bluuebunny/crossref_metadata_2025_split huggingface dataset:
The use of AFLP to find an informative SNP: genetic differences across a migratory divide in willow warblers
Authors: Bensch Staffan , Åkesson Susanne , Irwin Darren E. 
Published: March 2003

AbstractWe used the amplified fragment length polymorphism (AFLP) method to obtain genetic markers distinguishing two subspecies of willow warblersPhylloscopus trochilusthat have different migratory behaviours but are not differentiated in mitochondrial DNA or at several microsatellite loci. With the inverse‐polymerase chain reaction (PCR) approach we converted a dominant AFLP‐marker to a codominant single nucleotide polymorphism (SNP). Across Scandinavia we typed 621 birds at the SNP locus AFLP‐WW1 and we found a sigmoid change in allele frequencies centred around 62 degrees latitude. North of the latitudinal cline was a west‐east cline. Both clines are narrower than one would expect from dispersal distances in willow warblers, which suggests that these are maintained by selection. The latitudinal cline at the locus AFLP‐WW1 is paralleled by changes in several other traits, all of which might be maintained by a single selective force. The most plausible selection factor that we have identified is selection against hybrids because of inferior migratory behaviour. The selective force maintaining the east–west cline is less obvious. We discuss alternatives to the selection scenario, involving colonization history and asymmetric gene flow.
Mitochondrial DNA variation in Indo‐Pacific populations of the giant tiger prawn, Penaeus monodon
Authors: Benzie J. A. H. , Ballment E. , Forbes A. T. , Demetriades N. T. , Sugama K. , Haryanti  , Moria S. 
Published: March 2003

AbstractSurveys of mitochondrial DNA (mtDNA) variation in the giant tiger prawn, Penaeus monodon, using restriction fragment length polymorphisms have provided the first clear evidence that the Indo‐West Pacific region is a site of accumulation of genetic diversity rather than a site of origin of genetic diversity. No haplotyes were found in common between a group of five southeast African populations and a group of five Australian (including Western Australia) and three southeast Asian populations. The dominant haplotype was different in the Australian and southeast Asian population groups. Genetic diversity (π) was greatest in Indonesia (π averaged 0.05), less in the Philippines and Australia (π averaged 0.01), and markedly less in the southeast African and the West Australian populations (π averaged 0.003). The high diversity of the southeast Asian populations resulted from the occurrence in those populations of a set of haplotypes found only in southeast Asia but derived from the southeast African haplotypes. These genetic variants therefore evolved in the Indian Ocean and later migrated into the Indo‐West Pacific region. Low genetic variation in the geographically marginal populations in southeast Africa and Western Australia is considered to be the result of bottlenecks, but mismatch distributions suggest that large population sizes have been maintained in Indonesian populations for long periods.
Bacterial diversity in maize rhizospheres: conclusions on the use of genetic profiles based on PCR‐amplified partial small subunit rRNA genes in ecological studies
Authors: Schmalenberger Achim , Tebbe Christoph C. 
Published: March 2003

AbstractA cultivation‐independent approach based on polymerase chain reaction (PCR)‐amplified partial small subunit rRNA genes and genetic profiling by single‐strand conformation polymorphism (SSCP) was used to characterize the bacterial diversity inhabiting the rhizosphere of maize plants grown on an agricultural field. The community structures of two cultivars, a genetically engineered and a nonengineered variety, different herbicide regimes and soil tillage were compared with each other at two sampling dates. SSCP‐profiles were generated with DNA from bacterial cell consortia with primers hybridizing to evolutionarily highly conserved rRNA gene regions. On silver‐stained gels, each profile consisted of approx. 50 distinguishable bands. Similarity analyses of patterns recorded by digital image analyses could not detect any difference between cultivars or treatments that was greater than the variability between replicates. A total of 54 sequences recovered from different bands were identified and grouped into operational taxonomical units (OTUs). Surprisingly, only five of 40 OTUs contained sequences of both samplings. Three different bands from a profile were selected to test whether this small overlap was due to an incomplete recovery of sequences. From a faint band, two different OTUs were found when 12 clones were analysed, and from two strong bands 24 and 22 OTUs were detected from a total of 26 and 36 clones, respectively. The OTUs belonged to phylogenetically different groups of bacteria. Gene probes that were developed to target different bands of the profiles, however, indicated in Southern blot analyses that patterns between treatments, replicates and samplings, and even from two different growing seasons were highly conserved. Our study demonstrates that community profiles can consist of more sequences than detectable by staining and that gene probes in Southern blot can be a useful control to investigate the composition of microbial communities by genetic profiles.
Tracing the geographical origin of Megastigmus transvaalensis (Hymenoptera: Torymidae): an African wasp feeding on a South American plant in North America
Authors: Scheffer Sonja J. , Grissell E. E. 
Published: March 2003

