bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeography of field voles (Microtus agrestis) in Eurasia inferred from mitochondrial DNA sequences
Authors: Jaarola Maarit , Searle Jeremy B. 
Published: March 2003

AbstractIn a distribution‐wide phylogeographic survey of the field vole (Microtus agrestis), 75 specimens from 56 localities across Eurasia were examined for DNA sequence variation along the whole 1140 base pair (bp) mitochondrial (mt) cytochrome b gene. The species is subdivided into three main mtDNA phylogeographic groups — western, eastern and southern — with largely allopatric distributions. The western phylogeographical group is found in west and central Europe and spread most probably from a glacial refugium in the Carpathians. The eastern group covers a large range from Lithuania to central Asia, and probably originated from a southeast European source (e.g. the southern Urals or the Caucasus). The southern group occupies an area from Portugal to Hungary, with division into two distinct mtDNA sublineages that presumably derive from separate glacial refugia in the Iberian Peninsula. Molecular clock estimates suggest that the western and eastern field vole populations separated during the last glaciation, whereas the southern population dates back 0.5–0.9 Myr. High levels of mtDNA variation indicate relatively large population sizes and subdivisions within phylogeographic groups during the last glaciation. We report a possible new suture zone in east Europe.
Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review
Authors: Li You‐Chun , Korol Abraham B. , Fahima Tzion , Beiles Avigdor , Nevo Eviatar 
Published: March 2003

AbstractMicrosatellites, or tandem simple sequence repeats (SSR), are abundant across genomes and show high levels of polymorphism. SSR genetic and evolutionary mechanisms remain controversial. Here we attempt to summarize the available data related to SSR distribution in coding and noncoding regions of genomes and SSR functional importance. Numerous lines of evidence demonstrate that SSR genomic distribution is nonrandom. Random expansions or contractions appear to be selected against for at least part of SSR loci, presumably because of their effect on chromatin organization, regulation of gene activity, recombination, DNA replication, cell cycle, mismatch repair system, etc. This review also discusses the role of two putative mutational mechanisms, replication slippage and recombination, and their interaction in SSR variation.
Migration and genetic structure of the grain aphid (Sitobion avenae) in Britain related to climate and clonal fluctuation as revealed using microsatellites
Authors: Llewellyn K. S. , Loxdale H. D. , Harrington R. , Brookes C. P. , Clark S. J. , Sunnucks P. 
Published: March 2003

AbstractGenetic structuring of populations reflects the interaction of genetic drift, mutation, migration and selection, with influences from life history. Aphids are interesting in this regard as they have the potential for unusually high levels of dispersal and natural selection, which typically counter each other. In the present study, winged grain aphidsSitobion avenae(F.) were collected in four 12.2‐m high suction traps along a north–south transect in Britain in order to eliminate sampling bias from plant hosts (cereals and grasses; Poaceae), it being known that these insects show host adaptation demonstrable using molecular markers. Samples were analysed at four polymorphic microsatellite loci over two consecutive years. Population allele frequencies were similar nationally during the two years, although clonal diversity varied greatly between sites and years. In the first sampling year following a harsh winter, diversity was found to display a latitudinal clinal trend: the proportion of unique clones (genotypes) increased with latitude. However, this pattern was less apparent the following year, after a milder winter. Nonetheless, overallFSTanalysis showed that there was little spatial genetic structuring in either sampling year. These data support the view that the insect is highly migratory and also support a theoretical model and previous data suggesting that the reproductive mode is clinal inS. avenae. This appears to be because natural selection (reduced reproductive success of asexual genotypes under cold conditions) is sufficiently powerful to overcome the homogenizing effects of strong migration. There was no clear evidence for isolation by distance for the genetic data obtained. The data are compared with similar data from other aphid species and other insects. Only by the collection of such data sets can an accurate picture be built up relating genetic variability to flight behaviour, including migratory ambit in this group of insects since, due to their small size and rapid dilution in the air, other marking approaches are impracticable over large geographical distances.
Demographic and genetic estimates of effective population size (Ne) reveals genetic compensation in steelhead trout
Authors: Ardren William R. , Kapuscinski Anne R. 
Published: March 2003

