bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long‐term effective population sizes, temporal stability of genetic composition and potential for local adaptation in anadromous brown trout (Salmo trutta) populations
Authors: Hansen Michael M. , Ruzzante Daniel E. , Nielsen Einar E. , Bekkevold Dorte , Mensberg Karen‐Lise D. 
Published: March 2003

AbstractWe examined the long‐term temporal (1910s to 1990s) genetic variation at eight microsatellite DNA loci in brown trout (Salmo truttaL) collected from five anadromous populations in Denmark to assess the long‐term stability of genetic composition and to estimate effective population sizes (Ne). Contemporary and historical samples consisted of tissue and archived scales, respectively. Pairwise θSTestimates, a hierarchical analysis of molecular variance (amova) and multidimensional scaling analysis of pairwise genetic distances between samples revealed much closer genetic relationships among temporal samples from the same populations than among samples from different populations. Estimates ofNe, using a likelihood‐based implementation of the temporal method, revealedNe ≥ 500 in two of three populations for which we have historical data. A third population in a small (3 km) river showedNe ≥ 300. Assuming a stepping‐stone model of gene flow we considered the relative roles of gene flow, random genetic drift and selection to assess the possibilities for local adaptation. The requirements for local adaptation were fulfilled, but only adaptations resulting from strong selection were expected to occur at the level of individual populations. Adaptations resulting from weak selection were more likely to occur on a regional basis, i.e. encompassing several populations.Neappears to have declined recently in at least one of the studied populations, and the documented recent declines of many other anadromous brown trout populations may affect the persistence of local adaptation.
On the correlation between heterozygosity and fitness in natural populations
Authors: Hansson Bengt , Westerberg Lars 
Published: March 2003

AbstractThree primary hypotheses currently prevail for correlations between heterozygosity at a set of molecular markers and fitness in natural populations. First, multilocus heterozygosity–fitness correlations might result from selection acting directly on the scored loci, such as at particular allozyme loci. Second, significant levels of linkage disequilibrium, as in recently bottlenecked‐and‐expanded populations, might cause associations between the markers and fitness loci in the local chromosomal vicinity. Third, in partially inbred populations, heterozygosity at the markers might reflect variation in the inbreeding coefficient and might associate with fitness as a result of effects of homozygosity at genome‐wide distributed loci. Despite years of research, the relative importance of these hypotheses remains unclear. The screening of heterozygosity at polymorphic DNA markers offers an opportunity to resolve this issue, and relevant empirical studies have now emerged. We provide an account of the recent progress on the subject, and give suggestions on how to distinguish between the three hypotheses in future studies.
Extremely low levels of genetic polymorphism in endosymbionts (Buchnera) of aphids (Pemphigus)
Authors: Abbot P. , Moran N. A. 
Published: March 2003

AbstractMolecular evolutionary studies have suggested that vertically transmitted endosymbionts are subject to accumulation of deleterious mutations through genetic drift. Predictions of this hypothesis for patterns of intraspecific polymorphism were borne out in the single relevant study available, on the symbiont Buchnera aphidicola of Uroleucon ambrosiae. In order to examine the generality of this result, we surveyed DNA sequence variation in Buchnera of the distantly related aphid, Pemphigus obesinymphae. In contrast to Uroleucon species, Pemphigus species have complex life cycles with few dispersal stages. Despite these differences, P. obesinymphae showed patterns of variation at two Buchnera loci and one mitochondrial locus that were remarkably similar to those reported previously for Buchnera of U. ambrosiae. In the western US, Buchnera was nearly monomorphic, and in the eastern US, synonymous divergence ranged from 0.08 to 0.16%. Most polymorphisms involved rare alleles, consistent with a recent range of ancestral polymorphism, probably due to demographic fluctuations in aphid populations. These results support the generality of small effective population size in Buchnera and their aphid hosts.
Several Pleistocene refugia detected in the high alpine plant Phyteuma globulariifolium Sternb. & Hoppe (Campanulaceae) in the European Alps
Authors: Schönswetter P. , Tribsch A. , Barfuss M. , Niklfeld H. 
Published: March 2003

