Comparative Genomics of Two Jute Species and Insight Into Fibre
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microorganisms Article Label-Free Quantitative Proteomics Analysis in Susceptible and Resistant Brassica napus Cultivars Infected with Xanthomonas campestris pv. campestris Md Tabibul Islam 1,2, Bok-Rye Lee 1,3 , Van Hien La 1, Dong-Won Bae 4, Woo-Jin Jung 5 and Tae-Hwan Kim 1,* 1 Department of Animal Science, Institute of Agricultural Science and Technology, College of Agriculture & Life Science, Chonnam National University, Gwangju 61186, Korea; [email protected] (M.T.I.); [email protected] (B.-R.L.); [email protected] (V.H.L.) 2 Alson H. Smith Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Tech, Winchester, VA 22602, USA 3 Asian Pear Research Institute, Chonnam National University, Gwangju 61186, Korea 4 Central Instrument Facility, Gyeongsang National University, Jinju 52828, Korea; [email protected] 5 Division of Applied Bioscience and Biotechnology, Institute of Environmentally Friendly Agriculture (IEFA), College of Agriculture and Life Science, Chonnam National University, Gwangju 61186, Korea; [email protected] * Correspondence: [email protected]; Tel.: +82-62-530-2126 Abstract: Black rot, caused by Xanthomonas campestris pv. campestris (Xcc), is the main disease of cruciferous vegetables. To characterize the resistance mechanism in the Brassica napus–Xcc pathosys- tem, Xcc-responsive proteins in susceptible (cv. Mosa) and resistant (cv. Capitol) cultivars were investigated using gel-free quantitative proteomics and analysis of gene expression. This allowed us to identify 158 and 163 differentially expressed proteins following Xcc infection in cv. Mosa and cv. Citation: Islam, M.T.; Lee, B.-R.; Capitol, respectively, and to classify them into five major categories including antioxidative systems, La, V.H.; Bae, D.-W.; Jung, W.-J.; proteolysis, photosynthesis, redox, and innate immunity. -
PANNZER 2: Annotate a Complete Proteome in Minutes!
PANNZER 2: Annotate a complete proteome in minutes! Alan J Medlar#, Petri Törönen#, Elaine Zosa, Liisa Holm* Structural Genomics Group, Institute of Biotechnology PO Box 56, 00014 University of Helsinki, Finland #These authors contributed equally *To whom correspondence should be addressed: [email protected] 1. INTRODUCTION As high-throughput sequencing has become increasingly efficient, downstream analysis has become the main bottleneck in genome sequencing projects. For example, a critical and time-consuming step is the annotation of the organism’s proteome: assigning molecular functions, involvement in biological processes and the cellular localizations of all identified protein sequences. The process of protein annotation involves classifying each protein using the Gene Ontology (GO) and selecting suitable free text descriptions, which are required for submission into sequence databases. We refer to these as GO and DE predictions, respectively. Although servers are available that perform functional annotation, none perform both GO and DE predictions concurrently, they tend to be slow and are restricted in the number of queries that can be submitted. Finally, many of the existing methods do not return an estimate of the prediction accuracy. 2. METHODS AND RESULTS The above shortcomings are remedied by PANNZER 2, an interactive web server and standalone program for protein function prediction. It is, to our knowledge, the only tool that performs both DE and GO prediction. It uses SANS-parallel [1], a high-throughput sequence search program that is thousands of times faster than BLAST, to identify homologous sequences. It is, therefore, capable of analyzing tens of thousands of proteins interactively. Results are displayed as an HTML table summarizing both DE and GO predictions, including a statistical estimate for the reliability of each prediction. -
Stability Analysis of Selected Jute (Corchorus Capsularis L.) Genotypes in Saline and Non-Saline Soils of Bangladesh