AbstractEstimates of effective population size (Ne) are required to predict the impacts of genetic drift and inbreeding on the evolutionary dynamics of populations. How the ratio of Ne to the number of sexually mature adults (N) varies in natural vertebrate populations has not been addressed. We examined the sensitivity of Ne/N to fluctuations of N and determined the major variables responsible for changing the ratio over a period of 17 years in a population of steelhead trout (Oncorhynchus mykiss) from Washington State. Demographic and genetic methods were used to estimate Ne. Genetic estimates of Ne were gained via temporal and linkage disequilibrium methods using data from eight microsatellite loci. DNA for genetic analysis was amplified from archived smolt scales. The Ne/N from 1977 to 1994, estimated using the temporal method, was 0.73 and the comprehensive demographic estimate of Ne/N over the same time period was 0.53. Demographic estimates of Ne indicated that variance in reproductive success had the most substantial impact on reducing Ne in this population, followed by fluctuations in population size. We found increased Ne/N ratios at low N, which we identified as genetic compensation. Combining the information from the demographic and genetic methods of estimating Ne allowed us to determine that a reduction in variance in reproductive success must be responsible for this compensation effect. Understanding genetic compensation in natural populations will be valuable for predicting the effects of changes in N (i.e. periods of high population density and bottlenecks) on the fitness and genetic variation of natural populations.
Habitat differentiation vs. isolation‐by‐distance: the genetic population structure of Elymus athericus in European salt marshes
Authors: Bockelmann A.‐C. , Reusch T. B. H. , Bijlsma R. , Bakker J. P. 
Published: March 2003

AbstractWe investigated genetic differentiation among populations of the clonal grass Elymus athericus, a common salt‐marsh species occurring along the Wadden Sea coast of Europe. While E. athericus traditionally occurs in the high salt marsh, it recently also invaded lower parts of the marsh. In one of the first analyses of the genetic population structure in salt‐marsh species, we were interested in population differentiation through isolation‐by‐distance, and among strongly divergent habitats (low and high marsh) in this wind‐ and water‐dispersed species. High and low marsh habitats were sampled at six sites throughout the Wadden Sea. Based on reciprocal transplantation experiments conducted earlier revealing lower survival of foreign genotypes we predicted reduced gene flow among habitats. Accordingly, an analysis with polymorphic cross‐species microsatellite primers revealed significant genetic differentiation between high and low marsh habitats already on a very small scale (< 100 m), while isolation‐by‐distance was present only on larger scales (60–443 km). In an analysis of molecular variance we found that 14% of the genetic variance could be explained by the differentiation between habitats, as compared to only 8.9% to geographical (isolation‐by‐distance) effects among six sites 2.5–443 km distant from each other. This suggests that markedly different selection regimes between these habitats, in particular intraspecific competition and herbivory, result in habitat adaptation and restricted gene flow over distances as small as 80 m. Hence, the genetic population structure of plant species can only be understood when considering geographical and selection‐mediated restrictions to gene flow simultaneously.
Associations between mycophagous Drosophila and their Howardula nematode parasites: a worldwide phylogenetic shuffle
Authors: Perlman Steve J. , Spicer Greg S. , Shoemaker D. Dewayne , Jaenike John 
Published: March 2003

AbstractLittle is known about what determines patterns of host association of horizontally transmitted parasites over evolutionary timescales. We examine the evolution of associations between mushroom‐feeding Drosophila flies (Diptera: Drosophilidae), particularly in the quinaria and testacea species groups, and their horizontally transmitted Howardula nematode parasites (Tylenchida: Allantonematidae). Howardula species were identified by molecular characterization of nematodes collected from wild‐caught flies. In addition, DNA sequence data is used to infer the phylogenetic relationships of both host Drosophila (mtDNA: COI, II, III) and their Howardula parasites (rDNA: 18S, ITS1; mtDNA: COI). Host and parasite phylogenies are not congruent, with patterns of host association resulting from frequent and sometimes rapid host colonizations. Drosophila‐parasitic Howardula are not monophyletic, and host switches have occurred between Drosophila and distantly related mycophagous sphaerocerid flies. There is evidence for some phylogenetic association between parasites and hosts, with some nematode clades associated with certain host lineages. Overall, these host associations are highly dynamic, and appear to be driven by a combination of repeated opportunities for host colonization due to shared breeding sites and large potential host ranges of the nematodes.
Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects
Authors: Zhang De‐Xing , Hewitt Godfrey M. 
Published: March 2003

