Plant & Animal Genome V
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(Arachis Hypogaea) and Its Most Closely Related Wild Species Using
Annals of Botany 111: 113–126, 2013 doi:10.1093/aob/mcs237, available online at www.aob.oxfordjournals.org A study of the relationships of cultivated peanut (Arachis hypogaea) and its most closely related wild species using intron sequences and microsatellite markers Downloaded from https://academic.oup.com/aob/article-abstract/111/1/113/182224 by University of Georgia Libraries user on 29 November 2018 Ma´rcio C. Moretzsohn1,*, Ediene G. Gouvea1,2, Peter W. Inglis1, Soraya C. M. Leal-Bertioli1, Jose´ F. M. Valls1 and David J. Bertioli2 1Embrapa Recursos Gene´ticos e Biotecnologia, C.P. 02372, CEP 70.770-917, Brası´lia, DF, Brazil and 2Universidade de Brası´lia, Instituto de Cieˆncias Biolo´gicas, Campus Darcy Ribeiro, CEP 70.910-900, Brası´lia-DF, Brazil * For correspondence. E-mail [email protected] Received: 25 June 2012 Returned for revision: 17 August 2012 Accepted: 2 October 2012 Published electronically: 6 November 2012 † Background and Aims The genus Arachis contains 80 described species. Section Arachis is of particular interest because it includes cultivated peanut, an allotetraploid, and closely related wild species, most of which are diploids. This study aimed to analyse the genetic relationships of multiple accessions of section Arachis species using two complementary methods. Microsatellites allowed the analysis of inter- and intraspecific vari- ability. Intron sequences from single-copy genes allowed phylogenetic analysis including the separation of the allotetraploid genome components. † Methods Intron sequences and microsatellite markers were used to reconstruct phylogenetic relationships in section Arachis through maximum parsimony and genetic distance analyses. † Key Results Although high intraspecific variability was evident, there was good support for most species. -
Reproductive Biology and Endocrinology Biomed Central
Reproductive Biology and Endocrinology BioMed Central Research Open Access Identification, cloning and functional characterization of novel beta-defensins in the rat (Rattus norvegicus) Suresh Yenugu1,3, Vishnu Chintalgattu2, Christopher J Wingard2, Yashwanth Radhakrishnan1, Frank S French1 and Susan H Hall*1 Address: 1Laboratories for Reproductive Biology, Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina 27599, USA, 2Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, North Carolina 27834, USA and 3Department of Biochemistry and Molecular Biology, Pondicherry University, Pondicherry, 605014, India Email: Suresh Yenugu - [email protected]; Vishnu Chintalgattu - [email protected]; Christopher J Wingard - [email protected]; Yashwanth Radhakrishnan - [email protected]; Frank S French - [email protected]; Susan H Hall* - [email protected] * Corresponding author Published: 04 February 2006 Received: 23 November 2005 Accepted: 04 February 2006 Reproductive Biology and Endocrinology2006, 4:7 doi:10.1186/1477-7827-4-7 This article is available from: http://www.rbej.com/content/4/1/7 © 2006Yenugu et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: beta-defensins are small cationic peptides that exhibit broad spectrum antimicrobial properties. The majority of beta-defensins identified in humans are predominantly expressed in the male reproductive tract and have roles in non-immunological processes such as sperm maturation and capacitation. Characterization of novel defensins in the male reproductive tract can lead to increased understanding of their dual roles in immunity and sperm maturation. -
Genome Amplification 81
