bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal and spatial dynamics of a parapatric boundary between two Australian reptile ticks
Authors: Bull C. Michael , Burzacott Dale 
Published: March 2003

AbstractTwo tick species Aponomma hydrosauri and Amblyomma limbatum that infest large reptiles have an abrupt parapatric boundary near Mt Mary in South Australia. A previous model has suggested that the boundary is maintained at population density troughs resulting from habitat heterogeneity along a gradual environmental gradient. This paper describes the dynamics of the boundary on three transects over 17 years, 1982–98. Over the last seven years of that period there has been a significant increase in rainfall. At the same time, the boundary position has moved 1–2 km on the transects, with the more mesic adapted Ap. hydrosauri advancing into the distribution of the more xeric adapted Amb. limbatum. Also over the same time the density of ticks on lizards in regions flanking the boundary zone has increased for Ap. hydrosauri and decreased for Amb. limbatum. These results suggest that the environmental gradient has been altered, perhaps by increased rainfall, to favour Ap. hydrosauri, which has been able to colonize more successfully across the density troughs and extend its distribution.
Population subdivision in marine environments: the contributions of biogeography, geographical distance and discontinuous habitat to genetic differentiation in a blennioid fish, Axoclinus nigricaudus
Authors: Riginos C. , Nachman M. W. 
Published: March 2003

AbstractThe relative importance of factors that may promote genetic differentiation in marine organisms is largely unknown. Here, contributions to population structure from a biogeographic boundary, geographical distance and the distribution of suitable habitat were investigated in Axoclinus nigricaudus, a small subtidal rock‐reef fish, throughout its range in the Gulf of California. A 408‐bp fragment of the mitochondrial control region was sequenced from 105 individuals. Variation was significantly partitioned between 28 of 36 possible combinations of population pairs. Phylogenetic analyses, hierarchical analyses of variance and a modified Mantel test substantiated a major break between two putative biogeographic regions. This genetic discontinuity coincides with an abrupt change in ecological characteristics, including temperature and salinity, but does not coincide with known oceanographic circulation patterns or any known historic barriers. There was an overall relationship of increasing genetic distance with increasing geographical distance between population pairs, in a manner consistent with isolation‐by‐distance. A significant habitat‐by‐geographical‐distance interaction term indicated that, for a given geographical distance, populations separated by discontinuous habitat (sand) are more distinct genetically than are populations separated by continuous habitat (rock). In addition, populations separated by deep open waters were more genetically distinct than populations separated by continuous habitat (rock). These results indicate that levels of genetic differentiation among populations of A. nigricaudus cannot be explained by a single factor, but are due to the combined influences of biogeography, geographical distance and availability of suitable habitat.
Comparative phylogeography of the two pink salmon broodlines: an analysis based on a mitochondrial DNA genealogy
Authors: Churikov D. , Gharrett A. J. 
Published: March 2003

AbstractOver most of their natural northern Pacific Ocean range, pink salmon (Oncorhynchus gorbuscha) spawn in a habitat that was repeatedly and profoundly affected by Pleistocene glacial advances. A strictly two‐year life cycle of pink salmon has resulted in two reproductively isolated broodlines, which spawn in alternating years and evolved as temporal replicates of the same species. To study the influence of historical events on phylogeographical and population genetic structure of the two broodlines, we first reconstructed a fine‐scale mtDNA haplotype genealogy from a sample of 80 individuals and then determined the geographical distribution of the major genealogical assemblages for 718 individuals sampled from nine Alaskan and eastern Asian even‐ and nine odd‐year pink salmon populations. Analysis of restriction site states in seven polymerase chain reaction (PCR)‐amplified mtDNA regions (comprising 97% of the mitochondrial genome) using 13 endonucleases resolved 38 haplotypes, which clustered into five genealogical lineages that differed from 0.065 to 0.225% in net sequence divergence. The lineage sorting between broodlines was incomplete, which suggests a recent common ancestry. Within each lineage, haplotypes exhibited star‐like genealogies indicating recent population growth. The depth of the haplotype genealogy is shallow (∼0.5% of nucleotide sequence divergence) and probably reflects repeated decreases in population size due to Pleistocene glacial advances. Nested clade analysis (NCA) of geographical distances showed that the geographical distribution observed for mitochondrial DNA (mtDNA) haplotypes resulted from alternating influences of historical range expansions and episodes of restricted dispersal. Analyses of molecular variance showed weak geographical structuring of mtDNA variation, except for the strong subdivision between Asian and Alaskan populations within the even‐year broodline. The genetic similarities observed among and within geographical regions probably originated from postglacial recolonizations from common sources rather than extensive gene flow. The phylogeographical and population genetic structures differ substantally between broodlines. This can be explained by stochastic lineage sorting in glacial refugia and perhaps different recolonization routes in even‐ and odd‐year broodlines.
An exceptional case of historical outbreeding in African sable antelope populations
Authors: Pitra Christian , Hansen Anders J. , Lieckfeldt Dietmar , Arctander Peter 
Published: March 2003

