1
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Hoque MM, Valentine MJ, Kelly PJ, Barua S, Murillo DFB, Wang C. Modification of the Folmer primers for the cytochrome c oxidase gene facilitates identification of mosquitoes. Parasit Vectors 2022; 15:437. [PMID: 36419198 PMCID: PMC9682724 DOI: 10.1186/s13071-022-05494-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/17/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Accurate identification of mosquito species is essential for the development and optimization of strategies to control mosquitoes and mosquito-borne diseases. Problems with the morphological identification of mosquito species have led to the use of molecular identification techniques, in particular the Folmer cytochrome c oxidase subunit I (COI) PCR system (FCOS), originally designed to identify a range of other invertebrates. METHODS As there can be difficulties identifying mosquitoes using FCOS, we re-evaluated the FCOS primers and developed a new COI-based SYBR PCR (the Auburn COI system-AUCOS) to improve the molecular identification of mosquitoes. Sequence data in GenBank for 33 species from 10 genera of mosquitoes were used to develop our AUCOS primers. Two molecular assays (AUCOS, FCOS) and morphological identification were carried out on mosquitoes collected from the field in Auburn, Alabama (USA) and on Saint Kitts. RESULTS With a convenience sample of individual mosquitoes comprising 19 species from six genera in Saint Kitts (n = 77) and Auburn (n = 48), our AUCOS provided higher-quality sequence data than FCOS. It also proved more sensitive than FCOS, successfully amplifying 67.5% (85/126) as opposed to 16.7% (21/126) of the samples. The species determined by morphology, or genus with damaged samples, matched that as determined by AUCOS for 84.9% (62/73) of the samples. Morphological classification was confirmed by FCOS with 81.0% (17/21) of samples producing utilizable sequences. While both FCOS and AUCOS correctly identified all the Aedes, Anopheles, Deinocerites, and Uranotaenia species in the study, identification of Culex species was less successful with both methods: 50.0% (3/6) by FCOS and 35.7% (5/14) by AUCOS. CONCLUSIONS The AUCOS DNA barcoding system for mosquito species described in this study is superior to the existing FCOS for the identification of mosquito species. As AUCOS and FCOS amplify the same variable region of the COI, the large amount of existing data on GenBank can be used to identify mosquito species with sequences produced by either PCR.
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Affiliation(s)
- Md Monirul Hoque
- grid.252546.20000 0001 2297 8753College of Veterinary Medicine, College of Veterinary Medicine, Auburn University, Auburn, AL 36849-5519 USA
| | | | | | - Subarna Barua
- grid.252546.20000 0001 2297 8753College of Veterinary Medicine, College of Veterinary Medicine, Auburn University, Auburn, AL 36849-5519 USA
| | - Daniel Felipe Barrantes Murillo
- grid.252546.20000 0001 2297 8753College of Veterinary Medicine, College of Veterinary Medicine, Auburn University, Auburn, AL 36849-5519 USA
| | - Chengming Wang
- grid.252546.20000 0001 2297 8753College of Veterinary Medicine, College of Veterinary Medicine, Auburn University, Auburn, AL 36849-5519 USA
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2
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Hinckley A, Camacho-Sanchez M, Ruedi M, Hawkins MTR, Mullon M, Cornellas A, Tuh Yit Yuh F, Leonard JA. Evolutionary history of Sundaland shrews (Eulipotyphla: Soricidae: Crocidura) with a focus on Borneo. Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Abstract
The hyperdiverse shrew genus Crocidura is one of few small mammal genera distributed across Sundaland and all of its boundaries. This represents a rare opportunity to study the geological history of this region through the evolutionary history of these shrews. We generate a phylogeny of all recognized species of Sundaland Crocidura and show that most speciation events took place during the Pleistocene, prior to the inundation of the Sunda Shelf around 400 000 years ago. We find east–west differentiation within two separate lineages on Borneo, and that the current taxonomy of its two endemic species does not reflect evolutionary history, but ecophenotypic variation of plastic traits related to elevation. Sulawesi shrews are monophyletic, with a single notable exception: the black-footed shrew (C. nigripes). We show that the black-footed shrew diverged from its relatives on Borneo recently, suggesting a human-assisted breach of Wallace’s line. Overall, the number of Crocidura species, especially on Borneo, probably remains an underestimate.
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Affiliation(s)
- Arlo Hinckley
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | - Miguel Camacho-Sanchez
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
- Instituto Andaluz de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica (IFAPA) Centro Las Torres, Alcalá del Río, Spain
| | | | - Melissa T R Hawkins
- National Museum of Natural History, Department of Vertebrate Zoology, Smithsonian Institution, USA
| | | | - Anna Cornellas
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
| | | | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville, Spain
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3
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Bartolomé C, Buendía-Abad M, Benito M, Sobrino B, Amigo J, Carracedo A, Martín-Hernández R, Higes M, Maside X. Longitudinal analysis on parasite diversity in honeybee colonies: new taxa, high frequency of mixed infections and seasonal patterns of variation. Sci Rep 2020; 10:10454. [PMID: 32591554 PMCID: PMC7319982 DOI: 10.1038/s41598-020-67183-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/19/2020] [Indexed: 12/18/2022] Open
Abstract
To evaluate the influence that parasites have on the losses of Apis mellifera it is essential to monitor their presence in the colonies over time. Here we analysed the occurrence of nosematids, trypanosomatids and neogregarines in five homogeneous colonies for up to 21 months until they collapsed. The study, which combined the use of several molecular markers with the application of a massive parallel sequencing technology, provided valuable insights into the epidemiology of these parasites: (I) it enabled the detection of parasite species rarely reported in honeybees (Nosema thomsoni, Crithidia bombi, Crithidia acanthocephali) and the identification of two novel taxa; (II) it revealed the existence of a high rate of co-infections (80% of the samples harboured more than one parasite species); (III) it uncovered an identical pattern of seasonal variation for nosematids and trypanosomatids, that was different from that of neogregarines; (IV) it showed that there were no significant differences in the fraction of positive samples, nor in the levels of species diversity, between interior and exterior bees; and (V) it unveiled that the variation in the number of parasite species was not directly linked with the failure of the colonies.