Application of high performance compute technology in bioinformatics Sven Warris Thesis committee Promotor Prof. Dr D. de Ridder Professor of Bioinformatics Wageningen University & Research Co-promotor Dr J.P. Nap Professor of Life Sciences & Renewable Energy Hanze University of Applied Sciences Groningen Other members Prof. Dr B. Tekinerdogan, Wageningen University & Research Prof. Dr R.C.H.J. van Ham, Delft University of Technology & KeyGene N.V., Wageningen Dr P. Prins, University of Tennessee, USA Prof. Dr R.V. van Nieuwpoort, Netherlands eScience Center, Amsterdam Application of high performance compute technology in bioinformatics Sven Warris Thesis submitted in fulfilment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. Dr A.P.J. Mol in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Tuesday 22 October 2019 at 4:00 p.m. in the Aula Sven Warris Application of high performance compute technology in bioinformatics, 159 pages. PhD thesis, Wageningen University, Wageningen, the Netherlands (2019) With references, with summaries in English and Dutch ISBN: 978-94-6395-112-8 DOI: https://doi.org/10.18174/499180 Table of contents 1 Introduction 9 2 Fast selection of miRNA candidates based on large- scale pre-computed MFE sets of randomized sequences 27 3 Flexible, fast and accurate sequence alignment profiling on GPGPU with PaSWAS 47 4 pyPaSWAS: Python-based multi-core CPU and GPU sequence alignment 67 5 Correcting palindromes in long reads after whole- genome amplification 81 6 Mining functional annotations across species 103 7 General discussion 125 Summary 141 Samenvatting 145 Acknowledgements 149 Curriculum vitae 153 List of publications 155 Propositions 159 7 1 Introduction 9 Advances in DNA sequencing technology In recent years, technological developments in the life sciences have progressed enormously. -
CITOGENÉTICA MOLECULAR DA VARIEDADE BRS PÉROLA BRANCA (Arachis Hypogaea L.) E DE SEUS GENITORES
VANESSA EMANUELLE DE OLIVEIRA MACIEL CITOGENÉTICA MOLECULAR DA VARIEDADE BRS PÉROLA BRANCA (Arachis hypogaea L.) E DE SEUS GENITORES RECIFE 2014 VANESSA EMANUELLE DE OLIVEIRA MACIEL CITOGENÉTICA MOLECULAR DA VARIEDADE BRS PÉROLA BRANCA (Arachis hypogaea L.) E DE SEUS GENITORES Dissertação apresentada ao Programa de Pós-Graduação em Agronomia– Melhoramento Genético de Plantas (PPGAMGP) da Universidade Federal Rural de Pernambuco, como parte dos requisitos para obtenção do título de mestre. Orientador: Prof. Dr. Reginaldo De Carvalho Co-Orientadoras: Dra. Roseane Cavalcanti dos Santos Dra. Lidiane de Lima Feitoza RECIFE 2014 MACIEL, V.E.O. Citogenética molecular da variedade BRS Pérola Branca (Arachis hypogaea L.)... i VANESSA EMANUELLE DE OLIVEIRA MACIEL CITOGENÉTICA MOLECULAR DA VARIEDADE BRS PÉROLA BRANCA (Arachis hypogaea L.) E DE SEUS GENITORES Dissertação apresentada ao Programa de Pós-Graduação em Agronomia–Melhoramento Genético de Plantas (PPGAMGP) da Universidade Federal Rural de Pernambuco, como parte dos requisitos para obtenção do título de mestre em Melhoramento Genético de Plantas. Dissertação defendida e aprovada pela banca examinadora em: 28/07/2014. ORIENTADOR: Dr. Reginaldo de Carvalho Departamento de Biologia/UFRPE EXAMINADORES: Dr. Edson Ferreira da Silva Departamento de Biologia/UFRPE Dra. Maria Rita Cabral Sales de Melo MACIEL, V.E.O. Citogenética molecular da variedade BRS Pérola Branca (Arachis hypogaea L.)... ii Dedico a minha amada avó, Maria da Glória Rodrigues (In memoriam). MACIEL, V.E.O. Citogenética molecular da variedade BRS Pérola Branca (Arachis hypogaea L.)... iii AGRADECIMENTOS Primeiramente, a Deus por me proporcionar a conclusão de mais uma etapa em minha formação profissional. Aos meus pais, Ivônia Rodrigues de Oliveira e Manoel José Alves Maciel e, a minha querida avó, Maria da Glória Rodrigues (In memoriam), que são os meus pilares, por todo incentivo e ensinamento de valores fundamentais para a minha vida. -
