bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microsatellite DNA markers for three toad‐headed lizard species (Phrynocephalus vlangalii, P. przewalskii and P. guttatus)
Authors: ZHAN AIBIN , FU JINZHONG 
Published: January 2009

AbstractTo assess the impact of natural landscapes on the population structure of lizards, 10 polymorphic microsatellite DNA markers were developed for the Qinghai toad‐headed lizard, Phrynocephalus vlangalii. The number of alleles at these informative loci ranged from four to 28. The novel markers and those previously developed for Phrynocephalus przewalskii were cross‐tested among three toad‐headed lizard species P. vlangalii, P. przewalskii and P. guttatus. A high cross‐utility rate of more than 58% was observed among these three species. These markers are expected to be useful tools for taxonomic considerations as well as population genetic analysis and future conservation management.
Isolation of ten tetranucleotide microsatellite loci in the Northern Wheatear (Oenanthe oenanthe)
Authors: KUDERNATSCH DAGMAR , WEIS‐DOOTZ TANJA , SEGELBACHER GERNOT 
Published: January 2009

AbstractWe isolated 10 polymorphic microsatellite DNA loci from the Northern Wheatear (Oenanthe oenanthe) and optimized these for future studies in population genetics and behavioural ecology. The loci were screened for polymorphism using 107 individuals from one population in Germany. The primers amplified loci with high numbers of alleles ranging from two to 20 alleles per locus.
Isolation and characterization of 23 microsatellite loci in the yellow tang, Zebrasoma flavescens (Pisces: Acanthuridae)
Authors: CHRISTIE MARK R. , EBLE JEFF A. 
Published: January 2009

AbstractTwenty‐three microsatellites were isolated from the yellow tang (Zebrasoma flavescens), an ecologically and commercially important reef fish. Genetic diversity was assessed in 90 adults collected from Honokohau, Hawaii. The number of alleles per locus varied from four to 29 (mean = 13.8) and observed and expected heterozygosities ranged from 0.15 to 0.94 (mean = 0.70) and from 0.29 to 0.93 (mean = 0.81), respectively. Eight loci exhibited significant departure from Hardy–Weinberg equilibrium due to the presence of null alleles. Exact tests showed no evidence of genotypic disequilibrium between loci. Overall, loci were well resolved, easy to score and highly polymorphic.
Development of nine new microsatellite loci for the American beaver,Castor canadensis(Rodentia: Castoridae), and cross‐species amplification in the European beaver,Castor fiber
Authors: PELZ‐SERRANO KARLA , MUNGUIA‐VEGA ADRIAN , PIAGGIO ANTOINETTE J. , NEUBAUM MELISSA , MUNCLINGER PAVEL , PÁRTL ADAM , VAN RIPER III CHARLES , CULVER MELANIE 
Published: January 2009

AbstractWe developed nine new nuclear dinucleotide microsatellite loci forCastor canadensis. All loci were polymorphic, except for one. The number of alleles ranged from two to four and from five to 12 in populations from Arizona and Wisconsin, respectively. Average heterozygosity ranged from 0.13 to 0.86 per locus. Since cross‐species amplification inCastor fiberwas successful only in four loci, we tested also nine recently publishedC. canadensisloci in the Eurasian species. Eight of the published loci amplified; however, three were monomorphic. The number of alleles was lower inC. fiberthan inC. canadensisat all loci tested.
Isolation and characterization of nine polymorphic microsatellite loci of the kelp greenling, Hexagrammos decagrammus, a temperate reef fish
Authors: FREIWALD JAN , STEWART NATHAN L. , YATES DEVONA C. , BERNARDI GIACOMO 
Published: January 2009

AbstractNine polymorphic microsatellite loci were developed and characterized for the temperate reef fish species, Hexagrammos decagrammus (kelp greenling). The number of alleles varied from three to 22 in a sample of 22 individuals from one population. Expected heterozygosities ranged from 0.354 to 0.979. These microsatellites allow us to investigate reproductive success of individuals, alternative mating strategies as well as population structure and metapopulation dynamics of this species.
Laser‐assisted microdissection for the study of the ecology of parasites in their hosts
Authors: POST R. J. , CRAINEY J. L. , BIVAND A. , RENZ A. 
Published: January 2009