AbstractPhyteuma globulariifolium is a high alpine plant species growing in the European Alps and the Pyrenees. In order to elucidate its glacial history, 325 individuals from 69 populations were analysed using the amplified fragment length polymorphism (AFLP) technique. A strongly hierarchical phylogeographical pattern was detected: Two major east–west vicariant groups can be separated along a gap in the distributional area. A further subdivision into at least four populational groups is in congruence with presumed peripheral glacial refugia. There is no indication for survival on unglaciated mountain tops (nunataks) in the interior of the Pleistocene ice shield covering the Alps. Our results favour glacial survival in peripheral, unglaciated or not fully glaciated areas. Populations of P. globulariifolium in the Pyrenees are the result of relatively recent long‐distance dispersal. Within the Alps, there is strong differentiation among groups of populations, whereas within them the differentiation is weak. This suggests high levels of gene‐flow over short to middle distances.
Palaeoclimatic changes explain Anatolian mountain frog evolution: a test for alternating vicariance and dispersal events
Authors: Veith M. , Schmidtler J. F. , Kosuch J. , Baran I. , Seitz A. 
Published: March 2003

AbstractHolarctic biodiversity has been influenced by climatic fluctuations since the Pliocene. Asia Minor was one of the major corridors for postglacial invasions in the Palearctic. Today this area is characterized by an extraordinarily rich fauna with close affiliation to European, Asian and Indo‐African biota. However, exact scenarios of range expansion and contraction are lacking. Using a phylogeographical approach we (i) identify monophyletic lineages among Anatolian mountain frogs and (ii) derive a spatio‐temporal hypothesis for the invasion process in Anatolia. We sequenced 540 bp of the mitochondrial 16S rRNA gene from 40 populations of mountain frogs from Anatolia, the Elburz Mountains and the Caucasus. Our samples comprise all known species and subspecies: Rana macrocnemis macrocnemis, R. m. tavasensis, R. m. pseudodalmatina, R. camerani and R. holtzi. They include the type localities of four of these taxa. We used a nested clade analysis (NCA) to infer historical and recurrent events that account for the observed geographical distribution of haplotypes. None of the extant species is monophyletic. Based on a molecular clock calibration using homologous sequences of Western Palearctic water frogs of the same genus, we estimated that a basic radiation into three lineages c. 2 Mya was followed by several dispersal and fragmentation events. The geographical distribution of resident and widespread haplotypes allows us to infer and date scenarios of range expansion and fragmentation that are aligned with dramatic climatic oscillations that have occurred during the last 600 000 years. Consequently, Pliocene and Pleistocene climatic oscillations triggered the evolution of Anatolian mountain frogs through an interplay of vicariance and dispersal events.
Polymorphism of a complex resistance gene candidate family in wild populations of common bean (Phaseolus vulgaris) in Argentina: comparison with phenotypic resistance polymorphism
Authors: De Meaux J. , Cattan‐Toupance I. , Lavigne C. , Langin T. , Neema C. 
Published: March 2003

AbstractFifteen populations of wild bean (Phaseolus vulgaris), located in three provinces in Argentina, were analysed for their polymorphism for a complex resistance gene candidate (RGC) family clustered on the genome and for resistance phenotypes to strains of Colletotrichum lindemuthianum. Results indicate that RGC polymorphism is high. Population structure obtained for markers related to resistance was compared to population structure obtained for RAPD markers in order to infer the evolutionary forces driving polymorphism for resistance in wild populations at both molecular and phenotypic levels. Hierarchical analysis of differentiation showed that, within provinces, populations were differentiated for RAPD as well as for molecular and phenotypic markers of resistance. In contrast, provinces were differentiated only for RAPD and RGC markers and not for resistance phenotypes. The discrepancies found between diversity structures for molecular markers (RAPD and RGCs) and for resistance phenotypes suggest an effect of selection and indicate that diversity for resistance may not be driven by the same selective forces at the molecular and phenotypic levels. We further discuss whether specific selective forces are exerted on RGC markers and underline the importance of spatial scale of analysis for demonstrating an impact of selection.
Postglacial recolonization and cpDNA variation of silver birch, Betula pendula
Authors: Palmé A. E. , Su Q. , Rautenberg A. , Manni F. , Lascoux M. 
Published: March 2003

