772,496 results match your criteria method gene

Influence of estradiol on bovine trophectoderm and uterine gene transcripts around maternal recognition of pregnancy.

Biol Reprod 2021 May 7. Epub 2021 May 7.

Department of Animal Science, South Dakota State University, Brookings SD; USA.

Embryo survival and pregnancy success is increased among animals that exhibit estrus prior to fixed time artificial insemination (AI), but there are no differences in conceptus survival to d16. The objective of this study was to determine effects of preovulatory estradiol on uterine transcriptomes, select trophectoderm transcripts, and uterine luminal fluid (ULF) proteins. Beef cows/heifers were synchronized, artificially inseminated (d0), and grouped into either high (highE2) or low (lowE2) preovulatory estradiol. Read More

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Ketogenic diet-mediated steroid metabolism reprogramming improves the immune microenvironment and myelin growth in spinal cord injury rats according to gene and co-expression network analyses.

Aging (Albany NY) 2021 May 6;13. Epub 2021 May 6.

Department of Rehabilitation Medicine, Peking University Third Hospital, Beijing 100191, China.

The ketogenic diet has been widely used in the treatment of various nervous system and metabolic-related diseases. Our previous research found that a ketogenic diet exerts a protective effect and promotes functional recovery after spinal cord injury. However, the mechanism of action is still unclear. Read More

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Time-of-day effects of consumption of fish oil-enriched sausages on serum lipid parameters and fatty acid composition in normolipidemic adults: A randomized, double-blind, placebo-controlled, and parallel-group pilot study.

Nutrition 2021 Mar 24;90:111247. Epub 2021 Mar 24.

Healthy Food Science Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan; Department of Applied Biological Science, Graduate School of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan; School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Ibaraki, Japan. Electronic address:

Objectives: The body clock controls diurnal rhythms of nutrient digestion, absorption, and metabolism. Fish oil (FO) contains abundant ω-3 polyunsaturated fatty acids (PUFA), including docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), that are thought to lower triglyceride (TG) levels. This randomized, placebo-controlled, double-blind, parallel-group trial aimed to confirm the effects of the time of FO intake on TG in healthy Japanese adults. Read More

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Intratumour microbiome associated with the infiltration of cytotoxic CD8+ T cells and patient survival in cutaneous melanoma.

Eur J Cancer 2021 May 4;151:25-34. Epub 2021 May 4.

Department of Chronic Disease Epidemiology, Yale School of Public Health, School of Medicine, Yale Cancer Center, Yale University, New Haven, CT, USA. Electronic address:

Objective: The gut microbiome plays an important role in systemic inflammation and immune response. Microbes can translocate and reside in tumour niches. However, it is unclear how the intratumour microbiome affects immunity in human cancer. Read More

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PM2.5 aggravates NQO1-induced mucus hyper-secretion through release of neutrophil extracellular traps in an asthma model.

Ecotoxicol Environ Saf 2021 May 4;218:112272. Epub 2021 May 4.

Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, the Third People's Hospital of Chengdu, Chengdu 610031, China; Department of Pulmonary and Critical Care Medicine, Chengdu third people's hospital branch of National Clinical Research Center for Respiratory Disease, Affiliated Hospital of ChongQing Medical University, Chengdu 610031, China. Electronic address:

Background: Particulate matter of 2.5 µm or less in diameter (PM2.5) is one of the most complex pollutants in the atmospheric environment and harmful to human health. Read More

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Early time-point cell morphology classifiers successfully predict human bone marrow stromal cell differentiation modulated by fiber density in nanofiber scaffolds.

Biomaterials 2021 Apr 26;274:120812. Epub 2021 Apr 26.

National Institute of Standards & Technology, Biosystems & Biomaterials Division, 100 Bureau Dr. Stop 8543, Gaithersburg, MD, 20899, USA. Electronic address:

Nanofiber scaffolds can induce osteogenic differentiation and cell morphology alterations of human bone marrow stromal cells (hBMSCs) without introduction of chemical cues. In this study, we investigate the predictive power of day 1 cell morphology, quantified by a machine learning based method, as an indicator of osteogenic differentiation modulated by nanofiber density. Nanofiber scaffolds are fabricated via electrospinning. Read More

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Molecular characterisation and epidemiology of enterovirus-associated aseptic meningitis in the Western and Eastern Cape Provinces, South Africa 2018-2019.