AbstractDetermining the geographical origin of an introduced organism can be critical to understanding or managing a non‐native species, but is often difficult when the organism is small or inconspicuous. We used a phylogeographical approach to identify the region of endemism and determine the geographical origin of world populations of the seed‐feeding wasp Megastigmus transvaalensis (Hussey). This wasp feeds on African Rhus species and South American Schinus species in various locations around the world. Because it is present both in Africa and in South America, it is unclear whether the wasp was originally an African Rhus‐feeder that has begun feeding on Schinus or a South American Schinus‐feeder that has started feeding on Rhus. Phylogenetic analysis of 800 bp of mitochondrial cytochrome oxidase I sequence data found extensive variation and phylogeographical structure within African M. transvaalensis. Specimens from other locations around the world were all identical in COI sequence and were phylogenetically nested within the African samples. We conclude that M. transvaalensis was originally an African Rhus‐feeder that readily attacks Schinus. We evaluate potential pathways of introduction of this wasp to the New World, and we discuss implications of our results for biocontrol efforts against invasive Schinus populations.
A molecular genetic analysis of the communal nesting of the ostrich (Struthio camelus)
Authors: Kimwele C. N. , Graves J. A. 
Published: March 2003

AbstractThe ostrich breeding system is complex and unique; communal clutches are laid by several females, although only one female, the major female, and the resident territorial male provide parental care. More eggs are laid in the nest than can be incubated and the major female ejects surplus eggs from the incubated central clutch. Microsatellite markers were used to analyse the parentage of communal nests in Nairobi National Park. This revealed that major females contributed a disproportionate number of fertile eggs to the central, incubated clutch and that multiple paternity and maternity within a nest were common; 68.9% of all incubated eggs on a nest were not parented by both the resident territorial male and the major female of that nest. All the males fertilized eggs on the clutches of neighbouring males. Unexpectedly, every major female with her own nest was also simultaneously a minor female with incubated eggs on neighbouring clutches. The relatedness between females laying in the same nest was not significantly different from the population average and significantly less than that between chicks hatched from the same nest.
Associations among cytoplasmic molecular markers, gender, and components of fitness in Silene vulgaris, a gynodioecious plant
Authors: Mccauley D. E. , Olson M. S. 
Published: March 2003

AbstractIt has been suggested that the dynamics of chloroplast DNA (cpDNA) or mitochondrial DNA (mtDNA) genetic markers used in studies of plant populations could be influenced by natural selection acting elsewhere in the genome. This could be particularly true in gynodioecious plants if cpDNA or mtDNA genetic markers are in gametic disequilibrium with genes responsible for sex expression. In order to investigate this possibility, a natural population of the gynodioecious plant Silene vulgaris was used to study associations among mtDNA haplotype, cpDNA haplotype, sex and some components of fitness through seed. Individuals were sampled for mtDNA and cpDNA haplotype as determined using restriction fragment length polymorphism (RFLP) methods, sex (female or hermaphrodite), fruit number, fruit set, seeds/fruit and seed germination. The sex of surviving germinating seeds was also noted. All individuals in the population fell into one of two cytoplasmic categories, designated haplotypes f and g by a unique electrophoretic signature in both the mtDNA and cpDNA. The subset of the population carrying haplotype g included a significantly higher proportion of females when compared with the sex ratio of the subset carrying the f haplotype. Haplotype g had a significantly higher fitness when measured by fruit number, fruit set and seeds/fruit, whereas haplotype f had significantly higher fitness when measured by seed germination. Offspring of individuals carrying haplotype g included a significantly greater proportion of females when compared with offspring of individuals carrying the f haplotype. Other studies of gynodioecious plants have shown that females generally have higher fitness through seed than hermaphrodites, but in this study not all fitness differences between haplotypes could be predicted from differences in haplotype‐specific sex ratio alone. Rather, some differences in haplotype‐specific fitness were due to differences in fitness between individuals of the same sex, but carrying different haplotypes. The results are discussed with regard to the potential for hitchhiking selection to influence the dynamics of the noncoding regions used to designate the cpDNA and mtDNA haplotypes.
Population genetics of a successful invader: the marsh frog Rana ridibunda in Britain
Authors: Zeisset Inga , Beebee Trevor J. C. 
Published: March 2003

