Exploration of the genetic landscape of bacterial dsDNA viruses reveals an ANI gap amid extensive mosaicism.

Average nucleotide identity (ANI) is a widely used metric to estimate genetic relatedness, especially in microbial species delineation. While ANI calculation has been well optimized for bacteria and closely related viral genomes, accurate estimation of ANI below 80%, particularly in large reference data sets, has been challenging due to a lack of accurate and scalable methods. To bridge this gap, we introduce MANIAC, an efficient computational pipeline optimized for estimating ANI and alignment fraction (AF) in viral genomes with divergence around ANI of 70%.

The cell colony development is connected with the accumulation of embryogenesis-related proteins and dynamic distribution of cell wall components in in vitro cultures of Fagopyrum tataricum and Fagopyrum esculentum.

Background: Due to the totipotency of plant cells, which allows them to reprogram from a differentiated to a dedifferentiated state, plants exhibit a remarkable regenerative capacity, including under in vitro culture conditions. When exposed to plant hormones, primarily auxins and cytokinins, explant cells cultured in vitro can undergo differentiation through callus formation. Protoplast culture serves as a valuable research model for studying these processes in detail.

Efficacy of Rose Stem Cell-Derived Exosomes (RSCEs) in Skin Treatment: From Healing to Hyperpigmentation Management: Case Series and Review.

Objective: To present and analyze eight clinical cases illustrating the use of rose stem cell-derived exosomes (RSCEs) in treating various dermatological conditions and to review current literature on plant-derived exosomes in medicine and dermatology.

Background: RSCEs possess low cytotoxicity, high biocompatibility, and effective cellular uptake, making them promising agents for dermatological therapies. A literature review included in the introduction and discussion covers the broader role of plant-derived exosomes, highlighting their therapeutic potential in skin treatment.

The endonuclease activity of MCPIP1 controls the neoplastic transformation of epithelial cells via the c-Met/CD44 axis.

The RNase activity of MCPIP1 is essential for regulating cellular homeostasis, proliferation, and tumorigenesis. Our study elucidates the effects of downregulation of MCPIP1 expression and an RNase-inactivating mutation (D141N) on normal epithelial kidney cells, indicating that MCPIP1 expression is a key factor that suppresses neoplastic transformation. We observed that either expression downregulation or mutation of MCPIP1 significantly increased its clonogenicity and altered the expression of cancer stem cell (CSC) markers and factors involved in epithelial-to-mesenchymal transition (EMT).

The structural biology of deoxyhypusination complexes.

Deoxyhypusination is the first rate-limiting step of the unique post-translational modification-hypusination-that is catalyzed by deoxyhypusine synthase (DHS) and deoxyhypusine hydroxylase (DOHH). This modification is essential for the activation of translation factor 5A in eukaryotes (eIF5A) and Archaea (aIF5A). This perspective focuses on the structural biology of deoxyhypusination complexes in eukaryotic and archaeal organisms.

Effects of data transformation and model selection on feature importance in microbiome classification data.

Background: Accurate classification of host phenotypes from microbiome data is crucial for advancing microbiome-based therapies, with machine learning offering effective solutions. However, the complexity of the gut microbiome, data sparsity, compositionality, and population-specificity present significant challenges. Microbiome data transformations can alleviate some of the aforementioned challenges, but their usage in machine learning tasks has largely been unexplored.

LCRAnnotationsDB: a database of low complexity regions functional and structural annotations.

Low Complexity Regions (LCRs) are segments of proteins with a low diversity of amino acid composition. These regions play important roles in proteins. However, annotations describing these functions are dispersed across databases and scientific literature.

Chromosome-scale assembly of the African yam bean genome.