AbstractEmpirical investigations of intraspecific outbreeding and subsequent introgressive hybridization in natural populations are rare, particularly among conspecific populations of large mammals. Using mitochondrial DNA data [partial control region (496 basepairs — bp) and cytochrome b gene (343 bp) sequences analysed from 95 individuals representing 17 sampling locations scattered through the African miombo (Brachystegia) woodland ecosystem] and phylogeographical statistical procedures (gene genealogy, nested cladistic and admixture proportion analyses), we (i) give a detailed dissection of the geographical genetic structure of Hippotragus niger; (ii) infer the processes and events potentially involved in the population history; and (iii) trace extensive introgressive hybridization in the species. The present‐day sable antelope population shows a tripartite pattern of genetic subdivision representing West Tanzanian, Kenya/East Tanzanian and Southern Africa locations. Nested clade analysis revealed that past allopatric fragmentation, caused probably by habitat discontinuities associated with the East African Rift Valley system, together with intermediary episodic long‐distance colonization and restricted, recurrent gene flow have played an predominant role in shaping the extent of maternal genetic diversity (10.4%) and population structure. An extensive (average rate of admixture = 20.0%), but geographically circumscribed and unidirectional hybridization event in the past was inferred, resulting in an extreme (the highest discovered so far in mammals) intraspecific difference of 18.2% among morphologically monotypic sable antelopes from West Tanzania. The results are used to provide an evolutionary framework within which taxonomic implications and conservation decisions can be evaluated.
Exploring the potential of life‐history key innovation: brook breeding in the radiation of the Malagasy treefrog genus Boophis
Authors: Vences M. , Andreone F. , Glaw F. , Kosuch J. , Meyer A. , Schaefer H.‐C. , Veith M. 
Published: March 2003

AbstractThe treefrog genus Boophis is one of the most species‐rich endemic amphibian groups of Madagascar. It consists of species specialized to breeding in brooks (48 species) and ponds (10 species). We reconstructed the phylogeny of Boophis using 16S ribosomal DNA sequences (558 bp) from 27 species. Brook‐breeders were monophyletic and probably derived from an ancestral pond‐breeding lineage. Pond‐breeders were paraphyletic. The disparity in diversification among pond‐breeders and brook‐breeders was notable among endemic Malagasy frogs, although it was not significant when considering Boophis alone. Sibling species which have different advertisement calls but are virtually indistinguishable by morphology were common among brook‐breeders; genetic divergence between these species was high (modal 8% total pairwise divergence). Substitution rates in brook‐breeding species were significantly higher than in pond‐breeders. Speciation of pond‐breeders may be hindered by their usually more synchronous reproduction and a higher vagility which enhances gene flow, while a higher potential of spatial segregation and speciation may exist along brooks.
Natural selection and the genetic differentiation of coastal and Arctic populations of the Atlantic cod in northern Norway: a test involving nucleotide sequence variation at the pantophysin (PanI) locus
Authors: Pogson Grant H. , Fevolden Svein‐Erik 
Published: March 2003

AbstractTo examine the role of contemporary selection in maintaining significant allele frequency differences at the pantophysin (PanI) locus among populations of the Atlantic cod,Gadus morhua, in northern Norway, we sequenced 127PanIAalleles sampled from six coastal and two Barents Sea populations. The distributions of variable sites segregating within thePanIAallelic class were then compared among the populations. Significant differences were detected in the overall frequencies ofPanIAalleles among populations within coastal and Arctic regions that was similar in magnitude to heterogeneity in the distributions of polymorphic sites segregating within thePanIAallelic class. The differentiation observed at silent sites in thePanIAallelic class contradicts the predicted effects of widescale gene flow and suggests that postsettlement selection acting on cohorts cannot be responsible for the genetic differences described between coastal and Arctic populations. Our results suggest that the marked differences observed between coastal and Arctic populations ofG. morhuain northern Norway at thePanI locus reflect the action of recent diversifying selection and that populations throughout the region may be more independent than suggested by previous studies.
Two atypical mobilization proteins are involved in plasmid CloDF13 relaxation
Authors: Núñez Belén , De La Cruz Fernando 
Published: March 2003

