bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isolation and characterization of microsatellite loci in tropical forage Stylosanthes capitata Vogel
Authors: SANTOS M. O. , SASSAKI R. P. , CHIARI L. , RESENDE R. M. S. , DE SOUZA A. P. 
Published: January 2009

Abstract Stylosanthes capitata is an important tropical pasture legume. Knowledge of genetic diversity and structure of S. capitata populations is of great importance for the conservation and germplasm management of this species. Thus, eight microsatellite markers were developed from an S. capitata‐enriched library. They were characterized in 20 accessions from the germplasm collection of the Empresa Brasileira de Pesquisa Agropecuária (Embrapa). The observed and expected heterozygosities ranged from 0.16 to 0.85 and from 0.40 to 0.85, respectively. These microsatellites are the first set of molecular markers from this species and will contribute towards studies of genetic diversity, conservation and breeding of S. capitata.
Development of 16 polymorphic simple sequence repeat markers for Lycoris longituba from expressed sequence tags
Authors: HE QIULING , SHEN YE , CHEN YING , ZHOU YAN , BERG ARTHUR , WU RONGLING , HUANG MINREN 
Published: January 2009

Abstract Lycoris longituba is a tulip‐like ornamental plant in China. We report on the data mining of L. longituba expressed sequence tags (ESTs) to generate simple sequence repeat (SSRs) markers. Eighteen EST‐SSRs were isolated and validated for 32 individuals. These markers will be valuable for studying the genetic structure and diversity of populations for L. longituba.
Isolation and characterization of microsatellite loci in an endangered tree species, Afzelia xylocarpa (Kurz) Craib (Caesalpinioideae)
Authors: PAKKAD GREUK , UENO SANEYOSHI , YOSHIMARU HIROSHI 
Published: January 2009

Abstract Afzelia xylocarpa is listed as an endangered species on the International Union for the Conservation of Nature and Natural Resources World list of Threatened Trees, due to overexploitation for its valuable timber and habitat loss. We isolated eight polymorphic microsatellite loci from A. xylocarpa using dual suppression polymerase chain reaction technique. These loci provide microsatellite markers with high polymorphism, as the number of alleles ranged from two to seven, and the estimate of gene diversity was between 0.285 and 0.795. The markers are now available for more detailed investigation of population genetic structure and gene flow among A. xylocarpa populations.
New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach
Authors: VALENTINI ALICE , MIQUEL CHRISTIAN , NAWAZ MUHAMMAD ALI , BELLEMAIN EVA , COISSAC ERIC , POMPANON FRANÇOIS , GIELLY LUDOVIC , CRUAUD CORINNE , NASCETTI GIUSEPPE , WINCKER PATRICK , SWENSON JON E. , TABERLET PIERRE 
Published: January 2009

AbstractThe development of DNA barcoding (species identification using a standardized DNA sequence), and the availability of recent DNA sequencing techniques offer new possibilities in diet analysis. DNA fragments shorter than 100–150 bp remain in a much higher proportion in degraded DNA samples and can be recovered from faeces. As a consequence, by using universal primers that amplify a very short but informative DNA fragment, it is possible to reliably identify the plant taxon that has been eaten. According to our experience and using this identification system, about 50% of the taxa can be identified to species using the trnL approach, that is, using the P6 loop of the chloroplast trnL (UAA) intron. We demonstrated that this new method is fast, simple to implement, and very robust. It can be applied for diet analyses of a wide range of phytophagous species at large scales. We also demonstrated that our approach is efficient for mammals, birds, insects and molluscs. This method opens new perspectives in ecology, not only by allowing large‐scale studies on diet, but also by enhancing studies on resource partitioning among competing species, and describing food webs in ecosystems.
Isolation, characterization and cross‐species testing of microsatellites obtained from a sand smelt (Atherina boyeri) genomic library
Authors: MILANA VALENTINA , SOLA LUCIANA , ROSSI ANNA R. , BARBISAN FEDERICA , CONGIU LEONARDO 
Published: January 2009