The Agriculturists 13(2): 25-35 (2015) ISSN 2304-7321 (Online), ISSN 1729-5211 (Print) A Scientific Journal of Krishi Foundation Indexed Journal Stability Analysis of Selected Jute (Corchorus capsularis L.) Genotypes in Saline and Non-saline Soils of Bangladesh M. Billah, B. Sikder, M. A. Latif* and A. K. Chowdhury Department of Genetic and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali-8602, Bangladesh *Corresponding author and Email: [email protected] Received: 04 April 2015 Accepted: 12 December 2015 Abstract Ten white jute genotypes (Corchorus capsularis L.) were evaluated across three different locations including saline and non-saline soils of Bangladesh during 2014 to assess genotype × environment interaction and stability for plant height, base diameter, fresh weight with leaves, dry stick weight and dry fiber weight. Additive Main Effect Multiplicative Interaction (AMMI) model was used to assess the additive and multiplicative interaction of jute genotypes for these characters across three environments. Significant variations in genotype environment interaction were observed for all characters except plant height and base diameter. Based on stability parameters bi 1 and bi o, the genotype C-3465 showed stability for plant height, D-154 for base diameter and fresh weight with leaves. The genotypes C-2753 showed stability for fresh weight with leaves, without leaves and dry stick weight, CVL-1 for fresh weight without leaves, C-2760 for fresh weight with leaves, without leaves and for dry fiber weight across saline and non- saline area. Heritability in broad sense was quite high for all characters (85-90%) except plant height (17%) indicating less environmental fluctuation. -
Pan-Genome-Wide Analysis of Pantoea Ananatis Identified Genes Linked to Pathogenicity In
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.24.219337; this version posted July 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Pan-genome-wide analysis of Pantoea ananatis identified genes linked to pathogenicity in onion Gaurav Agarwal1*, Divya Choudhary1, Shaun P. Stice2, Brendon K. Myers1, Ronald D. Gitaitis1, Stephanus N. Venter3, Brian H. Kvitko2, Bhabesh Dutta1* 1Department of Plant Pathology, Coastal Plain Experimental Station, University of Georgia, Tifton, Georgia, USA 2Department of Plant Pathology, University of Georgia, Athens, Georgia, USA 3Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa *Corresponding authors: [email protected] (BD); [email protected] (GA) 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.24.219337; this version posted July 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Abstract Pantoea ananatis is a member of a Pantoea spp. complex that causes center rot of onion, which significantly affects onion yield and quality. This pathogen does not have typical virulence factors like type II or type III secretion systems but appears to require a biosynthetic gene-cluster, HiVir/PASVIL (located chromosomally), for a phosphonate secondary metabolite, and the onion- virulence regions, OVR (localized on a megaplasmid), for onion pathogenicity and virulence, respectively. -
Corchorus L. and Hibiscus L.: Molecular Phylogeny Helps to Understand Their Relative Evolution and Dispersal Routes
Corchorus L. and Hibiscus L.: Molecular Phylogeny Helps to Understand Their Relative Evolution and Dispersal Routes Arif Mohammad Tanmoy1, Md. Maksudul Alam1,2, Mahdi Muhammad Moosa1,3, Ajit Ghosh1,4, Waise Quarni1,5, Farzana Ahmed1, Nazia Rifat Zaman1, Sazia Sharmin1,6, Md. Tariqul Islam1, Md. Shahidul Islam1,7, Kawsar Hossain1, Rajib Ahmed1 and Haseena Khan1* 1Molecular Biology Lab, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh. 2Department of Molecular and Cell Biology, Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080, USA. 3Graduate Studies in Biological Sciences, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. 4Plant Molecular Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India. 5Department of Pathology and Cell Biology, University of South Florida, 12901 Bruce B. Downs Blvd., Tampa, FL 33612, USA. 6Department of Kidney Development, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Kumamoto 860-0811, Japan. 7Breeding Division, Bangladesh Jute Research Institute (BJRI), Dhaka 1207, Bangladesh. ABSTRACT: Members of the genera Corchorus L. and Hibiscus L. are excellent sources of natural fibers and becoming much important in recent times due to an increasing concern to make the world greener. The aim of this study has been to describe the molecular phylogenetic relationships among the important members of these two genera as well as to know their relative dispersal throughout the world. Monophyly of Corchorus L. is evident from our study, whereas paraphyletic occurrences have been identified in case of Hibiscus L. -
