10,069 results match your criteria sequenced characterized

Genetic diversity and phylogenetic analysis of the surface layer protein A gene (slpA) among Clostridioides difficile clinical isolates from Tehran, Iran.

Anaerobe 2021 Jun 7:102403. Epub 2021 Jun 7.

Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.

Clostridioides difficile is the most common causative agent of healthcare-associated diarrhea. C. difficile strains produce a crystalline surface layer protein (SlpA), encoded by the slpA gene. Read More

View Article and Full-Text PDF

The complete mitochondrial genome and phylogeny of (Pavlovales, Pavlovophyceae).

Mitochondrial DNA B Resour 2021 May 21;6(6):1702-1703. Epub 2021 May 21.

Marine Ecosystem Research Center, Korea Institute of Ocean Science & Technology, Busan, Republic of Korea.

The complete mitochondrial genome of the pavlovophycean microalga CCMP 620 was sequenced and characterized. The circular mitogenome is a total 29,282 bp in length with 39.2% GC content and contains 47 genes, including 20 protein-coding, three rRNA, and 24 tRNA genes. Read More

View Article and Full-Text PDF

Clostridioides difficile specific DNA adenine methyltransferase CamA squeezes and flips adenine out of DNA helix.

Nat Commun 2021 06 8;12(1):3436. Epub 2021 Jun 8.

Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Clostridioides difficile infections are an urgent medical problem. The newly discovered C. difficile adenine methyltransferase A (CamA) is specified by all C. Read More

View Article and Full-Text PDF

Potential G-quadruplexes and i-Motifs in the SARS-CoV-2.

PLoS One 2021 8;16(6):e0250654. Epub 2021 Jun 8.

Advanced (Magnetic) Theranostic Nanostructures Lab, INL-International Iberian Nanotechnology Laboratory, Braga, Portugal.

Quadruplex structures have been identified in a plethora of organisms where they play important functions in the regulation of molecular processes, and hence have been proposed as therapeutic targets for many diseases. In this paper we report the extensive bioinformatic analysis of the SARS-CoV-2 genome and related viruses using an upgraded version of the open-source algorithm G4-iM Grinder. This version improves the functionality of the software, including an easy way to determine the potential biological features affected by the candidates found. Read More

View Article and Full-Text PDF

Phylogenomic Characterization of a Novel Species Associated with Fatal Diphtheritic Stomatitis in Endangered Yellow-Eyed Penguins.

mSystems 2021 Jun 8:e0032021. Epub 2021 Jun 8.

Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom.

Yellow-eyed penguins, Megadyptes antipodes, are an endangered species that are endemic to New Zealand. Outbreaks of diphtheritic stomatitis have caused significant mortality for this species, especially among young chicks. In this study, we isolated 16 sp. Read More

View Article and Full-Text PDF

First Report of Brown Leaf Spot of Caused by in China.

Plant Dis 2021 Jun 7. Epub 2021 Jun 7.

chengdu, China;

"Chuanzao 2" is a walnut variety derived from the hybridization of L. and Dode distributed in southwest China, where it is an economically important tree species in rural regions (Xiao et al. 2012). Read More

View Article and Full-Text PDF

Enhanced characterization of the thyA system for mutational analysis in Escherichia coli: Defining mutationally "hot" regions of the gene.

Mutat Res 2021 May 25;823:111754. Epub 2021 May 25.

Department of Microbiology, Immunology, and Molecular Genetics, and The Molecular Biology Institute, University of California, and the David Geffen School of Medicine, Los Angeles, CA 90095, United States. Electronic address:

We have extensively characterized base substitution mutations in the 795 base pair (bp) long E. coli thyA gene to define as many of the base substitution mutational sites that inactivate the gene as possible. The resulting catalog of mutational sites constitutes a system with up to 5 times as many sites for monitoring each of the six base substitution mutations as the widely used rpoB/Rif system. Read More

View Article and Full-Text PDF

Leveraging Microbial Genomes and Genomic Context for Chemical Discovery.

Acc Chem Res 2021 Jun 4. Epub 2021 Jun 4.

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.

ConspectusThe genomic era has dramatically changed how we discover and investigate microbial biochemistry. In particular, the exponential expansion in the number of sequenced microbial genomes provides investigators with a vast wealth of sequence data to exploit for the discovery of biochemical functions and mechanisms, as well as novel enzymes and metabolites. In contrast to early biochemical work, which was largely characterized by "forward" approaches that proceed from biomass to enzyme to gene, the availability of genome sequences enables the discovery of new microbial metabolic activities, enzymes, and metabolites by "reverse" approaches that originate with genetic information or by approaches that incorporate features of both forward and reverse methodologies. Read More

View Article and Full-Text PDF

Three Novel Homozygous Mutations of the Gene in a Gitelman Syndrome Patient.