AbstractThis study reports the isolation and characterization of 11 polymorphic microsatellites from a sand smelt (Atherina boyeri) genomic library. Enrichment was performed with di‐, tri‐ and tetranucleotide motifs following the FIASCO procedure (fast isolation by AFLP of sequences containing repeats). All loci were found to be in linkage and in Hardy–Weinberg equilibrium. This represents the first microsatellite isolation for the family Atherinidae and the isolated loci were accordingly tested on four additional species of the family: two recognized (A. presbyter and A. hepsetus) and two proposed (‘punctata’ and ‘non‐punctata’ forms). Moreover their cross‐species suitability on Menidia menidia, belonging to the same order but to the family Atherinopsidae, was also tested.
Ten microsatellite markers for the freshwater diatomSellaphora capitata
Authors: EVANS KATHARINE M. , CHEPURNOV VICTOR A. , MANN DAVID G. 
Published: January 2009

AbstractTen polymorphic microsatellite markers were developed for the benthic freshwater diatomSellaphora capitataand tested on 40 isolates from a Belgian pond. Genotyping was very successful (95%). The number of alleles per locus ranged from three to 12 (mean 6.6) and expected heterozygosities from 0.2 to 0.86 (mean 0.67). This is the first time that microsatellite markers have been developed for a freshwater or benthic diatom.
Assessing statistical power of SNPs for population structure and conservation studies
Authors: MORIN PHILLIP A. , MARTIEN KAREN K. , TAYLOR BARBARA L. 
Published: January 2009

AbstractSingle nucleotide polymorphisms (SNPs) have been proposed by some as the new frontier for population studies, and several papers have presented theoretical and empirical evidence reporting the advantages and limitations of SNPs. As a practical matter, however, it remains unclear how many SNP markers will be required or what the optimal characteristics of those markers should be in order to obtain sufficient statistical power to detect different levels of population differentiation. We use a hypothetical case to illustrate the process of designing a population genetics project, and present results from simulations that address several issues for maximizing statistical power to detect differentiation while minimizing the amount of effort in developing SNPs. Results indicate that (i) while ~30 SNPs should be sufficient to detect moderate (FST = 0.01) levels of differentiation, studies aimed at detecting demographic independence (e.g. FST < 0.005) may require 80 or more SNPs and large sample sizes; (ii) different SNP allele frequencies have little affect on power, and thus, selection of SNPs can be relatively unbiased; (iii) increasing the sample size has a strong effect on power, so that the number of loci can be minimized when sample number is known, and increasing sample size is almost always beneficial; and (iv) power is increased by including multiple SNPs within loci and inferring haplotypes, rather than trying to use only unlinked SNPs. This also has the practical benefit of reducing the SNP ascertainment effort, and may influence the decision of whether to seek SNPs in coding or noncoding regions.
Microsatellite markers for the grapevine pathogen, Eutypa lata
Authors: BAUMGARTNER K. , BERGEMANN S. E. , FUJIYOSHI P. , ROLSHAUSEN P. E. , GUBLER W. D. 
Published: January 2009

AbstractWe isolated and characterized nine polymorphic microsatellite markers for Eutypa lata, a fungal pathogen responsible for Eutypa dieback of grapevine, in populations from two California vineyards (24 isolates per vineyard). Allele frequency ranged from two to 11 alleles per locus and haploid gene diversity ranged from 0.33 to 0.83. All samples comprised unique haplotypes. Our results suggest that there is sufficient allelic polymorphism to estimate fine‐scale spatial structure, and to identify possible sources of inoculum from habitats outside of vineyards.
Isolation and characterization of polymorphic microsatellite loci in two primary parasitoids of the noctuid Spodoptera frugiperda: Chelonus insularis and Campoletis sonorensis (Hymenoptera)
Authors: JOURDIE VIOLAINE , ALVAREZ NADIR , TURLINGS TED C. J. , FRANCK PIERRE 
Published: January 2009

AbstractFifteen and 13 microsatellite loci were isolated, respectively, from Campoletis sonorensis Cameron and from Chelonus insularis Cresson. These two parasitic Hymenoptera are primary parasitoids of Lepidoptera in North, Central and South America, including the important agricultural pest Spodoptera frugiperda. Allelic diversity and heterozygosity were quantified in samples from Mexico. Each locus was polymorphic, with the number of alleles ranging from two to 16 in C. sonorensis and from four to 18 in C. insularis. Heterozygosity ranged from 0.088 to 0.403 in C. sonorensis and from 0.106 to 0.458 in C. insularis.
Isolation and characterization of expressed sequence tag‐linked microsatellite loci for the European eel (Anguilla anguilla)
Authors: PUJOLAR J. M. , MAES G. E. , VAN HOUDT J. K. J. , ZANE L. 
Published: January 2009