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Affiliation(s)
- Carolina Bartolomé
- Grupo de Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Galicia, Spain. .,Instituto de Investigación Sanitaria de Santiago (IDIS), 15706, Santiago de Compostela, Galicia, Spain.
| | - María Buendía-Abad
- Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal (IRIAF), Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, 19180, Marchamalo, Spain
| | - María Benito
- Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal (IRIAF), Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, 19180, Marchamalo, Spain
| | - Beatriz Sobrino
- Instituto de Investigación Sanitaria de Santiago (IDIS), 15706, Santiago de Compostela, Galicia, Spain.,Fundación Pública Galega de Medicina Xenómica, Servicio Galego de Saúde (SERGAS), 15706, Santiago de Compostela, Spain
| | - Jorge Amigo
- Instituto de Investigación Sanitaria de Santiago (IDIS), 15706, Santiago de Compostela, Galicia, Spain.,Fundación Pública Galega de Medicina Xenómica, Servicio Galego de Saúde (SERGAS), 15706, Santiago de Compostela, Spain
| | - Angel Carracedo
- Grupo de Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Galicia, Spain.,Instituto de Investigación Sanitaria de Santiago (IDIS), 15706, Santiago de Compostela, Galicia, Spain.,Fundación Pública Galega de Medicina Xenómica, Servicio Galego de Saúde (SERGAS), 15706, Santiago de Compostela, Spain.,Departamento de CC. Forenses, Anatomía Patolóxica, Xinecoloxía e Obstetricia, e Pediatría, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Galicia, Spain
| | - Raquel Martín-Hernández
- Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal (IRIAF), Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, 19180, Marchamalo, Spain.,Instituto de Recursos Humanos para la Ciencia y la Tecnología, Fundación Parque Científico Tecnológico de Albacete, 02006, Albacete, Spain
| | - Mariano Higes
- Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal (IRIAF), Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, 19180, Marchamalo, Spain
| | - Xulio Maside
- Grupo de Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Galicia, Spain.,Instituto de Investigación Sanitaria de Santiago (IDIS), 15706, Santiago de Compostela, Galicia, Spain.,Departamento de CC. Forenses, Anatomía Patolóxica, Xinecoloxía e Obstetricia, e Pediatría, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Galicia, Spain
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4
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Belair CD, Hu T, Chu B, Freimer JW, Cooperberg MR, Blelloch RH. High-throughput, Efficient, and Unbiased Capture of Small RNAs from Low-input Samples for Sequencing. Sci Rep 2019; 9:2262. [PMID: 30783180 PMCID: PMC6381177 DOI: 10.1038/s41598-018-38458-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 12/05/2018] [Indexed: 12/29/2022] Open
Abstract
MicroRNAs hold great promise as biomarkers of disease. However, there are few efficient and robust methods for measuring microRNAs from low input samples. Here, we develop a high-throughput sequencing protocol that efficiently captures small RNAs while minimizing inherent biases associated with library production. The protocol is based on early barcoding such that all downstream manipulations can be performed on a pool of many samples thereby reducing reagent usage and workload. We show that the optimization of adapter concentrations along with the addition of nucleotide modifications and random nucleotides increases the efficiency of small RNA capture. We further show, using unique molecular identifiers, that stochastic capture of low input RNA rather than PCR amplification influences the biased quantitation of intermediately and lowly expressed microRNAs. Our improved method allows the processing of tens to hundreds of samples simultaneously while retaining high efficiency quantitation of microRNAs in low input samples from tissues or bodily fluids.
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Affiliation(s)
- Cassandra D Belair
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, 94143, USA.,Department of Urology, University of California, San Francisco, CA, 94143, USA
| | - Tianyi Hu
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, 94143, USA.,Department of Urology, University of California, San Francisco, CA, 94143, USA
| | - Brandon Chu
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, 94143, USA.,Department of Urology, University of California, San Francisco, CA, 94143, USA
| | - Jacob W Freimer
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, 94143, USA.,Department of Urology, University of California, San Francisco, CA, 94143, USA
| | | | - Robert H Blelloch
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, 94143, USA. .,Department of Urology, University of California, San Francisco, CA, 94143, USA.