Workflows for Rapid Functional Annotation of Diverse
insects Article Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes Surya Saha 1,2 , Amanda M. Cooksey 2,3, Anna K. Childers 4 , Monica F. Poelchau 5 and Fiona M. McCarthy 2,* 1 Boyce Thompson Institute, 533 Tower Rd., Ithaca, NY 14853, USA; [email protected] 2 School of Animal and Comparative Biomedical Sciences, University of Arizona, 1117 E. Lowell St., Tucson, AZ 85721, USA; [email protected] 3 CyVerse, BioScience Research Laboratories, University of Arizona, 1230 N. Cherry Ave., Tucson, AZ 85721, USA 4 Bee Research Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, 10300 Baltimore Ave., Beltsville, MD 20705, USA; [email protected] 5 National Agricultural Library, Agricultural Research Service, USDA, 10301 Baltimore Ave., Beltsville, MD 20705, USA; [email protected] * Correspondence: fi[email protected] Simple Summary: Genomic technologies are accumulating information about genes faster than ever before, and sequencing initiatives, such as the Earth BioGenome Project, i5k, and Ag100Pest Initiative, are expected to increase this rate of acquisition. However, if genomic sequencing is to be used for the improvement of human health, agriculture, and our understanding of biological systems, it is necessary to identify genes and understand how they contribute to biological outcomes. While there are several well-established workflows for assembling genomic sequences and identifying genes, understanding gene function is essential to create actionable knowledge. Moreover, this functional annotation process must be easily accessible and provide information at a genomic scale to keep up Citation: Saha, S.; Cooksey, A.M.; with new sequence data. We report a well-defined workflow for rapid functional annotation of whole Childers, A.K.; Poelchau, M.F.; proteomes to produce Gene Ontology and pathways information. -
How the Energy Sensor, AMPK, Impact the Testicular Function Pascal Froment, Mélanie Faure, Edith Guibert, Jean-Pierre Brillard
How the energy sensor, AMPK, impact the testicular function Pascal Froment, Mélanie Faure, Edith Guibert, Jean-Pierre Brillard To cite this version: Pascal Froment, Mélanie Faure, Edith Guibert, Jean-Pierre Brillard. How the energy sensor, AMPK, impact the testicular function. 27. Conference of European Comparative Endocrinologists, Aug 2014, Rennes, France. 2014. hal-02742016 HAL Id: hal-02742016 https://hal.inrae.fr/hal-02742016 Submitted on 3 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Copyright 27th Conference of European Comparative Endocrinologists CECE 2014 25-29 August 2014 Rennes, France 3 27th Conference of European Comparative Endocrinologists Organized with the generous support and help of our sponsors Université de Rennes 1 European Society for Comparative Endocrinology (Grants) European Union INTEREG TC2N Rennes Métropole European Society of Endocrinology (Grants) Institut National de la Recherche Agronomique Société de Neuroendocrinologie (Grants) Institut National de l'Environnement Industriel et des Risques !"#$%$&$'()'*)+,)*+,)'#&*'-.'#."$/ -
Copper Uptake and Accumulation, Ultra-Structural Alteration, and Bast