AbstractA European eel (Anguilla anguilla) expressed sequence tag database consisting of 795 contigs and 4008 singletons was screened for microsatellites sequences. Primers were designed to amplify 96 repeats, of which 86 gave good quality amplification products. Twenty‐eight microsatellites were selected for further microsatellite genotyping. Only two loci were found to be monomorphic; out of the 26 polymorphic loci, number of alleles per locus ranged from two to 14, while the observed and expected heterozygosities ranged from 0.05 to 0.93, and from 0.05 to 0.95, respectively. All 28 primer sets tested revealed positive amplification in American eel (Anguilla rostrata).
Characterization of 31 EST‐derived microsatellite markers for the pearl oyster Pinctada martensii (Dunker)
Authors: SHI YAOHUA , WANG YAN , HONG KUI , HOU ZHANHUI , WANG AIMIN , GUO XIMING 
Published: January 2009

AbstractWe developed and characterized 31 microsatellite markers from expressed sequence tags of Pinctada martensii (Dunker). The number of alleles per locus ranged from 4 to 18 as determined in 44 individuals from a wild population. The expected heterozygosity ranged from 0.4121 to 0.9436, while the observed heterozygosity ranged from 0.4054 to 0.7273. Most of the loci are in Hardy–Weinberg equilibrium. These markers should be useful for population genetics studies, parentage and genome mapping in this species.
Characterization of 32 novel microsatellite loci for population and mating system studies using Campostoma anomalum (central stoneroller)
Authors: LANDIS J. B. , HUDMAN S. P. , GROSE M. J. , SKALSKI G. T. , WILEY E. O. 
Published: January 2009

AbstractThe central stoneroller (Campostoma anomalum) is an abundant, widespread and sexually dimorphic stream minnow that is a useful model for mating system studies as well as a sentinel species for understanding population‐level processes for fishes in headwater communities. We developed one genomic library enriched for dinucleotide repeats and isolated 48 putative, novel microsatellite loci. Of those, we present 32 polymorphic and independent microsatellite markers with 3 to 16 alleles per locus and heterozygosity ranging from 0.23 to 0.95. Hence, these markers will be useful for future behavioural, ecological and evolutionary studies using C. anomalum.
Twelve nuclear microsatellite loci for rice stem borer (Chilo suppressalis W.)
Authors: LIU YU‐DI , HOU MAO‐LIN , HAO LI‐XIA 
Published: January 2009

AbstractWe developed 12 polymorphic microsatellite markers for the rice stem borer Chilo suppressalis (Walker). These loci were screened for 96 individuals from eight populations across China. The total number of alleles ranged from 3 to 33 and the expected heterozygosity at these loci ranged from 0.131 to 0.671. These molecular markers will be useful for fully investigating the population structure and host preference of C. suppressalis at fine spatial scales.
Development of 10 microsatellite loci in the pulmonate snail Biomphalaria kuhniana (Mollusca, Gastropoda)
Authors: DUPUY VIRGINIE , NICOT ANTOINE , JARNE PHILIPPE , DAVID PATRICE 
Published: January 2009

AbstractWe characterized 10 variable microsatellite loci in the freshwater snail Biomphalaria kuhniana, as well as conditions for multiplexing and co‐loading sets of loci. Two to five alleles were detected per locus over the two studied populations in Venezuela. High inbreeding coefficients suggest high selfing rates. Cross‐species amplification provided some variability at eight and three loci in the other species belonging to the Biomphalaria straminea complex (B. straminea and B. intermedia), but was unsuccessful in more divergent species.
Isolation and characterization of 15 polymorphic microsatellite DNA loci from Argyrosomus japonicus (mulloway), a new aquaculture species in Australia
Authors: ARCHANGI B. , CHAND V. , MATHER P. B. 
Published: January 2009