The mobilization region of plasmid CloDF13 was localized to a 3.6 kb DNA segment that was analysed by transposon mutagenesis and DNA sequencing. Analysis of the DNA sequence allowed us to identify two mobilization genes and the CloDF13 origin of conjugative transfer (oriT), which was localized to a 661 bp segment at one end of the mobilization (Mob) region. Thus, the overall organization was oriT–mobB–mobC. Plasmid CloDF13 DNA was isolated mainly as a relaxed form that contained a unique strand and site‐specific cleavage site (nic). The position of nic was mapped to the sequence 5′‐GGGTG/GTCGGG‐3′ by primer extension and sequencing reactions. Analysis of Mob− insertion mutants showed that mobC was essential for CloDF13 relaxation in vivo. The sequence of mobC predicts a protein (MobC) of 243 amino acids without significant similarity to previously reported relaxases. In addition to MobC, the product of mobB was also required for CloDF13 mobilization and for oriT relaxation in vivo. mobB codes for a protein (MobB) of 653 amino acids with three predicted transmembrane segments at the N‐terminus and the NTP‐binding motifs characteristic of the TraG family of conjugative coupling proteins. Membership of the TraG family was confirmed by the fact that CloDF13 mobilization by plasmid R388 was independent of TrwB and only required PILW. However, contrary to the activities found for other coupling proteins, MobB was required for efficient oriT cleavage in vivo, suggesting an additional role for this particular protein during oriT processing for mobilization. Additionally, the cleavage site produced by the joint activities of MobB and MobC was shown to contain unblocked ends, suggesting that no stable covalent intermediates between relaxase and DNA were formed during the nic cleavage reaction. This is the first report of a conjugative transfer system in which niccleavage results in a free nicked‐DNA intermediate.
The Caulobacter crescentus flagellar gene, fliX, encodes a novel trans‐acting factor that couples flagellar assembly to transcription
Authors: Muir Rachel E. , O'Brien Tina M. , Gober James W. 
Published: March 2003

The first flagellar assembly checkpoint of Caulobacter crescentus couples assembly of the early class II components of the basal body complex to the expression of class III and IV genes, which encode extracytoplasmic structures of the flagellum. The transcription of class III/IV flagellar genes is activated by the response regulator factor, FlbD. Gain of function mutations in flbD, termed bfa, can bypass the transcriptional requirement for the assembly of class II flagellar structures. Here we show that the class II flagellar gene fliX encodes a trans‐acting factor that couples flagellar assembly to FlbD‐dependent transcription. We show that the overexpression of fliX can suppress class III/IV gene expression in both wild‐type and flbD‐bfa cells. Introduction of a bfa allele of flbD into cells possessing a deletion in fliX restores motility indicating that FliX is not a structural component of the flagellum, but rather a trans‐acting factor. Furthermore, extragenic motile suppressors which arise in ΔfliX cells map to the flbD locus. These results indicate that FlbD functions downstream of FliX in activating class III/IV transcription. β‐Lactamase fusions to FliX and analysis of cellular fractions demonstrate that FliX is a cytosolic protein that demonstrates some peripheral association with the cytoplasmic membrane. In addition, we have isolated a mutant allele of fliX that exhibits a bfa‐like phenotype, restoring flbD‐dependent class III/IV transcription in strains that contain mutations in class II flagellar structural genes. Taken together, these results indicated both a positive and negative regulatory function for FliX in coupling the assembly of class II basal body components to gene expression.
The CbrA–CbrB two‐component regulatory system controls the utilization of multiple carbon and nitrogen sources in Pseudomonas aeruginosa
Authors: Nishijyo Takayuki , Haas Dieter , Itoh Yoshifumi 
Published: March 2003

