3,562 results match your criteria trends high-throughput

Association between biofilm formation gene bla exoU and metallo and extend spectrum beta-lactamase production of multidrug resistance Pseudomonas aeruginosa in clinical samples.

Fattma Abodi Ali

Comb Chem High Throughput Screen 2021 Apr 18. Epub 2021 Apr 18.

Department of Medical microbiology, College of Health Sciences, Hawler Medical University. Iraq.

Background: The presence of biofilm formation exoU gene is significant challenge to infection control management in hospitals and exposure by Pseudomonas aeruginosa may lead to further spread and development of antimicrobial resistance.

Methods: Out of 227 samples 40 clinical isolates of P. aeruginosa were collected from patients attending public hospitals ( Rizgary, Teaching hospital, Laboratory center, Raparin, Nanakaly hospitals)in Erbil city/Iraq over a period during 2018 to march 2019 and fully characterized by standard bacteriological procedures and antimicrobial susceptibility test and ESBL has been carried out by Vitek 2 compact system and. Read More

View Article and Full-Text PDF

Metabolic pathways inferred from a bacterial marker gene illuminate ecological changes across South Pacific frontal boundaries.

Nat Commun 2021 04 13;12(1):2213. Epub 2021 Apr 13.

Ocean Frontier Institute and Department of Oceanography, Dalhousie University, Halifax, NS, Canada.

Global oceanographic monitoring initiatives originally measured abiotic essential ocean variables but are currently incorporating biological and metagenomic sampling programs. There is, however, a large knowledge gap on how to infer bacterial functions, the information sought by biogeochemists, ecologists, and modelers, from the bacterial taxonomic information (produced by bacterial marker gene surveys). Here, we provide a correlative understanding of how a bacterial marker gene (16S rRNA) can be used to infer latitudinal trends for metabolic pathways in global monitoring campaigns. Read More

View Article and Full-Text PDF

Phylogenetic classification of the whole-genome sequences of SARS-CoV-2 from India & evolutionary trends.

Indian J Med Res 2021 Jan & Feb;153(1 & 2):166-174

Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune, India.

Background & Objectives: Several phylogenetic classification systems have been devised to trace the viral lineages of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, inconsistency in the nomenclature limits uniformity in its epidemiological understanding. This study provides an integration of existing classifications and describes evolutionary trends of the SARS-CoV-2 strains circulating in India. Read More

View Article and Full-Text PDF

An Information Theoretical Multilayer Network Approach to Breast Cancer Transcriptional Regulation.

Front Genet 2021 18;12:617512. Epub 2021 Mar 18.

Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.

Breast cancer is a complex, highly heterogeneous disease at multiple levels ranging from its genetic origins and molecular processes to clinical manifestations. This heterogeneity has given rise to the so-called intrinsic or molecular breast cancer subtypes. Aside from classification, these subtypes have set a basis for differential prognosis and treatment. Read More

View Article and Full-Text PDF

Molecular Diversity and Distribution of Arbuscular Mycorrhizal Fungi at Different Elevations in Mt. Taibai of Qinling Mountain.

Front Microbiol 2021 4;12:609386. Epub 2021 Mar 4.

College of Agriculture, Henan University of Science and Technology, Luoyang, China.

Arbuscular mycorrhizal fungi (AMFs) play a vital role in ecosystems, especially in ecosystem variability, diversity, and function. Understanding the AMF diversity, distribution, and their driver at different altitudinal gradients is a benefit for understanding the ecological function of AMF in mountain ecosystems. In this study, we explored the AMF molecular diversity and their distribution from 660 to 3,500 m a. Read More

View Article and Full-Text PDF

Assessing the Statistical Training in Animal Science Graduate Programs in the US: Survey on Statistical Training.

J Anim Sci 2021 Mar 19. Epub 2021 Mar 19.

Department of Animal Science, Iowa State University, Ames, IA, United States of America.