AbstractChloroplast PCR‐RFLP markers were used to reconstruct the history of the silver birch, Betula pendula Roth, in Europe since the last glacial maximum (LGM). In birch, fossil pollen maps do not reveal a clear chronological sequence of postglacial spread. If anything, the pollen record suggests that most of Europe was recolonized by birches as early as 10 000 bp, probably from populations that remained close to the ice sheets during the LGM. The geographical distribution of haplotypes supports a scenario of early colonization. Two of the 13 haplotypes that were observed are common, representing 35% and 49% of the total sample, respectively. Although one of the common haplotypes is predominant in the NW and the other in the SE, both are present throughout most of the investigated geographical area. Rare haplotypes are geographically restricted. The distribution of the haplotypes reveals five genetic boundaries between groups of haplotypes and allows us to infer patterns of postglacial recolonization. Europe was re‐occupied by two main waves of recolonization: one eastern and one western, with origins at intermediate latitudes. Populations in the Iberian Peninsula and in Italy did not take part in the postglacial recolonization of Europe.
A rapid population expansion retains genetic diversity within European rabbits in Australia
Authors: Zenger K. R. , Richardson B. J. , Vachot‐Griffin A‐M. 
Published: March 2003

AbstractThe well documented historical translocations of the European rabbit (Oryctolagus cuniculus) offer an excellent framework to test the genetic effects of reductions in effective population size. It has been proposed that rabbits went through an initial bottleneck at the time of their establishment in Australia, as well as multiple founder events during the rabbit's colonization process. To test these hypotheses, genetic variation at seven microsatellite loci was measured in 252 wild rabbits from five populations across Australia. These populations were compared to each other and to data from Europe. No evidence of a genetic bottleneck was observed with the movement of 13 rabbits from Europe to Australia when compared to French data. Within Australia the distribution of genetic diversity did not reflect the suggested pattern of sequential founder effects. In fact, the current pattern of genetic variation in Australia is most likely a result of multiple factors including mutation, genetic drift and geographical differentiation. The absence of reduced genetic diversity is almost certainly a result of the rabbit's rapid population expansion at the time of establishment in Australia. These results highlight the importance of population growth following a demographic bottleneck, which largely determines the severity of genetic loss.
A new cytotoxin from Bacillus cereus that may cause necrotic enteritis
Authors: Lund Terje , De Buyser Marie‐Laure , Granum Per Einar 
Published: March 2003

A cytotoxin (CytK) has been isolated from a Bacillus cereus strain that caused a severe food poisoning outbreak killing three people. A protein of 34 kDa was highly cytotoxic, and the addition of other secreted proteins gave no synergistic effect. CytK was also necrotic and haemolytic. No known B. cereus enterotoxins were produced by this strain. A DNA sequence from 1.8 kb upstream to 0.2 kb downstream of the toxin gene was sequenced. The deduced amino acid sequence of the toxin showed similarity to Staphylococcus aureus leucocidins, γ‐haemolysin and α‐haemolysin, Clostridium perfringensβ‐toxin and B. cereus haemolysin II, all belonging to a family of β‐barrel channel‐forming toxins. There was no sequence similarity between CytK and enterotoxins of B. cereus. The upstream sequence contained a partial sequence of a putative histidine kinase gene. A recognition site for PlcR, which regulates the transcription of enterotoxins HBL and Nhe of B. cereus, was found in the promoter region of the toxin. This new cytotoxin may be responsible for a disease that is similar to, although not as severe as, the necrotic enteritis caused by the β‐toxin of C. perfringens type C.
A 76‐residue polypeptide of colicin E9 confers receptor specificity and inhibits the growth of vitamin B12‐dependent Escherichia coli 113/3 cells
Authors: Penfold Christopher N. , Garinot‐Schneider Carole , Hemmings Andrew M. , Moore Geoffrey R. , Kleanthous Colin , James Richard 
Published: March 2003