AbstractFifteen microsatellite loci were isolated for population genetic studies of mulloway (Argyrosomus japonicus), a commercial/recreational fish species in Southern Australia. A genomic library was screened randomly for di‐ tri‐ and tetranucleotide repeats. Fifteen microsatellite marker loci were developed that were highly polymorphic (allele number ranged from four to 18).Observed and expected heterozygosities ranged from 0.17 to 1 and from 0.27 to 0.91, respectively. These markers have proven useful for estimating genetic variation and for evaluating population structure across the species’ natural distribution. They also provide powerful tools for optimizing hatchery practices to conserve genetic diversity.
Influence of DNA isolation from historical otoliths on nuclear–mitochondrial marker amplification and age determination in an overexploited fish, the common sole (Solea solea L.)
Authors: CUVELIERS E. L. , BOLLE L. J. , VOLCKAERT F. A. M. , MAES G. E. 
Published: January 2009

AbstractHistorical otolith collections are crucial in assessing the evolutionary consequences of natural and anthropogenic changes on the demography and connectivity of commercially important fish species. Hence, it is important to define optimal protocols for purifying DNA from such valuable information sources while avoiding any damage to the physical structure of the otolith. Before being able to conclude on the harmlessness of a method, it is important to validate protocols on different kinds of otoliths by testing purification methodologies under standardized conditions. Here we compare the effect of two DNA extraction methods on the success in identifying the age in an overexploited marine fish, the common sole (Solea solea L.). To ensure optimal future population genetic and demographic analyses, we assessed DNA quantity and tested the DNA quality by investigating the amplification success of a mitochondrial and nuclear marker. Our results show that the choice of the DNA extraction method had a significant effect on the success of using these otoliths in age and growth analyses. Standard commercial and published protocols resulted in a severe damaging of the otolith structure, hampering accurate preparation and analyses of the morphological structures of the otoliths. Shortening the lysis time and lowering the EDTA (ethylene diamine tetraacetic acid) and SDS (sodium dodecylsulphate) concentration turned out to be beneficial for the stability of otolith structure, while maintaining an overall high DNA quality measured through polymerase chain reaction amplification success. We therefore recommend that care should be taken when choosing the extraction method for a molecular study on archived samples, in order to enable the maximal use of information embedded in historical material.
Isolation and characterization of microsatellite loci for alligator gar (Atractosteus spatula) and their variability in two other species (Lepisosteus oculatus and L. osseus) of Lepisosteidae
Authors: MOYER GREGORY R. , SLOSS BRIAN L. , KREISER BRIAN R. , FELDHEIM KEVIN A. 
Published: January 2009

AbstractWe report on the isolation of 17 polymorphic microsatellite loci from alligator gar (Atractosteus spatula), a large‐bodied species that has experienced population declines across much of its range. These loci possessed 2–19 alleles and observed heterozygosities of 0–0.974. All loci conformed to Hardy–Weinberg equilibrium expectations, and none exhibited linkage disequilibrium. Nine and eight of these loci were found to be polymorphic in the related species Lepisosteus oculatus and L. osseus, respectively. These microsatellite loci should prove useful in conservation efforts of A. spatula through the study of population structure and hatchery broodstock management.
Isolation and characterization of microsatellite loci in the western pearlshell mussel, Margaritifera falcata (Gould)
Authors: CHONG JER PIN , BOX JAYNE BRIM , NEZ DONNA A. , MOCK KAREN E. 
Published: January 2009

AbstractTen microsatellite loci were isolated from the western pearlshell, Margaritifera falcata (Gould, 1850) and characterized in populations from Washington and Montana, USA. We also assessed eight microsatellite loci developed in M. margaritifera, two of which showed utility. Both of our test populations showed significant heterozygote deficiencies at most loci, consistent with a hermaphroditic life history. Populations differed markedly with respect to allelic richness, allele frequencies and numbers of identical multilocus genotypes. This panel of loci should prove useful in describing gene flow and genetic diversity patterns among M. falcata populations, information that should aid future conservation efforts.
The Ecological and Spatial Structure of the Socio‐Economic Characteristics of Winnipeg,1961
Authors: Nicholson T. G. , Yeates Maurice H. 
Published: January 2009