AbstractPopulation‐genetic studies have been remarkably productive and successful in the last decade following the invention of PCR technology and the introduction of mitochondrial and microsatellite DNA markers. While mitochondrial DNA has proven powerful for genealogical and evolutionary studies of animal populations, and microsatellite sequences are the most revealing DNA markers available so far for inferring population structure and dynamics, they both have important and unavoidable limitations. To obtain a fuller picture of the history and evolutionary potential of populations, genealogical data from nuclear loci are essential, and the inclusion of other nuclear markers, i.e. single copy nuclear polymorphic (scnp) sequences, is clearly needed. Four major uncertainties for nuclear DNA analyses of populations have been facing us, i.e. the availability of scnp markers for carrying out such analysis, technical laboratory hurdles for resolving haplotypes, difficulty in data analysis because of recombination, low divergence levels and intraspecific multifurcation evolution, and the utility of scnp markers for addressing population‐genetic questions. In this review, we discuss the availability of highly polymorphic single copy DNA in the nuclear genome, describe patterns and rate of evolution of nuclear sequences, summarize past empirical and theoretical efforts to recover and analyse data from scnp markers, and examine the difficulties, challenges and opportunities faced in such studies. We show that although challenges still exist, the above‐mentioned obstacles are now being removed. Recent advances in technology and increases in statistical power provide the prospect of nuclear DNA analyses becoming routine practice, allowing allele‐discriminating characterization of scnp loci and microsatellite loci. This certainly will increase our ability to address more complex questions, and thereby the sophistication of genetic analyses of populations.
An essential dimeric membrane protein of trypanosome glycosomes
Authors: Maier Alexander , Lorenz Patrick , Voncken Frank , Clayton Christine 
Published: March 2003

Kinetoplastid parasites compartmentalize the first seven enzymes of glycolysis in a peroxisome‐like microbody, the glycosome. Genes encoding the most abundant protein of the glycosomal membrane, GIM5, have been cloned and the protein characterized. Two genes, GIM5A and GIM5B, encode 26 kDa proteins. Although many microbody membrane proteins are conserved in evolution, the only homologues of GIM5 in the available databases are from the closely related kinetoplastids Trypanosoma cruzi and Leishmania. The N‐ and C‐termini are conserved between the two genes, and between species, and are oriented towards the cytosol. They are separated by a short loop that is located between two transmembrane domains and shows almost no sequence conservation. This suggests that the N‐ and C‐terminal domains are more important for function. GIM5 forms dimers in vivo. Overexpression of GIM5B inhibits growth, whereas depletion of GIM5 to below 10% of wild‐type levels is very rapidly lethal. This novel organellar membrane protein is therefore essential for bloodstream trypanosome survival.
Identification and characterization of the Cryptococcus neoformans phosphomannose isomerase‐encoding gene, MAN1, and its impact on pathogenicity
Authors: Wills Elizabeth A. , Roberts Ian S. , Del Poeta Maurizio , Rivera Johanna , Casadevall Arturo , Cox Gary M. , Perfect John R. 
Published: March 2003

The polysaccharide capsule surrounding Cryptococcus neoformans comprises manose, xylose and glucuronic acid, of which mannose is the major constituent. The GDP‐mannose biosynthesis pathway is highly conserved in fungi and consists of three key enzymes: phosphomannose isomerase (PMI), phosphomannomutase (PMM) and GDP‐mannose pyrophosphorylase (GMP). The MAN1 gene, encoding for the PMI enzyme, was isolated and sequenced from C. neoformans, and a disruption of the MAN1 gene was generated. One MAN1 disruption mutant, man1, which showed poor capsule formation, reduced polysaccharide secretion and morphological abnormalities, was chosen for virulence studies. In both the rabbit and the mouse models of invasive cryptococcosis, man1 was shown to be severely impaired in its virulence, with complete elimination of the yeast from the host. A reconstituted strain of man1 was constructed using gene replacement at the native locus. The wild‐type and reconstituted strains were significantly more virulent than the knock‐out mutant in both animal models. Our findings reveal that PMI activity is essential for the survival of C. neoformans in the host. The fact that the man1 mutant was not pathogenic suggests that blocking mannose synthesis could be fungicidal in the mammalian host and thus an excellent target for antifungal drug development.
The KEX2 gene of Candida glabrata is required for cell surface integrity
Authors: Bader Oliver , Schaller Martin , Klein Sabine , Kukula Janine , Haack Katja , Mühlschlegel Fritz , Korting Hans Christian , Schäfer Wilhelm , Hube Bernhard 
Published: March 2003

