bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intensive genetic assessment of the mating system and reproductive success in a semi‐closed population of the mottled sculpin, Cottus bairdi
Authors: Fiumera Anthony C. , Porter Brady A. , Grossman Gary D. , Avise John C. 
Published: March 2003

AbstractMost genetic surveys of parentage in nature sample only a small fraction of the breeding population. Here we apply microsatellite markers to deduce the genetic mating system and assess the reproductive success of females and males in an extensively collected, semi‐closed stream population of the mottled sculpin fish, Cottus bairdi. In this species, males guard nest rocks where females deposit the eggs for fertilization. The potential exists for both males and females to mate with multiple partners and for males to provide parental care to genetically unrelated offspring. Four hundred and fifty‐five adults and subadults, as well as 1259 offspring from 23 nests, were genotyped at five polymorphic microsatellite loci. Multilocus maternal genotypes, deduced via genetic analyses of embryos, were reconstructed for more than 90% of the analysed nests, thus allowing both male and female reproductive success to be estimated accurately. There was no genetic evidence for cuckoldry, but one nest probably represents a takeover event. Successful males spawned with a mean of 2.8 partners, whereas each female apparently deposited her entire clutch of eggs in a single nest (mean fecundity = 66 eggs/female). On average, genetically deduced sires and dams were captured 1.6 and 9.3 metres from their respective nests, indicating little movement by breeders during the spawning season. Based on a ‘genetic mark–recapture’ estimate, the total number of potentially breeding adults (c. 570) was an order‐of‐magnitude larger than genetically based estimates of the effective number of breeders (c. 54). In addition, significantly fewer eggs per female were deposited in single than in multidam nests. Not only were perceived high‐quality males spawning with multiple partners, but they were receiving more eggs from each female.
Population differentiation of Potamogeton pectinatus in the Baltic Sea with reference to waterfowl dispersal
Authors: King R. A. , Gornall R. J. , Preston C. D. , Croft J. M. 
Published: March 2003

AbstractForty populations of Potamogeton pectinatus L. were sampled from around the Baltic Sea basin. Analysis of 62 ISSR ‘loci’ showed that the number of clones per population is very variable but shows a tendency to decrease with latitude. Analysis of molecular variance revealed that, overall, just over half the variability is stored within populations and just under half between them (φST 0.496). In pairwise comparisons, most populations are significantly differentiated. Genetic distance between populations, as measured by φST, increases with geographical distance. Levels of population differentiation, however, are lower on the southeastern Swedish coast than elsewhere, a reduction correlated with the importance of this area as a staging post for the massive migrations of waterfowl from arctic Russia and western Siberia. Cumulative plots of φST against geographical distance along this coast suggest that, although it does not prevent significant population differentiation, bird traffic reduces it over distances of 150–200 km.
The Baltic Sea as a model system for studying postglacial colonization and ecological differentiation, exemplified by the red alga Ceramium tenuicorne
Authors: Gabrielsen T. M. , Brochmann C. , Rueness J. 
Published: March 2003