Chromosomal Microarray Analysis in Turkish Patients with Unexplained Developmental Delay and Intellectual Developmental Disorders
177 Arch Neuropsychitry 2020;57:177−191 RESEARCH ARTICLE https://doi.org/10.29399/npa.24890 Chromosomal Microarray Analysis in Turkish Patients with Unexplained Developmental Delay and Intellectual Developmental Disorders Hakan GÜRKAN1 , Emine İkbal ATLI1 , Engin ATLI1 , Leyla BOZATLI2 , Mengühan ARAZ ALTAY2 , Sinem YALÇINTEPE1 , Yasemin ÖZEN1 , Damla EKER1 , Çisem AKURUT1 , Selma DEMİR1 , Işık GÖRKER2 1Faculty of Medicine, Department of Medical Genetics, Edirne, Trakya University, Edirne, Turkey 2Faculty of Medicine, Department of Child and Adolescent Psychiatry, Trakya University, Edirne, Turkey ABSTRACT Introduction: Aneuploids, copy number variations (CNVs), and single in 39 (39/123=31.7%) patients. Twelve CNV variant of unknown nucleotide variants in specific genes are the main genetic causes of significance (VUS) (9.75%) patients and 7 CNV benign (5.69%) patients developmental delay (DD) and intellectual disability disorder (IDD). were reported. In 6 patients, one or more pathogenic CNVs were These genetic changes can be detected using chromosome analysis, determined. Therefore, the diagnostic efficiency of CMA was found to chromosomal microarray (CMA), and next-generation DNA sequencing be 31.7% (39/123). techniques. Therefore; In this study, we aimed to investigate the Conclusion: Today, genetic analysis is still not part of the routine in the importance of CMA in determining the genomic etiology of unexplained evaluation of IDD patients who present to psychiatry clinics. A genetic DD and IDD in 123 patients. diagnosis from CMA can eliminate genetic question marks and thus Method: For 123 patients, chromosome analysis, DNA fragment analysis alter the clinical management of patients. Approximately one-third and microarray were performed. Conventional G-band karyotype of the positive CMA findings are clinically intervenable. -
Characterization of the Arachis (Leguminosae) D Genome Using Fluorescence in Situ Hybridization (FISH) Chromosome Markers and Total Genome DNA Hybridization
Genetics and Molecular Biology, 31, 3, 717-724 (2008) Copyright © 2008, Sociedade Brasileira de Genética. Printed in Brazil www.sbg.org.br Research Article Characterization of the Arachis (Leguminosae) D genome using fluorescence in situ hybridization (FISH) chromosome markers and total genome DNA hybridization Germán Robledo1 and Guillermo Seijo1,2 1Instituto de Botánica del Nordeste, Corrientes, Argentina. 2Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina. Abstract Chromosome markers were developed for Arachis glandulifera using fluorescence in situ hybridization (FISH) of the 5S and 45S rRNA genes and heterochromatic 4’-6-diamidino-2-phenylindole (DAPI) positive bands. We used chro- mosome landmarks identified by these markers to construct the first Arachis species ideogram in which all the ho- mologous chromosomes were precisely identified. The comparison of this ideogram with those published for other Arachis species revealed very poor homeologies with all A and B genome taxa, supporting the special genome con- stitution (D genome) of A. glandulifera. Genomic affinities were further investigated by dot blot hybridization of biotinylated A. glandulifera total DNA to DNA from several Arachis species, the results indicating that the D genome is positioned between the A and B genomes. Key words: chromosome markers, DAPI bands, rDNA loci, dot blot hybridization, genome relationships. Received: June 29, 2007; Accepted: November 22, 2007. Introduction row et al., 2001; Simpson, 2001; Mallikarjuna, 2002; Mal- The genus Arachis comprises 80 wild species and the likarjuna et al., 2004). For this reason, great efforts have cultivated crop Arachis hypogaea L. (Fabales, Legumi- been directed towards understanding the relationships be- nosae) commonly known as groundnut or peanut. -