plants Article Copper Uptake and Accumulation, Ultra-Structural Alteration, and Bast Fibre Yield and Quality of Fibrous Jute (Corchorus capsularis L.) Plants Grown under Two Different Soils of China Muhammad Hamzah Saleem 1, Shafaqat Ali 2,3,* , Sana Irshad 4, Muhammad Hussaan 5, Muhammad Rizwan 2 , Muhammad Shoaib Rana 6, Abeer Hashem 7,8, Elsayed Fathi Abd_Allah 9 and Parvaiz Ahmad 7,10,* 1 MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; [email protected] 2 Department of Environmental Sciences and Engineering, Government College University Allama Iqbal Road, 38000 Faisalabad, Pakistan; [email protected] 3 Department of Biological Sciences and Technology, China Medical University, Taichung 40402, Taiwan 4 School of Environmental Studies, China University of Geosciences, Wuhan 430070, China; [email protected] 5 Department of Botany, Government College University, Allama Iqbal Road, 38000 Faisalabad, Pakistan; [email protected] 6 Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, Microelements Research Center, College of Resource and Environment, Huazhong Agricultural University, Wuhan 430070, China; [email protected] 7 Botany and Microbiology Department, College of Science, King Saud University, P.O. Box. 2460, Riyadh 11451, Saudi Arabia; [email protected] 8 Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, ARC, Giza 12511, Egypt 9 Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box. 2460, Riyadh 11451, Saudi Arabia; [email protected] 10 Department of Botany, S.P. -
Gene Co-Expression Network Analysis Identifies Porcine Genes Associated
www.nature.com/scientificreports OPEN Gene co-expression network analysis identifies porcine genes associated with variation in Received: 16 September 2016 Accepted: 29 March 2017 metabolizing fenbendazole and Published: xx xx xxxx flunixin meglumine in the liver Jeremy T. Howard1, Melissa S. Ashwell1, Ronald E. Baynes2, James D. Brooks2, James L. Yeatts2 & Christian Maltecca1 Identifying individual genetic variation in drug metabolism pathways is of importance not only in livestock, but also in humans in order to provide the ultimate goal of giving the right drug at the right dose at the right time. Our objective was to identify individual genes and gene networks involved in metabolizing fenbendazole (FBZ) and flunixin meglumine (FLU) in swine liver. The population consisted of female and castrated male pigs that were sired by boars represented by 4 breeds. Progeny were randomly placed into groups: no drug (UNT), FLU or FBZ administered. Liver transcriptome profiles from 60 animals with extreme (i.e. fast or slow drug metabolism) pharmacokinetic (PK) profiles were generated from RNA sequencing. Multiple cytochrome P450 (CYP1A1, CYP2A19 and CYP2C36) genes displayed different transcript levels across treated versus UNT. Weighted gene co-expression network analysis identified 5 and 3 modules of genes correlated with PK parameters and a portion of these were enriched for biological processes relevant to drug metabolism for FBZ and FLU, respectively. Genes within identified modules were shown to have a higher transcript level relationship (i.e. connectivity) in treated versus UNT animals. Investigation into the identified genes would allow for greater insight into FBZ and FLU metabolism. Drug use and how it is currently regulated in livestock has received increased attention due to animal welfare concerns, food safety and the prevalence of antibiotic resistance1. -
Corchorus Olitorius Linn) and Scent Leaf (Ocimum Gratissimum Linn) Diet Supplementation on Mnu-Induced Colon Cancer in Wistar Rats
PREVENTIVE EFFECT OF DIFFERENT LEVELS OF JEW‟S MALLOW (CORCHORUS OLITORIUS LINN) AND SCENT LEAF (OCIMUM GRATISSIMUM LINN) DIET SUPPLEMENTATION ON MNU-INDUCED COLON CANCER IN WISTAR RATS BY KUNLE OGUNGBEMI DEPARTMENT OF BIOCHEMISTRY FACULTY OF SCIENCE AHMADU BELLO UNIVERSITY, ZARIA, NIGERIA SEPTEMBER, 2015 i PREVENTIVE EFFECT OF DIFFERENT LEVELS OF CORCHORUS OLITORIUS LINN AND OCIMUM GRATISSIMUM LINN DIET SUPPLEMENTATION ON MNU-INDUCED COLON CANCER IN WISTAR RATS BY Kunle OGUNGBEMI BSC BIOCHEMISTRY (ABU) 2011 MSc/SCIEN/22990/2012-2013 A THESIS SUBMITTED TO THE SCHOOL OF POSTGRADUATE STUDIES, AHMADU BELLO UNIVERSITY, ZARIA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE AWARD OF A MASTERS DEGREE IN BIOCHEMISTRY DEPARTMENT OF BIOCHEMISTRY FACULTY OF SCIENCE AHMADU BELLO UNIVERSITY, ZARIA NIGERIA SEPTEMBER, 2015 ii DECLARATION I declare that the work in this Dissertation entitled „PREVENTIVE EFFECT OF DIFFERENT LEVELS OF CORCHORUS OLITORIUS LINN AND OCIMUM GRATISSIMUM LINN DIET SUPPLEMENTATION ON MNU INDUCED COLON CANCER IN