systemic therapy. It is therefore important to look for possible biological markers that could tell the prognosis and the progression of SARC.

Methods: A combined evaluation of the Cancer Genome Atlas (TCGA) and genotypic tissue expression (GTEx) portal was used to analyzeLMNB2 expression level in different types of cancer.

Endothelial-secreted Endocan activates PDGFRA and regulates vascularity and spatial phenotype in glioblastoma.

Extensive neovascularization is a hallmark of glioblastoma (GBM). In addition to supplying oxygen and nutrients, vascular endothelial cells provide trophic support to GBM cells via paracrine signaling. Here we report that Endocan (ESM1), an endothelial-secreted proteoglycan, confers enhanced proliferative, migratory, and angiogenic properties to GBM cells and regulates their spatial identity.

In vitro biological evaluation of silver nanoparticles synthesized using zingiber officinale and ocimum gratissimum herbal formulation.

Introduction: The biomedical potential of silver nanoparticles (Ag NPs) synthesized with Zingiber officinale and Ocimum gratissimum herbal formulation was investigated in this study. The study aims to reveal their applications in various biomedical fields. The study evaluates the antioxidant, thrombolytic, and antimicrobial potential of Zingiber officinale and Ocimum gratissimum herbal formulation-mediated Ag NPs.

Combined single-photon emission computed tomography-myocardial perfusion imaging with coronary calcium score for assessing coronary disease.

Purpose: Coronary artery disease (CAD) underestimation represents a major pitfall of single-photon emission computed tomography-myocardial perfusion imaging (SPECT-MPI). Coronary artery calcium score (CACS) has emerged as a sensitive tool for the assessment of suspect CAD; however, the integration of SPECT-MPI with CACS has been seldom evaluated, so far, and was therefore the aim of the present study.

Methods: Patients undergoing SPECT-MPI with CACS and subsequent coronary angiography were included.

A review of optical and thermal eye tissue parameters for improved computational models in retinal laser therapy.

Laser surgery is recognized as a highly effective method for managing retinal diseases. However, the thermal effects of the laser on different eye tissues are not entirely understood yet. In this context, computational modeling can be a useful tool to predict therapy outcomes.