Simple Approach for Species Discrimination of Fabaceae Family on the Basis of Length Variation in PCR Amplified Products Using Barcode Primers
Int.J.Curr.Microbiol.App.Sci (2018) 7(12): 921-928 International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 12 (2018) Journal homepage: http://www.ijcmas.com Original Research Article https://doi.org/10.20546/ijcmas.2018.712.115 Simple Approach for Species Discrimination of Fabaceae Family on the Basis of Length Variation in PCR Amplified Products Using Barcode Primers Sumana Sikdar1*, Sharad Tiwari2, Swapnil Sapre1 and Vishwa Vijay Thakur3 1Biotechnology Centre, Jawaharlal Nehru Agricultural University, Jabalpur 482004, India 2Department of Plant breeding and Genetics, College of Agriculture, Jawaharlal Nehru Agricultural University, Jabalpur 482004, India 3ICAR-IINRG, Namkum Ranchi- 834010, India *Corresponding author ABSTRACT Fabaceae is one of the most diversified and complex family of flowering plants. The important pulses and the medicinally important plant species under this family have a high market value. Now a day, adulteration in the food and herbal medicinal products has become a severe problem. Adulteration of therapeutic herbs and major pulses with related K e yw or ds or conflicting species has proved to be hazardous to human health in several cases. We Barcode primers, have projected here, a PCR-based method using some of the major universal DNA barcode PCR, Agarose gel primers from the plastid region to address this problem. The basic idea behind this study electrophoresis, was to utilize the amplicon length polymorphisms exhibited by these primers to Adulteration, differentiate the plant species. PCR amplification success and species discrimination Fabaceae ability of five major DNA barcode primers (trnH-psbA, trnL, atpF-atpH, matK and rbcL) Article Info was studied among 24 representative plant species of Fabaceae family. -
Visual Gene Network Analysis of Aging-Specific Gene Co-Expression
4open 2018, 1,4 © B.P. Parida et al., Published by EDP Sciences 2018 https://doi.org/10.1051/fopen/2018004 Available online at: www.4open-sciences.org RESEARCH ARTICLE Visual gene network analysis of aging-specific gene co-expression in human indicates overlaps with immuno-pathological regulations Bibhu Prasad Parida1,*, Biswapriya Biswavas Misra2, Amarendra Narayan Misra3,4 1 Post-Graduate Department of Biosciences and Biotechnology, School of Biotechnology, Fakir Mohan University, Balasore 756020, Odisha, India 2 Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem 27157, NC, USA 3 Central University of Jharkhand, Brambe, Ratu-Lohardaga Road, Ranchi 835205, Jharkhand, India 4 Khallikote University, Berhampur 760001, Odisha, India Received 19 September 2017, Accepted 4 July 2018 Abstract- - Introduction: Aging is a complex biological process that brings about a gradual decline of physiological and metabolic machineries as a result of maturity. Also, aging is irreversible and leads ultimately to death in biological organisms. Methods: We intend to characterize aging at the gene expression level using publicly available human gene expression arrays obtained from gene expression omnibus (GEO) and ArrayExpress. Candidate genes were identified by rigorous screening using filtered data sets, i.e., GSE11882, GSE47881, and GSE32719. Using Aroma and Limma packages, we selected the top 200 genes showing up and down regulation (p < 0.05 and fold change >2.5) out of which 185 were chosen for further comparative analysis. Results: This investigation enabled identification of candidate genes involved in aging that are associated with several signaling cascades demonstrating strong correlation with ATP binding and protease functions. -