The mechanism by which E colicins recognize and then bind to BtuB receptors in the outer membrane of Escherichia coli cells is a poorly understood first step in the process that results in cell killing. Using N‐ and C‐terminal deletions of the N‐terminal 448 residues of colicin E9, we demonstrated that the smallest polypeptide encoded by one of these constructs that retained receptor‐binding activity consisted of residues 343–418. The results of the in vivo receptor‐binding assay were supported by an alternative competition assay that we developed using a fusion protein consisting of residues 1–497 of colicin E9 fused to the green fluorescent protein as a fluorescent probe of binding to BtuB in E. coli cells. Using this improved assay, we demonstrated competitive inhibition of the binding of the fluorescent fusion protein by the minimal receptor‐binding domain of colicin E9 and by vitamin B12. Mutations located in the minimum R domain that abolished or reduced the biological activity of colicin E9 similarly affected the competitive binding of the mutant colicin protein to BtuB. The sequence of the 76‐residue R domain in colicin E9 is identical to that found in colicin E3, an RNase type E colicin. Comparative sequence analysis of colicin E3 and cloacin DF13, which is also an RNase‐type colicin but uses the IutA receptor to bind to E. coli cells, revealed significant sequence homology throughout the two proteins, with the exception of a region of 92 residues that included the minimum R domain. We constructed two chimeras between cloacin DF13 and colicin E9 in which (i) the DNase domain of colicin E9 was fused onto the T+R domains of cloacin DF13; and (ii) the R domain and DNase domain of colicin E9 were fused onto the T domain of cloacin DF13. The killing activities of these two chimeric colicins against indicator strains expressing BtuB or IutA receptors support the conclusion that the 76 residues of colicin E9 confer receptor specificity. The minimum receptor‐binding domain polypeptide inhibited the growth of the vitamin B12‐dependent E. coli 113/3 mutant cells, demonstrating that vitamin B12 and colicin E9 binding is mutually exclusive.
Evidence for the secretion of Chlamydia trachomatis CopN by a type III secretion mechanism
Authors: Fields K. A. , Hackstadt T. 
Published: March 2003

The medically significant, obligate intracellular pathogen Chlamydia trachomatis replicates within vacuoles termed inclusions. A developmental cycle is initiated after entry into a host cell and is manifested by the transformation of infectious elementary bodies (EBs) to larger, non‐infectious reticulate bodies (RBs). Analysis of the C. trachomatis genome has revealed that chlamydiae possess genes that may encode a type III secretion apparatus. In other Gram‐negative pathogens, the type III secretion mechanism is used to target virulence factors directly to the host cell cytoplasm and is essential for full virulence. To evaluate the possibility of a functional type III secretion mechanism in C. trachomatis, we initially focused on a locus containing genes encoding products with similarity to chaperones (Scc1), secretion pore components (Cds1 and Cds2) and secreted proteins (CopN) from other type III systems. Gene expression was tested by reverse transcriptase–polymerase chain reaction (RT–PCR) of total RNA extracted from infected HeLa cell monolayers at 2, 6, 12 and 20 h after infection and normalized for the number of C. trachomatis genomes present. Message was detected for Scc1 at all times, whereas message for all other tested genes was detected in significant amounts at 12 h and 20 h. Immunoblot analysis with Scc1‐ and CopN‐specific antibodies revealed that CopN and Scc1 were present in EBs, RBs and whole‐culture extracts harvested 20 h after infection. CopN is homologous to the secreted protein YopN of Yersinia sp., and analysis of monolayers 20 h after infection via indirect immunofluorescence showed specific labelling of inclusion membranes when probed with CopN‐specific antibodies but not with Scc1‐specific antibodies. His‐tagged CopN and a chlamydial cytoplasmic control protein (NrdB) were expressed in Yersinia enterocolitica containing or lacking the virulence plasmid pYV. CopN, but not NrdB, was secreted by Y. enterocolitica in a Ca2+‐ and pYV‐dependent fashion. These data indicate that components of the putative type III apparatus of C. trachomatis are expressed and that at least one of these products is secreted by chlamydiae to the inclusion membrane. The observation that CopN is also secreted by the Yersinia type III apparatus provides support for the notion that chlamydiae secrete proteins via a type III mechanism.
The Nudix hydrolases of Deinococcus radiodurans
Authors: Xu WenLian , Shen JianYing , Dunn Christopher A. , Desai Seema , Bessman Maurice J. 
Published: March 2003