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5
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Kumar V, Sharma N, Sharma A. DNA barcoding of the Indian blackbuck (Antilope cervicapra) and their correlation with other closely related species. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2017. [DOI: 10.1186/s41935-017-0034-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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6
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Phylogeography and population genetics of introduced Silver Carp (Hypophthalmichthys molitrix) and Bighead Carp (H. nobilis) in North America. Biol Invasions 2017. [DOI: 10.1007/s10530-017-1484-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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7
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Leveraging Comparative Genomics to Identify and Functionally Characterize Genes Associated with Sperm Phenotypes in Python bivittatus (Burmese Python). GENETICS RESEARCH INTERNATIONAL 2016; 2016:7505268. [PMID: 27200191 PMCID: PMC4855019 DOI: 10.1155/2016/7505268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 01/30/2016] [Accepted: 02/18/2016] [Indexed: 11/22/2022]
Abstract
Comparative genomics approaches provide a means of leveraging functional genomics information from a highly annotated model organism's genome (such as the mouse genome) in order to make physiological inferences about the role of genes and proteins in a less characterized organism's genome (such as the Burmese python). We employed a comparative genomics approach to produce the functional annotation of Python bivittatus genes encoding proteins associated with sperm phenotypes. We identify 129 gene-phenotype relationships in the python which are implicated in 10 specific sperm phenotypes. Results obtained through our systematic analysis identified subsets of python genes exhibiting associations with gene ontology annotation terms. Functional annotation data was represented in a semantic scatter plot. Together, these newly annotated Python bivittatus genome resources provide a high resolution framework from which the biology relating to reptile spermatogenesis, fertility, and reproduction can be further investigated. Applications of our research include (1) production of genetic diagnostics for assessing fertility in domestic and wild reptiles; (2) enhanced assisted reproduction technology for endangered and captive reptiles; and (3) novel molecular targets for biotechnology-based approaches aimed at reducing fertility and reproduction of invasive reptiles. Additional enhancements to reptile genomic resources will further enhance their value.
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8
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A new problem with cross-species amplification of microsatellites: generation of non-homologous products. DONG WU XUE YAN JIU = ZOOLOGICAL RESEARCH 2016; 31:131-40. [PMID: 20545002 DOI: 10.3724/sp.j.1141.2010.02131] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Microsatellites have been widely used in studies on population genetics, ecology and evolutionary biology. However, microsatellites are not always available for the species to be studied and their isolation could be time-consuming. In order to save time and effort researchers often rely on cross-species amplification. We revealed a new problem of microsatellite cross-species amplification in addition to size homoplasy by analyzing the sequences of electromorphs from seven catfish species belonging to three different families (Clariidae, Heteropneustidae and Pimelodidae). A total of 50 different electromorphs were amplified from the seven catfish species by using primers for 4 microsatellite loci isolated from the species Clarias batrachus. Two hundred and forty PCR-products representing all 50 electromorphs were sequenced and analyzed. Primers for two loci amplified specific products from orthologous loci in all species tested, whereas primers for the other two loci produced specific and polymorphic bands from some non-orthologous loci, even in closely related non-source species. Size homoplasy within the source species was not obvious, whereas extensive size homoplasy across species were detected at three loci, but not at the fourth one. These data suggest that amplification of products from non-orthologous loci and appearance of size homoplasy by cross-amplification are locus dependent, and do not reflect phylogenetic relationship. Amplification of non-orthologous loci and appearance of size homoplasy will lead to obvious complications in phylogenetic interference, population genetic and evolutionary studies. Therefore, we propose that sequence analysis of cross-amplification products should be conducted prior to application of cross-species amplification of microsatellites.
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9
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Liu WL, Shih HC, Weng IS, Ko YZ, Tsai CC, Chou CH, Chiang YC. Characterization of Genomic Inheritance of Intergeneric Hybrids between Ascocenda and Phalaenopsis Cultivars by GISH, PCR-RFLP and RFLP. PLoS One 2016; 11:e0153512. [PMID: 27055268 PMCID: PMC4824505 DOI: 10.1371/journal.pone.0153512] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 03/30/2016] [Indexed: 11/18/2022] Open
Abstract
Background The intergeneric hybrids between Ascocenda John De Biase ‘Blue’ and Phalaenopsis Chih Shang's Stripes have been generated to introduce the blue color into the Phalaenopsis germplasm in prior study. In order to confirm the inheritance in hybrid progenies, genomic in situ hybridization (GISH) and restriction fragment length polymorphism (RFLP) analysis were conducted to confirm the intergeneric hybridization status. Methods/Results GISH analysis showed the presence of both maternal and paternal chromosomes in the cells of the putative hybrids indicating that the putative hybrid seedlings were intergeneric hybrids of the two parents. Furthermore, twenty-seven putative hybrids were randomly selected for DNA analysis, and the external transcribed spacer (ETS) regions of nrDNA were analyzed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and RFLP analyses to identify the putative hybrids. RFLP analysis showed that the examined seedlings were intergeneric hybrids of the two parents. However, PCR-RFLP analysis showed bias to maternal genotype. Conclusions Both GISH and RFLP analyses are effective detection technology to identify the intergeneric hybridization status of putative hybrids. Furthermore, the use of PCR-RFLP analysis to identify the inheritance of putative hybrids should be carefully evaluated.