AbstractWe investigated the genetic outcome of successful invasion by an alien species, the marsh frog Rana ridibunda, in Britain. Twelve adults translocated from Hungary into Kent (Romney) in 1935 resulted rapidly in a large localized population. A further successful translocation in 1973 from Romney to Sussex (Lewes), together with other range extensions, provided an opportunity to test bottleneck effects during colonization events. Romney and Lewes frogs had similar genetic diversities to those in Hungary at 14 random amplified polymorphic DNA marker (RAPD) and five microsatellite loci. The introduced populations were, however, differentiated genetically from each other and from a reference population in Hungary. Fitness assessments (larval growth and survival) revealed no differences between the Lewes and Romney populations. Despite starting with few founders, significant bottleneck effects on R. ridibunda in Britain were therefore undetectable, presumably because population expansions were rapid immediately after the translocations.
A Rox1‐independent hypoxic pathway in yeast. Antagonistic action of the repressor Ord1 and activator Yap1 for hypoxic expression of the SRP1/TIR1 gene
Authors: Bourdineaud Jean‐Paul , De Sampaïo Guillaume , Lauquin Guy J.‐M. 
Published: March 2003

Hypoxic SRP1/TIR1 gene expression depends on the absence of haem but is independent of Rox1‐mediated repression. We have found a new hypoxic pathway involving an antagonistic interaction between the Ixr1/Ord1 repressor and the Yap1 factor, a transcriptional activator involved in oxidative stress response. Here, we show that Ord1 repressed SRP1 gene expression under normoxia and hypoxia, whereas Yap1 activated it. Ord1 and Yap1 have been shown to bind the SRP1 promoter in a region extending from −299 to −156 bp upstream of the start codon. A typical AP‐1 responsive element lying from −247 to −240 bp allows Yap1 binding. Internal deletion of sequences within the SRP1 promoter were introduced. Two regions were characterized at positions −299/−251 and −218/−156 that, once removed, resulted in a constitutive expression of SRP1 in a wild‐type strain under normoxic conditions. Deletion of both these two sequences allowed the bypass of YAP1 requirement in a Δyap1 strain, whereas these two internal deletions did not yield increased expression in a Δord1 strain compared with the full‐length promoter. Both a single Δord1 mutant and a doubly disrupted Δyap1 Δord1 strain yielded normoxic constitutive SRP1 expression and increased hypoxic SRP1 induction, thereby demonstrating that ord1 is epistatic to yap1. Thus, Yap1 is not directly involved in SRP1 induction by hypoxia, but is necessary to counteract the Ord1 effect.
The absence of a flagellum leads to altered colony morphology, biofilm development and virulence in Vibrio cholerae O139
Authors: Watnick Paula I. , Lauriano Crystal M. , Klose Karl E. , Croal Laura , Kolter Roberto 
Published: March 2003