Int J Gen Med 2021 24;14:1999-2002. Epub 2021 May 24.

Department of Endocrinology, The Peoples Hospital of Guangxi Zhuang Autonomous Region, Guangxi, People's Republic of China.

Aim: Gitelman syndrome (GS) is an autosomal recessive disorder characterized by hypokalemic metabolic alkalosis. In this study, we investigated the clinical presentation and sequenced 26 exons of gene in a patient with a clinical suspicion of GS.

Methods: Clinical work-up including clinical examination, electrocardiography (ECG), chest X-ray, bone mineral density (BMD), and ultrasound examination was conducted and all exons of gene were analyzed by whole-exome sequencing. Read More

View Article and Full-Text PDF

Circulating tumor cells, circulating tumor DNA, and disease characteristics in young women with metastatic breast cancer.

Breast Cancer Res Treat 2021 Jun 2;187(2):397-405. Epub 2021 Jun 2.

Robert H. Lurie Comprehensive Cancer Center of Northwestern University, 676 N St. Clair St Suite 850, Chicago, IL, 60611, USA.

Background: Clinical and genomic data from patients with early-stage breast cancer suggest more aggressive disease in premenopausal women. However, the association between age, disease course, and molecular profile from liquid biopsy in metastatic breast cancer (MBC) is not well characterized.

Methods: Patients were classified as premenopausal (< 45 years), perimenopausal (45-55 years), or postmenopausal (> 55 years). Read More

View Article and Full-Text PDF

Characterization of glutamine synthetase from the ammonium-excreting strain HM053 of Azospirillum brasilense.

Braz J Biol 2021 28;82:e235927. Epub 2021 May 28.

Universidade Federal do Paraná - UFPR, Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Curitiba, PR, Brasil.

Glutamine synthetase (GS), encoded by glnA, catalyzes the conversion of L-glutamate and ammonium to L-glutamine. This ATP hydrolysis driven process is the main nitrogen assimilation pathway in the nitrogen-fixing bacterium Azospirillum brasilense. The A. Read More

View Article and Full-Text PDF

Characterization of the Highly Efficient Acid-Stable Xylanase and β-Xylosidase System from the Fungus ATHUM 8891 ( ATHUM 8891).

J Fungi (Basel) 2021 May 29;7(6). Epub 2021 May 29.

Enzyme and Microbial Biotechnology Unit, Department of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece.

Two novel xylanolytic enzymes, a xylanase and a β-xylosidase, were simultaneously isolated and characterized from the extracellular medium of ATHUM 8891 (anamorph ATHUM 8891), grown on Brewer's Spent Grain as a sole carbon source. They represent the first pair of characterized xylanolytic enzymes of the genus and the first extensively characterized xylanolytic enzymes of the family . In contrast to other xylanolytic enzymes isolated from the same family, both enzymes are characterized by exceptional thermostability and stability at low pH values, in addition to activity optima at temperatures around 65 °C and acidic pH values. Read More

View Article and Full-Text PDF

DNA Aptamers against Vaccinia-Related Kinase (VRK) 1 Block Proliferation in MCF7 Breast Cancer Cells.

Pharmaceuticals (Basel) 2021 May 17;14(5). Epub 2021 May 17.

Grupo de Aptámeros, Departamento de Bioquímica-Investigación, IRYCIS-Hospital Universitario Ramón y Cajal, Carretera de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain.

Vaccinia-related kinase (VRK) 1 is a serin/threonine kinase that plays an important role in DNA damage response (DDR), phosphorylating some proteins involved in this process such as 53BP1, NBS1 or H2AX, and in the cell cycle progression. In addition, VRK1 is overexpressed in many cancer types and its correlation with poor prognosis has been determined, showing VRK1 as a new therapeutic target in oncology. Using in vitro selection, high-affinity DNA aptamers to VRK1 were selected from a library of ssDNA. Read More

View Article and Full-Text PDF

Missense Variant in a Cat with L-2-Hydroxyglutaric Aciduria.

Genes (Basel) 2021 May 1;12(5). Epub 2021 May 1.

Anderson Moores Veterinary Specialists, Winchester SO21 2LL, Hampshire, UK.

A 7-month-old, spayed female, domestic longhair cat with L-2-hydroxyglutaric aciduria (L-2-HGA) was investigated. The aim of this study was to investigate the clinical signs, metabolic changes and underlying genetic defect. The owner of the cat reported a 4-month history of multiple paroxysmal seizure-like episodes, characterized by running around the house, often in circles, with abnormal behavior, bumping into obstacles, salivating and often urinating. Read More

View Article and Full-Text PDF

Polysaccharide utilization loci-driven enzyme discovery reveals BD-FAE: a bifunctional feruloyl and acetyl xylan esterase active on complex natural xylans.