Genomics-informed breeding of locally adapted, nutritious, albeit underutilised African crops can help mitigate food and nutrition insecurity challenges in Africa, particularly against the backdrop of climate change. However, utilisation of modern genome-assisted crop improvement tools including genomic selection and genome editing for many African indigenous crops is hampered by the scarcity of genomic resources. Here we report on the assembly of the genome of African yam bean (Sphenostylis stenocarpa), a tuberous legume crop that is indigenous to Africa.

Designed, Programmable Protein Cages Utilizing Diverse Metal Coordination Geometries Show Reversible, pH-Dependent Assembly.

The rational design and production of a novel series of engineered protein cages are presented, which have emerged as versatile and adaptable platforms with significant applications in biomedicine. These protein cages are assembled from multiple protein subunits, and precise control over their interactions is crucial for regulating assembly and disassembly, such as the on-demand release of encapsulated therapeutic agents. This approach employs a homo-undecameric, ring-shaped protein scaffold with strategically positioned metal binding sites.

Molecular basis for thiocarboxylation and release of Urm1 by its E1-activating enzyme Uba4.

Ubiquitin-related modifier 1 (Urm1) is a highly conserved member of the ubiquitin-like (UBL) family of proteins. Urm1 is a key component of the eukaryotic transfer RNA (tRNA) thiolation cascade, responsible for introducing sulfur at wobble uridine (U34) in several eukaryotic tRNAs. Urm1 must be thiocarboxylated (Urm1-SH) by its E1 activating enzyme UBL protein activator 4 (Uba4).

Optimization of Selection Agent Concentrations and Expanding G418 Utility for Gentamicin Resistance in Marchantia polymorpha.

Genetic transformation of plants is pivotal for advancing biotechnology, with success depending largely on effective selection methods. has emerged as a model plant due to its evolutionary importance, ease of manipulation, and simple genetic structure. However, inconsistent antibiotic performance and limited studies on optimal selection agent concentrations have posed challenges.

Structural basis of chiral wrap and T-segment capture by DNA gyrase.

Type II topoisomerase DNA gyrase transduces the energy of ATP hydrolysis into the negative supercoiling of DNA. The postulated catalytic mechanism involves stabilization of a chiral DNA loop followed by the passage of the T-segment through the temporarily cleaved G-segment resulting in sign inversion. The molecular basis for this is poorly understood as the chiral loop has never been directly observed.

Development of selective ssDNA micro-probe for PD1 detection as a novel strategy for cancer imaging.

Programmed death receptor 1, PD1, modulates the function of immune cells by providing inhibitory signals and constitutes the marker of immune exhaustion. Monitoring the level of PD1 promises a useful diagnostic approach in autoimmune diseases and cancer. Here we describe the development of an ssDNA aptamer-based molecular probe capable of specific recognition of human PD1 receptor.

Distinguishable topology of the task-evoked functional genome networks in HIV-1 reservoirs.

HIV-1 reservoirs display a heterogeneous nature, lodging both intact and defective proviruses. To deepen our understanding of such heterogeneous HIV-1 reservoirs and their functional implications, we integrated basic concepts of graph theory to characterize the composition of HIV-1 reservoirs. Our analysis revealed noticeable topological properties in networks, featuring immunologic signatures enriched by genes harboring intact and defective proviruses, when comparing antiretroviral therapy (ART)-treated HIV-1-infected individuals and elite controllers.

RNA sample optimization for cryo-EM analysis.

RNAs play critical roles in most biological processes. Although the three-dimensional (3D) structures of RNAs primarily determine their functions, it remains challenging to experimentally determine these 3D structures due to their conformational heterogeneity and intrinsic dynamics. Cryogenic electron microscopy (cryo-EM) has recently played an emerging role in resolving dynamic conformational changes and understanding structure-function relationships of RNAs including ribozymes, riboswitches and bacterial and viral noncoding RNAs.

Refined Protein-Sugar Interactions in the Martini Force Field.

Sugar molecules play important roles as mediators of biomolecular interactions in cellular functions, disease, and infections. Molecular dynamics simulations are an indispensable tool to explore these interactions at the molecular level. The large time and length scales involved frequently necessitate the use of coarse-grained representations, which heavily depend on the parametrization of sugar-protein interactions.