AbstractThe Baltic Sea provides a unique model system for studying genetic effects of postglacial colonization and ecological differentiation, because all marine organisms must have immigrated after the opening of the Danish Straits 8000 years ago and responded to the development of the steep Skagerrak‐Baltic salinity gradient. The red alga Ceramium tenuicorne shows conspicuous variation in growth and reproduction along this gradient. Herein we obtained reproductive data coupled with two types of molecular markers, one organellar (cox2–3 spacer sequences of mitochondrial DNA; mtDNA) and one mainly nuclear (random amplified polymorphic DNAs; RAPDs). Nine main populations were sampled in a nested spatial hierarchy including three salinity regions (Oslofjorden, Kattegat, and the Baltic Sea), and nine additional populations were sampled for the mtDNA analysis. Asexuality was frequent at low (Baltic) and medium (Kattegat) salinities but virtually absent at the highest salinity (Oslofjorden). Five mtDNA haplotypes were observed, of which two highly divergent ones were common. One was restricted to and fixed in Oslofjorden, and the other, which was closely related to the three rare haplotypes, was found from southernmost Norway via Kattegat into the Baltic. The RAPD data revealed, on the other hand, a continuous cline corresponding to the salinity gradient, with 27.4% divergence among salinity regions and most of the variation stored at the smallest spatial scale analysed (64.2%; within 1 m2 subpopulations). The combined data suggest colonization from a diverse Atlantic glacial gene pool followed by (1) lineage sorting of ancestral mtDNA polymorphisms and (2) strong differential selection among nuclear genotypes along the salinity gradient, including selection for nonrecombinant multiplication of those best fit to the marginal low‐salinity habitats.
Faecal genetic analysis to determine the presence and distribution of elusive carnivores: design and feasibility for the Iberian lynx
Authors: Palomares F. , Godoy J. A. , Piriz A. , O'Brien S. J. , W. E. Johnson  
Published: March 2003

AbstractNoninvasive methods using genetic markers have been suggested as ways to overcome difficulties associated with documenting the presence of elusive species. We present and assess a novel, reliable and effective molecular genetic technique for the unequivocal genetic identification of faeces from the endangered Iberian lynx (Lynx pardinus). From mitochondrial DNA (mtDNA) cytochrome bandD‐loop region sequences, we designed four species‐specific primers (for products 130–161 bp long) that were considered to be likely to amplify degraded DNA. We compared two DNA extraction methods, various DNA amplification conditions and the robustness and specificity of the primer pairs with 87 lynx samples from 5 potentially different lynx populations and with 328 samples of other carnivore species. The utility of the identification technique was tested with faeces of different ages, with faeces from controlled field experiments, and with faeces collected from locales with possible lynx populations from throughout the state of Andalusia, Spain (8052 km2). Faecal mtDNA extraction was more efficient using PBS wash of the faeces instead of a faeces homogenate. Our assay increased from 92.6 to 99% efficiency with a second amplification and a reduction in template concentration to overcome polymerase chain reaction (PCR) inhibition. Our assay never produced false positives, and correctly identified all lynx faeces. Of 252 faeces samples of unknown species collected throughout Andalusia, 26.6% (from three different areas) were classified as Iberian lynx, 1.4% showed evidence of PCR inhibition and 1.2% were of uncertain origin. This method has proven to be a reliable technique that can be incorporated into large‐scale surveys of Iberian lynx populations and exemplifies an approach that can easily be extended to other species.
Genetic differences among three colour morphotypes of the black rockfish, Sebastes inermis, inferred from mtDNA and AFLP analyses
Authors: Kai Yoshiaki , Nakayama Kouji , Nakabo Tetsuji 
Published: March 2003

AbstractThe genetic differences among three colour morphotypes of the black rockish, Sebastes inermis, were determined from mitochondrial DNA (mtDNA) and amplified fragment length polymorphisms (AFLP) analyses. In the AFLP analysis, each morphotype could be distinguished by the presence or absence matrix of five AFLP loci. These diagnostic loci indicated that the three morphotypes represented independent gene pools, indicating reproductive isolation. Furthermore, 14 significant frequency differences in AFLP fragments were observed between morphotypes A and B, 12 between morphotypes A and C and six between morphotypes B and C. These significant differences also supported the likelihood of reproductive isolation among the morphotypes. In the mtDNA analysis, variations in partial sequences of the control region failed to distinguish clearly between the three morphotypes, but restrictions of gene flow and genetic differentiation among the morphotypes were supported by significant FST estimates. The absence of diagnostic mtDNA differences in this study may have been due to introgressive hybridization among the morphotypes and/or incomplete lineage sorting, due to the recency of speciation.
The genetic impact of demographic decline and reintroduction in the wild boar (Sus scrofa): A microsatellite analysis
Authors: Vernesi C. , Crestanello B. , Pecchioli E. , Tartari D. , Caramelli D. , Hauffe H. , Bertorelle G. 
Published: March 2003