J Clin Virol 2021 Apr 24;139:104845. Epub 2021 Apr 24.

Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, South Africa and the National Health Laboratory Service, Anzio Road, Observatory, Cape Town, South Africa.

Background: Enteroviruses are amongst the most common causes of aseptic meningitis. Between November 2018 and May 2019, an outbreak of enterovirus-associated aseptic meningitis cases was noted in the Western and Eastern Cape Provinces, South Africa.

Objectives: To describe the epidemiology and phylogeography of enterovirus infections during an aseptic meningitis outbreak in the Western and Eastern Cape Provinces of South Africa. Read More

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A survey of the mouse hindbrain in the fed and fasted state using single-nucleus RNA sequencing.

Mol Metab 2021 May 4:101240. Epub 2021 May 4.

MRC Metabolic Diseases Unit, University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK. Electronic address:

Objective: The area postrema (AP) and the nucleus tractus solitaris (NTS), located in the hindbrain, are key nuclei that sense and integrate peripheral nutritional signals and, consequently, regulate feeding behaviour. While single cell transcriptomics have been used in mice to reveal the gene expression profile and heterogeneity of key hypothalamic populations, similar in-depth studies have not yet been performed in the hindbrain.

Methods: Using single-nucleus RNA sequencing, we provide a detailed survey of 16,034 cells within the AP and NTS of the mouse, in the fed and fasted state. Read More

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Evolution of host use in fungivorous ciid beetles (Coleoptera: Ciidae): molecular phylogeny focusing on Japanese taxa.

Mol Phylogenet Evol 2021 May 4:107197. Epub 2021 May 4.

Department of Zoology, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake, Sakyo, Kyoto 606 8502 Japan.

Consumer-resource interactions between trophic levels are ubiquitous and important factors in shaping the diversity of insects. However, dietary patterns such as host specificity and conservatism have been insufficiently examined in fungivorous insects. Here we reconstructed the evolutionary history of host use in fungivorous ciid beetles (Coleoptera: Ciidae) and tested for host conservatism. Read More

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Replication competence of canine distemper virus in cell lines expressing signaling lymphocyte activation molecule (SLAM) of goat, sheep and dog origin.

Microb Pathog 2021 May 4:104940. Epub 2021 May 4.

Indian Council of Agricultural Research (ICAR)-Indian Veterinary Research Institute (IVRI), Izatnagar, 243122, Bareilly, Uttar Pradesh, India.

Cellular receptors play an important role in entry and cell to cell spread of morbillivirus infections. The cells expressing SLAM and Nectin-4 have been used for successful and efficient isolation of canine distemper virus (CDV) in high titre. There are several methods for generation of cells expressing receptor molecules. Read More

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Vitamin D pathway gene polymorphisms, vitamin D level, and cytokines in children with type 1 diabetes.

Gene 2021 May 4:145691. Epub 2021 May 4.

Siriraj Diabetes Center of Excellence, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Division of Endocrinology and Metabolism, Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand. Electronic address:

Aims: The study aimed to examine genetic polymorphism of vitamin D-related genes and association between those genes and vitamin D and cytokines levels in children with type 1 diabetes (T1D).

Materials And Methods: This study was conducted among 100 T1D children and 100 controls at Division of Endocrinology and Metabolism, Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand, during 2016 to 2018. Vitamin D metabolite levels were measured by liquid chromatography-tandem mass spectrometry method, serum cytokine levels of IFN- ɣ, IL-10, IL-13, IL-17α, IL-2, IL-4, IL-6, and TNF-α by immunoassay, and genetic variations at VDR, CYP2R1, CYP27B1, GC, DHCR7, and CYP24A1 by polymerase chain reaction-restriction fragment length polymorphism method. Read More

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Genetic mosaicism, intrafamilial phenotypic heterogeneity, and molecular defects of a novel missense SLC6A1 mutation associated with epilepsy and ADHD.

Exp Neurol 2021 May 4:113723. Epub 2021 May 4.

Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, 37232, United States of America. Electronic address:

Background: Mutations in SLC6A1, encoding γ-aminobutyric acid (GABA) transporter 1 (GAT-1), have been recently associated with a spectrum of neurodevelopmental disorders ranging from variable epilepsy syndromes, intellectual disability (ID), autism and others. To date, most identified mutations are de novo. We here report a pedigree of two siblings associated with myoclonic astatic epilepsy, attention deficit hyperactivity disorder (ADHD), and ID. Read More

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mA demethylase ALKBH5 suppresses proliferation and migration of enteric neural crest cells by regulating TAGLN in Hirschsprung's disease.

Life Sci 2021 May 4:119577. Epub 2021 May 4.

Department of Pediatric Surgery, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, China. Electronic address:

Objectives: This study aims to investigate the role of demethylase ALKBH5 mediated demethylation of TAGLN mRNA in the occurrence of Hirschsprung's disease (HSCR), and to clarify how ALKBH5 reduces the mA level of TAGLN mRNA and inhibits its degradation, thereby inhibiting the proliferation and migration of neural crest cells, and potentially contributing to the occurrence of HSCR.

Material And Methods: Quantitative real-time PCR (qRT-PCR) and Western-Blot (WB) were conducted to test the expression level of ALKBH5 and TAGLN genes. Cell function assays were adopted to detect cell phenotypes. Read More

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lncRNA UCA1 induced by SP1 and SP3 forms a positive feedback loop to facilitate malignant phenotypes of colorectal cancer via targeting miR-495.

Life Sci 2021 May 4:119569. Epub 2021 May 4.

Department of Gastroenterology, The Third Xiangya Hospital, Central South University, Changsha 410013, Hunan Province, PR China; Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha 410013, Hunan Province, PR China. Electronic address:

Aims: Long noncoding RNA (LncRNA) urothelial cancer associated 1 (UCA1) was dysregulated in colorectal cancers (CRC) and promoted tumor progression of CRC. The aims of this study are to further investigate the underlying mechanism.

Main Methods: Short hairpin RNAs (shRNAs) were applied for gene knockdown. Read More

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The sputum microbiome and clinical outcomes in patients with bronchiectasis: a prospective observational study.

Lancet Respir Med 2021 May 4. Epub 2021 May 4.

Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK. Electronic address:

Background: Infection is a key component of bronchiectasis pathophysiology. Characterisation of the microbiome offers a higher degree of sensitivity and resolution than does traditional culture methods. We aimed to evaluate the role of the microbiome in determining the risk of exacerbation and long-term outcomes, including all-cause mortality, in bronchiectasis. Read More

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Classification of triple-negative breast cancers through a Boolean network model of the epithelial-mesenchymal transition.

Cell Syst 2021 May 6. Epub 2021 May 6.

Center for Complexity and Biosystems, Department of Environmental Science and Policy, University of Milan, via Celoria 26, 20133 Milano, Italy; CNR - Consiglio Nazionale delle Ricerche, Istituto di Biofisica, via Celoria 26, 20133 Milano, Italy. Electronic address:

Predicting the metastasis risk in patients with a primary breast cancer tumor is of fundamental importance to decide the best therapeutic strategy in the framework of personalized medicine. Here, we present ARIADNE, a general algorithmic strategy to assess the risk of metastasis from transcriptomic data of patients with triple-negative breast cancer, a subtype of breast cancer with poorer prognosis with respect to the other subtypes. ARIADNE identifies hybrid epithelial/mesenchymal phenotypes by mapping gene expression data into the states of a Boolean network model of the epithelial-mesenchymal pathway. Read More

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An effective method for establishing animal models of azoospermia and oligospermia.

Andrologia 2021 May 7:e14095. Epub 2021 May 7.

Department of Biology and Anatomical Sciences, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

The current study aims to develop a validated animal model to predict successful spermatogenesis retrieval in azoospermia and oligospermia men. Thirty-two mice were equally divided into 4 groups: control, scrotal hyperthermia (15 times), scrotal hyperthermia group (10 times), scrotal hyperthermia group (5 times). In the scrotal hyperthermia groups, their scrotum exposed to water at a temperature of 43°C for 20 min every other day. Read More

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A method for achieving complete microbial genomes and improving bins from metagenomics data.

