Morphogenesis of Aragonite Biomineral Structures by the Nonclassical Colloidal Crystal Growth Mechanism Revisited on the Nanoscale: The Noah's Ark Shell (, L.) Case Study.

Characterization and formation of the biomineral aragonite structures of the Noah's Ark shell ( L.,1758) were studied from structural, morphogenetic, and biochemical points of view. Structural and morphological features were examined using X-ray diffraction, field-emission scanning electron microscopy, and atomic force microscopy, while thermal properties were determined by thermogravimetric and differential thermal analyses.

An alternative approach to biokinetic modelling for phenol pollutant degradation and microbial growth using Genetic Programming.

Biokinetic models can optimise pollutant degradation and enhance microbial growth processes, aiding to protect ecosystem protection. Traditional biokinetic approaches (such as Monod, Haldane, etc.) can be challenging, as they require detailed knowledge of the organism's metabolism and the ability to solve numerous kinetic differential equations based on the principles of micro, molecular biology and biochemistry (first engineering principles) which can lead to discrepancies between predicted and actual degradation rates.

Sequence-based Identification of Polyamine Oxidase Genes in Sorghum bicolor L.

Polyamine oxidase (PAOs) are enzymes associated with polyamine catabolism and play important roles in growth and development and stress tolerance of plants. In the present study, genome-wide discovery and analysis of the PAO family in sorghum was done utilizing model PAO of Arabidopsis. Six PAO genes were found using publicly available genomic data.

Oral Regimens for Rifampin-Resistant, Fluoroquinolone-Susceptible Tuberculosis.

Background: For decades, poor treatment options and low-quality evidence plagued care for patients with rifampin-resistant tuberculosis. The advent of new drugs to treat tuberculosis and enhanced funding now permit randomized, controlled trials of shortened-duration, all-oral treatments for rifampin-resistant tuberculosis.

Methods: We conducted a phase 3, multinational, open-label, randomized, controlled noninferiority trial to compare standard therapy for treatment of fluoroquinolone-susceptible, rifampin-resistant tuberculosis with five 9-month oral regimens that included various combinations of bedaquiline (B), delamanid (D), linezolid (L), levofloxacin (Lfx) or moxifloxacin (M), clofazimine (C), and pyrazinamide (Z).

Helping authors produce FAIR taxonomic data: evaluation of an author-driven phenotype data production prototype.

It is well-known that the use of vocabulary in phenotype treatments is often inconsistent. An earlier survey of biologists who create or use phenotypic characters revealed that this lack of standardization leads to ambiguities, frustrating both the consumers and producers of phenotypic data. Such ambiguities are challenging for biologists, and more so for Artificial Intelligence, to resolve.

Chromosome length genome assembly of the stone marten (Martes foina, Mustelidae): a new view on one of the cornerstones in carnivore cytogenetics.

The stone marten (Martes foina) is an important species for cytogenetic studies in the order Carnivora. ZooFISH probes created from its chromosomes provided a strong and clean signal in chromosome painting experiments and were valuable for studying the evolution of carnivoran genome architecture. The research revealed that the stone marten chromosome set is similar to the presumed ancestral karyotype of the Carnivora, which added an additional value for the species.

Fatuamide A, a Hybrid PKS/NRPS Metallophore from a sp. Marine Cyanobacterium Collected in American Samoa.

A structurally novel metabolite, fatuamide A (), was discovered from a laboratory cultured strain of the marine cyanobacterium sp., collected from Faga'itua Bay, American Samoa. A bioassay-guided approach using NCI-H460 human lung cancer cells directed the isolation of fatuamide A, which was obtained from the most cytotoxic fraction.

Study of the role of transmembrane emp24 domain-containing protein 2 in oral squamous cell carcinoma.

Objective: This study aimed to investigate the role of transmembrane emp24 domain-containing protein 2 (TMED2) in oral squamous cell carcinoma (OSCC).

Methodology: A bioinformatics analysis was first conducted to explore TMED2 expression in OSCC and its relation with overall survival. The analysis results were further verified by assessing TMED2 expression levels in human normal oral keratinocyte cells and human OSCC cell lines using quantitative real-time polymerase chain reaction and the Western blot.

Classification-based pathway analysis using GPNet with novel P-value computation.

Pathway analysis plays a critical role in bioinformatics, enabling researchers to identify biological pathways associated with various conditions by analyzing gene expression data. However, the rise of large, multi-center datasets has highlighted limitations in traditional methods like Over-Representation Analysis (ORA) and Functional Class Scoring (FCS), which struggle with low signal-to-noise ratios (SNR) and large sample sizes. To tackle these challenges, we use a deep learning-based classification method, Gene PointNet, and a novel $P$-value computation approach leveraging the confusion matrix to address pathway analysis tasks.

Inferring the genetic relationships between unsupervised deep learning-derived imaging phenotypes and glioblastoma through multi-omics approaches.

This study aimed to investigate the genetic association between glioblastoma (GBM) and unsupervised deep learning-derived imaging phenotypes (UDIPs). We employed a combination of genome-wide association study (GWAS) data, single-nucleus RNA sequencing (snRNA-seq), and scPagwas (pathway-based polygenic regression framework) methods to explore the genetic links between UDIPs and GBM. Two-sample Mendelian randomization analyses were conducted to identify causal relationships between UDIPs and GBM.

SAMURAI: shallow analysis of copy number alterations using a reproducible and integrated bioinformatics pipeline.

Shallow whole-genome sequencing (sWGS) offers a cost-effective approach to detect copy number alterations (CNAs). However, there remains a gap for a standardized workflow specifically designed for sWGS analysis. To address this need, in this work we present SAMURAI, a bioinformatics pipeline specifically designed for analyzing CNAs from sWGS data in a standardized and reproducible manner.