AbstractThe reintroduction of wild boar from central Europe after World War II has contributed substantially to the range expansion of this species in Italy, where indiscriminate hunting in earlier times resulted in extreme demographic reduction. However, the genetic impact of such processes is not well‐understood. In this study, 105 individuals from Italian and Hungarian wild boar populations were characterized for nine autosomal microsatellite loci. The Hungarian samples, and two central Italian samples from protected areas (parks) where reintroduction is not documented, were assumed to be representative of the genetic composition of the source and the target populations in the reintroduction process, respectively. Animals hunted in the wild in the Florence area of Tuscany (Italy) were then studied to identify the effects of reintroduction. The results we obtained can be summarized as follows: (i) none of the populations analysed shows genetic evidence of demographic decline; (ii) the three parental populations from Italy and Hungary are genetically distinct; however, the low level of divergence appears in conflict with the naming of the Italian and the European subspecies (Sus scrofa majori and Sus scrofa scrofa, respectively); in addition, the Italian groups appear to be as divergent from each other as they are from the Hungarian population; (iii) most of the individuals hunted near Florence are genetically intermediate between the parental groups, suggesting that hybridization has occurred in this area, the average introgression of Hungarian genotypes is 13%, but ≈ 45% of the genetic pool of these individuals can not be directly attributed to any of the parental populations we analysed; (iv) analysis of microsatellite loci, though in a limited number, is an important tool for estimating the genetic effect of reintroduction in the wild boar, and therefore for the development of conservation and management strategies for this species.
The city‐fox phenomenon: genetic consequences of a recent colonization of urban habitat
Authors: Wandeler P. , Funk S. M. , Largiadèr C. R. , Gloor S. , Breitenmoser U. 
Published: March 2003

AbstractThe red fox (Vulpes vulpes) is one of the best‐documented examples of a species that has successfully occupied cities and their suburbs during the last century. The city of Zurich (Switzerland) was colonized by red foxes 15 years ago and the number of recorded individuals has increased steadily since then. Here, we assessed the hypothesis that the fox population within the city of Zurich is isolated from adjacent rural fox populations against the alternative hypothesis that urban habitat acts as a constant sink for rural dispersers. We examined 11 microsatellite loci in 128 foxes from two urban areas, separated by the main river crossing the city, and three adjacent rural areas from the region of Zurich. Mean observed heterozygosity across individuals and the number of detected alleles were lower for foxes collected within the city as compared with their rural conspecifics. Genetic differentiation was significantly lower between rural than between rural and urban populations, and highest value of pairwise FST was recorded between the two urban areas. Our results indicate that the two urban areas were independently founded by a small number of individuals from adjacent rural areas resulting in genetic drift and genetic differentiation between rural and urban fox populations. Population admixture and immigration analysis revealed that urban–rural gene flow was higher than expected from FST statistics. In the five to seven generations since colonization, fox density has dramatically increased. Currently observed levels of migration between urban and rural populations will probably erode genetic differentiation over time.
Host adaptation and the emergence of infectious disease: the Salmonella paradigm
Authors: Kingsley Robert A. , Bäumler Andreas J. 
Published: March 2003

SummaryThe recent emergence of food‐borne pathogens, such as Salmonella enterica serotype Enteritidis (S. enteritidis) and Escherichia coli O157:H7, has generated increasing interest in how infectious diseases can invade, persist and spread within new host populations. To alter their host range pathogens require adaptations, which ensure their circulation in a new animal population. Adaptations for circulation in different populations of vertebrate hosts seem to have been acquired multiple times within the genus Salmonella because extant Salmonella serotypes differ greatly with regard to host range. In this article, mechanisms involved in host adaptation are deduced by considering the influence of the host immune response on circulation of Salmonella serotypes within populations of vertebrate animals. This approach contributes to the identification of genes involved in host adaptation and provides new insights into the emergence of food‐borne pathogens.
Surface expression of O‐specific lipopolysaccharide in Escherichia coli requires the function of the TolA protein
Authors: Gaspar Joe A. , Thomas John A. , Marolda Cristina L. , Valvano Miguel A. 
Published: March 2003