L'application de l'analyse des composantes principales aux donnees socio‐economiques de 1961 pour Winnipeg nous permet d'extraire les dimensions sous‐jacentes de la structure socio‐economique de la population de la ville. On y fait la demonstration que les dimensions derivees correspondent dans une large mesure aux dimensions obtenues par l'analyse de l'aire sociale. II est de plus souligne que l'analyse des composantes principales constitue un instrument utile dans l'analyse des donnees urbaines multivariees; elle est egalement tres utile‐a Pinterieur de certaines limites‐dans les etudes empiriques portant sur la structure ecologique de la ville.The application of principal components analysis to 1961 socio‐economic data for Winnipeg derives the underlying dimensions of the socio‐economic structure of the city's population. It is generally shown that the derived dimensions are quite similar to “social area analysis” dimensions. It is further indicated that principal components analysis provides a useful tool in the analysis of multivariate urban data and, subject to certain limitations, is extremely useful in empirical studies of the ecological structure of cities.
Multidrug‐Resistant E. coli and Enterobacter Extraintestinal Infection in 37 Dogs
Authors: Gibson J.S. , Morton J.M. , Cobbold R.N. , Sidjabat H.E. , Filippich L.J. , Trott D.J. 
Published: January 2009

Background: Extraintestinal infections caused by multidrug‐resistant (MDR) Escherichia coli and Enterobacter are becoming more common in veterinary medicine.Objective: To generate hypotheses for risk factors for dogs acquiring extraintestinal infection caused by MDR E. coli and Enterobacter, describe antimicrobial resistance profiles and analyze treatment and clinical outcomes.Animals: Thirty‐seven dogs diagnosed with extraintestinal infection caused by MDR E. coli and Enterobacter spp. between October 1999 and June 2006.Methods: Retrospective case series assembled from hospital records data, including clinical history before 1st MDR isolation and treatment outcome. Identity and antimicrobial susceptibility profiles were confirmed by standard microbiological techniques for 57 isolates.Results: Most dogs had an underlying disease condition (97%), received prior antimicrobial treatment (87%), were hospitalized for ≥3 days (82%), and had a surgical intervention (57%). The urinary tract was the most common infection site (62%), and urinary catheterization, bladder stasis, or both were common among dogs (24%). Some dogs were treated with high doses of co‐amoxyclavulanate (n = 14) and subsequently recovered even though the isolates showed in vitro resistance to this antimicrobial. Other dogs were successfully treated with chloramphenicol (n = 11) and imipenem (n = 2).Conclusion and Clinical Importance: Predisposing disease condition, any prior antimicrobial use rather than a specific class of antimicrobial, duration of hospitalization, and type of surgical procedure might be risk factors for acquiring MDR extraintestinal infections. Whereas culture and sensitivity results can indicate use of last‐resort antimicrobials such as imipenem for MDR infections, some affected dogs can recover after administration of high doses of co‐amoxyclavulanate.
Antigen and Antibody Testing for the Diagnosis of Blastomycosis in Dogs
Authors: Spector D. , Legendre A.M. , Wheat J. , Bemis D. , Rohrbach B. , Taboada J. , Durkin M. 
Published: January 2009

Background:Early diagnosis and treatment are associated with an improved prognosis in blastomycosis. The diagnosis of blastomycosis may be missed by cytology, histopathology, culture, or serology. An enzyme immunoassay (EIA) for detection ofBlastomyces dermatitidisgalactomannan antigen in body fluids has been used for rapid diagnosis of blastomycosis in humans.Hypothesis:Measurement ofBlastomycesantigen in urine or serum by the MVistaBlastomycesantigen EIA is more sensitive than measurement of anti‐Blastomycesantibodies for diagnosis of blastomycosis in dogs.Methods:Serum and urine samples from 46 dogs with confirmed blastomycosis were tested forBlastomycesantigen and serum was tested for anti‐Blastomycesantibodies.Results:The sensitivity for the detection of antigen in urine was 93.5% and it was 87.0% in serum. The sensitivity of antibody detection by agar gel immunodiffusion (AGID) was 17.4% and it was 76.1% by EIA. Antigen and antibody decreased during itraconazole treatment.Conclusions and Clinical Importance:Antigen detection is a more sensitive test for diagnosis of blastomycosis than antibody testing by AGID, the only commercially available method. Antigen concentrations decreased with treatment.