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Affiliation(s)
- Wen-Lin Liu
- Kaohsiung District Agricultural Research and Extension Station, Pingtung 900, Taiwan
| | - Huei-Chuan Shih
- Department of Nursing, Meiho University, Pingtung 912, Taiwan
| | - I-Szu Weng
- Kaohsiung District Agricultural Research and Extension Station, Pingtung 900, Taiwan
| | - Ya-Zhu Ko
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Chi-Chu Tsai
- Kaohsiung District Agricultural Research and Extension Station, Pingtung 900, Taiwan
- National Pingtung University of Science and Technology, Pingtung 912, Taiwan
- * E-mail: (CCT); (CHC); (YCC)
| | - Chang-Hung Chou
- Research Center for Biodiversity, China Medical University, Taichung 404, Taiwan
- * E-mail: (CCT); (CHC); (YCC)
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- Department of Biomedical Science and Environment Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- * E-mail: (CCT); (CHC); (YCC)
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10
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Gaubert P, Njiokou F, Olayemi A, Pagani P, Dufour S, Danquah E, Nutsuakor MEK, Ngua G, Missoup AD, Tedesco PA, Dernat R, Antunes A. Bushmeat genetics: setting up a reference framework for the DNA typing of African forest bushmeat. Mol Ecol Resour 2014; 15:633-51. [DOI: 10.1111/1755-0998.12334] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 09/17/2014] [Accepted: 09/19/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Philippe Gaubert
- Institut des Sciences de l'Evolution de Montpellier - UM2-CNRS-IRD; Université Montpellier 2; Place Eugène Bataillon - CC 64 34095 Montpellier Cedex 05 France
| | - Flobert Njiokou
- Laboratoire de Parasitologie et d'Ecologie; Faculté des Sciences; Université de Yaoundé I; BP 812 Yaoundé Cameroon
| | - Ayodeji Olayemi
- Natural History Museum; Obafemi Awolowo University; Ho 220005 Ile-Ife Osun State Nigeria
| | - Paolo Pagani
- Dutch Wildlife Health Centre; Faculty of Veterinary Medicine; Yalelaan 1 3584 CL Utrecht The Netherlands
| | | | - Emmanuel Danquah
- Department of Wildlife and Range Management; Faculty of Renewable Natural Resources; Kwame Nkrumah University of Science and Technology; University Post Office; Kumasi Ghana
| | - Mac Elikem K. Nutsuakor
- Department of Wildlife and Range Management; Faculty of Renewable Natural Resources; Kwame Nkrumah University of Science and Technology; University Post Office; Kumasi Ghana
| | - Gabriel Ngua
- Amigos de la Naturaleza y del Desarrollo de Guinea Ecuatorial (ANDEGE); Barrió Ukomba, S/N Bata Equatorial Guinea
| | - Alain-Didier Missoup
- Biologie de l'Evolution - Mammalogie; Département de Biologie des Organismes Animaux; Faculté des Sciences; Université de Douala; BP 24157 Douala Cameroon
| | - Pablo A. Tedesco
- Département Milieux et Peuplements Aquatiques; Muséum National d'Histoire Naturelle; UMR Biologie des ORganismes et des Ecosystèmes Aquatiques (UMR BOREA IRD 207-CNRS 7208-UPMC-MNHN); 43 rue Cuvier FR-75231 Paris Cedex France
| | - Rémy Dernat
- Institut des Sciences de l'Evolution - CNRS UMR 5554; Plateforme Bioinformatique LabEx; Université Montpellier 2; Place Eugène Bataillon 34095 Montpellier Cedex 05 France
| | - Agostinho Antunes
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental; Universidade do Porto; Rua dos Bragas, 177 4050-123 Porto Portugal
- Departamento de Biologia; Faculdade de Ciências; Universidade do Porto; Rua do Campo Alegre 4169-007 Porto Portugal
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Wultsch C, Waits LP, Kelly MJ. Noninvasive individual and species identification of jaguars (Panthera onca), pumas (Puma concolor) and ocelots (Leopardus pardalis) in Belize, Central America using cross-species microsatellites and faecal DNA. Mol Ecol Resour 2014; 14:1171-82. [DOI: 10.1111/1755-0998.12266] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/28/2014] [Accepted: 03/31/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Claudia Wultsch
- Department of Fish and Wildlife Conservation; Virginia Tech; 100 Cheatham Hall Blacksburg VA 24061 USA
- Sackler Institute for Comparative Genomics; American Museum of Natural History; 79th Street at Central Park West New York NY 10024 USA
| | - Lisette P. Waits
- Department of Fish and Wildlife Resources; University of Idaho; 875 Perimeter Drive MS 1136 Moscow ID 83844 USA
| | - Marcella J. Kelly
- Department of Fish and Wildlife Conservation; Virginia Tech; 100 Cheatham Hall Blacksburg VA 24061 USA
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Specific primer design for the polymerase chain reaction. Biotechnol Lett 2013; 35:1541-9. [PMID: 23794048 DOI: 10.1007/s10529-013-1249-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Accepted: 05/23/2013] [Indexed: 02/07/2023]
Abstract
The design of primers has a major impact on the success of PCR in relation to the specificity and yield of the amplified product. Here, we introduce the applications of PCR as well as the definition and characteristics for PCR primer design. Recent primer design tools based on Primer3, along with several computational intelligence-based primer design methods which have been applied in primer design, are also reviewed. In addition, characteristics of population-based methods used in primer design are discussed in detail.