We investigated the involvement of Tol proteins in the surface expression of lipopolysaccharide (LPS). tolQ, ‐R, ‐A and ‐B mutants of Escherichia coli K‐12, which do not form a complete LPS‐containing O antigen, were transformed with the O7+ cosmid pJHCV32. The tolA and tolQ mutants showed reduced O7 LPS expression compared with the respective isogenic parent strains. No changes in O7 LPS expression were found in the other tol mutants. The O7‐deficient phenotype in the tolQ and tolA mutants was complemented with a plasmid encoding the tolQRA operon, but not with a similar plasmid containing a frameshift mutation inactivating tolA. Therefore, the reduction in O7 LPS was attributed to the lack of a functional tolA gene, caused either by a direct mutation of this gene or by a polar effect on tolA gene expression exerted by the tolQ mutation. Reduced surface expression of O7 LPS was not caused by changes in lipid A‐core structure or downregulation of the O7 LPS promoter. However, an abnormal accumulation of radiolabelled mannose was detected in the plasma membrane. As mannose is a sugar unique to the O7 subunit, this result suggested the presence of accumulated O7 LPS biosynthesis intermediates. Attempts to construct a tolA mutant in the E. coli O7 wild‐type strain VW187 were unsuccessful, suggesting that this mutation is lethal. In contrast, a polar tolQ mutation affecting tolA expression in VW187 caused slow growth rate and serum sensitivity in addition to reduced O7 LPS production. VW187 tolQ cells showed an elongated morphology and became permeable to the membrane‐impermeable dye propidium iodide. All these phenotypes were corrected upon complementation with cloned tol genes but were not restored by complementation with the tolQRA operon containing the frameshift mutation in tolA. Our results demonstrate that the TolA protein plays a critical role in the surface expression of O antigen subunits by an as yet uncharacterized involvement in the processing of O antigen.
Differential fluorescence induction reveals Streptococcus pneumoniae loci regulated by competence stimulatory peptide
Authors: Bartilson Magdalena , Marra Andrea , Christine Jillian , Asundi Jyoti S. , Schneider William P. , Hromockyj Alexander E. 
Published: March 2003

Differential fluorescence induction (DFI) in Streptococcus pneumoniae was used as a method for the discovery of genes activated in specific growth environments. Competence stimulatory peptide (CSP) was used as the model inducing system to identify differentially expressed genes. To identify CSP‐induced promoters, a plasmid library was constructed by inserting random pieces of S. pneumoniae chromosomal DNA upstream of the promoterless gfpmut2 gene in an Escherichia coli/S. pneumoniae shuttle vector. S. pneumoniae carrying the library were induced with CSP and enriched for green fluorescent protein (GFP)‐expressing bacteria using fluorescence‐activated cell sorting. A total of 886 fluorescent clones was screened, and 12 differentially activated promoter elements were identified. Sequence analysis of these clones revealed that three were associated with novel competence loci, one of which we show is essential for DNA uptake, and six are known CSP‐inducible promoters. We also explored whether competence proteins have a role in virulence and found that mutations in three CSP‐inducible genes resulted in attenuated virulence phenotypes in either of two murine infection models. These results demonstrate the utility of DFI as a method for identifying differentially expressed genes in S. pneumoniae and the potential utility of applying DFI to other Gram‐positive bacteria.
A tripeptide sequence within the nascent DaaP protein is required for mRNA processing of a fimbrial operon in Escherichia coli
Authors: Loomis Wendy P. , Koo Jovanka T. , Cheung Teresa P. , Moseley Steve L. 
Published: March 2003