Throughout most of history, epidemic and pandemic cholera was caused by Vibrio cholerae of the serogroup O1. In 1992, however, a V. cholerae strain of the serogroup O139 emerged as a new agent of epidemic cholera. Interestingly, V. cholerae O139 forms biofilms on abiotic surfaces more rapidly than V. cholerae O1 biotype El Tor, perhaps because regulation of exopolysaccharide synthesis in V. cholerae O139 differs from that in O1 El Tor. Here, we show that all flagellar mutants of V. cholerae O139 have a rugose colony morphology that is dependent on the vps genes. This suggests that the absence of the flagellar structure constitutes a signal to increase exopolysaccharide synthesis. Furthermore, although exopolysaccharide production is required for the development of a three‐dimensional biofilm, inappropriate exopolysaccharide production leads to inefficient colonization of the infant mouse intestinal epithelium by flagellar mutants. Thus, precise regulation of exopolysaccharide synthesis is an important factor in the survival of V. cholerae O139 in both aquatic environments and the mammalian intestine.
The microsatellites of Escherichia coli: rapidly evolving repetitive DNAs in a non‐pathogenic prokaryote
Authors: Metzgar David , Thomas Elizabeth , Davis Clara , Field Dawn , Wills Christopher 
Published: March 2003

We have demonstrated hypervariability of native short‐motif repeats (microsatellites) in Escherichia coli. Twenty‐five of the longest microsatellites in the E. coli genome were identified. These were analysed for length variability among 22 wild‐type (non‐mutator) isolates from the E. coli collection of reference (ECOR). Non‐coding mononucleotide repeats are consistently polymorphic among these genetically diverse E. coli. Length differences in variable microsatellites allowed all E. coli strains examined to be uniquely differentiated. Phylogenetic analysis of the variable repeats shows ubiquitous homoplasy at the level of divergence represented by the sample set, suggesting that these markers are hypermutable and should prove valuable for the discrimination of closely related strains that are not otherwise genetically differentiable. Genomic analyses suggest that similar markers are also likely to be found in all other prokaryotes.
Extensive alanine scanning reveals protein–protein and protein–DNA interaction surfaces in the global regulator FlhD from Escherichia coli
Authors: Campos Andrés , Matsumura Philip 
Published: March 2003

FlhD and FlhC are the transcriptional activators of the flagellar regulon. The heterotetrameric complex formed by these two proteins activates the transcription of the class II flagellar genes. The flagellar regulon consists not only of flagellar genes, but also of the chemotactic genes and some receptor proteins. Recently, a connection between the flagellar regulon and some virulence genes has been found in some species. Furthermore, FlhD, but not FlhC, regulates another non‐flagellar target. As a first attempt to understand the mechanism of the flagellar transcriptional activation by FlhD and FlhC, the structure of FlhD has been solved. In order to understand the mechanism of the action of FlhD when it regulates the flagellar genes, we conducted site‐directed mutagenesis based on its three‐dimensional structure. Six interaction surfaces in the FlhD dimer were mapped by alanine scanning mutagenesis. Two of them are surface clusters formed by residues His‐2, Asp‐28, Arg‐35, Phe‐34 and Asn‐61 located at each side of the dimer core. The other four are located in the flexible arms of the dimer. The residues Ser‐82, Arg‐83, Val‐84, His‐91, Thr‐92, Ile‐94 and Leu‐96 are located at this region. All these residues are involved in the FlhD/FlhC interaction with the exception of Ser‐82, Arg‐83 and Val‐84. These three residues affect the DNA‐binding ability of the complex. The three‐dimensional topology of FlhD and the site‐directed mutagenesis results support the hypothesis of FlhC as an allosteric effector that activates FlhD for the recognition of the DNA.
CueR (YbbI) of Escherichia coli is a MerR family regulator controlling expression of the copper exporter CopA
Authors: Stoyanov Jivko V. , Hobman Jon L. , Brown Nigel L. 
Published: March 2003