WISTAR RATS‟ has been carried out by me in the Department of Biochemistry. The information derived from the literature has been duly acknowledged in the text and a list of references provided. No part of this thesis was previously presented for another degree at this or any other institution. Ogungbemi Kunle __________________ _______________ MSc/Sci/22990/2012-2013 Signature Date iii CERTIFICATION I declare that the work in this Dissertation entitled PREVENTIVE EFFECT OF DIFFERENT LEVELS OF CORCHORUS OLITORIUS LINN AND OCIMUM GRATISSIMUM LINN DIET SUPPLEMENTATION ON MNU INDUCED COLON CANCER IN WISTAR RATS by Ogungbemi Kunle (MSc/Sci/22990/2012-2013), meets the regulations governing the award of the degree of Masters in Biochemistry of the Ahmadu Bello University, and is approved for its contribution to knowledge and literary presentation. -
Potential Healing Powers with Jute Plant- a Review
International Journal of Sciences: Basic and Applied Research (IJSBAR) ISSN 2307-4531 (Print & Online) http://gssrr.org/index.php?journal=JournalOfBasicAndApplied -------------------------------------------------------------------------------------------------------------------------- Potential Healing Powers with Jute Plant- A Review Md. Mahabub Alia, Balaram Rayb, Begum Rokeyac, Mst. Aleya Nasreend, Zakaria Ahmede* a,d,eBiochemistry and Microbiology Department, Bangladesh Jute research Institute, Manik Mia Avenue, Dhaka–1207, Bangladesh bDepartment of Chemistry, Hajee Danesh Science & Technology University, Dinajpur, Bangladesh cDepartment of Pharmacology, Bangladesh University of Health Science, Mirpur, Dhaka, Bangladesh aEmail: [email protected] , dEmail: [email protected] eEmail: [email protected] bEmail: [email protected] cEmail: [email protected] , cEmail: [email protected] Abstract Jute (Corchorus spp) can be a potential medicinal product for the treatment of many diseases. In traditional medicinal practices, it is used to treat constipation, demulcent, dysentery, worm, carminative anthalmitic, intestinal antiseptic, ascites, pain, piles, tumors, dysuria, febrifuge, stomachic, cystitis etc. Till now more than 80 compounds, including glycosides, triterpenes, ionones, phenolics, phytosterols, organic acids, lignins, alkaloids have been isolated and identified from jute plant. The main phytochemical compounds are cardiac glycosides, corchorin, corchotoxin, helveticoside, corchoroside A and B, olitoriside, -
JRC 9057 (Ishani): a Newly Developed White Jute (Corchorus Capsularis L
The Pharma Innovation Journal 2018; 7(7): 164-167 ISSN (E): 2277- 7695 ISSN (P): 2349-8242 NAAS Rating: 5.03 JRC 9057 (Ishani): a newly developed white jute TPI 2018; 7(7): 164-167 © 2018 TPI (Corchorus capsularis L.) variety for enhanced fibre www.thepharmajournal.com Received: 23-05-2018 yield and improved quality textile fibre Accepted: 24-06-2018 Sanjoy Shil Sanjoy Shil and Jiban Mitra Asst. Professor, Bidhan Chandra Krishi Viswavidyalaya (Bankura Campus), Chhatna, Susunia, Abstract Bankura, West Bengal, India Jute is one of the most affordable natural fibers and it is second only to cotton in amount produced and variety of uses of vegetable fibers. Jute fibres are eco-friendly, biodegradable and recyclable in nature Jiban Mitra and hence it create pollution free environment. In modern era of growing environmental friendly crops, DUS Testing Laboratory, the role of jute as ‘Green Crop’ may be highlighted and the significance of this commercial crop will be Division of Crop Improvement, not only to produce fibre for industries as raw material but also the equivalent impact on balancing and ICAR-Central Research Institute conditioning the soil-air-environment. So the production of jute fibres assumes high socio-economic as Jute & Allied Fibres (ICAR- well as environmental significance. Among the two species of jute (Corchorus olitorius L. and CRIJAF), Barrackpore, Kolkata, Corchorus capsularis L.) fibre made from C. capsularis is whiter and of a higher quality than that made West Bengal, India from C. olitorius. The cultivation of white jute (C. capsularis L.) is very specific and native to India particularly to Eastern states.