A novel two‐component system, CbrA–CbrB, was discovered in Pseudomonas aeruginosa;cbrA and cbrB mutants of strain PAO were found to be unable to use several amino acids (such as arginine, histidine and proline), polyamines and agmatine as sole carbon and nitrogen sources. These mutants were also unable to use, or used poorly, many other carbon sources, including mannitol, glucose, pyruvate and citrate. A 7 kb EcoRI fragment carrying the cbrA and cbrB genes was cloned and sequenced. The cbrA and cbrB genes encode a sensor/histidine kinase (Mr 108 379, 983 residues) and a cognate response regulator (Mr 52 254, 478 residues) respectively. The amino‐terminal half (490 residues) of CbrA appears to be a sensor membrane domain, as predicted by 12 possible transmembrane helices, whereas the carboxy‐terminal part shares homology with the histidine kinases of the NtrB family. The CbrB response regulator shows similarity to the NtrC family members. Complementation and primer extension experiments indicated that cbrA and cbrB are transcribed from separate promoters. In cbrA or cbrB mutants, as well as in the allelic argR9901 and argR9902 mutants, the aot–argR operon was not induced by arginine, indicating an essential role for this two‐component system in the expression of the ArgR‐dependent catabolic pathways, including the aruCFGDB operon specifying the major aerobic arginine catabolic pathway. The histidine catabolic enzyme histidase was not expressed in cbrAB mutants, even in the presence of histidine. In contrast, proline dehydrogenase, responsible for proline utilization (Pru), was expressed in a cbrB mutant at a level comparable with that of the wild‐type strain. When succinate or other C4‐dicarboxylates were added to proline medium at 1 mM, the cbrB mutant was restored to a Pru+ phenotype. Such a succinate‐dependent Pru+ property was almost abolished by 20 mM ammonia. In conclusion, the CbrA–CbrB system controls the expression of several catabolic pathways and, perhaps together with the NtrB–NtrC system, appears to ensure the intracellular carbon: nitrogen balance in P. aeruginosa.
The role of HetN in maintenance of the heterocyst pattern in Anabaena sp. PCC 7120
Authors: Callahan Sean M. , Buikema William J. 
Published: March 2003

The gene hetN encodes a putative oxidoreductase that is known to suppress heterocyst differentiation when present on a multicopy plasmid in Anabaena sp. PCC 7120. To mimic the hetN null phenotype and to examine where HetN acts in the regulatory cascade that controls heterocyst differentiation, we replaced the native chromosomal hetN promoter with the copper‐inducible petE promoter. In the presence of copper, heterocyst formation was suppressed in undifferentiated filaments. When hetN expression was turned off by transferring cells to media lacking copper, the filaments initially displayed the wild‐type pattern of single heterocysts but, 48 h after the induction of heterocyst formation, a pattern of multiple contiguous heterocysts predominated. Suppression of heterocyst formation by HetN appears to occur both upstream and downstream of the positive regulator HetR: overexpression of hetN in undifferentiated filaments prevents the wild‐type pattern of hetR expression as well as the multiheterocyst phenotype normally observed when hetR is expressed from an inducible promoter. Green fluorescent protein fusions show that the expression of hetN in wild‐type filaments normally occurs primarily in heterocysts. We propose that HetN is normally involved in the maintenance of heterocyst spacing after the initial heterocyst pattern has been established, but ectopic expression of hetN can also block the initial establishment of the pattern.
The yeast transcriptome in aerobic and hypoxic conditions: effects of hap1, rox1, rox3 and srb10 deletions
Authors: Becerra Manuel , Lombardía‐Ferreira Luis J. , Hauser Nicole C. , Hoheisel Jörg D. , Tizon Belén , Cerdán M. Esperanza 
Published: March 2003

