Precision enzyme discovery through targeted mining of metagenomic data.

Metagenomics has opened new avenues for exploring the genetic potential of uncultured microorganisms, which may serve as promising sources of enzymes and natural products for industrial applications. Identifying enzymes with improved catalytic properties from the vast amount of available metagenomic data poses a significant challenge that demands the development of novel computational and functional screening tools. The catalytic properties of all enzymes are primarily dictated by their structures, which are predominantly determined by their amino acid sequences.

Lignocellulose degradation by rumen bacterial communities: New insights from metagenome analyses.

Ruminant animals house a dense and diverse community of microorganisms in their rumen, an enlarged compartment in their stomach, which provides a supportive environment for the storage and microbial fermentation of ingested feeds dominated by plant materials. The rumen microbiota has acquired diverse and functionally overlapped enzymes for the degradation of plant cell wall polysaccharides. In rumen Bacteroidetes, enzymes involved in degradation are clustered into polysaccharide utilization loci to facilitate coordinated expression when target polysaccharides are available.

Efficiency of an alkaline, thermostable, detergent compatible, and organic solvent tolerant lipase with hydrolytic potential in biotreatment of wastewater.

Discharging the tannery wastewater into the environment is a serious challenge worldwide due to the release of severe recalcitrant pollutants such as oil compounds and organic materials. The biological treatment through enzymatic hydrolysis is a cheap and eco-friendly method for eliminating fatty substances from wastewater. In this context, lipases can be utilized for bio-treatment of wastewater in multifaceted industrial applications.

Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation.

Understanding the genetic mechanisms of phenotypic variation in hybrids between domestic animals and their wild relatives may aid germplasm innovation. Here, we report the high-quality genome assemblies of a male Pamir argali ( , 2 = 56), a female Tibetan sheep ( , 2 = 54), and a male hybrid of Pamir argali and domestic sheep, and the high-throughput sequencing of 425 ovine animals, including the hybrids of argali and domestic sheep. We detected genomic synteny between Chromosome 2 of sheep and two acrocentric chromosomes of argali.

Functional and phylogenetic analyses of camel rumen microbiota associated with different lignocellulosic substrates.

Rumen microbiota facilitates nutrition through digestion of recalcitrant lignocellulosic substrates into energy-accessible nutrients and essential metabolites. Despite the high similarity in rumen microbiome structure, there might be distinct functional capabilities that enable different ruminant species to thrive on various lignocellulosic substrates as feed. Here, we applied genome-centric metagenomics to explore phylogenetic diversity, lignocellulose-degrading potential and fermentation metabolism of biofilm-forming microbiota colonizing 11 different plant substrates in the camel rumen.

Microwave-Assisted Synthesis of Silver Nanoparticles for Multimode Colorimetric Sensing of Multiplex Metal Ions and Molecular Informatization Applications.

Plasmonic materials have been widely used in chemo/biosensing and biomedicine. However, little attention has been paid to the application of plasmonic materials in terms of the transition from molecular sensing to molecular informatization. Herein, we demonstrated that silver nanoparticles (AgNPs) prepared through facile and rapid microwave heating have multimode colorimetric sensing capabilities to different metal ions (Cr, Hg, and Ni), which can be further transformed into interesting and powerful molecular information technology (massively parallel molecular logic computing and molecular information protection).

Dynamics of rumen bacterial composition of yak () in response to dietary supplements during the cold season.

This study aimed to explore the rumen bacterial community of yak in response to dietary supplements during the cold season. In addition, the rumen fermentation products were also analyzed. Twenty-one female domestic yaks were randomly divided into three groups i.

Diversity of microbes colonizing forages of varying lignocellulose properties in the sheep rumen.

Background: The rumen microbiota contributes strongly to the degradation of ingested plant materials. There is limited knowledge about the diversity of taxa involved in the breakdown of lignocellulosic biomasses with varying chemical compositions in the rumen.

Method: We aimed to assess how and to what extent the physicochemical properties of forages influence the colonization and digestion by rumen microbiota.

MicroRNAome: Potential and Veritable Immunomolecular Therapeutic and Diagnostic Baseline for Lingering Bovine Endometritis.

The bovine endometrium is a natural pathogen invasion barrier of the uterine tissues' endometrial epithelial cells that can resist foreign pathogen invasion by controlling the inflammatory immune response. Some pathogens suppress the innate immune system of the endometrium, leading to prolonged systemic inflammatory response through the blood circulation or cellular degradation resulting in bovine endometritis by bacterial endotoxins. The microRNA (miRNA) typically involves gene expression in multicellular organisms in post-transcription regulation by affecting both the stability and the translation of messenger RNA.