Statistical analysis of data and understanding of experimental design are critical skills needed by Animal Science Graduate Students (ASGS). These skills are even more valuable with the increased development of high-throughput technologies. The objective of this study was to evaluate the perceived statistical training of US ASGS. Read More

View Article and Full-Text PDF

Distribution of Chromophytic Phytoplankton in the Eddy-Induced Upwelling Region of the West Pacific Ocean Revealed Using L Genes.

Front Microbiol 2021 2;12:596015. Epub 2021 Mar 2.

College of Marine Science and Technology, China University of Geosciences, Wuhan, China.

Marine chromophytic phytoplankton are a diverse group of algae and contribute significantly to the total oceanic primary production. However, the spatial distribution of chromophytic phytoplankton is understudied in the West Pacific Ocean (WPO). In this study, we have investigated the community structure and spatial distribution of chromophytic phytoplankton using RuBisCO genes (Form ID L). Read More

View Article and Full-Text PDF

A streamlined solution for processing, elucidating and quality control of cyclobutane pyrimidine dimer sequencing data.

Nat Protoc 2021 Apr 17;16(4):2190-2212. Epub 2021 Mar 17.

Comprehensive Cancer Center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA.

UV radiation may lead to melanoma and nonmelanoma skin cancers by causing helix-distorting DNA damage such as cyclobutane pyrimidine dimers (CPDs). These DNA lesions, if located in important genes and not repaired promptly, are mutagenic and may eventually result in carcinogenesis. Examining CPD formation and repair processes across the genome can shed light on the mutagenesis mechanisms associated with UV damage in relevant cancers. Read More

View Article and Full-Text PDF

Chemistry Informer Libraries: Conception, Early Experience, and Role in the Future of Cheminformatics.

Acc Chem Res 2021 04 16;54(7):1586-1596. Epub 2021 Mar 16.

Chemistry Capabilities Accelerating Therapeutics, Merck & Co., Inc., Kenilworth, New Jersey 07033, United States.

The synthetic chemistry literature traditionally reports the scope of new methods using simple, nonstandardized test molecules that have uncertain relevance in applied synthesis. In addition, published examples heavily favor positive reaction outcomes, and failure is rarely documented. In this environment, synthetic practitioners have inadequate information to know whether any given method is suitable for the task at hand. Read More

View Article and Full-Text PDF

Single-Nanoparticle Coulometry Method with High Sensitivity and High Throughput to Study the Electrochemical Activity and Oscillation of Single Nanocatalysts.

Small 2021 Apr 14;17(14):e2007302. Epub 2021 Mar 14.

School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Suzhou, 215123, China.

To explore nanocatalysts with high electro-catalytic performance and less loading of precious metals, efforts have been made to develop electrochemical methods with high spatial resolution at the single nanoparticle level. Herein, a highly sensitive single-nanoparticle coulometry method is successfully developed to study the electrochemical activity and oscillation of single PtTe nanocatalysts. Based on microbattery reactions involving the formic acid electro-oxidation and the deposition of Ag on the single PtTe nanocatalyst surface, this method enables the transition from the undetectable sub-fA electric signal of the formic acid electro-oxidation into strong localized surface plasmon resonance scattering signal of Ag detected by dark-field microscopy. Read More

View Article and Full-Text PDF

A library preparation optimized for metagenomics of RNA viruses.

Mol Ecol Resour 2021 Mar 13. Epub 2021 Mar 13.

ASTRE, Cirad, INRAE, University of Montpellier, Montpellier, France.

Our understanding of the viral communities associated to animals has not yet reached the level attained on the bacteriome. This situation is due to, among others, technical challenges in adapting metagenomics using high-throughput sequencing to the study of RNA viromes in animals. Although important developments have been achieved in most steps of viral metagenomics, there is yet a key step that has received little attention: the library preparation. Read More

View Article and Full-Text PDF

RNA Dysregulation: An Expanding Source of Cancer Immunotherapy Targets.