Biotechnol Biofuels 2021 May 31;14(1):127. Epub 2021 May 31.

Department of Bioproduct Engineering, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.

Background: Nowadays there is a strong trend towards a circular economy using lignocellulosic biowaste for the production of biofuels and other bio-based products. The use of enzymes at several stages of the production process (e.g. Read More

View Article and Full-Text PDF

The evolution of hard tick-borne relapsing fever borreliae is correlated with vector species rather than geographical distance.

BMC Ecol Evol 2021 May 31;21(1):105. Epub 2021 May 31.

Joint Graduate School of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8515, Japan.

Background: Relapsing fever (RF) borreliae are arthropod-borne spirochetes and some of them cause human diseases, which are characterized by relapsing or recurring episodes of fever. Recently, it has been classified into two groups: soft tick-borne RF (STRF) borreliae and hard tick-borne RF (HTRF) borreliae. STRF borreliae include classical RF agents and HTRF borreliae, the latter of which include B. Read More

View Article and Full-Text PDF

First report of on roots of in Guangdong Province, China.

Plant Dis 2021 May 31. Epub 2021 May 31.

Guangzhou Institute of Forestry and Landscape Architecture, Soil environmental investigation department, Guangzhou, Guangdong, China;

(), a perennial herbaceous legume, is widely distributed in southern China. . has antipyretic, antiseptic and expectorant properties and can therefore be used as a phytomedicine (Ghosal et al. Read More

View Article and Full-Text PDF

Sequence and Phylogenetic Analysis of the First Complete Genome of Ricetungro spherical virus in Malaysia.

Iran J Biotechnol 2020 Oct 1;18(4):e2566. Epub 2020 Oct 1.

Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 Bangi, Malaysia.

Background: Rice tungro disease (RTD) is a viral disease mainly affecting rice in Asia. RTD caused by and . To date, there are only 5 RTSV isolates have been reported. Read More

View Article and Full-Text PDF
October 2020

Development, Identification, and Application of a Germplasm Specific SCAR Marker for Kimura et Migo.

Front Plant Sci 2021 14;12:669458. Epub 2021 May 14.

College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China.

The stems of have been used as a rare and valuable Chinese tonic medicine, known as "Tiepi Fengdou", since the Qing dynasty. Because of the increased market demand and continued exploitation of this plant, the reserves of wild resources have been depleted, and products on the market are being increasingly adulterated. Such changes have strongly affected the sustainable utilization of this valuable medicinal plant resource and the development of related industries. Read More

View Article and Full-Text PDF

Low bias multiple displacement amplification with confinement effect based on agarose gel.

Anal Bioanal Chem 2021 May 28. Epub 2021 May 28.

State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, Jiangsu, China.

Multiple displacement amplification (MDA) is a popular single-cell whole-genome amplification (WGA) technique that can greatly improve the amplification efficiency of single-cell genomes. However, there is an inherent problem that cannot be completely solved, that is, the amplification bias. We here propose an improved MDA method based on low melting agarose gel, named gelMDA. Read More

View Article and Full-Text PDF

A novel mutation in ext2 caused hereditary multiple exostoses through reducing the synthesis of heparan sulfate.

Genet Mol Biol 2021 21;44(2):e20200334. Epub 2021 May 21.

Guangzhou Medical University, Guangzhou Women and Children's Medical Center, Guangzhou Institute of Pediatrics, Guangzhou, Guangdong Province, P.R. China.

Hereditary multiple exostoses (HME) is a rare skeletal disorder characterized by the formation of multiple benign cartilage-capped tumors, usually in the metaphyseal region of the long bones. Over 70% of HME cases arise from monoallelic mutations in either of the two genes encoding the heparan sulfate (HS) synthesis enzymes, ext1 and ext2. To identify more HME-associated mutations, genomic DNA from members of five independent consanguineous families with HME was sequenced with whole exome sequencing (WES). Read More

View Article and Full-Text PDF

Next generation sequencing for pathogen detection in periprosthetic joint infections.

EFORT Open Rev 2021 Apr 1;6(4):236-244. Epub 2021 Apr 1.

Department of Orthopaedic Surgery, Stanford University, Stanford, California, USA.

Periprosthetic joint infections (PJI) represent one of the most catastrophic complications following total joint arthroplasty (TJA). The lack of standardized diagnostic tests and protocols for PJI is a challenge for arthroplasty surgeons.Next generation sequencing (NGS) is an innovative diagnostic tool that can sequence microbial deoxyribonucleic acids (DNA) from a synovial fluid sample: all DNA present in a specimen is sequenced in parallel, generating millions of reads. Read More

View Article and Full-Text PDF

Inhibition of cell migration and invasion by ICAM-1 binding DNA aptamers.

Anal Biochem 2021 May 24;628:114262. Epub 2021 May 24.