Serum Metabolomics Revealed the Differential Metabolic Pathway in Calves with Severe Clinical Diarrhea Symptoms.

The complex etiology, higher morbidity and mortality, poor prognosis, and expensive cost of calf diarrhea have made it a catastrophic disease in the dairy industry. This study aims to assess the biomarkers in calves with diarrhea and to predict the biomarkers related to the pathway. As subjects, nine calves with diarrhea and nine healthy calves were enrolled, according to strict enrollment criteria.

Temporal changes in microbial communities attached to forages with different lignocellulosic compositions in cattle rumen.

The attachment of rumen microbes to feed particles is critical to feed fermentation, degradation and digestion. However, the extent to which the physicochemical properties of feeds influence the colonization by rumen microbes is still unclear. We hypothesized that rumen microbial communities may have differential preferences for attachments to feeds with varying lignocellulose properties.

Matter, energy and information network of a graphene-peptide-based fluorescent sensing system for molecular logic computing, detection and imaging of cancer stem cell marker CD133 in cells and tumor tissues.

Tumorigenesis, metastasis, and the recurrence of cancer, which may result from the abnormal presence or activation of cancer stem cells (CSCs), are involved in disorders of exchanged matter (biomarkers), energy and information in living organisms. Rapid and sensitive detection and imaging of CSC biomarkers (such as CD133) are helpful for early diagnosis and therapeutic evaluation of tumors. Recently, a preliminary exploration of a few affinity molecules (like peptide-based probes) has just begun for chemical measurements and imaging of CSC biomarker CD133.

Graphene-Based Steganographically Aptasensing System for Information Computing, Encryption and Hiding, Fluorescence Sensing and in Vivo Imaging of Fish Pathogens.

Inspired by information processing and communication of life based on complex molecular interactions, some artificial (bio)chemical systems have been developed for applications in molecular information processing or chemo/biosensing and imaging. However, little attention has been paid to simultaneously and comprehensively utilize the information computing, encoding, and molecular recognition capabilities of molecular-level systems (such as DNA-based systems) for multifunctional applications. Herein, a graphene-based steganographically aptasensing system was constructed for multifunctional application, which relies on specific molecular recognition and information encoding abilities of DNA aptamers ( Aeromonas hydrophila and Edwardsiella tarda-binding aptamers as models) and the selective adsorption and fluorescence quenching capacities of graphene oxide (GO).

Genomic copy number variation of the CHKB gene alters gene expression and affects growth traits of Chinese domestic yak (Bos grunniens) breeds.

Copy number variation (CNV) influences the mRNA transcription levels and phenotypic traits through gene dosage, position effects, alteration of downstream pathways, and modulation of the structure and position of chromosomes. A previous study using the read depth approach to genome resequencing analysis revealed CNVs of the choline kinase beta (CHKB) gene in the copy number variable regions (CNVRs) of yak breeds may influence muscle development and therefore the phenotypic traits of yak breeds. Further work is required to attain a more complete understanding and validate the importance of the detected CNVR of the CHKB gene found in yak breeds, because there is no association studies of the CHKB gene with yak growth traits that have been reported.

The Boolean logic tree of molecular self-assembly system based on cobalt oxyhydroxide nanoflakes for three-state logic computation, sensing and imaging of pyrophosphate in living cells and in vivo.

Sensing of pyrophosphate (PPi) is helpful to better understand many life processes and diagnose various early-stage diseases. However, many traditional reported methods based on artificial receptors for sensing of PPi exhibit some disadvantages including difficulties in designing appropriate binding sites and complicated multi-step assembly/functionalization. Thus, it is significantly important and a big challenge to know how to use a simple molecular self-assembly or an interaction system to solve the above-mentioned limits to achieve the quantitative analysis of specific substances in the system.

Directly repurposing waste optical discs with prefabricated nanogrooves as a platform for investigation of cell-substrate interactions and guiding neuronal growth.

Due to rapid change in information technology, many consumer electronics become electronic waste which is the fastest-growing pollution problems worldwide. In fact, many discarded electronics with prefabricated micro/nanostructures may provide a good basis to fulfill special needs of other fields, such as tissue engineering, biosensors, and energy. Herein, to take waste optical discs as an example, we demonstrate that discarded electronics can be directly repurposed as highly anisotropic platforms for in vitro investigation of cell behaviors, such as cell adhesion, cell alignment, and cell-cell interactions.

Highly Tunable and Scalable Fabrication of 3D Flexible Graphene Micropatterns for Directing Cell Alignment.

