Discovering novel type I collagen fragments from Cyprinus carpio supporting bone regeneration.

Fish collagen is gaining increasing attention in tissue engineering due to its exceptional bioactivity. This study aimed to isolate functional fish collagen fragments capable of microbial biosynthesis and supporting bone tissue regeneration. Collagen fragments of 150 amino acids were extracted from Cyprinus carpio collagen I (CcCOL1), and their bioactivity, net charge, and hydrophobicity were calculated and analyzed for correlations, these physicochemical and sequential features were using to train the machine learning model, which classified the fragments into three subgroups.

Accelerating promoter identification and design by deep learning.

Promoters are DNA sequences that govern the location, direction, and strength of gene transcription, playing a pivotal role in cellular growth and lifespan. Engineered promoters facilitate precise control of recombinant protein expression and metabolic pathway modulation for natural product biosynthesis. Traditional methods such as rational design and directed evolution have established the foundation for promoter engineering, and recent advances in deep learning (DL) have revolutionized the field.

Discovering novel transglutaminases from Streptomyces species for efficient protein cross-linking in foods.

Transglutaminase (TG) is a key enzyme in food processing by catalyzing protein crosslinking. This study identified novel hyperactive TGs from Streptomyces species to enhance crosslinking efficiency. We integrated phylogenetic analysis for initial screening, followed by virtual docking for further selection.

Machine learning model for differentiating malignant from benign thyroid nodules based on the thyroid function data.

Objectives: To develop and validate a machine learning (ML) model to differentiate malignant from benign thyroid nodules (TNs) based on the routine data and provide diagnostic assistance for medical professionals.

Setting: A qualified panel of 1649 patients with TNs from one hospital were stratified by gender, age, free triiodothyronine (FT3), free thyroxine (FT4) and thyroid peroxidase antibody (TPOAB).

Participants: Thyroid function (TF) data of 1649 patients with TNs were collected in a single centre from January 2018 to June 2022, with a total of 273 males and 1376 females, respectively.

Engineering an Autolytic System for Overexpression of a Collagen-Mimetic Peptide with Enhanced Hemostatic Activity.

We previously identified that the collagen mimetic peptide (CMP)-E3 is sufficient to induce in vitro blood clotting. In this study, we further demonstrated its ability to induce in vivo blood coagulation through a rat tail bleeding assay. However, intracellular expression of CMP-E3 negatively impacted growth, causing cell density to fluctuate within an optical density at 600 nm (OD) range of 1.

A safety and absolute activity measurement method for Phi29 DNA polymerase based on chemiluminescent detection of dATP consumption.

Background: Phi29 DNA polymerase serves as a cornerstone enzyme in molecular biology, enabling critical applications such as rolling-circle amplification, multiple strand-displacement amplification, and single-molecule real-time sequencing. Despite its widespread use, traditional methods for assessing its activity-including radioactive labeling and fluorescence-based quantification-suffer from limitations such as operational complexity, low precision, and safety risks. These challenges have hindered standardized quality control in both academic and industrial settings.

Epimedii Folium decoction ameliorates osteoporosis in mice through NLRP3/caspase-1/IL-1β signalling pathway and gut-bone axis.

Aim Of The Study: This study aimed to determine the effect of Epimedium brevicornu Maxim. (EF) on osteoporosis (OP) and its underlying molecular mechanisms, and to explore the existence of the "Gut-Bone Axis".

Material And Methods: The impact of EF decoction (EFD) on OP was evaluated using istopathological examination and biochemical assays.

Single-cell phylotranscriptomics of developmental and cell type evolution.

Single-cell phylotranscriptomics is an emerging tool to reveal the molecular and cellular mechanisms of evolution. We summarize its utility in studying the hourglass pattern of ontogenetic evolution and for understanding the evolutionary history of cell types. The developmental hourglass model suggests that the mid-embryonic stage is the most conserved period of development across species, which is supported by morphological and molecular studies.

Young duplicate genes show developmental stage- and cell type-specific expression and function in Caenorhabditis elegans.

Gene duplication produces the material that fuels evolutionary innovation. The "out-of-testis" hypothesis suggests that sperm competition creates selective pressure encouraging the emergence of new genes in male germline, but the somatic expression and function of the newly evolved genes are not well understood. We systematically mapped the expression of young duplicate genes throughout development in Caenorhabditis elegans using both whole-organism and single-cell transcriptomic data.

NADH-dependent formate dehydrogenase mutants for efficient carbon dioxide fixation.

Bioconversion of CO to high-valuable products is a globally pursued sustainable technology for carbon neutrality. However, low CO activation with formate dehydrogenase (FDH) remains a major challenge for further upcycling due to the poor CO affinity, reduction activity and stability of currently used FDHs. Here, we present two recombined mutants, ΔFDHPa48 and ΔFDHPa4814, which exhibit high CO reduction activity and antioxidative activity.

[Advances in methods and applications of single-cell Hi-C data analysis].

