37 results match your criteria β-diversity estimated

First report of squash vein yellowing virus naturally infecting butternut squash () in Texas.

Plant Dis 2021 Apr 6. Epub 2021 Apr 6.

Texas A&M University, Department of Plant Pathology & Microbiology, 2401 E. Bus. Hwy. 83, Weslaco, Texas, United States, 78596.

Virus diseases are major constraints to the production of cucurbits in the Texas Lower Rio Grande Valley. In September 2020, a ~8.1 ha butternut squash () field in Hidalgo County, Texas, was observed with virus-like symptoms of vein yellowing, leaf curl, mosaic, and foliar chlorosis. Read More

View Article and Full-Text PDF

Analysis of the evolution and transmission dynamics of the field MDV in China during the years 1995-2020, indicating the emergence of a unique cluster with the molecular characteristics of vv+ MDV that has become endemic in southern China.

Transbound Emerg Dis 2020 Dec 23. Epub 2020 Dec 23.

Institute for Poultry Science and Health, Guangxi University, Nanning, China.

Marek's disease (MD) continues to threaten the sustainability of the world poultry industry. In this study, the sequences of the meq gene of 220 MDV strains isolated during the years 1964-2020 were analysed, including 50 from our group plus 170 isolates from the GenBank. Analyses, using phylogenetic trees, amino acid (aa)-mutation screening, evolutionary studies and transmission dynamics were all performed. Read More

View Article and Full-Text PDF
December 2020

Genetic diversity and inter-relationships of fruit bio-chemicals and antioxidant activity in Iranian wild blackberry species.

Sci Rep 2020 11 4;10(1):18983. Epub 2020 Nov 4.

Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz, Iran.

Blackberries are a rich source of bio-chemicals such as anthocyanins and polyphenolic antioxidants. The evaluation of the extent of variation among wild genetic resources can provide useful information for the establishment of effective conservation strategies and future breeding programs. In this study, variations and inter-relationship of berry weight, total phenol (TP), total soluble solids (TSS), titratable acidity (TA), ascorbic acid (AA), anthocyanin and antioxidant activity were estimated in their values among 57 accessions belonging to 4 different Rubus spp. Read More

View Article and Full-Text PDF
November 2020

Cannabis use, other drug use, and risk of subsequent acute care in primary care patients.

Drug Alcohol Depend 2020 11 8;216:108227. Epub 2020 Aug 8.

Kaiser Permanente Washington Health Research Institute, 1730 Minor Ave, Suite 1600, Seattle, WA, 98101-1466, USA; Department of Psychiatry and Behavioral Sciences, University of Washington, 1959 NE Pacific Street, Box 356560, Room BB1644, Seattle, WA, 98195-6560, USA. Electronic address:

Background: Cannabis and other drug use is associated with adverse health events, but little is known about the association of routine clinical screening for cannabis or other drug use and acute care utilization. This study evaluated whether self-reported frequency of cannabis or other drug use was associated with subsequent acute care.

Method: This retrospective cohort study used EHR and claims data from 8 sites in Washington State that implemented annual substance use screening. Read More

View Article and Full-Text PDF
November 2020

Genetic Mapping and Nucleotide Diversity of Two Powdery Mildew Resistance Loci in Melon ().

Phytopathology 2020 Dec 21;110(12):1970-1979. Epub 2020 Oct 21.

Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Harbin, Heilongjiang Province, 150030, China.

Powdery mildew (PM) significantly and negatively affects the yield and quality of melon () worldwide. Race 2F is the predominant physiological race of the pathogen in many regions. We used accessions PMR 6 (P; resistant to PM) and M1-7 (P; susceptible to PM) to analyze the inheritance of resistance to PM (race 2F). Read More

View Article and Full-Text PDF
December 2020

Screening of new cell cycle suppressive compounds from marine-derived microorganisms in Chinese hamster ovary cells.

J Biosci Bioeng 2020 Jul 3;130(1):106-113. Epub 2020 Apr 3.

Graduate School of Engineering. Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan. Electronic address:

Monoclonal antibodies (mAbs) are active pharmaceutical ingredients in antibody drugs, produced mainly using recombinant Chinese hamster ovary (CHO) cells. The regulation of recombinant CHO cell proliferation can improve the productivity of heterologous proteins. Chemical compound approaches for cell cycle regulation have the advantages of simplicity and ease of use in industrial processes. Read More

View Article and Full-Text PDF

Unraveling the genetic diversity of Belgian Milk Sheep using medium-density SNP genotypes.