AbstractThe population biology of internal parasites is difficult to study because the adult parasites are often inaccessible, deep within the host's body. Developing stages, such as eggs in the faeces or larvae in the skin are more easily obtained, but are difficult to handle because they are often very small and with a tough cuticle. This has limited their use in molecular ecology for estimating population biology parameters of the adults (their parents). We have usedOnchocerca ochengi(a filarial nematode parasite of cattle) to describe a novel and generally applicable method of easily and conveniently isolating individual larvae (microfilariae) from the host using laser‐assisted microdissection. Furthermore, we have been able to improve the isolation of DNA by using the laser to bisect the larva to release DNA from the tissues enclosed within the parasite cuticle, and in this way we have achieved amplification of fragments over 1400 bp, and routinely PCR‐amplified single‐copy sequences from 5% of the DNA from a single larva (the equivalent of approximately 15 nuclei), and regularly from 0.5%.
Characterization of 11 new microsatellite loci in taro (Colocasia esculenta)
Authors: HU KAN , HUANG XING FANG , KE WEI DONG , DING YI 
Published: January 2009

AbstractEleven new microsatellite markers were isolated from taro, Colocasia esculenta (L.) Schott, a root crop widely distributed all over the world. Forty‐eight primer pairs were designed from a microsatellite‐enriched genomic library, of which 11 primer pairs have polymorphisms in 30 individuals tested from a population in China, which revealed two to six alleles per locus with the observed and expected heterozygosity levels ranging from 0 to 0.733 and from 0.381 to 0.731, respectively. These new genetic markers will be useful for the study of taro germplasm management and population evolution in the future.
Isolation and characterization of microsatellite loci from Lochmaea suturalis, the heather beetle (Coleoptera: Chrysomelidae), a pest in Europe and a biocontrol agent in New Zealand
Authors: HARMAN HELEN M. , WEIR BEVAN S. , WELLS SARAH J. , HOWITT ROBYN L. J. 
Published: January 2009

AbstractThe heather beetle Lochmaea suturalis which is native to northwest Europe has been released as a biocontrol agent for heather in New Zealand. We have isolated and optimized eight microsatellite loci from New Zealand beetles. These loci provide markers with high polymorphism ranging from four to 20 alleles per locus. Observed heterozygosity averaged 0.631 per locus. These results suggest the markers are useful for population studies that will contribute to assessment of L. suturalis as a biocontrol agent.
Microsatellite loci for population and parentage analysis in the Amazon River dolphin (Inia geoffrensis de Blainville, 1817)
Authors: GRAVENA WALESKA , HRBEK TOMAS , DA SILVA VERA M. S. , ASTOLFI‐FILHO SPARTACO , FARIAS IZENI P. 
Published: January 2009

AbstractWe developed specific primers for microsatellite DNA regions for the Amazon River dolphin or boto Inia geoffrensis, for use in population and conservation genetic studies. We also tested their transferability for two other species, Pontoporia blainvillei (sister taxon of I. geoffrensis) and Sotalia guianensis. A total of 12 microsatellite loci were polymorphic for the boto. An additional 25 microsatellite loci previously isolated from other cetacean species were also tested in the boto. The 26 polymorphic microsatellite loci indicate they will be excellent markers for studies of population structure and kinship relations of the boto.
Polymorphic microsatellite loci in the widespread amphidromous goby Sicyopterus lagocephalus and cross‐genus amplification among Sicydiinae
Authors: HOAREAU T. B. , BARBISAN F. , DUBOIS S. , ZANE L. , BERREBI P. 
Published: January 2009

AbstractMicrosatellite DNA markers were isolated in an amphidromous goby (Sicyopterus lagocephalus) from a partial genomic library enriched for AC repeats. Eight microsatellites were highly polymorphic with six to 33 alleles per locus and expected heterozygosities ranging from 0.53 to 0.97. Cross‐species amplifications were performed within the sub‐family Sicydiinae by genotyping individuals from two species of the genus Cotylopus. Some of these loci were successfully amplified and showed polymorphism in the second genus.
Four cleaved amplified polymorphic sequence (CAPS) markers for the detection of the Juglans ailantifolia chloroplast in putatively native J. cinerea populations
Authors: MCCLEARY TIM S. , ROBICHAUD RODNEY L. , NUANES STEVE , ANAGNOSTAKIS SANDRA L. , SCHLARBAUM SCOTT E. , ROMERO‐SEVERSON JEANNE 
Published: January 2009