Trends Pharmacol Sci 2021 Apr;42(4):268-282

Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:

Cancer transcriptomes frequently exhibit RNA dysregulation. As the resulting aberrant transcripts may be translated into cancer-specific proteins, there is growing interest in exploiting RNA dysregulation as a source of tumor antigens (TAs) and thus novel immunotherapy targets. Recent advances in high-throughput technologies and rapid accumulation of multiomic cancer profiling data in public repositories have provided opportunities to systematically characterize RNA dysregulation in cancer and identify antigen targets for immunotherapy. Read More

View Article and Full-Text PDF

Clinical prediction rule for SARS-CoV-2 infection from 116 U.S. emergency departments 2-22-2021.

PLoS One 2021 10;16(3):e0248438. Epub 2021 Mar 10.

Department of Emergency Medicine, Wayne State University School of Medicine, Detroit, Michigan, United States of America.

Objectives: Accurate and reliable criteria to rapidly estimate the probability of infection with the novel coronavirus-2 that causes the severe acute respiratory syndrome (SARS-CoV-2) and associated disease (COVID-19) remain an urgent unmet need, especially in emergency care. The objective was to derive and validate a clinical prediction score for SARS-CoV-2 infection that uses simple criteria widely available at the point of care.

Methods: Data came from the registry data from the national REgistry of suspected COVID-19 in EmeRgency care (RECOVER network) comprising 116 hospitals from 25 states in the US. Read More

View Article and Full-Text PDF

Trends in CRISPR-Cas9 technology application in cancer.

Prog Mol Biol Transl Sci 2021 2;178:175-192. Epub 2021 Feb 2.

Department of Life Science, National Institute of Technology, Rourkela, Odisha, India. Electronic address:

The evolution of the CRISPR-Cas9 technology in cancer research has tremendous potential to shape the future of oncology. Although this gene-editing tool's pre-clinical progress is into its nascent stage, there are many unanswered questions regarding health benefits and therapy precision using CRISPR. The application of CRISPR is highly specific, economically sustainable, and is a high throughput technique, but on the other hand, its application involves measured risk of countering the toxic immune response of Cas protein, off-target effects, limitation of delivering the edited cells back into cancer patients. Read More

View Article and Full-Text PDF
February 2021

Comparison of methodologies used to determine aromatic lignin unit ratios in lignocellulosic biomass.

Biotechnol Biofuels 2021 Mar 6;14(1):58. Epub 2021 Mar 6.

Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.

Background: Multiple analytical methods have been developed to determine the ratios of aromatic lignin units, particularly the syringyl/guaiacyl (S/G) ratio, of lignin biopolymers in plant cell walls. Chemical degradation methods such as thioacidolysis produce aromatic lignin units that are released from certain linkages and may induce chemical changes rendering it difficult to distinguish and determine the source of specific aromatic lignin units released, as is the case with nitrobenzene oxidation methodology. NMR methods provide powerful tools used to analyze cell walls for lignin composition and linkage information. Read More

View Article and Full-Text PDF

Sex Determination and Differentiation in Decapod and Cladoceran Crustaceans: An Overview of Endocrine Regulation.

Genes (Basel) 2021 Feb 21;12(2). Epub 2021 Feb 21.

Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa 236-0027, Japan.

Mechanisms underlying sex determination and differentiation in animals are known to encompass a diverse array of molecular clues. Recent innovations in high-throughput sequencing and mass spectrometry technologies have been widely applied in non-model organisms without reference genomes. Crustaceans are no exception. Read More

View Article and Full-Text PDF
February 2021

Error-Free Synthetic DNA by Molecular Dictation.

Trends Biotechnol 2021 Feb 27. Epub 2021 Feb 27.

Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK. Electronic address:

Synthetic DNA is the linchpin of the rapidly accelerating biotechnological era and is perhaps the most promising candidate for long-term digital data storage. Despite huge advances, manufacturing error-free DNA at low cost and high throughput remains challenging. Borrowing from well-established sequencing-by-synthesis technologies, we describe a new solution for DNA error correction. Read More

View Article and Full-Text PDF
February 2021

Sexually transmitted infections (STIs) and its changing scenario: A scoping review.

Comb Chem High Throughput Screen 2021 Feb 28. Epub 2021 Feb 28.

Department of lab medicine, Max Super speciality hospital, Saket Delhi -110017. India.

Sexually transmitted infections (STIs) and reproductive tract infections (RTIs) have existed worldwide since ancient time, causing significant morbidity and mortality. To maintain healthy sexual and reproductive life, it is highly essential to prevent STIs, RTIs and related illnesses. STIs are transmitted by swapping body fluids among people during sexual intercourse. Read More

View Article and Full-Text PDF
February 2021

Discovery of sultam-containing small-molecule disruptors of the huntingtin-calmodulin protein-protein interaction.

Med Chem Res 2020 Jul 12;29(7):1187-1198. Epub 2020 Jun 12.

Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, 125 Mason Farm Road, Chapel Hill, NC 27599, USA.

The aberrant protein-protein interaction between calmodulin and mutant huntingtin protein in Huntington's disease patients has been found to contribute to Huntington's disease progression. A high-throughput screen for small molecules capable of disrupting this interaction revealed a sultam series as potent small-molecule disruptors. Diversification of the sultam scaffold afforded a set of 24 analogs or further evaluation. Read More

View Article and Full-Text PDF

Outer Membrane Structural Defects in Salmonella enterica Serovar Typhimurium Affect Neutrophil Chemokinesis but Not Chemotaxis.

mSphere 2021 02 24;6(1). Epub 2021 Feb 24.

Department of Mechanical Engineering, Virginia Tech, Blacksburg, Virginia, USA

Neutrophils, the first line of defense against pathogens, are critical in the host response to acute and chronic infections. In Gram-negative pathogens, the bacterial outer membrane (OM) is a key mediator of pathogen detection; nonetheless, the effects of variations in its molecular structure on the neutrophil migratory response to bacteria remain largely unknown. Here, we developed a quantitative microfluidic assay that precludes physical contact between bacteria and neutrophils while maintaining chemical communication, thus allowing investigation of both transient and steady-state responses of neutrophils to a library of serovar Typhimurium OM-related mutants at single-cell resolution. Read More

View Article and Full-Text PDF
February 2021

Pro-biomics: Omics Technologies To Unravel the Role of Probiotics in Health and Disease.

Adv Nutr 2021 Feb 24. Epub 2021 Feb 24.

Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, Alexandroupolis, Greece.

The comprehensive characterization of probiotic action has flourished during the past few decades, alongside the evolution of high-throughput, multiomics platforms. The integration of these platforms into probiotic animal and human studies has provided valuable insights into the holistic effects of probiotic supplementation on intestinal and extraintestinal diseases. Indeed, these methodologies have informed about global molecular changes induced in the host and residing commensals at multiple levels, providing a bulk of metagenomic, transcriptomic, proteomic, and metabolomic data. Read More

View Article and Full-Text PDF
February 2021

Uncovering the Mechanical Code of DNA Using 'Loop-seq'.

Marek Marzec

Trends Genet 2021 Feb 20. Epub 2021 Feb 20.

University of Silesia in Katowice, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellonska 28, 40-032 Katowice, Poland. Electronic address:

DNA mechanical properties play a critical role in different biological processes. Basu and coworkers described a method that measures DNA mechanics on the genome scale. Access to a high-throughput tool for measuring DNA mechanics opens up new possibilities to investigate this phenomenon with respect to establishing the chromatin regulatory landscape. Read More

View Article and Full-Text PDF
February 2021

Next generation sequencing approaches to evaluate water and wastewater quality.

Water Res 2021 Apr 4;194:116907. Epub 2021 Feb 4.