Anim Genet 2020 Mar 27;51(2):258-265. Epub 2019 Dec 27.

Livestock Genetics, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 30 - 2472, 3001, Leuven, Belgium.

The present study focuses on the Belgian Milk Sheep in Flanders (Belgium) and compares its genetic diversity and relationship with the Flemish Sheep, the Friesian Milk Sheep, the French Lacaune dairy sheep and other Northern European breeds. For this study, 94 Belgian Milk Sheep, 23 Flemish Sheep and 22 Friesian Milk Sheep were genotyped with the OvineSNP50 array. In addition, 29 unregistered animals phenotypically similar to Belgian Milk Sheep were genotyped using the 15K ISGC chip. Read More

View Article and Full-Text PDF

Isolation of Yasminevirus, the First Member of Klosneuvirinae Isolated in Coculture with Vermamoeba vermiformis, Demonstrates an Extended Arsenal of Translational Apparatus Components.

J Virol 2019 12 12;94(1). Epub 2019 Dec 12.

Aix-Marseille Université, MEPHI (Microbes, Evolution, Phylogeny and Infections), IRD, APHM, Faculté de Médecine, Marseille, France

The family of giant viruses is still expanding, and evidence of a translational machinery is emerging in the virosphere. The Klosneuvirinae group of giant viruses was first reconstructed from studies, and then a unique member was isolated, Bodo saltans virus. Here we describe the isolation of a new member in this group using coculture with the free-living amoeba This giant virus, called Yasminevirus, has a 2. Read More

View Article and Full-Text PDF
December 2019

Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes.

Microbiome 2019 06 27;7(1):97. Epub 2019 Jun 27.

Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.

Background: Hospital wastewaters contain fecal material from a large number of individuals, of which many are undergoing antibiotic therapy. It is, thus, plausible that hospital wastewaters could provide opportunities to find novel carbapenemases and other resistance genes not yet described in clinical strains. Our aim was therefore to investigate the microbiota and antibiotic resistome of hospital effluent collected from the city of Mumbai, India, with a special focus on identifying novel carbapenemases. Read More

View Article and Full-Text PDF

[Podophyllotoxin analogue with bicyclo[3.2.1]octane moiety annelated with indole: synthesis, molecular modeling, and biological testing].

Biomed Khim 2019 Feb;65(2):86-90

Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia; Institute of Physiologically active compounds, Russian Academy of Sciences, Chernogolovka, Russia.

C4-Ester derivatives of the anticancer agent podophyllotoxin with bridged moieties can either inhibit polymerization of alpha,beta-tubulin with the formation of microtubules (analogously to the parent molecule) or cause an unusual effect of "curling and shortening" of the microtubules (MT). In order to predict the effect of bridged podophyllotoxin derivatives on the MT network using computer molecular modeling it is desirable to enhance the structural diversity of their bridged substituents. In the present work we synthesized novel podophyllotoxin ester with bicyclo[3. Read More

View Article and Full-Text PDF
February 2019

Addition of a polygenic risk score, mammographic density, and endogenous hormones to existing breast cancer risk prediction models: A nested case-control study.

PLoS Med 2018 09 4;15(9):e1002644. Epub 2018 Sep 4.

Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.

Background: No prior study to our knowledge has examined the joint contribution of a polygenic risk score (PRS), mammographic density (MD), and postmenopausal endogenous hormone levels-all well-confirmed risk factors for invasive breast cancer-to existing breast cancer risk prediction models.

Methods And Findings: We conducted a nested case-control study within the prospective Nurses' Health Study and Nurses' Health Study II including 4,006 cases and 7,874 controls ages 34-70 years up to 1 June 2010. We added a breast cancer PRS using 67 single nucleotide polymorphisms, MD, and circulating testosterone, estrone sulfate, and prolactin levels to existing risk models. Read More

View Article and Full-Text PDF
September 2018

Lipid peroxidation diminishing perspective of isolated theaflavins and thearubigins from black tea in arginine induced renal malfunctional rats.

Lipids Health Dis 2018 Jul 18;17(1):157. Epub 2018 Jul 18.

Department of Food Science and Human Nutrition, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan.