AbstractHybridization between butternut (Juglans cinerea), a forest tree native to eastern North America, and Japanese walnut (J. ailantifolia), a tree tolerant to the lethal fungal disease butternut canker, casts doubt on the genetic identity of the remaining butternuts. We report a diagnostic test to distinguish the J. cinerea chloroplast from the J. ailantifolia chloroplast using cleaved amplified polymorphic sequences resolvable in 1.5% agarose gels. J. ailantifolia maternal ancestry in naturally regenerated stands provides a site selection criterion for studies of introgression dynamics when the non‐native parent and the hybrids tolerate a disease to which the native species is susceptible.
Rapid polymerase chain reaction–restriction fragment length polymorphism method for discrimination of the two Atlantic cryptic deep‐sea species of scabbardfish
Authors: STEFANNI SERGIO , BETTENCOURT RAUL , KNUTSEN HALVOR , MENEZES GUI 
Published: January 2009

AbstractThe present investigation provides an efficient diagnostic method based on polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis to discriminate between two cryptic species of scabbardfish, Aphanopus carbo and A. intermedius, with commercial relevance in several European fish markets. Two DNA fragments from the mtDNA, including control region and partial cytochrome oxidase subunit I genes of about 1100 bp and 700 bp, respectively, were isolated by PCR amplification. Digestion of the amplicon including the control region with HaeII and the amplicon including the COI gene with Sau3AI restriction enzymes allowed an unequivocal discrimination between the two scabbardfish species. This PCR–RFLP method allowed a clear and rapid discrimination of the trichiurid species studied.
Eight microsatellite loci for the sexually transmitted, parasitic mite Coccipolipus hippodamiae
Authors: GORDON LAURA K. , HURST GREGORY D. D. , WATTS PHILLIP C. 
Published: January 2009

AbstractSeven dinucleotide and one trinucleotide polymorphic microsatellite loci were isolated from the mite Coccipolipus hippodamiae. This mite is an ectoparasite of coccinellid beetles (ladybirds), principally the European two‐spot ladybird Adalia bipunctata, where it causes sterility in the female host. Levels of genetic diversity were assessed using 32 mites from Warsaw, Poland. We observed moderate variability, with the number of alleles per locus varying between 2 and 4, and observed and expected heterozygosities ranging from 0.031 to 0.267 and between 0.062 and 0.526, respectively. This is the first description of microsatellite loci from the genus Coccipolipus and these loci are currently being employed to answer fundamental questions about the epidemiology of C. hippodamiae infections on A. bipunctata.
Eight novel tetranucleotide and five cross‐species dinucleotide microsatellite loci for the ornate chorus frog (Pseudacris ornata)
Authors: DEGNER JACOB F. , HETHER TYLER D. , HOFFMAN ERIC A. 
Published: January 2009

AbstractWe describe the cloning and characterization of eight novel tetranucleotide microsatellite loci in the ornate chorus frog (Pseudacris ornata). We also screened 26 loci from GenBank that were isolated from other Pseudacris species and obtained consistent product from five of these dinucleotide loci. All loci are polymorphic. In our sample of 26 frogs from a natural population, polymorphism ranged from 1 to 22 alleles per locus with expected heterozygosities ranging from 0 to 0.958. These loci enable high‐resolution studies of P. ornata. Moreover, cross‐species amplification success suggests they will also be useful for other chorus frog species.
Isolation of 11 polymorphic tri‐ and tetranucleotide microsatellite loci in a North American sedge (Carex scoparia: Cyperaceae) and cross‐species amplification in three additional Carex species
Authors: HIPP ANDREW L. , KETTENRING KARIN M. , FELDHEIM KEVIN A. , WEBER JAIME A. 
Published: January 2009

AbstractWe report on the isolation and evaluation of 11 microsatellites from a widespread eastern North American wetland sedge, Carex scoparia. Loci exhibit 3–9 alleles over five populations and significant FIS (0.204–0.717) in most populations. All primers cross‐amplify in at least two other species, and 10 cross‐amplify in the more distantly related C. stipata. These markers will be used to examine population genetics and patterns of chromosomal diversification in this ecologically important sedge species and its relatives.
Microsatellites in the Karoo scrub‐robin, Cercotrichas coryphaeus (Passeriformes: Muscicapinae): isolation and characterization of 13 autosomal and two sex‐linked loci
Authors: RIBEIRO ÂNGELA , LLOYD PENN , FELDHEIM KEVIN A. , BOWIE RAURI C. K. 
Published: January 2009