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Bornholdt R, Helgen K, Koepfli KP, Oliveira L, Lucherini M, Eizirik E. Taxonomic revision of the genusGalictis(Carnivora: Mustelidae): species delimitation, morphological diagnosis, and refined mapping of geographical distribution. Zool J Linn Soc 2013. [DOI: 10.1111/j.1096-3642.2012.00859.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Diopere E, Hellemans B, Volckaert FA, Maes GE. Identification and validation of single nucleotide polymorphisms in growth- and maturation-related candidate genes in sole (Solea solea L.). Mar Genomics 2013; 9:33-8. [DOI: 10.1016/j.margen.2012.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/27/2012] [Accepted: 09/28/2012] [Indexed: 11/29/2022]
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15
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Hollenbeck CM, Portnoy DS, Gold JR. Use of comparative genomics to develop EST-SSRs for red drum (Sciaenops ocellatus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2012; 14:672-680. [PMID: 22527270 DOI: 10.1007/s10126-012-9449-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 03/03/2012] [Indexed: 05/31/2023]
Abstract
Microsatellites physically linked to expressed sequence tags (EST-SSRs) are an important resource for linkage mapping and comparative genomics, and data mining in publicly available EST databases is a common strategy for EST-SSR discovery. At present, many species lack species-specific EST sequence data needed for the efficient characterization of EST-SSRs. This paper describes the discovery and development of EST-SSRs for red drum (Sciaenops ocellatus), an estuarine-dependent sciaenid species of economic importance in the USA and elsewhere, using a phylogenetically informed, comparative genomics approach to primer design. The approach entailed comparing existing genomic resources from species closely allied phylogenetically to red drum, with resources from more distantly related outgroup species. By taking into account the degree to which flanking regions are conserved across taxa, the efficiency of PCR primer design was increased greatly. The amplification success rate for primers designed for red drum was 100 % when using EST libraries from confamilial species and 92 % when using an EST library from a species in the same suborder. The primers developed also amplified EST-SSRs in a wide range of perciform fishes, suggesting potential use in comparative genomics. This study demonstrates that EST-SSRs can be efficiently developed for an organism when limited species-specific data are available by exploiting genomic resources from well-studied species, even those at extended phylogenetic distances.
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Affiliation(s)
- Christopher M Hollenbeck
- Department of Wildlife and Fisheries Sciences, Center for Biosystematics and Biodiversity, Texas A&M University, TAMU 2258, College Station, TX 77843-2258, USA.
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Chuang LY, Cheng YH, Yang CH. URPD: a specific product primer design tool. BMC Res Notes 2012; 5:306. [PMID: 22713312 PMCID: PMC3494561 DOI: 10.1186/1756-0500-5-306] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 05/20/2012] [Indexed: 11/16/2022] Open
Abstract
Background Polymerase chain reaction (PCR) plays an important role in molecular biology. Primer design fundamentally determines its results. Here, we present a currently available software that is not located in analyzing large sequence but used for a rather straight-forward way of visualizing the primer design process for infrequent users. Findings URPD (yoUR Primer Design), a web-based specific product primer design tool, combines the NCBI Reference Sequences (RefSeq), UCSC In-Silico PCR, memetic algorithm (MA) and genetic algorithm (GA) primer design methods to obtain specific primer sets. A friendly user interface is accomplished by built-in parameter settings. The incorporated smooth pipeline operations effectively guide both occasional and advanced users. URPD contains an automated process, which produces feasible primer pairs that satisfy the specific needs of the experimental design with practical PCR amplifications. Visual virtual gel electrophoresis and in silico PCR provide a simulated PCR environment. The comparison of Practical gel electrophoresis comparison to virtual gel electrophoresis facilitates and verifies the PCR experiment. Wet-laboratory validation proved that the system provides feasible primers. Conclusions URPD is a user-friendly tool that provides specific primer design results. The pipeline design path makes it easy to operate for beginners. URPD also provides a high throughput primer design function. Moreover, the advanced parameter settings assist sophisticated researchers in performing experiential PCR. Several novel functions, such as a nucleotide accession number template sequence input, local and global specificity estimation, primer pair redesign, user-interactive sequence scale selection, and virtual and practical PCR gel electrophoresis discrepancies have been developed and integrated into URPD. The URPD program is implemented in JAVA and freely available at http://bio.kuas.edu.tw/urpd/.
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Affiliation(s)
- Li-Yeh Chuang
- Department of Chemical Engineering, Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan
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Jordan I, Munster VJ, Sandig V. Authentication of the R06E fruit bat cell line. Viruses 2012; 4:889-900. [PMID: 22754654 PMCID: PMC3386627 DOI: 10.3390/v4050889] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 05/18/2012] [Accepted: 05/21/2012] [Indexed: 11/16/2022] Open
Abstract
Fruit bats and insectivorous bats are believed to provide a natural reservoir for a wide variety of infectious diseases. Several lines of evidence, including the successful isolation of infectious viruses, indicate that Marburg virus and Ravn virus have found a major reservoir in colonies of the Egyptian rousette (Rousettus aegyptiacus). To facilitate molecular studies on virus-reservoir host interactions and isolation of viruses from environmental samples, we established cell lines from primary cells of this animal. The cell lines were given to several laboratories until we realized that a contamination with Vero cells in one of the cultures had occurred. Here we describe a general diagnostic procedure for identification of cross-species contamination with the focus on Vero and Rousettus cell lines, and summarize newly discovered properties of the cell lines that may pertain to pathogen discovery.