Background: Recently oxidative stress induced maladies have amplified owing to sedentary lifestyle and monotonous diet. Introduction of plant based biomolecules may be a suitable strategy to cope with the lipid peroxidation. In this context, black tea polyphenols (theaflavin & thearubigins) are in fame among the scientific community as cost effective therapeutic agents owing to their safety, economics, structural diversity and ability to modulate various lipid peroxidation responses by halting the expression of different metabolic targets. Read More

View Article and Full-Text PDF

Evaluating the impact of synthetic herbicides on soil dwelling macrobes and the physical state of soil in an agro-ecosystem.

Ecotoxicol Environ Saf 2018 Jul 20;156:205-215. Epub 2018 Mar 20.

Biotechnology and Nuclear Agriculture Research Institute, Ghana Atomic Energy Commission, Post Office Box L.G. 80, Legon, Accra, Ghana; Radiation, Entomology and Pest Management Centre, Ghana. Electronic address:

This study evaluated three herbicides active ingredients: Paraquat, Glyphosate and 2,4-D Amine in commercial formulations as Frankoquat, Roundup and Agriherb respectively under field conditions to determine their influence on soil dwelling macrobes and the physical state of soil. Herbicides were serially diluted to three treatment concentrations for each plus three controls. Herbicide concentrations were applied to the demarcated field on three consecutive occasions in splits. Read More

View Article and Full-Text PDF

Mutation spectrum and risk of colorectal cancer in African American families with Lynch syndrome.

Gastroenterology 2015 Nov 3;149(6):1446-53. Epub 2015 Aug 3.

Center for Clinical Cancer Genetics, the University of Chicago, Chicago, Illinois. Electronic address:

Background & Aims: African Americans (AAs) have the highest incidence of and mortality resulting from colorectal cancer (CRC) in the United States. Few data are available on genetic and nongenetic risk factors for CRC among AAs. Little is known about cancer risks and mutations in mismatch repair (MMR) genes in AAs with the most common inherited CRC condition, Lynch syndrome. Read More

View Article and Full-Text PDF
November 2015

Unknown aspect of the old disease: does dyslipidemia in systemic AA amyloidosis differ from the dyslipidemia in primary glomerulonephritis?

Ren Fail 2015 16;37(8):1273-9. Epub 2015 Jul 16.

a Department of Nephrology , Ankara Numune Educational and Research Hospital , Ankara , Turkey and.

Aim: To investigate the nature of dyslipidemia and its diversity in patients with systemic AA amyloidosis.

Methods: The reports of the kidney biopsies performed due to nephrotic proteinuria (>3.5 g/day/1. Read More

View Article and Full-Text PDF

DISTMIX: direct imputation of summary statistics for unmeasured SNPs from mixed ethnicity cohorts.

Bioinformatics 2015 Oct 9;31(19):3099-104. Epub 2015 Jun 9.

Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA.

Motivation: To increase the signal resolution for large-scale meta-analyses of genome-wide association studies, genotypes at unmeasured single nucleotide polymorphisms (SNPs) are commonly imputed using large multi-ethnic reference panels. However, the ever increasing size and ethnic diversity of both reference panels and cohorts makes genotype imputation computationally challenging for moderately sized computer clusters. Moreover, genotype imputation requires subject-level genetic data, which unlike summary statistics provided by virtually all studies, is not publicly available. Read More

View Article and Full-Text PDF
October 2015

Saccharina genomes provide novel insight into kelp biology.

Nat Commun 2015 Apr 24;6:6986. Epub 2015 Apr 24.

Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.

Seaweeds are essential for marine ecosystems and have immense economic value. Here we present a comprehensive analysis of the draft genome of Saccharina japonica, one of the most economically important seaweeds. The 537-Mb assembled genomic sequence covered 98. Read More

View Article and Full-Text PDF

Hormonal contraception and the risk of HIV acquisition: an individual participant data meta-analysis.

PLoS Med 2015 Jan 22;12(1):e1001778. Epub 2015 Jan 22.

Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.

Background: Observational studies of a putative association between hormonal contraception (HC) and HIV acquisition have produced conflicting results. We conducted an individual participant data (IPD) meta-analysis of studies from sub-Saharan Africa to compare the incidence of HIV infection in women using combined oral contraceptives (COCs) or the injectable progestins depot-medroxyprogesterone acetate (DMPA) or norethisterone enanthate (NET-EN) with women not using HC.

Methods And Findings: Eligible studies measured HC exposure and incident HIV infection prospectively using standardized measures, enrolled women aged 15-49 y, recorded ≥15 incident HIV infections, and measured prespecified covariates. Read More

View Article and Full-Text PDF
January 2015

Genetic characterization of local Criollo pig breeds from the Americas using microsatellite markers.