We have shown that the open reading frame ybbI in the genomic sequence of Escherichia coli K‐12 encodes the regulator of expression of the copper‐exporting ATPase, CopA. In vivo studies showed that ybbI (designated cueR for copper export regulator gene) was required for copper tolerance during growth, that disruption of cueR caused loss of copA expression and that copA gene expression was regulated by cueR and by copper or silver ions. Expression of a lacZ reporter gene under the control of the copA promoter was approximately proportional to the concentration of cupric ions in the medium, but increased more rapidly in response to silver ion concentrations. The start of the copA transcript was located by primer extension mapping, and DNase I protection assays showed that the CueR protein binds in vitro to a dyad symmetrical sequence within a 19 bp spacer sequence in the copA promoter. CueR binding occurs in vitro in both the presence and the absence of RNA polymerase with or without copper ions present but, in the presence of CueR, RNA polymerase and copper ions, permanganate‐sensitive transcription complexes were formed. CueR is predicted to have an N‐terminal helix–turn–helix sequence and shows similarity to MerR family regulators.
Two‐hybrid analysis of domain interactions involving NtrB and NtrC two‐component regulators
Authors: Martínez‐Argudo Isabel , Martín‐Nieto José , Salinas Paloma , Maldonado Rafael , Drummond Martin , Contreras Asunción 
Published: March 2003

Signal transduction by two‐component regulatory systems involves phosphorylation of the receiver domain of a response regulator by the transmitter domain of the cognate histidine kinase. In the NtrBC system, phosphorylation of NtrC by NtrB results in transcriptional activation of nitrogen‐regulated genes. We have used the yeast two‐hybrid system to probe interactions between domains of the NtrB and NtrC proteins fromKlebsiella pneumoniae. We constructed fusions from each of a series of proteins or protein domains to the activation and the DNA‐binding domains of GAL4 and analysed expression of GAL1:lacZandGAL1:HIS3reporters in yeast. The DNA‐binding domain of NtrC and the so‐called sensor domain of NtrB appeared to provide the major determinants for dimerization of the fusion proteins. A strong and specific interaction was also shown between NtrB and NtrC, localized to the HN region of the NtrB transmitter module and to the NtrC receiver domain, whereas other domains of these proteins do not appear to contribute to the recognition specificity. The results presented here indicate that communication between two‐component partners also involves protein–protein interactions that can be detectedin vivo, suggesting that the yeast two‐hybrid system is a powerful genetic tool for identifying functional partners of prokaryotic signal transduction pathways.
Beta‐helix model for the filamentous haemagglutinin adhesin of Bordetella pertussis and related bacterial secretory proteins
Authors: Kajava Andrey V. , Cheng Naiqian , Cleaver Ryan , Kessel Martin , Simon Martha N. , Willery Eve , Jacob‐Dubuisson Francoise , Locht Camille , Steven Alasdair C. 
Published: March 2003

Bordetella pertussis establishes infection by attaching to epithelial cells of the respiratory tract. One of its adhesins is filamentous haemagglutinin (FHA), a 500‐Å‐long secreted protein that is rich in β‐structure and contains two regions, R1 and R2, of tandem 19‐residue repeats. Two models have been proposed in which the central shaft is (i) a hairpin made up of a pairing of two long antiparallel β‐sheets; or (ii) a β‐helix in which the polypeptide chain is coiled to form three long parallel β‐sheets. We have analysed a truncated variant of FHA by electron microscopy (negative staining, shadowing and scanning transmission electron microscopy of unstained specimens): these observations support the latter model. Further support comes from detailed sequence analysis and molecular modelling studies. We applied a profile search method to the sequences adjacent to and between R1 and R2 and found additional ‘covert’ copies of the same motifs that may be recognized in overt form in the R1 and R2 sequence repeats. Their total number is sufficient to support the tenet of the β‐helix model that the shaft domain – a 350 Å rod – should consist of a continuous run of these motifs, apart from loop inserts. The N‐terminus, which does not contain such repeats, was found to be weakly homologous to cyclodextrin transferase, a protein of known immunoglobulin‐like structure. Drawing on crystal structures of known β‐helical proteins, we developed structural models of the coil motifs putatively formed by the R1 and R2 repeats. Finally, we applied the same profile search method to the sequence database and found several other proteins – all large secreted proteins of bacterial provenance – that have similar repeats and probably also similar structures.