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Journal of Integrative Agriculture 2017年第3期16卷 532-539页

作者： shesh kumari Division of Crop Protection and Plant Health Crop Research Institute Prague 16106 Czech Republic

The cereal cyst nematode,Heterodera avenae Wollenweber,1924,is a major pest of cereal crops throughout the world and causes serious yield losses,especially of *** studies have shown that this species is widely distributed in the Czech *** this study,seven populations of *** were molecularly studied,and one population was morphologically *** regions（18S,28S,and internal transcribed spacer 1）of ribosomal DNA were sequenced and the analysis of the 18S gene of six populations did not reveal any variation,whereas the internal transcribed spacer 1and 28S sequences of six populations differed by only two nucleotides from a population in？*** and quick identification of cereal cyst nematodes is important for effective control measures and ribosomal sequence analyses of seven populations in this study will be useful in future phylogenetic studies of Heterodera *** in the Czech Republic.

关键词： Heterodera avenae PCR ribosomal DNA sequencing nematode

Genetic polymorphisms predict response to anti-tumor necrosis factor treatment in Crohn's disease

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World Journal of Gastroenterology 2017年第27期23卷 4958-4967页

作者： Uri Netz Jane Victoria Carter Maurice Robert Eichenberger Gerald Wayne Dryden Jianmin Pan shesh Nath Rai Susan Galandiuk Price Institute of Surgical Research the Hiram C.Polk Jr.MD Department of SurgeryUniversity of Louisville School of Medicine Department of Surgery A Soroka University Medical Center Faculty of Health Sciences Ben-Gurion University of the Negev Department of Medicine Division of GastroenterologyHepatology and Nutrition University of Louisville School of Medicine Louisville Department of Bioinformatics and Biostatistics University of Louisville School of Public Health and Information Sciences

To investigate genetic factors that might help define which Crohn’s disease (CD) patients are likely to benefit from anti-tumor necrosis factor (TNF) therapy. METHODSThis was a prospective cohort study. Patients were recruited from a university digestive disease practice database. We included CD patients who received anti-TNF therapy, had available medical records (with information on treatment duration and efficacy) and who consented to participation. Patients with allergic reactions were excluded. Patients were grouped as ever-responders or non-responders. Genomic DNA was extracted from peripheral blood, and 7 single nucleotide polymorphisms (SNPs) were assessed. The main outcome measure (following exposure to the drug) was response to therapy. The patient genotypes were assessed as the predictors of outcome. Possible confounders and effect modifiers included age, gender, race, and socioeconomic status disease, as well as disease characteristics (such as Montreal criteria). RESULTS121 patients were included. Twenty-one were non-responders, and 100 were ever-responders. Fas ligand SNP (rs763110) genotype frequencies, TNF gene -308 SNP (rs1800629) genotype frequencies, and their combination, were significantly different between groups on multivariable analysis controlling for Montreal disease behavior and perianal disease. The odds of a patient with a Fas ligand CC genotype being a non-responder were four-fold higher as compared to a TC or TT genotype (P = 0.009, OR = 4.30, 95%CI: 1.45-12.80). The presence of the A (minor) TNF gene -308 allele correlated with three-fold higher odds of being a non-responder (P = 0.049, OR = 2.88, 95%CI: 1.01-8.22). Patients with the combination of the Fas ligand CC genotype and the TNF -308 A allele had nearly five-fold higher odds of being a non-responder (P = 0.015, OR = 4.76, 95%CI: 1.35-16.77). No difference was seen for the remaining SNPs. CONCLUSIONThe Fas-ligand SNP and TNF gene -308 SNP are associated with anti-TNF treatment

关键词： Anti-tumor necrosis factor Fas ligand Antibody Response Crohn’s disease Single nucleotide polymorphisms Genotype Tumor necrosis factor gene

Proteomics and metabolic phenotyping define principal roles for the aryl hydrocarbon receptor in mouse liver