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Affiliation(s)
- Ingo Jordan
- ProBioGen AG, Goethestr. 54, Berlin 13086, Germany;
- Author to whom correspondence should be addressed; ; Tel.: +49 30 924006-71; Fax: +49 30 914006-49
| | - Vincent J. Munster
- Rocky Mountain Laboratories, NIAID, NIH, 903 S 4th Street, Hamilton, MT 59840, USA;
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18
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Zuccon D, Brisset J, Corbari L, Puillandre N, Utge J, Samadi S. An optimised protocol for barcoding museum collections of decapod crustaceans: a case-study for a 10 - 40-years-old collection. INVERTEBR SYST 2012. [DOI: 10.1071/is12027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The sequencing of the crustacean collection of the MNHN, Paris, constitutes a promising yet very challenging barcoding project. For the collection’s crustacean specimens preserved in ethanol, some of which were collected up to 40 years ago, the conventional COI barcoding procedure of amplification with Folmer primers failed for more than half of the specimens (58%, n = 1920). We hypothesised that this failure may have been due to incompatible mismatches between the crustaceans targeted and the Folmer primer sequences and/or the amount of degradation of the DNA extracted from museum specimens. The comparison of the Folmer primers against the COI sequences from GenBank complete decapod mitochondrial genomes revealed that the annealing regions were, in fact, rather conserved, suggesting that the amplification failures were due more likely to the low quality of the DNA isolated. Using an alignment of all available decapod sequences we designed two internal primers in the middle of the barcoding COI region and also selected two additional external primers to be used as alternative to the standard Folmer primers. Using a two-overlapping-fragments amplification strategy and different primer combinations, our new protocol significantly increased the amplification success rate of the collection material from 42% with the Folmer primers to 84%, recovering an additional 364 complete barcodes and 443 minibarcodes (i.e. fragments of less than 400 base pairs), and expanding the species coverage from 254 to 397 barcoded crustaceans.
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Chaves PB, Graeff VG, Lion MB, Oliveira LR, Eizirik E. DNA barcoding meets molecular scatology: short mtDNA sequences for standardized species assignment of carnivore noninvasive samples. Mol Ecol Resour 2011; 12:18-35. [PMID: 21883979 DOI: 10.1111/j.1755-0998.2011.03056.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although species assignment of scats is important to study carnivore biology, there is still no standardized assay for the identification of carnivores worldwide, which would allow large-scale routine assessments and reliable cross-comparison of results. Here, we evaluate the potential of two short mtDNA fragments [ATP6 (126 bp) and cytochrome oxidase I gene (COI) (187 bp)] to serve as standard markers for the Carnivora. Samples of 66 species were sequenced for one or both of these segments. Alignments were complemented with archival sequences and analysed with three approaches (tree-based, distance-based and character-based). Intraspecific genetic distances were generally lower than between-species distances, resulting in diagnosable clusters for 86% (ATP6) and 85% (COI) of the species. Notable exceptions were recently diverged species, most of which could still be identified using diagnostic characters and uniqueness of haplotypes or by reducing the geographic scope of the comparison. In silico analyses were also performed for a 110-bp cytochrome b (cytb) segment, whose identification success was lower (70%), possibly due to the smaller number of informative sites and/or the influence of misidentified sequences obtained from GenBank. Finally, we performed case studies with faecal samples, which supported the suitability of our two focal markers for poor-quality DNA and allowed an assessment of prey DNA co-amplification. No evidence of prey DNA contamination was found for ATP6, while some cases were observed for COI and subsequently eliminated by the design of more specific primers. Overall, our results indicate that these segments hold good potential as standard markers for accurate species-level identification in the Carnivora.
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Affiliation(s)
- Paulo B Chaves
- Programa de Pós-Graduação em Zoologia, Pontifícia Universidade Católica do Rio Grande do Sul, Faculdade de Biociências, Av. Ipiranga, 6681, 90619-900 Porto Alegre, RS, Brazil
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20
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Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis. Genomics 2011; 98:137-44. [PMID: 21569836 DOI: 10.1016/j.ygeno.2011.04.009] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 04/22/2011] [Accepted: 04/25/2011] [Indexed: 11/23/2022]
Abstract
The polymerase chain reaction is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. We have developed and tested efficient tools for PCR primer and probe design, which also predict oligonucleotide properties based on experimental studies of PCR efficiency. The tools provide comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, unique, group-specific, bisulphite modification assays, Overlap-Extension PCR Multi-Fragment Assembly, as well as a programme to design oligonucleotide sets for long sequence assembly by ligase chain reaction. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. It calculates the melting temperature for standard and degenerate oligonucleotides including LNA and other modifications, provides analyses for a set of primers with prediction of oligonucleotide properties, dimer and G-quadruplex detection, linguistic complexity, and provides a dilution and resuspension calculator.