Department of Bioengineering, Karamanoğlu Mehmetbey University, Karaman, Turkey.

Cancer is the second leading cause of death worldwide and most of the cancer-related deaths result from metastasis. As expressed on the surface of various cancer cell types, intercellular adhesion molecule-1 (ICAM-1) has been shown to play a role in the attachment, invasion and migration of tumor cells. In this study, DNA aptamers were generated against ICAM-1 by cell-SELEX and protein SELEX method using ICAM-1 CHO-ICAM-1 cells and ICAM-1 protein, respectively. Read More

View Article and Full-Text PDF

Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors.

PLoS One 2021 26;16(5):e0252181. Epub 2021 May 26.

InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea.

GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. Due to the low cost of genome sequencing, multiple strains of specific species have been sequenced: e.g. Read More

View Article and Full-Text PDF

Cholesterol metabolism is a potential therapeutic target in Duchenne muscular dystrophy.

J Cachexia Sarcopenia Muscle 2021 May 26. Epub 2021 May 26.

Généthon, Evry, France.

Background: Duchenne muscular dystrophy (DMD) is a lethal muscle disease detected in approximately 1:5000 male births. DMD is caused by mutations in the DMD gene, encoding a critical protein that links the cytoskeleton and the extracellular matrix in skeletal and cardiac muscles. The primary consequence of the disrupted link between the extracellular matrix and the myofibre actin cytoskeleton is thought to involve sarcolemma destabilization, perturbation of Ca homeostasis, activation of proteases, mitochondrial damage, and tissue degeneration. Read More

View Article and Full-Text PDF

Two novel mutations in PADI6 and TLE6 genes cause female infertility due to arrest in embryonic development.

J Assist Reprod Genet 2021 May 26. Epub 2021 May 26.

Prenatal Diagnosis Center, Guizhou Provincial People's Hospital, Guiyang, China.

Purpose: This study aims to identify genetic causes of female infertility associated with recurrent failure of assisted reproductive technology (ART) characterized by embryonic developmental arrest.

Methods: We recruited infertile patients from two consanguineous families from the Reproductive Medicine Center of Guizhou Provincial People's Hospital. Peripheral blood was collected for genomic DNA extraction. Read More

View Article and Full-Text PDF

Taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism.

Mol Med 2021 May 24;27(1):50. Epub 2021 May 24.

Laboratorio de Líquido Sinovial, Instituto Nacional de Rehabilitación "Luis Guillermo Ibarra Ibarra", Calz México-Xochimilco 289, Arenal de Guadalupe, 14389, Mexico City, Mexico.

Objective: To evaluate the taxonomic composition of the gut microbiome in gout patients with and without tophi formation, and predict bacterial functions that might have an impact on urate metabolism.

Methods: Hypervariable V3-V4 regions of the bacterial 16S rRNA gene from fecal samples of gout patients with and without tophi (n = 33 and n = 25, respectively) were sequenced and compared to fecal samples from 53 healthy controls. We explored predictive functional profiles using bioinformatics in order to identify differences in taxonomy and metabolic pathways. Read More

View Article and Full-Text PDF

Use of Zebrafish Genetic Models to Study Etiology of the Amyloid-Beta and Neurofibrillary Tangle Pathways in Alzheimer's Disease.

Curr Neuropharmacol 2021 May 24. Epub 2021 May 24.

School of Health Sciences, Purdue University, West Lafayette, Indiana, United States.

The prevalence of neurodegenerative diseases is increasing globally, with an imperative need to identify and expand the availability of pharmaceutical treatment strategies. Alzheimer's disease is the most common neurodegenerative disease for which there is no cure or has limited treatments. Rodent models are primarily used in Alzheimer's disease research to investigate causes, pathology, molecular mechanisms, and pharmaceutical therapies. Read More

View Article and Full-Text PDF

Discovery of Cyclohexadepsipeptides with Anti-Zika Virus Activities and Biosynthesis of the Nonproteinogenic Building Block (3S)-Methyl-l-Proline.

J Biol Chem 2021 May 21:100822. Epub 2021 May 21.

State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China; Institute of Ocean Research, Peking University, Beijing 100191, China. Electronic address:

The fungal cyclohexadepsipeptides destruxins (DTXs), isaridins (ISDs) and isariins (ISRs) are nonribosomal peptides whose structures include a 19-membered ring composed of five amino acid residues and one α- or β-hydroxy acid residue. These cyclohexadepsipeptides contain unusual nonproteinogenic amino acid-building blocks and possess a range of antiviral, antibacterial and other activities. The biosynthetic gene clusters for ISDs and ISRs have not been identified, and the biosynthesis of the nonproteinogenic (3S)-methyl-l-proline residue, which is found in DTXs, ISDs and many other natural products, lacks full characterization. Read More

View Article and Full-Text PDF