Charles E. Via, Jr. Department of Civil and Environmental Engineering, Virginia Tech, 1145 Perry Street, Blacksburg, VA 24061, United States. Electronic address:

The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. Read More

View Article and Full-Text PDF

Machine learning identifies candidates for drug repurposing in Alzheimer's disease.

Nat Commun 2021 02 15;12(1):1033. Epub 2021 Feb 15.

Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, MA, USA.

Clinical trials of novel therapeutics for Alzheimer's Disease (AD) have consumed a large amount of time and resources with largely negative results. Repurposing drugs already approved by the Food and Drug Administration (FDA) for another indication is a more rapid and less expensive option. We present DRIAD (Drug Repurposing In AD), a machine learning framework that quantifies potential associations between the pathology of AD severity (the Braak stage) and molecular mechanisms as encoded in lists of gene names. Read More

View Article and Full-Text PDF
February 2021

Acoustic vibration technology: Toward a promising fruit quality detection method.

Compr Rev Food Sci Food Saf 2021 Mar 15;20(2):1655-1680. Epub 2021 Feb 15.

College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China.

Understanding fruit quality is an effective way to reduce fruit loss and waste by providing proper strategies for fruit processing and management. Various noninvasive technologies have been developed for assessing fruit quality. Among them, acoustic vibration technology has received considerable attention from academics. Read More

View Article and Full-Text PDF

Sinomenine Inhibits the Growth of Ovarian Cancer Cells Through the Suppression of Mitosis by Down-Regulating the Expression and the Activity of CDK1.

Onco Targets Ther 2021 5;14:823-834. Epub 2021 Feb 5.

Department of Gynecology and Obstetrics, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200072, People's Republic of China.

Introduction: Ovarian cancer is one of the most common gynecological cancers worldwide. While, therapies against ovarian cancer have not been completely effective, sinomenine has been proved to have anti-tumor activity in various cancer cells. However, study of its anti-ovarian cancer effect is still rare, and the underlying mechanism has not been elucidated. Read More

View Article and Full-Text PDF
February 2021

Data-Driven Modeling of Pregnancy-Related Complications.

Trends Mol Med 2021 Feb 8. Epub 2021 Feb 8.

Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University School of Medicine, Stanford, CA, USA. Electronic address:

A healthy pregnancy depends on complex interrelated biological adaptations involving placentation, maternal immune responses, and hormonal homeostasis. Recent advances in high-throughput technologies have provided access to multiomics biological data that, combined with clinical and social data, can provide a deeper understanding of normal and abnormal pregnancies. Integration of these heterogeneous datasets using state-of-the-art machine-learning methods can enable the prediction of short- and long-term health trajectories for a mother and offspring and the development of treatments to prevent or minimize complications. Read More

View Article and Full-Text PDF
February 2021

Comparative transcriptome sequencing analysis and functional identification of a NAM-2-like gene in jute (Corchorus capsularis L.).

Plant Physiol Biochem 2021 Apr 30;161:25-35. Epub 2021 Jan 30.

Fujian Agriculture and Forestry University, Fuzhou, China. Electronic address:

Jute (Corchorus capsularis L.) is one of the most important sources of natural fibre. Drought is among the main factors affecting the production of jute. Read More

View Article and Full-Text PDF

Sustainable green solvents for microextraction techniques: Recent developments and applications.

J Chromatogr A 2021 Mar 28;1640:461944. Epub 2021 Jan 28.

Departamento de Farmacociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS 90050-170, Brazil.

The development and application of alternative green solvents in analytical techniques consist of trends in sample preparation, since this subject represents an important step toward sustainability in experimental procedures. This review is focused on the main theoretical aspects related to deep eutectic solvents (DES), switchable hydrophilicity solvents (SHS) and supramolecular solvents (SUPRAS). Recent applications are highlighted, particularly for the extraction of different analytes from environmental, biological and food matrices. Read More

View Article and Full-Text PDF