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21
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Shinoda N, Yoshida T, Kusama T, Takagi M, Hayakawa T, Onodera T, Sugiura K. High GC contents of primer 5'-end increases reaction efficiency in polymerase chain reaction. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2010; 28:324-30. [PMID: 20183585 DOI: 10.1080/15257770902963400] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Many studies have suggested that regulation of the polymerase chain reaction (PCR) is influenced by several factors. However, the understanding of reaction efficiency factors is not sufficient. Here we propose that high GC contents of primer 5'-end increases reaction efficiency in PCR. Using 71 primers (45 pairs), we analyzed factors that affect reaction efficiency, and statistically tested the correlation between the amplification signals and several factors. As a result, there were significant correlations between the amplification signals and the GC contents in the first 1 approximately 3 bps of primer 5'-end.
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Affiliation(s)
- Naoki Shinoda
- Food and Agricultural Materials Inspection Center, Saitama, Japan.
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22
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DAWSON DEBORAHA, HORSBURGH GAVINJ, KÜPPER CLEMENS, STEWART IANRK, BALL ALEXANDERD, DURRANT KATEL, HANSSON BENGT, BACON IDA, BIRD SUSANNAH, KLEIN ÁKOS, KRUPA ANDREWP, LEE JIN, MARTÍN‐GÁLVEZ DAVID, SIMEONI MICHELLE, SMITH GEMMA, SPURGIN LEWISG, BURKE TERRY. New methods to identify conserved microsatellite loci and develop primer sets of high cross‐species utility – as demonstrated for birds. Mol Ecol Resour 2010; 10:475-94. [DOI: 10.1111/j.1755-0998.2009.02775.x] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- DEBORAH A. DAWSON
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - GAVIN J. HORSBURGH
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - CLEMENS KÜPPER
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - IAN R. K. STEWART
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - ALEXANDER D. BALL
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - KATE L. DURRANT
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - BENGT HANSSON
- Department of Animal Ecology, Ecology Building, Lund University SE‐223 62 Lund, Sweden
| | - IDA BACON
- Institute of Evolutionary Biology, School of Biological Sciences, King’s Building, University of Edinburgh, Edinburgh, EH9 3JT, Scotland, UK
| | - SUSANNAH BIRD
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - ÁKOS KLEIN
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - ANDREW P. KRUPA
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - JIN‐WON LEE
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - DAVID MARTÍN‐GÁLVEZ
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - MICHELLE SIMEONI
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - GEMMA SMITH
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - LEWIS G. SPURGIN
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - TERRY BURKE
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
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VAN HOUDT JKJ, BREMAN FC, VIRGILIO M, DE MEYER M. Recovering full DNA barcodes from natural history collections of Tephritid fruitflies (Tephritidae, Diptera) using mini barcodes. Mol Ecol Resour 2010; 10:459-65. [DOI: 10.1111/j.1755-0998.2009.02800.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- J. K. J. VAN HOUDT
- Royal Museum for Central Africa, Leuvensesteenweg 13, B‐3080 Tervuren, Belgium
| | - F. C. BREMAN
- Royal Museum for Central Africa, Leuvensesteenweg 13, B‐3080 Tervuren, Belgium
| | - M. VIRGILIO
- Royal Museum for Central Africa, Leuvensesteenweg 13, B‐3080 Tervuren, Belgium
- Royal Belgian Institute for Natural Sciences, Vautierstraat 29, B‐1000 Brussels, Belgium
| | - M. DE MEYER
- Royal Museum for Central Africa, Leuvensesteenweg 13, B‐3080 Tervuren, Belgium
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Blume F, Bergmann I, Nettmann E, Schelle H, Rehde G, Mundt K, Klocke M. Methanogenic population dynamics during semi‐continuous biogas fermentation and acidification by overloading. J Appl Microbiol 2010; 109:441-450. [DOI: 10.1111/j.1365-2672.2010.04682.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- F. Blume
- Technische Universität Berlin, Institut für Technischen Umweltschutz, Fachgebiet Umweltmikrobiologie, Franklinstrasse 29, Berlin, Germany
| | - I. Bergmann
- Technische Universität Berlin, Institut für Technischen Umweltschutz, Fachgebiet Umweltmikrobiologie, Franklinstrasse 29, Berlin, Germany
- Leibniz‐Institut für Agrartechnik Potsdam‐Bornim e.V. (ATB), Abteilung Bioverfahrenstechnik, Max‐Eyth‐Allee 100, Potsdam, Germany
| | - E. Nettmann
- Technische Universität Berlin, Institut für Technischen Umweltschutz, Fachgebiet Umweltmikrobiologie, Franklinstrasse 29, Berlin, Germany
- Leibniz‐Institut für Agrartechnik Potsdam‐Bornim e.V. (ATB), Abteilung Bioverfahrenstechnik, Max‐Eyth‐Allee 100, Potsdam, Germany
| | - H. Schelle
- Leibniz‐Institut für Agrartechnik Potsdam‐Bornim e.V. (ATB), Abteilung Bioverfahrenstechnik, Max‐Eyth‐Allee 100, Potsdam, Germany
| | - G. Rehde
- Leibniz‐Institut für Agrartechnik Potsdam‐Bornim e.V. (ATB), Abteilung Bioverfahrenstechnik, Max‐Eyth‐Allee 100, Potsdam, Germany
| | - K. Mundt
- Leibniz‐Institut für Agrartechnik Potsdam‐Bornim e.V. (ATB), Abteilung Bioverfahrenstechnik, Max‐Eyth‐Allee 100, Potsdam, Germany
| | - M. Klocke
- Leibniz‐Institut für Agrartechnik Potsdam‐Bornim e.V. (ATB), Abteilung Bioverfahrenstechnik, Max‐Eyth‐Allee 100, Potsdam, Germany
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Tuefferd M, De Bondt A, Van Den Wyngaert I, Talloen W, Verbeke T, Carvalho B, Clevert DA, Alifano M, Raghavan N, Amaratunga D, Göhlmann H, Broët P, Camilleri-Broët S. Genome-wide copy number alterations detection in fresh frozen and matched FFPE samples using SNP 6.0 arrays. Genes Chromosomes Cancer 2008; 47:957-64. [PMID: 18663747 DOI: 10.1002/gcc.20599] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