Candida glabrata has emerged as one of the most common causes of candidosis. In order to identify factors that are necessary for viability and pathogenicity of this fungal pathogen, we analysed the role of the KEX2 gene, which codes for a regulatory endoproteinase that is known to process certain virulence factors in Candida albicans. The KEX2 gene from C. glabrata was cloned and found to have 51% and 62% identity and high structural similarities to the homologous counterparts in C. albicans and Saccharomyces cerevisiae. KEX2 was expressed at all time points investigated during growth in complex medium. In order to investigate the role of this putative regulatory proteinase, Kex2‐deficient mutants were produced. In addition to known kex2 phenotypes, such as pH and calcium hypersensitivity, the mutants grew in cellular aggregates and were found to be hypersensitive to several antifungal drugs that target the cell membrane, including azoles, amorolfine and amphotericin B. Ultrastructural investigation after exposure to low doses of itraconazole showed azole‐specific alterations such as enlarged vacuoles and proliferation of the cytoplasmatic membrane in the kex2 mutants, but not in the control strains. In contrast, antifungals such as 5‐flucytosine and hydroxypyridones inhibited growth of the kex2 mutants and the control strains to the same extent. In an in vitro model of oral candidosis, kex2 mutants showed reduced tissue damage in the presence of itraconazole compared with the control infections. These data suggest that Kex2 is involved in the processing of proteins that are essential for cell surface integrity of C. glabrata.
A two‐component signal transduction system involved in nickel sensing in the cyanobacterium Synechocystis sp. PCC 6803
Authors: López‐Maury Luis , García‐Domínguez Mario , Florencio Francisco J. , Reyes José C. 
Published: March 2003

SummaryIn the cyanobacterium Synechocystis sp. PCC 6803, genes for Ni2+, Co2+, and Zn2+ resistance are grouped in a 12 kb gene cluster. The nrsBACD operon is composed of four genes, which encode proteins involved in Ni2+ resistance. Upstream from nrsBACD, and in opposite orientation, a transcription unit formed by the two genes rppA and rppB has been reported previously to encode a two‐component signal transduction system involved in redox sensing. In this report, we demonstrate that rppA and rppB (here redesigned nrsR and nrsS respectively) control the Ni2+‐dependent induction of the nrsBACD operon and are involved in Ni2+ sensing. Thus, expression of the nrsBACD operon was not induced by Ni2+ in a nrsRS mutant strain. Furthermore, nrsRS mutant cells showed reduced tolerance to Ni2+. Whereas the nrsBACD operon is transcribed from two different promoters, one constitutive and the other dependent on the presence of Ni2+ in the medium, the nrsRS operon is transcribed from a single Ni2+‐inducible promoter. The nrsRS promoter is silent in a nrsRS mutant background suggesting that the system is autoregulated. Purified full length NrsR protein is unable to bind to the nrsBACD‐nrsRS intergenic region; however, an amino‐terminal truncated protein that contains the DNA binding domain of NrsR binds specifically to this region. Our nrsRS mutant, which carries a deletion of most of the nrsR gene and part of the nrsS gene, does not show redox imbalance or photosynthetic gene mis‐expression, contrasting with the previously reported nrsR mutant.
Fractionation of Escherichia coli cell populations at different stages during growth transition to stationary phase
Authors: Makinoshima Hideki , Nishimura Akiko , Ishihama Akira 
Published: March 2003