PLoS Comput Biol 2021 May 7;17(5):e1008972. Epub 2021 May 7.

Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America.

Metagenomics facilitates the study of the genetic information from uncultured microbes and complex microbial communities. Assembling complete genomes from metagenomics data is difficult because most samples have high organismal complexity and strain diversity. Some studies have attempted to extract complete bacterial, archaeal, and viral genomes and often focus on species with circular genomes so they can help confirm completeness with circularity. Read More

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Genome-wide identification of ABCC gene family and their expression analysis in pigment deposition of fiber in brown cotton (Gossypium hirsutum).

PLoS One 2021 7;16(5):e0246649. Epub 2021 May 7.

School of Life Sciences, Anhui Agricultural University, Hefei, PR China.

ABC (ATP-binding cassette) transporters are a class of superfamily transmembrane proteins that are commonly observed in natural organisms. The ABCC (ATP-binding cassette C subfamily) protein belongs to a subfamily of the ABC protein family and is a multidrug resistance-associated transporter that localizes to the tonoplast and plays a significant role in pathogenic microbial responses, heavy metal regulation, secondary metabolite transport, and plant growth. Recent studies have shown that the ABCC protein is also involved in the transport of anthocyanins/proanthocyanidins (PAs). Read More

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MiR-485-3p promotes proliferation of osteoarthritis chondrocytes and inhibits apoptosis via Notch2 and the NF-κB pathway.

Immunopharmacol Immunotoxicol 2021 May 7:1-10. Epub 2021 May 7.

Department of Foot and Ankle Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China.

Context: Osteoarthritis (OA) is one of the leading causes of disability worldwide. microRNAs (miRs) has been shown to be involved in multiple pathological processes during OA. But the possible mechanism of miR-485-3p in OA remains unclear. Read More

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Rescue of an infection clone of barley yellow dwarf virus -GAV.

Phytopathology 2021 May 7. Epub 2021 May 7.

Northwest A&F University, College of Plant Protection; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, China;

Barley yellow dwarf virus-GAV (BYDV-GAV) is one of the most prevalent viruses causing yellow dwarf disease in wheat in China. The biology and pathology of BYDV-GAV are well studied; however, gene functions and molecular mechanisms of BYDV-GAV disease development are unclear due to the lack of a reverse genetics system. In this study, a full-length cDNA clone of BYDV-GAV was constructed and expressed using Agrobacterium-mediated inoculation of Nicotiana benthamiana. Read More

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Vitamin B12 Induces Hepatic Fatty Infiltration through Altered Fatty Acid Metabolism.

Cell Physiol Biochem 2021 May;55(3):241-255

Division of Metabolic and Vascular Health, Clinical Sciences Research Laboratories, Warwick Medical School, University of Warwick, University Hospital-Walsgrave Campus, Coventry, UK,

Background/aims: Rise in global incidence of obesity impacts metabolic health. Evidence from human and animal models show association of vitamin B12 (B12) deficiency with elevated BMI and lipids. Human adipocytes demonstrated dysregulation of lipogenesis by low B12 via hypomethylation and altered microRNAs. Read More

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EPO transgene detection in Dried Blood Spots for antidoping application.

Drug Test Anal 2021 May 7. Epub 2021 May 7.

Analysis Department - Agence Française de Lutte contre le Dopage (AFLD), 143 avenue Roger Salengro-, 92290, Châtenay-Malabry, France.

The modification of gene expression to treat diseases is a field of research with exponential growth. As doping in sport closely follows emerging therapies, a surveillance of the modification of gene expression to enhance performance is needed. The gene coding for erythropoietin (EPO), is one target of interest. Read More

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Genomic appraisal of Klebsiella PGPB isolated from soil to enhance the growth of barley.

Genes Genomics 2021 May 7. Epub 2021 May 7.

Department of Microbiology and Biotechnology, School of Sciences, Gujarat University, Ahmedabad, 380009, India.

Background: PGPR has substituted chemical fertilizers to enhance the nutrient profile of the soil. Although gene encoding for PGP activity is present in PGPB their activity changes in response to conditions.