SummaryThe transcriptome of Saccharomyces cerevisiae was screened using the high‐density membrane hybridization method, under aerobic and hypoxic conditions, in wild‐type and mutant backgrounds obtained by the disruption of the genes encoding the regulatory proteins Hap1, Rox1 and the Srb10 and Rox3 subunits of RNA polymerase II holoenzyme. None of the mutations studied was able to fully overcome the wild‐type hypoxic response. Deletion of the hap1 gene changed the expression profiles of individual open reading frames (ORFs) under both aerobic and hypoxic conditions. Major changes associated with rox3 deletion were related to the hypoxic activation. Rox3 also caused a repressor effect (oxygen‐independent) on a subset of genes related to subtelomeric proteins. With regard to the effect brought about by the deletion of rox1 and srb10, correspondence cluster analysis revealed that the transcriptome profile in aerobic conditions is very similar in the wild‐type and both deletion strains. In contrast, however, differences were found during hypoxia between the subgroup formed by wild‐type and the Δrox1 deletant compared with the Δsrb10 deletant. An analysis of selected ORFs responding to hypoxia, in association with a dependence on the regulatory factors studied, made it possible to identify the clusters that are related to different regulatory circuits.
Lateral flagella of Aeromonas species are essential for epithelial cell adherence and biofilm formation
Authors: Gavín Rosalina , Rabaan Ali A. , Merino Susana , Tomás Juan M. , Gryllos Ioannis , Shaw Jonathan G. 
Published: March 2003

SummaryMesophilic Aeromonas strains express a single polar flagellum in all culture conditions and produce lateral flagella on solid media. Such hyperflagellated cells demonstrate increased adherence. Nine lateral flagella genes, lafA–U for Aeromonas hydrophila, and four Aeromonas caviae genes, lafA1, lafA2, lafB and fliU, were isolated. Mutant characterization, nucleotide and N‐terminal sequencing demonstrated that the A. hydrophila and A. caviae lateral flagellins were almost identical, but were distinct from their polar flagellum counterparts. The aeromonad lateral flagellins exhibited higher molecular masses on SDS–PAGE, and this aberrant migration was thought to result from post‐translational modification through glycosylation. Mutation of the Aeromonas lafB, lafS or both A. caviae lateral flagellins caused the loss of lateral flagella and a reduction in adherence and biofilm formation. Mutations in lafA1, lafA2, fliU or lafT resulted in strains that expressed lateral flagella, but had reduced adherence levels. Mutation of the lateral flagella loci did not affect polar flagellum synthesis, but the polarity of the transposon insertions on the A. hydrophila lafT/U genes resulted in non‐motility. However, mutations that abolished polar flagellum production also inhibited lateral flagella expression. We conclude that Aeromonas lateral flagella: (i) play a role in adherence and biofilm formation; (ii) are distinct from the polar flagellum; (iii) synthesis is dependent upon the presence of a polar flagellum filament; and (iv) that the motor proteins of the polar and lateral flagella systems appear to be shared.
Plasticity of a transcriptional regulation network among alpha‐proteobacteria is supported by the identification of CtrA targets in Brucella abortus
Authors: Bellefontaine Anne‐Flore , Pierreux Christophe E. , Mertens Pascal , Vandenhaute Jean , Letesson Jean‐Jacques , Bolle Xavier De 
Published: March 2003

SummaryCtrA is a master response regulator found in many alpha‐proteobacteria. In Caulobacter crescentus and Sinorhizobium meliloti, this regulator is essential for viability and is transcriptionally autoregulated. In C. crescentus, it is required for the regulation of multiple cell cycle events, such as DNA methylation, DNA replication, flagella and pili biogenesis and septation. Here, we report the characterization of the ctrA gene homologue in the α2‐proteobacteria Brucella abortus, a facultative intracellular pathogen responsible for brucellosis. We detected CtrA expression in the main Brucella species, and its overproduction led to a phenotype typical of cell division defect, consistent with its expected role. A purified B. abortus CtrA recombinant protein (His6–CtrA) was shown to protect the B. abortus ctrA promoter from DNase I digestion, suggesting transcriptional autoregulation, and this protection was enhanced under CtrA phosphorylation on a conserved Asp residue. Despite the similarities shared by B. abortus and C. crescentus ctrA, the pathway downstream from CtrA may be distinct, at least partially, in both bacteria. Indeed, beside ctrA itself, only one (the ccrM gene) out of four B. abortus homologues of known C. crescentus CtrA targets is bound in vitro by phosphorylated B. abortus CtrA. Moreover, further footprinting experiments support the hypothesis that, in B. abortus, CtrA might directly regulate the expression of the rpoD, pleC, minC and ftsE homologues. Taken together, these results suggest that, in B. abortus and C. crescentus, similar cellular processes are regulated by CtrA through the control of distinct target genes. The plasticity of the regulation network involving CtrA in these two bacteria may be related to their distinct lifestyles.