SNP arrays offer the opportunity to get a genome-wide view on copy number alterations and are increasingly used in oncology. DNA from formalin-fixed paraffin-embedded material (FFPE) is partially degraded which limits the application of those technologies for retrospective studies. We present the use of Affymetrix GeneChip SNP6.0 for identification of copy number alterations in fresh frozen (FF) and matched FFPE samples. Fifteen pairs of adenocarcinomas with both frozen and FFPE embedded material were analyzed. We present an optimization of the sample preparation and show the importance of correcting the measured intensities for fragment length and GC-content when using FFPE samples. The absence of GC content correction results in a chromosome specific "wave pattern" which may lead to the misclassification of genomic regions as being altered. The highest concordance between FFPE and matched FF were found in samples with the highest call rates. Nineteen of the 23 high level amplifications (83%) seen using FF samples were also detected in the corresponding FFPE material. For limiting the rate of "false positive" alterations, we have chosen a conservative False Discovery Rate (FDR). We observed better results using SNP probes than CNV probes for copy number analysis of FFPE material. This is the first report on the detection of copy number alterations in FFPE samples using Affymetrix GeneChip SNP6.0.
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Affiliation(s)
- Marianne Tuefferd
- JE2492 Department, Faculté de Médecine Paris-Sud, IFR69, Villejuif, France.
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26
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Küpper C, Burke T, Székely T, Dawson DA. Enhanced cross-species utility of conserved microsatellite markers in shorebirds. BMC Genomics 2008; 9:502. [PMID: 18950482 PMCID: PMC2588463 DOI: 10.1186/1471-2164-9-502] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Accepted: 10/24/2008] [Indexed: 11/24/2022] Open
Abstract
Background Microsatellite markers are popular genetic markers frequently used in forensic biology. Despite their popularity, the characterisation of polymorphic microsatellite loci and development of suitable markers takes considerable effort. Newly-available genomic databases make it feasible to identify conserved genetic markers. We examined the utility and characteristics of conserved microsatellite markers in Charadriiformes (plovers, sandpipers, gulls and auks). This order harbours many species with diverse breeding systems, life histories and extraordinary migration biology whose genetics warrant investigation. However, research has been largely restrained by the limited availability of genetic markers. To examine the utility of conserved microsatellite loci as genetic markers we collated a database of Charadriiformes microsatellites, searched for homologues in the chicken genome and tested conserved markers for amplification and polymorphism in a range of charadriiform species. Results Sixty-eight (42%) of 161 charadriiform microsatellite loci were assigned to a single location in the chicken genome based on their E-value. Fifty-five primers designed from conserved microsatellite loci with an E-value of E-10 or lower amplified across a wider range of charadriiform species than a control group of primers from ten anonymous microsatellite loci. Twenty-three of 24 examined conserved markers were polymorphic, each in on average 3 of 12 species tested. Conclusion Genomic sequence databases are useful tools to identify conserved genetic markers including those located in non-coding regions. By maximising primer sequence similarity between source species and database species, markers can be further improved and provide additional markers to study the molecular ecology of populations of non-model organisms.
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Affiliation(s)
- Clemens Küpper
- NERC Molecular Genetics Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.
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Development and experimental validation of a predictive threshold cycle equation for quantification of virulence and marker genes by high-throughput nanoliter-volume PCR on the OpenArray platform. Appl Environ Microbiol 2008; 74:3831-8. [PMID: 18424532 DOI: 10.1128/aem.02743-07] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Development of quantitative PCR (QPCR) assays typically requires extensive screening within and across a given species to ensure specific detection and lucid identification among various pathogenic and nonpathogenic strains and to generate standard curves. To minimize screening requirements, multiple virulence and marker genes (VMGs) were targeted simultaneously to enhance reliability, and a predictive threshold cycle (C(T)) equation was developed to calculate the number of starting copies based on an experimental C(T). The empirical equation was developed with Sybr green detection in nanoliter-volume QPCR chambers (OpenArray) and tested with 220 previously unvalidated primer pairs targeting 200 VMGs from 30 pathogens. A high correlation (R(2) = 0.816) was observed between the predicted and experimental C(T)s based on the organism's genome size, guanine and cytosine (GC) content, amplicon length, and stability of the primer's 3' end. The performance of the predictive C(T) equation was tested using 36 validation samples consisting of pathogenic organisms spiked into genomic DNA extracted from three environmental waters. In addition, the primer success rate was dependent on the GC content of the target organisms and primer sequences. Targeting multiple assays per organism and using the predictive C(T) equation are expected to reduce the extent of the validation necessary when developing QPCR arrays for a large number of pathogens or other targets.
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