AbstractFifteen polymorphic microsatellites were developed for the Karoo scrub‐robin, Cercotrichas coryphaeus. Here we describe and characterize microsatellite variation of 13 autosomal loci and two Z‐linked loci in 42 individuals from two distinct South African populations. The number of alleles per locus varied from three to 13 and values of observed heterozygosity ranged from 0.318 to 0.900. These loci will be used to test hypotheses relating to fine‐scale social structure and mating strategies in this cooperatively breeding species.
A novel manual pooling system for preparing three‐dimensional pools of a deep coverage soybean bacterial artificial chromosome library
Authors: XIA ZHENGJUN , WATANABE SATOSHI , CHEN QINGSHAN , SATO SHUSEI , HARADA KYUYA 
Published: January 2009

AbstractCompared with hybridization‐based techniques, polymerase chain reaction‐based screening of large insert libraries has been used widely as it is fast, easy and sensitive. However, various pooling strategies are needed to ensure efficient screening. It is time‐consuming and labourious to prepare three‐dimensional pools for a deep coverage bacterial artificial chromosome (BAC) library of soybean (1.12 × 109 bp) in the absence of robotic facility. In the present study, we describe a novel manual pooling system for preparing three‐dimensional pools of a soybean BAC library. This simple technique enables a single researcher to construct three‐dimensional pools for a deep‐coverage (12 haploid genome equivalents) BAC library of soybean in less than 2 months without any robotic manipulation. When the prepared three‐dimensional pools were screened with 29 polymerase chain reaction‐based markers, an average of 9.2 clones per marker were identified. These identified clones will be useful either in quantitative trait loci gene isolation or in synteny study between soybean and other legumes including Lotus japonicus. This efficient pooling system could be applied to any other BAC libraries without the need for robotic manipulation.
Development and characterization of microsatellite markers in Zanthoxylum ailanthoides (Rutaceae)
Authors: NAGAI H , YOSHIDA T , KAMIYA K , YAHARA T , TACHIDA H 
Published: January 2009

AbstractNine microsatellite markers were developed for Zanthoxylum ailanthoides, a typical pioneer tree. Averaged over the nine loci, the number of alleles per locus was 5.1. The observed and expected heterozygosities ranged from 0.233 to 0.833 and from 0.314 to 0.823, with averages of 0.606 and 0.641, respectively. No loci showed significant departures from Hardy–Weinberg equilibrium or linkage equilibrium after Bonferroni correction (P > 0.05). These markers will be useful for parentage analyses and studies of population genetic structure in the species.
Foveal function in children treated for amblyopia
Authors: Agervi Pia , Nilsson Maria , Martin Lene 
Published: January 2009

Abstract.Purpose:  This study aimed to evaluate foveal function, using three different methods, in children treated for monocular amblyopia.Methods:  A sample of 24 otherwise healthy children with treated amblyopia and an age‐matched control group of 25 healthy children were examined for best corrected visual acuity (BCVA) using a standard decimal (KM) chart and the computerized TriVA method at 50% and 10% contrasts. Foveal function was also measured with the rarebit fovea test (RFT), which is included in the rarebit perimetry program package. This test uses very small and bright dots against a dark background. The result is expressed as mean hit rate (MHR).Results:  Amblyopic eyes showed significantly lower BCVA when evaluated with the KM chart and with the TriVA test at different contrast levels, compared with both fellow eyes and control eyes. No statistically significant difference between amblyopic and fellow eyes was found when foveal function was evaluated with the RFT (median MHRs 91.5% and 94.5%, respectively), although results for both amblyopic and fellow eyes were statistically lower than those of the control group (median MHR 97%) (p = 0.001 and p = 0.046, respectively). This might indicate that the RFT provides different information about foveal function than conventional VA tests.Conclusions:  The findings in the current study accord with those of other studies reporting abnormalities in the fellow eyes of previously treated amblyopic patients. These findings may reflect a general disturbance in the visual system rather than a monocular adaptation to refractive error or ocular motor disturbance.
Indole-Diterpene Biosynthetic Capability ofEpichloëEndophytes as Predicted byltmGene Analysis
Authors: Young Carolyn A. , Tapper Brian A. , May Kimberley , Moon Christina D. , Schardl Christopher L. , Scott Barry 
Published: January 2009