The biogenesis of F1845 fimbriae, a member of the Dr family of Escherichia coli adhesins, is regulated by endonucleolytic cleavage of the daaABCDPE primary transcript and differential stability of the resulting cleavage products. Processing of daa mRNA is dependent upon translation of a small open reading frame, designated daaP, which flanks the daa processing site. Here, we demonstrate that daa mRNA processing is directly coupled to daaP translation. Cleavage of the daaA–E mRNA was shown to require the tripeptide Gly–Pro–Pro (GPP), encoded by daaP codons 49–51 downstream of the processing site. Processing also required active translation through RNA located upstream of the processing site; however, processing did not depend on the amino acid sequence encoded by the region of daaP upstream of the processing site. Finally, determination of the processing site was shown to involve its location relative to the codons encoding the GPP tripeptide. These data show that translation of daaP is required in cis to promote RNA processing. These data suggest a model involving interaction of the nascent GPP tripeptide portion of the DaaP polypeptide with the ribosome, triggering cleavage of the associated mRNA at a fixed distance upstream. A model of active involvement of the ribosome in this process is proposed.
Mutational analysis of RsrA, a zinc‐binding anti‐sigma factor with a thiol–disulphide redox switch
Authors: Paget Mark S. B. , Bae Jae‐Bum , Hahn Mi‐Young , Li Wei , Kleanthous Colin , Roe Jung‐Hye , Buttner Mark J. 
Published: March 2003

In the Gram‐positive bacterium, Streptomyces coelicolor A3(2), expression of the thioredoxin system is modulated by a sigma factor called σR in response to changes in the cytoplasmic thiol–disulphide status, and the activity of σR is controlled post‐translationally by an anti‐sigma factor, RsrA. In vitro, the anti‐sigma factor activity of RsrA, which contains seven cysteines, correlates with its thiol–disulphide redox status. Here, we investigate the function of RsrA in vivo. A constructed rsrA null mutant had very high constitutive levels of disulphide reductase activity and σR‐dependent transcription, confirming that RsrA is a negative regulator of σR and a key sensor of thiol–disulphide status. Targeted mutagenesis revealed that three of the seven cysteines in RsrA (C11, C41 and C44) were essential for anti‐sigma factor activity and that a mutant RsrA protein containing only these three cysteines was active and still redox sensitive in vivo. We also show that RsrA is a metalloprotein, containing near‐stoichiometric amounts of zinc. On the basis of these data, we propose that a thiol–disulphide redox switch is formed between two of C11, C41 and C44, and that all three residues play an essential role in anti‐sigma factor activity in their reduced state, perhaps by acting as ligands for zinc. Unexpectedly, rsrA null mutants were blocked in sporulation, probably as a consequence of an increase in the level of free σR.
Bile‐induced ‘pili’ in Campylobacter jejuni are bacteria‐independent artifacts of the culture medium
Authors: Gaynor Erin C. , Ghori Nafisa , Falkow Stanley 
Published: March 2003

In 1996, it was reported that the enteric pathogen Campylobacter jejuni produces pilus‐like appendages in response to bile salts such as deoxycholate (DOC), and that the formation of these appendages requires the putative peptidase PspA. Pili were known to be important virulence determinants in other pathogenic bacteria but had never before been observed for C. jejuni. We report here that these appendages are not pili, but are instead a bacteria‐independent morphological artifact of the growth medium. Furthermore, the pspA gene is not required for their formation. Broth cultures containing a threshold concentration of DOC inoculated with no bacteria produced identical abundant, fibrous, pilus‐like structures as those cultures that had been inoculated with C. jejuni. These fibres were also found in growth media from DOC‐containing pspA::CmR mutant cultures. These results are consistent with the absence of candidate pilin monomers in protein gel analyses as well as the dearth of pilin‐like genes and pilus formation gene clusters in the C. jejuni genome.