J Anim Sci 2014 Nov;92(11):4823-32

Departamento de Genética, Campus de Excelencia Internacional, Universidad de Córdoba, 14071 Córdoba, Spain.

Little is known about local Criollo pig genetic resources and relationships among the various populations. In this paper, genetic diversity and relationships among 17 Criollo pig populations from 11 American countries were assessed with 24 microsatellite markers. Heterozygosities, F-statistics, and genetic distances were estimated, and multivariate, genetic structure and admixture analyses were performed. Read More

View Article and Full-Text PDF
November 2014

Genome-wide admixture and association study of serum iron, ferritin, transferrin saturation and total iron binding capacity in African Americans.

Hum Mol Genet 2015 Jan 15;24(2):572-81. Epub 2014 Sep 15.

Department of Genetics Department of Biostatistics and

Iron is an essential component of many important proteins and enzymes, including hemoglobin, which is responsible for carrying oxygen to the cells. African Americans (AAs) have a greater prevalence of iron deficiency compared with European Americans. We conducted genome-wide admixture-mapping and association studies for serum iron, serum ferritin, transferrin saturation (SAT) and total iron binding capacity (TIBC) in 2347 AAs participating in the Jackson Heart Study (JHS). Read More

View Article and Full-Text PDF
January 2015

Traceability of polychlorinated dibenzo-dioxins/furans pollutants in soil and their ecotoxicological effects on genetics, functions and composition of bacterial community.

Chemosphere 2014 Aug 14;108:326-33. Epub 2014 Feb 14.

Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria (AECS), B.P. Box 6091, Damascus, Syria.

Dioxins (PCDD/Fs) are persistent organic pollutants. Their accumulation in soil is a crucial step in their transmission through the ecosystem. Traceability of dioxin in soil was evaluated in four sites A, B, C and D considered as potential industrial PCDD/Fs sources in Syria. Read More

View Article and Full-Text PDF

Vitamin D-binding protein and vitamin D status of black Americans and white Americans.

N Engl J Med 2013 Nov;369(21):1991-2000

From the Department of Medicine, Brigham and Women's Hospital (C.E.P.), Division of Nephrology, Massachusetts General Hospital (J.W., H.T., I.B., R.T.), Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School (A.H.B.), Division of Nephrology, Beth Israel Deaconess Medical Center (D.Z., S.A.K.), and Howard Hughes Medical Institute (D.Z., S.A.K.) - all in Boston; the Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore (M.K.E., A.B.Z.); the Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD (M.N.); and the Department of Medicine, San Francisco General Hospital and University of California, San Francisco, San Francisco (N.R.P.).

Background: Low levels of total 25-hydroxyvitamin D are common among black Americans. Vitamin D-binding protein has not been considered in the assessment of vitamin D deficiency.

Methods: In the Healthy Aging in Neighborhoods of Diversity across the Life Span cohort of blacks and whites (2085 participants), we measured levels of total 25-hydroxyvitamin D, vitamin D-binding protein, and parathyroid hormone as well as bone mineral density (BMD). Read More

View Article and Full-Text PDF
November 2013

DiffSplice: the genome-wide detection of differential splicing events with RNA-seq.

Nucleic Acids Res 2013 Jan 15;41(2):e39. Epub 2012 Nov 15.

Department of Computer Science, University of Kentucky, Lexington, KY 40506, USA.

The RNA transcriptome varies in response to cellular differentiation as well as environmental factors, and can be characterized by the diversity and abundance of transcript isoforms. Differential transcription analysis, the detection of differences between the transcriptomes of different cells, may improve understanding of cell differentiation and development and enable the identification of biomarkers that classify disease types. The availability of high-throughput short-read RNA sequencing technologies provides in-depth sampling of the transcriptome, making it possible to accurately detect the differences between transcriptomes. Read More

View Article and Full-Text PDF
January 2013

Why would plant species become extinct locally if growing conditions improve?

Int J Biol Sci 2012 7;8(8):1121-9. Epub 2012 Sep 7.

Alterra, Wageningen University and Research Centre, PO Box 47, 6700 AA Wageningen, Netherlands.