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Acta Pharmaceutica Sinica B 2021年第12期11卷 3806-3819页

作者： Jian Jin Banrida Wahlang Monika Thapa Kimberly Z.Head Josiah E.Hardesty Sudhir Srivastava Michael L.Merchant shesh N.Rai Russell A.Prough Matthew C.Cave Department of Pharmacology&Toxicology theUniversity of Louisville School ofMedicineLouisvilleKY 40202USA Department of Endocrinology the Second Affiliated Hospital&Yuying Children’s HospitalWenzhou Medical UniversityWenzhou 325027China Division of Gastroenterology Hepatology&NutritionDepartment of Medicinethe University of Louisville School of MedicineLouisvilleKY 40202USA Superfund Research Center the University of LouisvilleLouisvilleKY 40202USA eDepartment of Biochemistry and Molecular Geneticsthe University of Louisville School of MedicineLouisvilleKY 40202USA Department of Bioinformatics and Biostatistics the School of Public Health and Information Sciencesthe University of LouisvilleLouisvilleKY 40202USA Centre for Agricultural Bioinformatics ICAR-Indian Agricultural Statistics Research InstituteNew Delhi 110012India The Center for Integrative Environmental Health Sciences University of LouisvilleLouisvilleKY 40202USA Division of Nephrology&Hypertension Department of Medicinethe University of Louisville School of MedicineLouisvilleKY 40202USA The Hepatobiology and Toxicology Center University of LouisvilleLouisvilleKY 40202USA Alcohol Research Center University of LouisvilleLouisvilleKY 40202USA Biostatistics and Bioinformatics Facility James Graham Brown Cancer CenterLouisvilleKY 40202USA

Dioxin-like molecules have been associated with endocrine disruption and liver *** better understand aryl hydrocarbon receptor(AHR)biology,metabolic phenotyping and liver proteomics were performed in mice following ligand-activation or whole-body genetic ablation of this *** wild type(WT)and Ahr^(-/-) mice(Taconic)were fed a control diet and exposed to 3,3',4,4',5-pentachlorobiphenyl(PCB126)(61 nmol/kg by gavage)or vehicle for two ***126 increased expression of canonical AHR targets(Cyp1 a1 and Cyp1 a2)in WT but not Ahr^(-/-).Knockouts had increased adiposity with decreased glucose tolerance;smaller livers with increased steatosis and perilipin-2;and paradoxically decreased blood ***126 was associated with increased hepatic triglycerides in Ahr^(-/-).The liver proteome was impacted more so by Ahr^(-/-) genotype than ligandactivation,but top gene ontology(GO)processes were *** PCB126-associated liver proteome was *** principally regulated liver metabolism(e.g.,lipids,xenobiotics,organic acids)and bioenergetics,but it also impacted liver endocrine response(e.g.,the insulin receptor)and function,including the production of steroids,hepatokines,and pheromone binding *** effects could have been indirectly mediated by interacting transcription factors or *** biologic roles of the AHR and its ligands warrant more research in liver metabolic health and disease.

关键词： AHR Endocrine disruption Environmental liver disease Nonalcoholic fatty liver disease Perilipin-2 Pheromones PCB126

SWAT and Wavelet Analysis for Understanding the Climate Change Impact on Hydrologic Response

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Open Journal of Modern Hydrology 2012年第2期2卷 41-48页

作者： shesh Raj Koirala Randall W. Gentry 1Institute for a Secure and Sustainable Environment University of Tennessee Knoxville USA Institute for a Secure and Sustainable Environment University of Tennessee Knoxville USA 2Bechtel Corporation Houston USA.