New insights in the mechanism of the SARS-CoV-2 M inhibition by benzisoselenazolones and diselenides.

Although global vaccination campaigns alleviated the SARS-CoV-2 pandemic in terms of morbidity and mortality, the ability of the virus to originate mutants may reduce the efficacy of vaccines, posing a serious risk of a renewed pandemic. There is therefore a need to develop small molecules capable of targeting conserved viral targets, such as the main protease (M). Here, a series of benzisoselenazolones and diselenides were tested for their ability to inhibit M; then the most potent compounds were measured for antiviral activity in vitro, and the mechanism of action was investigated.

DNA methylation at AHRR as a master predictor of smoke exposure and a biomarker for sleep and exercise.

Background: DNA methylation profiling may provide a more accurate measure of the smoking status than self-report and may be useful in guiding clinical interventions and forensic investigations. In the current study, blood DNA methylation profiles of nearly 800 Polish individuals were assayed using Illuminia EPIC and the inference of smoking from epigenetic data was explored. In addition, we focused on the role of the AHRR gene as a top marker for smoking and investigated its responsiveness to other lifestyle behaviors.

Unravelling the potential of yolkin for nutraceutical use: the origin, structure, and functional insights of a hen egg yolk polypeptide complex.

Nutraceuticals can reduce the risk of many diseases, such as cardiovascular disease, immune deficiencies, neurodegeneration, and others. Their delivery remains a challenge because it depends on many factors, most notably the stability of the bioactive compounds. Yolkin is a peptide complex isolated from hen egg yolk with immunomodulatory and neuroprotective potential.

ERK1/2 interaction with DHPS regulates eIF5A deoxyhypusination independently of ERK kinase activity.

This study explores a non-kinase effect of extracellular regulated kinases 1/2 (ERK1/2) on the interaction between deoxyhypusine synthase (DHPS) and its substrate, eukaryotic translation initiation factor 5A (eIF5A). We report that Raf/MEK/ERK activation decreases the DHPS-ERK1/2 interaction while increasing DHPS-eIF5A association in cells. We determined the cryoelectron microscopy (cryo-EM) structure of the DHPS-ERK2 complex at 3.

Female-age-dependent changes in the lipid fingerprint of the mammalian oocytes.

Study Question: Can oocyte functionality be assessed by observing changes in their intracytoplasmic lipid droplets (LDs) profiles?

Summary Answer: Lipid profile changes can reliably be detected in human oocytes; lipid changes are linked with maternal age and impaired developmental competence in a mouse model.

What Is Known Already: In all cellular components, lipid damage is the earliest manifestation of oxidative stress (OS), which leads to a cascade of negative consequences for organelles and DNA. Lipid damage is marked by the accumulation of LDs.

Adaptation to space conditions of novel bacterial species isolated from the International Space Station revealed by functional gene annotations and comparative genome analysis.

Background: The extreme environment of the International Space Station (ISS) puts selective pressure on microorganisms unintentionally introduced during its 20+ years of service as a low-orbit science platform and human habitat. Such pressure leads to the development of new features not found in the Earth-bound relatives, which enable them to adapt to unfavorable conditions.

Results: In this study, we generated the functional annotation of the genomes of five newly identified species of Gram-positive bacteria, four of which are non-spore-forming and one spore-forming, all isolated from the ISS.

Molecular basis of plastoquinone reduction in plant cytochrome bf.

A multi-subunit enzyme, cytochrome bf (cytbf), provides the crucial link between photosystems I and II in the photosynthetic membranes of higher plants, transferring electrons between plastoquinone (PQ) and plastocyanin. The atomic structure of cytbf is known, but its detailed catalytic mechanism remains elusive. Here we present cryogenic electron microscopy structures of spinach cytbf at 1.