Chromatin three-dimensional genome structure plays a key role in cell function and gene regulation. Single-cell Hi-C techniques can capture genomic structure information at the cellular level, which provides an opportunity to study changes in genomic structure between different cell types. Recently, some excellent computational methods have been developed for single-cell Hi-C data analysis.

Interpretable machine-learning model for Predicting the Convalescent COVID-19 patients with pulmonary diffusing capacity impairment.

Introduction: The COVID-19 patients in the convalescent stage noticeably have pulmonary diffusing capacity impairment (PDCI). The pulmonary diffusing capacity is a frequently-used indicator of the COVID-19 survivors' prognosis of pulmonary function, but the current studies focusing on prediction of the pulmonary diffusing capacity of these people are limited. The aim of this study was to develop and validate a machine learning (ML) model for predicting PDCI in the COVID-19 patients using routinely available clinical data, thus assisting the clinical diagnosis.

A 3-D Chromosome Structure Reconstruction Method With High Resolution Hi-C Data Using Nonlinear Dimensionality Reduction and Divide-and-Conquer Strategy.

Chromosomes are fundamental components of genetic material, and their structural characteristics play an essential role in the regulation of gene expression. The advent of high-resolution Hi-C data has enabled scientists to explore the three-dimensional structure of chromosomes. However, most of the currently available methods for reconstructing chromosome structures are unable to achieve high resolutions, such as 5 Kilobase (KB).

Fluorescence coupling strategies in fluorescence-activated droplet sorting (FADS) for ultrahigh-throughput screening of enzymes, metabolites, and antibodies.

Fluorescence-activated droplet sorting (FADS) has emerged as a powerful tool for ultrahigh-throughput screening of enzymes, metabolites, and antibodies. Fluorescence coupling strategies (FCSs) are key to the development of new FADS methods through their coupling of analyte properties such as concentration, activities, and affinity with fluorescence signals. Over the last decade, a series of FCSs have been developed, greatly expanding applications of FADS.

Transcriptome age of individual cell types in .

The phylotranscriptomic analysis of development in several species revealed the expression of older and more conserved genes in midembryonic stages and younger and more divergent genes in early and late embryonic stages, which supported the hourglass mode of development. However, previous work only studied the transcriptome age of whole embryos or embryonic sublineages, leaving the cellular basis of the hourglass pattern and the variation of transcriptome ages among cell types unexplored. By analyzing both bulk and single-cell transcriptomic data, we studied the transcriptome age of the nematode throughout development.

All-in-One Digital Microfluidics System for Molecular Diagnosis with Loop-Mediated Isothermal Amplification.

In this study, an "all-in-one" digital microfluidics (DMF) system was developed for automatic and rapid molecular diagnosis and integrated with magnetic bead-based nucleic acid extraction, loop-mediated isothermal amplification (LAMP), and real-time optical signal monitoring. First, we performed on- and off-chip comparison experiments for the magnetic bead nucleic acid extraction module and LAMP amplification function. The extraction efficiency for the on-chip test was comparable to that of conventional off-chip methods.

Incidence and affecting factors of pulmonary diffusing capacity impairment with COVID-19 survivors 18 months after discharge in Wuhan, China.

The Publisher regrets that this article is an accidental duplication of an article that has already been published, http://dx.doi.org/10.

Improved thermostability of proteinase K and recognizing the synergistic effect of Rosetta and FoldX approaches.

Proteinase K (PRK) is a proteolytic enzyme that has been widely used in industrial applications. However, poor stability has severely limited the uses of PRK. In this work, we used two structure-guided rational design methods, Rosetta and FoldX, to modify PRK thermostability.

Genome-wide screen identifies curli amyloid fibril as a bacterial component promoting host neurodegeneration.

Growing evidence indicates that gut microbiota play a critical role in regulating the progression of neurodegenerative diseases such as Parkinson's disease. The molecular mechanism underlying such microbe-host interaction is unclear. In this study, by feeding expressing human α-syn with knockout mutants, we conducted a genome-wide screen to identify bacterial genes that promote host neurodegeneration.

Dynamic global analysis of transcription reveals the role of miRNAs in synergistic stabilization of gene expression.

Buffering exogenous perturbation is crucial to maintain transcriptional homeostasis during development. While miRNAs have been speculated to play a role in stability maintenance, previous studies seeking to check this conjecture focused on measurements of transcript levels at steady state or involved individual miRNA targets. We measured whole-genome expression dynamics by introducing a transient perturbation and establishing a perturbation and recovery system in Drosophila larvae.

Improved thermostability of creatinase from Alcaligenes Faecalis through non-biased phylogenetic consensus-guided mutagenesis.

Background: Enzymatic quantification of creatinine has become an essential method for clinical evaluation of renal function. Although creatinase (CR) is frequently used for this purpose, its poor thermostability severely limits industrial applications. Herein, we report a novel creatinase from Alcaligenes faecalis (afCR) with higher catalytic activity and lower K value, than currently used creatinases.