SummaryCultures of Escherichia coli could be separated into more than 15 cell populations, each forming a discrete band after Percoll gradient centrifugation. The cell separation was found to result from the difference in buoyant density but not the size difference. The cell density increases upon transition from exponential growth to stationary phase. Exponential phase cultures formed at least five discrete bands with lower densities, whereas stationary phase cultures formed more than 10 bands with higher densities. Two molecular markers characterizing each cell population were identified: the functioning promoter species, as identified by measuring the expression of green fluorescent protein under the control of test promoters; and the expressed protein species, as monitored by quantitative immunoblotting. These findings together suggest that the growth phase‐coupled transition of E. coli phenotype is discontinuous.
A cytoplasmic coiled‐coil domain is required for histidine kinase activity of the yeast osmosensor, SLN1
Authors: Tao Wei , Malone Cheryl L. , Ault Addison D. , Deschenes Robert J. , Fassler Jan S. 
Published: March 2003

SummaryThe yeast histidine kinase, Sln1p, is a plasma membrane‐associated osmosensor that regulates the activity of the osmotic stress MAP kinase pathway. Changes in the osmotic environment of the cell influence the autokinase activity of the cytoplasmic kinase domain of Sln1p. Neither the nature of the stimulus, the mechanism by which the osmotic signal is transduced nor the manner in which the kinase is regulated is currently clear. We have identified several mutations located in the linker region of the Sln1 kinase (just upstream of the kinase domain) that cause hyperactivity of the Sln1 kinase. This region of histidine kinases is largely uncharacterized, but its location between the transmembrane domains and the cytoplasmic kinase domain suggests that it may have a potential role in signal transduction. In this study, we have investigated the Sln1 linker region in order to understand its function in signal transduction and regulation of Sln1 kinase activity. Our results indicate that the linker region forms a coiled‐coil structure and suggest a mechanism by which alterations induced by osmotic stress influence kinase activity by altering the alignment of the phospho‐accepting histidine with respect to the catalytic domain of the kinase.
Identification of N‐acetylgalactosamine‐containing glycoproteins PEB3 and CgpA in Campylobacter jejuni
Authors: Linton Dennis , Allan Elaine , Karlyshev Andrey V. , Cronshaw Andrew D. , Wren Brendan W. 
Published: March 2003

SummaryIt was demonstrated recently that there is a system of general protein glycosylation in the human enteropathogen Campylobacter jejuni. To char‐ acterize such glycoproteins, we identified a lectin, Soybean agglutinin (SBA), which binds to multiple C. jejuni proteins on Western blots. Binding of lectin SBA was disrupted by mutagenesis of genes within the previously identified protein glycosylation locus. This lectin was used to purify putative glycoproteins selectively and, after sodium dodecyl sulphate‐ polyacrylamide gel electrophoresis (SDS–PAGE), Coomassie‐stained bands were cut from the gels. The bands were digested with trypsin, and peptides were identified by mass spectrometry and database searching. A 28 kDa band was identified as PEB3, a previously characterized immunogenic cell surface protein. Bands of 32 and 34 kDa were both identified as a putative periplasmic protein encoded by the C. jejuni NCTC 11168 coding sequence Cj1670c. We have named this putative glycoprotein CgpA. We constructed insertional knockout mutants of both the peb3 and cgpA genes, and surface protein extracts from mutant and wild‐type strains were analysed by one‐ and two‐dimensional polyacrylamide gel electrophoresis (PAGE). In this way, we were able to identify the PEB3 protein as a 28 kDa SBA‐reactive and immunoreactive glycoprotein. The cgpA gene encoded SBA‐reactive and immunoreactive proteins of 32 and 34 kDa. By using specific exoglycosidases, we demonstrated that the SBA binding property of acid‐glycine extractable C. jejuni glycoproteins, including PEB3 and CgpA, is a result of the presence of α‐linked N‐acetylgalactosamine residues. These data confirm the existence, and extend the boundaries, of the previously identified protein glycosylation locus of C. jejuni. Furthermore, we have identified two such glycoproteins, the first non‐flagellin campylobacter glycoproteins to be identified, and demonstrated that their glycan components contain α‐linked N‐acetylgalactosamine residues.