Recalibrating Protection Factors Using Millisecond Hydrogen/Deuterium Exchange Mass Spectrometry.

Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a powerful technique to interrogate protein structure and dynamics. With the ability to study almost any protein without a size limit, including intrinsically disordered ones, HDX-MS has shown fast growing importance as a complement to structural elucidation techniques. Current experiments compare two or more related conditions (sequences, interaction partners, excipients, conformational states, etc.

Role of the Mobile Active Site Flap in IMP Dehydrogenase Inhibitor Binding.

Inosine 5'-monophosphate dehydrogenase (IMPDH) is a promising antibiotic target. This enzyme catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5'-monophosphate (XMP), which is the rate-limiting step in guanine nucleotide biosynthesis. Bacterial IMPDH-specific inhibitors have been developed that bind to the NAD site.

Undocking of an extensive ciliary network induces proteostasis and cell fate switching resulting in severe primary ciliary dyskinesia.

Primary ciliary dyskinesia is a rare monogenic syndrome that is associated with chronic respiratory disease, infertility, and laterality defects. Although more than 50 genes causative of primary ciliary dyskinesia have been identified, variants in the genes encoding coiled-coil domain-containing 39 (CCDC39) and CCDC40 in particular cause severe disease that is not explained by loss of ciliary motility alone. Here, we sought to understand the consequences of these variants on cellular functions beyond impaired motility.

Correcting a pathogenic mitochondrial DNA mutation by base editing in mice.

Primary mitochondrial disorders are most often caused by deleterious mutations in the mitochondrial DNA (mtDNA). Here, we used a mitochondrial DddA-derived cytosine base editor (DdCBE) to introduce a compensatory edit in a mouse model that carries the pathological mutation in the mitochondrial transfer RNA (tRNA) alanine (mt-tRNA) gene. Because the original m.

Prior vaccination prevents overactivation of innate immune responses during COVID-19 breakthrough infection.

At this stage in the COVID-19 pandemic, most infections are "breakthrough" infections that occur in individuals with prior severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exposure. To refine long-term vaccine strategies against emerging variants, we examined both innate and adaptive immunity in breakthrough infections. We performed single-cell transcriptomic, proteomic, and functional profiling of primary and breakthrough infections to compare immune responses from unvaccinated and vaccinated individuals during the SARS-CoV-2 Delta wave.

Climate change aggravates bird mortality in pristine tropical forests.

Stable understory microclimates within undisturbed rainforests are often considered refugia against climate change. However, this assumption contrasts with emerging evidence of Neotropical bird population declines in intact rainforests. We assessed the vulnerability of resident rainforest birds to climatic variability, focusing on dry season severity characterized by hotter temperatures and reduced rainfall.

Epstein-Barr virus-driven cardiolipin synthesis sustains metabolic remodeling during B cell transformation.

The Epstein-Barr virus (EBV) infects nearly 90% of adults globally and is linked to over 200,000 annual cancer cases. Immunocompromised individuals from conditions such as primary immune disorders, HIV, or posttransplant immunosuppressive therapies are particularly vulnerable because of EBV's transformative capability. EBV remodels B cell metabolism to support energy, biosynthetic precursors, and redox equivalents necessary for transformation.

Ketogenesis supports hepatic polyunsaturated fatty acid homeostasis via fatty acid elongation.

Ketogenesis is a dynamic metabolic conduit supporting hepatic fat oxidation particularly when carbohydrates are in short supply. Ketone bodies may be recycled into anabolic substrates, but a physiological role for this process has not been identified. Here, we use mass spectrometry-based C-isotope tracing and shotgun lipidomics to establish a link between hepatic ketogenesis and lipid anabolism.

Parasitoid wasp venoms degrade imaginal discs for successful parasitism.

Parasitoid wasps, one of the most diverse and species-rich animal groups on Earth, produce venoms that manipulate host development and physiology to exploit resources. However, mechanisms of actions of these venoms remain poorly understood. Here, we discovered that the endoparasitoid wasp, , induces apoptosis, autophagy, and mitotic arrest in the adult tissue precursors of its host larvae.

A multi-analytical study of the Montelirio beaded attires: Marine resources, sumptuary crafts, and female power in copper age Iberia.

Excellent indicators of technology, social organization, exchange patterns, and even beliefs, beads are a topic of research in their own right. Findings made between 2010 and 2011 at the Montelirio tholos burial, part of the Valencina Copper Age mega-site, in south-western Spain, revealed what amounts to the largest single-burial ever-documented assemblage of beads. Furthermore, the Montelirio beads were part of unparalleled beaded attires worn by some of the people buried in the grave, mostly females.

Vascularization of human islets by adaptable endothelium for durable and functional subcutaneous engraftment.

Tissue-specific endothelial cells (ECs) are critical for the homeostasis of pancreatic islets and most other tissues. In vitro recapitulation of islet biology and therapeutic islet transplantation both require adequate vascularization, which remains a challenge. Using human reprogrammed vascular ECs (R-VECs), human islets were functionally vascularized in vitro, demonstrating responsive, dynamic glucose-stimulated insulin secretion and Ca influx.

Spherical harmonics texture extraction for versatile analysis of biological objects.

The characterization of phenotypes in cells or organisms from microscopy data largely depends on differences in the spatial distribution of image intensity. Multiple methods exist for quantifying the intensity distribution - or image texture - across objects in natural images. However, many of these texture extraction methods do not directly adapt to 3D microscopy data.