All 21 of the Nudix hydrolase genes from the radiation‐resistant organism Deinococcus radiodurans have been cloned into vectors under the control of T7 promoters and expressed as soluble proteins in Escherichia coli. Their sizes range from 9.8 kDa (91 amino acids) to 59 kDa (548 amino acids). Two novel proteins were identified, each with two Nudix boxes in its primary structure, unique among all other known Nudix hydrolases. Extracts of each of the expressed proteins were assayed by a generalized procedure that measures the hydrolysis of nucleoside diphosphate derivatives, and several enzymatic activities were tentatively identified. In addition to representatives of known Nudix hydrolase subfamilies active on ADP‐ribose, NADH, dinucleoside polyphosphates or (deoxy)nucleoside triphosphates, two new enzymes, a UDP‐glucose pyrophosphatase and a CoA pyrophosphatase, were identified.
Two‐partner secretion in Gram‐negative bacteria: a thrifty, specific pathway for large virulence proteins
Authors: Jacob‐Dubuisson Françoise , Locht Camille , Antoine Rudy 
Published: March 2003

A collection of large virulence exoproteins, including Ca2+‐independent cytolysins, an iron acquisition protein and several adhesins, are secreted by the two‐partner secretion (TPS) pathway in various Gram‐negative bacteria. The hallmarks of the TPS pathway are the presence of an N‐proximal module called the ‘secretion domain’ in the exoproteins that we have named the TpsA family, and the channel‐forming β‐barrel transporter proteins we refer to as the TpsB family. The genes for cognate exoprotein and transporter protein are usually organized in an operon. Specific secretion signals are present in a highly conserved region of the secretion domain of TpsAs. TpsBs probably serve as specific receptors of the TpsA secretion signals and as channels for the translocation of the exoproteins across the outer membrane. A subfamily of transporters also mediates activation of their cognate cytolysins upon secretion. The exoproteins are synthesized as precursors with an N‐terminal cleavable signal peptide, and a subset of them carries an extended signal peptide of unknown function. According to our current model, the exoproteins are probably translocated across the cytoplasmic membrane in a Sec‐dependent fashion, and their signal peptide is probably processed by a LepB‐type signal peptidase. The N‐proximal secretion domain directs the exoproteins towards their transporters early, so that translocation across both membranes is coupled. The exoproteins transit through the periplasm in an extended conformation and fold progressively at the cell surface before eventually being released into the extracellular milieu. Several adhesins also undergo extensive proteolytic processing upon secretion. The genes of many new TpsAs and TpsBs are found in recently sequenced genomes, suggesting that the TPS pathway is widespread.
A functional genomic analysis of type 3 Streptococcus pneumoniae virulence
Authors: Lau Gee W. , Haataja Sauli , Lonetto Michael , Kensit Sarah E. , Marra Andrea , Bryant Alexander P. , McDevitt Damien , Morrison Donald A. , Holden David W. 
Published: March 2003

Streptococcus pneumoniae remains a serious cause of morbidity and mortality in humans, but relatively little is known about the molecular basis of its pathogenesis. We used signature‐tagged mutagenesis together with an analysis of S. pneumoniae genome sequence to identify and characterize genes required for pathogenesis. A library of signature‐tagged mutants was created by insertion–duplication mutagenesis, and 1786 strains were analysed for their inability to survive and replicate in murine models of pneumonia and bacteraemia. One hundred and eighty‐six mutant strains were identified as attenuated, and 56 were selected for further genetic characterization based on their ability to excise the integrated plasmid spontaneously. The genomic DNA inserts of the plasmids were cloned in Escherichia coli and sequenced. These sequences were subjected to database searches, including the S. pneumoniae genome sequence, which allowed us to examine the chromosomal regions flanking these genes. Most of the insertions were in probable operons, but no pathogenicity islands were found. Forty‐two novel virulence loci were identified. Five strains mutated in genes involved in gene regulation, cation transport or stress tolerance were shown to be highly attenuated when tested individually in a murine respiratory tract infection model. Additional experiments also suggest that induction of competence for genetic transformation has a role in virulence.