Patterning graphene allows to precisely tune its properties to manufacture flexible functional materials or miniaturized devices for electronic and biomedical applications. However, conventional lithographic techniques are cumbersome for scalable production of time- and cost-effective graphene patterns, thus greatly impeding their practical applications. Here, we present a simple scalable fabrication of wafer-scale three-dimensional (3D) graphene micropatterns by direct laser tuning graphene oxide reduction and expansion using a LightScribe DVD writer.

Boolean Logic Tree of Label-Free Dual-Signal Electrochemical Aptasensor System for Biosensing, Three-State Logic Computation, and Keypad Lock Security Operation.

The most serious and yet unsolved problems of molecular logic computing consist in how to connect molecular events in complex systems into a usable device with specific functions and how to selectively control branchy logic processes from the cascading logic systems. This report demonstrates that a Boolean logic tree is utilized to organize and connect "plug and play" chemical events DNA, nanomaterials, organic dye, biomolecule, and denaturant for developing the dual-signal electrochemical evolution aptasensor system with good resettability for amplification detection of thrombin, controllable and selectable three-state logic computation, and keypad lock security operation. The aptasensor system combines the merits of DNA-functionalized nanoamplification architecture and simple dual-signal electroactive dye brilliant cresyl blue for sensitive and selective detection of thrombin with a wide linear response range of 0.

Radial versus femoral artery access for percutaneous coronary angiography and intervention: a systematic review and meta-analysis of randomized controlled trials in Chinese population.

To compare the feasibility, efficiency and safety of coronary angiography (CAG) and interventional procedures between the radial and femoral catheterization approaches in Chinese population using systematic review and meta-analysis, we conducted a search of the studies comparing radial and femoral catheterization approaches in patients underwent either CAG or percutaneous coronary intervention (PCI) in Chinese population. Fixed-effect relative risk (RR) for the primary end points and the second end points were compared between the two approaches. A total of 27 studies (n=8,749 patients) were finally included in the analysis.

Clinical impact of circulating miR-133, miR-1291 and miR-663b in plasma of patients with acute myocardial infarction.

Background: Acute myocardial infarction (AMI) is one of the leading causes for death in both developed and developing countries and it is the single largest cause of death in the United States, responsible for 1 out of every 6 deaths. The objective of this study was to determine microRNA (miRNA) expression in AMI and determine whether miR-133, miR-1291 and miR-663b could be measured in plasma as a biomarker for recurrence.

Methods: Patients with AMI and those without AMI were retrospectively recruited for a comparison of their plasma miR-133, miR-1291 and miR-663b expression.

[Measurement of methane and carbon dioxide emissions from ruminants based on the NDIR technique].

Methane (CH4) production in the rumen represents a loss of energy for the host animal; in addition, methane eructated by ruminants may contribute to a greenhouse effect or global warming. The dinumal CH4 and carbon dioxide (CO2) emissions from sheep were continuously recorded using the flow-through chamber method. A type new type of non-disperse infrared (NDIR) gas sensors based on pulse IR source was introduced, and by using the high performance pyroelectric IR sensor with built in interference filter and the "single light and two wavelengths" technology, CH4 and CO2 measurement from ruminants was achieved.

Residue 544 in domain III of the Bacillus thuringiensis Cry1Ac toxin is involved in protein structure stability.

A unique residue W544 in the beta18-beta19 loop of the Bacillus thuringiensis Cry1Ac toxin has been implicated in its toxicity. In this study, the effects of mutations at this residue on protein stability during protease treatment, UV irradiation, and preservation were examined. Residue 544 of Cry1Ac was involved in maintaining structural stability, and substitution of a polar group at this position was unfavorable to protein stability.

N546 in beta18-beta19 loop is important for binding and toxicity of the Bacillus thuringiensis Cry1Ac toxin.

Our previous mutagenic analysis showed that the unique residue N546 in the apex of beta18-beta19 loop of Bacillus thuringiensis Cry1Ac toxin is important for its toxicity. In this study, trypsin digestion susceptibility, binding to BBMV and oligomer formation activity was therefore analyzed to determine the mechanism of toxicity change of these mutant toxins. The results showed that residue N546 was not involved in toxin oligomerisation and maintaining the stability of toxin, the enhanced toxicity of mutant N546A was just because of increased binding to BBMV, and reduction in toxicity of other mutants were caused by reduction in initial or irreversible binding to BBMV.

The theoretical three-dimensional structure of Bacillus thuringiensis Cry5Aa and its biological implications.

Cry5Aa is a crystal protein produced by Bacillus thuringiensis serovar. damstadiensis during its stationary phase, this delta-endotoxin is active against nematodes and has great potential for nematodes control. The theoretical model of the three-dimensional structure of Cry5Aa was predicted by homology modeling on the structures of the Cry1Aa which is specific to Lepidopteran insects.