Quantifying the hydrological response to an increased atmospheric carbon dioxide concentration and climate change is important in a watershed scale particularly from the application point of view. The specific objectives are to evaluate the climate change impact on the future water yield at the outlet of Clinch River Watershed upstream of Norris Lake in Tennessee, USA and see how the frequency of extreme water yield (e.g. flood) changes compared to present condition. The predicted future climate change by climate change scenarios A2 from community climate system model (CCSM) is applied. The model was calibrated using monthly average streamflow data from 1970 to 1989 and validated using similar data from 1990 to 2009 collected at a USGS gauging station 03528000. Changes in monthly average streamflow were estimated for long term (around 2099). Results were also interpreted in the time-frequency domain approach by showing how frequency of occurrence changes based on A2 scenario.

关键词： Climate Change SWAT Wavelet Hydrologic Response

Microbiome data analysis with applications to pre-clinical studies using QIIME2: Statistical considerations

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Genes & Diseases 2021年第2期8卷 215-223页

作者： shesh N.Rai Chen Qian Jianmin Pan Jayesh P.Rai Ming Song Juhi Bagaitkar Michael Merchant Matthew Cave Nejat K.Egilmez Craig J.McClain Biostatistics and Bioinformatics Facility James Graham Brown Cancer CenterUniversity of LouisvilleLouisvilleKY40202USA Department of Biostatistics and Bioinformatics University of LouisvilleLouisvilleKY40202USA University of Louisville Alcohol Research Center University of LouisvilleLouisvilleKY40202USA University of Louisville Hepatobiology&Toxicology Center University of LouisvilleLouisvilleKY40202USA Department of Oral Immunology&Infectious Diseases University of LouisvilleLouisvilleKY40202USA Department of Medicine University of LouisvilleLouisvilleKY40202USA Robley Rex Louisville VAMC LouisvilleKY40206USA Department of Microbiology&Immunology University of LouisvilleLouisvilleKY40202USA

Diversity analysis and taxonomic profiles can be generated from marker-gene sequence data with the help of many available computational *** Quantitative Insights into Microbial Ecology Version 2(QIIME2)has been widely used for 16S rRNA data *** many articles have demonstrated the use of QIIME2 with suitable datasets,the application to preclinical data has rarely been talked *** issues involved in the pre-clinical data include the low-quality score and small sample size that should be addressed properly during *** addition,there are few articles that discuss the detailed statistical methods behind those alpha and beta diversity significance tests that researchers are eager to *** the program without knowing the logic behind it is extremely *** this article,we first provide a guideline for analyzing 16S rRNA data using *** we will talk about issues in pre-clinical data,and how they could impact the ***,we provide brief explanations of statistical methods such as group significance tests and sample size calculation.

关键词： 16S rRNA gene Alpha diversity ANOVA Beta diversity Bioinformatics Microbiome data QIIME Sample size calculation

Genetic variation in coronavirus disease 2019:a literature review

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Infectious Diseases Research 2021年第4期2卷 6-10页

作者： Sabah Mayahi Maryam Sadegh shesh Poli Hadi Koohsari Department of Medical Mycology and Parasitology School of MedicineMazandaran University of Medical SciencesSariIran School of New Technologies Golestan University of Medical SciencesGorganIran Department of Microbiology Azadshahr BranchIslamic Azad UniversityAzadshahrIran

Background:The first Coronavirus Disease 2019(COVID-19)outbreak occurred in Wuhan,Hubei Province,China,in December *** originated from a novel severe acute respiratory syndrome coronavirus 2(SARS-CoV-2).As of 12 November 2021,above 251,788,329 people have been infected and 5,077,907 deaths deaths have been reported *** new COVID-19 belongs to the genus Coronavirus with its high mutation rate in the *** present study aimed to investigate the problems caused by the mutation and its effects on the immune ***:We used Google Scholar,Web of science,Scopus,and PubMed for searching the literature regarding genetic variation in ***:The publicly available literature in this area was reviewed to summarize the information about the genetic variation of this virus,phylogeny and genome structure,its relationship with the ABO blood group,genome variation,mutations in hotspots,and spike surface ***:Finally,it was concluded that COVID-19 can mutate;therefore,health authorities are required to remain cautious and completely prepared.

关键词： Coronaviruses COVID-19 Virus Genetic variation