ABSTRACTBioprotective alkaloids produced byEpichloëand closely related asexualNeotyphodiumfungal endophytes protect their grass hosts from insect and mammalian herbivory. One class of these compounds, known for antimammalian toxicity, is the indole-diterpenes. TheLTMlocus ofNeotyphodium lolii(Lp19) andEpichloë festuce(Fl1), required for the biosynthesis of the indole-diterpene lolitrem, consists of 10ltmgenes. We have used PCR and Southern analysis to screen a broad taxonomic range of 44 endophyte isolates to determine why indole-diterpenes are present in so few endophyte-grass associations in comparison to that of the other bioprotective alkaloids, which are more widespread among the endophtyes. All 10ltmgenes were present in only three epichloë endophytes. A predominance of the asexualNeotyphodiumspp. examined contained 8 of the 10ltmgenes, with only oneN. loliicontaining the entireLTMlocus and the ability to produce lolitrems. Liquid chromatography-tandem mass spectrometry profiles of indole-diterpenes from a subset of endophyte-infected perennial ryegrass showed that endophytes that contained functional genes present inltmclusters 1 and 2 were capable of producing simple indole-diterpenes such as paspaline, 13-desoxypaxilline, and terpendoles, compounds predicted to be precursors of lolitrem B. Analysis of toxin biosynthesis genes by PCR now enables a diagnostic method to screen endophytes for both beneficial and detrimental alkaloids and can be used as a resource for screening isolates required for forage improvement.
Interaction of
Bacillus thuringiensis
Cry1 and Vip3A Proteins with
Spodoptera frugiperda
Midgut Binding Sites
Authors: Sena Janete A. D. , Hernández-Rodríguez Carmen Sara , Ferré Juan 
Published: January 2009

ABSTRACT
Vip3Aa, Vip3Af, Cry1Ab, and Cry1Fa were tested for their toxicities and binding interactions. Vip3A proteins were more toxic than Cry1 proteins. Binding assays showed independent specific binding sites for Cry1 and Vip3A proteins. Cry1Ab and Cry1Fa competed for the same binding sites, whereas Vip3Aa competed for those of Vip3Af.
Selection of
Sphingomonadaceae
at the Base of
Laccaria proxima
and
Russula exalbicans
Fruiting Bodies
Authors: Boersma F. G. Hidde , Warmink Jan A. , Andreote Fernando A. , van Elsas Jan Dirk 
Published: January 2009

ABSTRACT

The dense hyphal network directly underneath the fruiting bodies of ectomycorrhizal fungi might exert strong influences on the bacterial community of soil. Such fruiting bodies might serve as hot spots for bacterial activity, for instance by providing nutrients and colonization sites in soil. Here, we assessed the putative selection of specific members of the
Sphingomonadaceae
family at the bases of the fruiting bodies of the ectomycorrhizal fungi
Laccaria proxima
and
Russula exalbicans
in comparison to the adjacent bulk soil. To do so, we used a previously designed
Sphingomonadaceae
-specific PCR-denaturing gradient gel electrophoresis (DGGE) system and complemented this with analyses of sequences from a
Sphingomonadaceae
-specific clone library. The analyses showed clear selective effects of the fruiting bodies of both fungi on the
Sphingomonadaceae
community structures. The effect was especially prevalent with
R. exalbicans
. Strikingly, similar fungi sampled approximately 100 m apart showed similar DGGE patterns, while corresponding bulk soil-derived patterns differed from each other. However, the mycospheres of
L. proxima
and
R. exalbicans
still revealed divergent community structures, indicating that different fungi select for different members of the
Sphingomonadaceae
family. Excision of specific bands from the DGGE patterns, as well as analyses of the clone libraries generated from both habitats, revealed fruiting body-specific
Sphingomonadaceae
types. It further showed that major groups from the mycospheres of
R. exalbicans
and
L. proxima
did not cluster with known bacteria from the database, indicating new groups within the family of
Sphingomonadaceae
present in these environments.
Diverse and Novel
nifH
and
nifH
-Like Gene Sequences in the Deep-Sea Methane Seep Sediments of the Okhotsk Sea
Authors: Dang Hongyue , Luan Xiwu , Zhao Jingyi , Li Jing 
Published: January 2009

ABSTRACT

Diverse
nifH
and
nifH
-like gene sequences were obtained from the deep-sea surface sediments of the methane hydrate-bearing Okhotsk Sea. Some sequences formed novel families of the NifH or NifH-like proteins, of currently unresolved bacterial or archaeal origin. Comparison with other marine environments indicates environmental specificity of some of the sequences, either unique to the methane seep sediments of the Okhotsk Sea or to the general deep-sea methane seep sedimentary environments.