Two assumptions underlie current models of the geographical ranges of perennial plant species: 1. current ranges are in equilibrium with the prevailing climate, and 2. changes are attributable to changes in macroclimatic factors, including tolerance of winter cold, the duration of the growing season, and water stress during the growing season, rather than to biotic interactions. Read More

View Article and Full-Text PDF
February 2013

The rhesus macaque is three times as diverse but more closely equivalent in damaging coding variation as compared to the human.

BMC Genet 2012 Jun 29;13:52. Epub 2012 Jun 29.

Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA.

Background: As a model organism in biomedicine, the rhesus macaque (Macaca mulatta) is the most widely used nonhuman primate. Although a draft genome sequence was completed in 2007, there has been no systematic genome-wide comparison of genetic variation of this species to humans. Comparative analysis of functional and nonfunctional diversity in this highly abundant and adaptable non-human primate could inform its use as a model for human biology, and could reveal how variation in population history and size alters patterns and levels of sequence variation in primates. Read More

View Article and Full-Text PDF

Ethnic differentiation of copy number variation on chromosome 16p12.3 for association with obesity phenotypes in European and Chinese populations.

Int J Obes (Lond) 2013 Feb 6;37(2):188-90. Epub 2012 Mar 6.

Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China.

Objective: Genomic copy number variations (CNVs) have been strongly implicated as important genetic factors for obesity. A recent genome-wide association study identified a novel variant, rs12444979, which is in high linkage disequilibrium with CNV 16p12.3, for association with obesity in Europeans. Read More

View Article and Full-Text PDF
February 2013

Heterosis as investigated in terms of polyploidy and genetic diversity using designed Brassica juncea amphiploid and its progenitor diploid species.

PLoS One 2012 21;7(2):e29607. Epub 2012 Feb 21.

Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India.

Fixed heterosis resulting from favorable interactions between the genes on their homoeologous genomes in an allopolyploid is considered analogous to classical heterosis accruing from interactions between homologous chromosomes in heterozygous plants of a diploid species. It has been hypothesized that fixed heterosis may be one of the causes of low classical heterosis in allopolyploids. We used Indian mustard (Brassica juncea, 2n = 36; AABB) as a model system to analyze this hypothesis due to ease of its resynthesis from its diploid progenitors, B. Read More

View Article and Full-Text PDF

The toxicity of Roundup Original Max to 13 species of larval amphibians.

Environ Toxicol Chem 2009 Sep;28(9):2004-8

Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA.

With the increased use of glyphosate-based herbicides (marketed under several names, including Roundup and Vision), there has been a concomitant increased concern about the unintended impacts that particular formulations containing the popular surfactant polyethoxylated tallowamine (POEA) might have on amphibians. Published studies have examined a relatively small number of anuran species (primarily from Australia and eastern North America) and, surprisingly, no species of salamanders. Using a popular formulation of glyphosate (Roundup Original Max), the goal of the present study was to conduct tests of lethal concentrations estimated to kill 50% of a population after 96 h (LC50(96-h)) on a wider diversity of species from both eastern and western North America. Read More

View Article and Full-Text PDF
September 2009

Extensive oral shedding of human herpesvirus 8 in a renal allograft recipient.

Oral Microbiol Immunol 2009 Apr;24(2):109-15

UCL Eastman Dental Institute, Oral Medicine Department, London, UK.

Introduction: Studies were conducted to investigate changes in the extent of human herpesvirus 8 (HHV-8) shedding and diversity of HHV-8 strains in the mouth of a renal allograft recipient who developed cutaneous post-transplantation Kaposi's sarcoma.

Methods: Matched oral and blood samples were obtained from a Saudi Arabian renal allograft recipient from 3 days before to 38 weeks after transplantation, and from his kidney donor. Polymerase chain reaction (PCR) protocols to amplify selected HHV-8 sub-genomic regions were applied to detect and quantify HHV-8 DNA. Read More

View Article and Full-Text PDF

Evolutionary dynamics of variant genomes of human papillomavirus types 18, 45, and 97.

J Virol 2009 Feb 26;83(3):1443-55. Epub 2008 Nov 26.

Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA.

Human papillomavirus type 18 (HPV18) and HPV45 account for approximately 20% of all cervix cancers. We show that HPV18, HPV45, and the recently discovered HPV97 comprise a clade sharing a most recent common ancestor within HPV alpha7 species. Variant lineages of these HPV types were classified by sequence analysis of the upstream regulatory region/E6 region among cervical samples from a population-based study in Costa Rica, and 27 representative genomes from each major variant lineage were sequenced. Read More

View Article and Full-Text PDF
February 2009