A Study of Alterations in DNA Epigenetic Modifications (5Mc and 5Hmc) and Gene Expression Influenced by Simulated Microgravity I
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Digital Repository @ Iowa State University Genome Informatics Facility Publications Genome Informatics Facility 1-28-2016 A Study of Alterations in DNA Epigenetic Modifications (5mC and 5hmC) and Gene Expression Influenced by Simulated Microgravity in Human Lymphoblastoid Cells Basudev Chowdhury Purdue University Arun S. Seetharam Iowa State University, [email protected] Zhiping Wang Indiana University School of Medicine Yunlong Liu Indiana University School of Medicine Amy C. Lossie Purdue University See next page for additional authors Follow this and additional works at: https://lib.dr.iastate.edu/genomeinformatics_pubs Part of the Bioinformatics Commons, Genetics Commons, and the Genomics Commons Recommended Citation Chowdhury, Basudev; Seetharam, Arun S.; Wang, Zhiping; Liu, Yunlong; Lossie, Amy C.; Thimmapuram, Jyothi; and Irudayaraj, Joseph, "A Study of Alterations in DNA Epigenetic Modifications (5mC and 5hmC) and Gene Expression Influenced by Simulated Microgravity in Human Lymphoblastoid Cells" (2016). Genome Informatics Facility Publications. 4. https://lib.dr.iastate.edu/genomeinformatics_pubs/4 This Article is brought to you for free and open access by the Genome Informatics Facility at Iowa State University Digital Repository. It has been accepted for inclusion in Genome Informatics Facility Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. A Study of Alterations in DNA Epigenetic Modifications (5mC and 5hmC) and Gene Expression Influenced by Simulated Microgravity in Human Lymphoblastoid Cells Abstract Cells alter their gene expression in response to exposure to various environmental changes. Epigenetic mechanisms such as DNA methylation are believed to regulate the alterations in gene expression patterns. -
Reproductive Efficiency in Reciprocal Crosses of Arachis Monticoza with A
Reproductive Efficiency in Reciprocal Crosses of Arachis monticoZa with A. hypogaea Subspecies' H. E. Pattee2*, H. T. Stake? and F. G. Giesbrecht4 ABSTRACT pattern of reproductive development of A. hypogaea cv. Wild species of Arachis encompass a large number of Argentine, which lends support to the theory that A. specieswhich can provide valuable genetic resources for monticola is a weedy derivative of the cultivated peanut. improving A. hypogaea L., the domesticated peanut. Arachis monticola Krapov. and Rig. is the only species Key Words: Interspecific hybridization, fertilization which is both cross compatible with A. hypogaea and at timing, abortion, peanut, groundnut. the same ploidy level. An evaluation of reproductive efficiency in crosses between A. hypogaeu and A. monticola was conducted to better understand the po- tential for utilization of this germplasm. This study documents the reproductive efficiency of A. munticola Both subspecies of Arachis hypogaea L. are cultivated in reciprocal crosses with A. hypogaea subsp. hypogaea in the western hemisphere, but within the U.S., the var. hypogaea cvs. Florunner and NC 6; A. hypogaea subsp. hypogaea var. hypogaea (Virginia and runner subsp. fastigiata var. vulgaris cv. Argentine; and A. market types) predominates. Cultivars of subsp.fastigiata hypogaea subsp.fmtigiata var.fmtigiata cv. New Mexico include Spanish (var.vulgaris) and valencia (var.fmtigiata) Valencia C by using selfs as controls. A significant market types which are grown in the Southwest on a maternal effect was observed among selfs and hybrids more limited land area. Although genetic resources within for timing of fertilization. Selfs of Florunner and New the domesticated species may be adequate to solve many Mexico Valencia C initiated fertilization by 1 d afker production problems, genetic resistance to many dis- pollination, whereas syngamy did not occur in selfs of eases and insect pests is not readily available. -