Objective: To study comparative genomics for three Klebsiella strains and their PGPR activity in response to in vitro and soil condition. Read More

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A Protocol for Teaching Basic Next Generation Sequencing (NGS) Analysis Skills to Undergraduate Students Using Bash and R.

Methods Mol Biol 2021 ;2242:245-265

Department of Biology, University of Florence, Sesto Fiorentino, Italy.

Next generation sequencing (NGS) is routinely used to study crucial aspects of biological systems, including differentially expressed genes identification, microbiome taxonomic composition and structure, enrichment of specific cellular functions in a given environment, and so on. Current research laboratories are facing a serious lack in the availability of properly trained researchers capable of carrying out basic NGS analysis computational pipelines. This reflects a gap in most academic curricula concerning the basics of NGS data management, analysis, and interpretation. Read More

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January 2021

A Compendium of Bioinformatic Tools for Bacterial Pangenomics to Be Used by Wet-Lab Scientists.

Methods Mol Biol 2021 ;2242:233-243

Department of Agricultural and Food Science, University of Bologna, Bologna, Italy.

Making use of mathematics and statistics, bioinformatics helps biologists to quickly obtain information from a huge amount of experimental data. Nowadays, a large number of web- and computer-based tools are available, allowing more unskilled scientists to be familiar with data analysis techniques. The present chapter gives an overview of the most easy-to-use tools and software packages for bacterial genes and genome analysis present on the Web, with the aim to mainly help wet-lab researcher at undergraduate and postgraduate levels to introduce them to bioinformatics analysis of biological data. Read More

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January 2021

Simple, Reliable, and Time-Efficient Manual Annotation of Bacterial Genomes with MAISEN.

Methods Mol Biol 2021 ;2242:221-229

Faculty of Biology, Institute of Microbiology, Department of Environmental Microbiology and Biotechnology, University of Warsaw, Warsaw, Poland.

Over the last 15 years, the costs of DNA sequencing have sharply fallen, effectively shifting the costs of DNA analysis from sequencing to bioinformatic curation and storage. A huge number of available DNA sequences (including genomes and metagenomes) resulted in the development of various tools for sequence annotation. While much effort has been invested into the development of automatic annotation pipelines, manual curation of their results is still necessary in order to obtain a reliable and strictly validated data. Read More

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January 2021

Functional Metagenomics for Identification of Antibiotic Resistance Genes (ARGs).

Methods Mol Biol 2021 ;2242:173-183

Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.

The identification of antibiotic resistance genes (ARGs) in microbial communities is one of the most challenging tasks in biology. The evolution and improvement of genome sequencing techniques, combined with the improvement of computational analysis techniques, have allowed us to acquire increasingly detailed information on the complex and varied microbial community that coexists and coevolves in the most heterogeneous environment. This chapter describes how to identify and quantify ARGs, using specific tools (Bowtie2, Bedtools for coverage, G/C content, and the estimated number of reads mapping each open reading frame; RGI tool, with the support of CARD database, to inspect the distribution of antibiotic resistance genes). Read More

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January 2021

Accurate Annotation of Microbial Metagenomic Genes and Identification of Core Sets.

Chiara Vanni

Methods Mol Biol 2021 ;2242:115-138

Max Planck Institute for Marine Microbiology, Bremen, Germany.

In the past decade, metagenomics studies of microbial communities have added billions of sequences to the databases. This extensive amount of data and information has the potential to widen our understanding of the functioning of microbial communities and their roles in the environment. A fundamental step in this process is the functional and taxonomic profiling of the metagenomes, through an accurate gene annotation. Read More

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January 2021

Comparative Genomics, from the Annotated Genome to Valuable Biological Information: A Case Study.

Methods Mol Biol 2021 ;2242:91-112

Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk & Medical University of Gdansk, University of Gdansk, Gdansk, 58 Abrahama, Poland.

High availability of fast, cheap, and high-throughput next generation sequencing techniques resulted in acquisition of numerous de novo sequenced and assembled bacterial genomes. It rapidly became clear that digging out useful biological information from such a huge amount of data presents a considerable challenge. In this chapter we share our experience with utilization of several handy open source comparative genomic tools. Read More

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January 2021