Characterization of the Β-Defensin Genes in Giant Panda Zhi-Yi Zhang1, He-Min Zhang2, De-Sheng Li2, Tie-Yi Xiong3 & Sheng-Guo Fang 1
www.nature.com/scientificreports OPEN Characterization of the β-defensin genes in giant panda Zhi-Yi Zhang1, He-Min Zhang2, De-Sheng Li2, Tie-Yi Xiong3 & Sheng-Guo Fang 1 β-Defensins are small antimicrobial proteins expressed in various organisms and have great potential Received: 12 July 2017 for improving animal health and selective breeding programs. Giant pandas have a distinctive lineage Accepted: 12 June 2018 in Carnivora, and it is unclear whether β-defensin genes have experienced diferent selective pressures Published: xx xx xxxx during giant panda evolution. We therefore characterized the giant panda (Ailuropoda melanoleuca) β-defensin gene family through gap flling, TBLASTN, and HMM searches. Among 36 β-defensins identifed, gastrointestinal disease may induce the expression of the DEFB1 and DEFB139 genes in the digestive system. Moreover, for DEFB139, a signifcant positive selection diferent from that of its homologs was revealed through branch model comparisons. A Pro-to-Arg mutation in the giant panda DEFB139 mature peptide may have enhanced the peptide’s antimicrobial potency by increasing its stability, isoelectric point, surface charge and surface hydrophobicity, and by stabilizing its second β-sheet. Broth microdilution tests showed that the increase in net charge caused by the Pro-to-Arg mutation has enhanced the peptide’s potency against Staphylococcus aureus, although the increase was minor. We expect that additional gene function and expression studies of the giant panda DEFB139 gene could improve the existing conservation strategies for the giant panda. Defensins are a group of small antimicrobial peptides (AMPs) found in large variety of plants, invertebrates, and vertebrates that act against a broad spectrum of pathogens including enveloped viruses, gram-positive and gram-negative bacteria, mycobacteria, and fungi1. -
DEFB119 (NM 153289) Human Tagged ORF Clone – RC209341
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for RC209341 DEFB119 (NM_153289) Human Tagged ORF Clone Product data: Product Type: Expression Plasmids Product Name: DEFB119 (NM_153289) Human Tagged ORF Clone Tag: Myc-DDK Symbol: DEFB119 Synonyms: DEFB-19; DEFB-20; DEFB20; DEFB120; ESC42-RELA; ESC42-RELB Vector: pCMV6-Entry (PS100001) E. coli Selection: Kanamycin (25 ug/mL) Cell Selection: Neomycin ORF Nucleotide >RC209341 ORF sequence Sequence: Red=Cloning site Blue=ORF Green=Tags(s) TTTTGTAATACGACTCACTATAGGGCGGCCGGGAATTCGTCGACTGGATCCGGTACCGAGGAGATCTGCC GCCGCGATCGCC ATGAAACTTCTTTACCTGTTTCTTGCCATCCTTCTGGCCATAGAAGAACCAGTGATATCAGGCAAACGCC ACATCCTTCGATGCATGGGTAACAGTGGAATTTGTAGGGCCTCTTGCAAAAAGAACGAACAGCCCTACCT CTATTGCAGAAATTGTCAGTCCTGCTGCCTCCAGTCCTACATGAGGATAAGCATTTCTGGCAAAGAGGAA AATACCGACTGGTCTTATGAGAAGCAGTGGCCAAGACTACCT ACGCGTACGCGGCCGCTCGAGCAGAAACTCATCTCAGAAGAGGATCTGGCAGCAAATGATATCCTGGATT ACAAGGATGACGACGATAAGGTTTAA Protein Sequence: >RC209341 protein sequence Red=Cloning site Green=Tags(s) MKLLYLFLAILLAIEEPVISGKRHILRCMGNSGICRASCKKNEQPYLYCRNCQSCCLQSYMRISISGKEE NTDWSYEKQWPRLP TRTRPLEQKLISEEDLAANDILDYKDDDDKV Chromatograms: https://cdn.origene.com/chromatograms/mk6548_h10.zip Restriction Sites: SgfI-MluI This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850,