bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA RFLPs at a highly polymorphic locus distinguish European and African subspecies of the honey bee Apis mellifera L. and suggest geographical origins of New World honey bees
Authors: MCMICHAEL M. , HALL H. G. 
Published: November 2003

AbstractA highly polymorphic locus in the honey bee, Apis mellifera L., was detected with genomic probe pB178. Eighty‐five alleles, consisting of MspI and DdeI RFLPs, were found among the Old and New World bees tested. Forty‐one MspI and 43 DdeI restriction fragment patterns, or variants, were identified. Variants and alleles were discontinuously distributed in Old World European and African subspecies. Principal coordinate analysis of the genetic distances between the alleles resulted in the identification of three distinct groups corresponding to three groups of honey bee races with historically different geographical distributions: east European A. m. ligustica and A. m. caucasica; west European A. m. mellifera; and South African A. m. scutellata. The clustering of alleles into these groups is consistent with previous honey bee phylogeographic studies, employing other nuclear and mitochondrial DNA markers, which in part support the evolutionary history of the honey bee hypothesized by Ruttner based on morphometric and allozyme data. The majority of alleles in bees from the USA grouped with those found in east European bees, while other alleles grouped with alleles found in A. m. mellifera. While the majority of the alleles in neotropical bees grouped with or were identical to African alleles, other alleles grouped with alleles found in A. m. mellifera, A. m. ligustica, and A. m. caucasica. Clues to the ancestry of neotropical bees may be found in the identification of alleles that were identical or more similar to alleles found in South African and west European bees; evidence for west European ancestry has been suggested using other taxonomic characters that were not unique to west European bees. Both west European and African alleles were found in individual neotropical colonies, which may indicate that honey bee subspecies which evolved allopatrically have hybridized in the human‐assisted extension of their original geographical ranges.
RAPD analysis reveals low genetic variability in the endangered light‐footed clapper rail
Authors: Nusser J. A. , Goto R. M. , Ledig D. B. , Fleischer R. C. , Miller M. M. 
Published: November 2003

Numbers of light‐footed clapper rails Rallus longirostris levipes, an endangered bird inhabiting southern California salt marshes, have substantially declined from historic levels. RAPD (randomly amplified polymorphic DNA) analysis was employed to assess the genetic variability within and among four of the largest remaining light‐footed clapper rail populations. A single, larger population of the endangered Yuma clapper rail Rallus longirostris yumanensis was used for comparison.A total of 325 RAPD primers were tested on DNA from a subset of five clapper rails composed of a single representative for each of the four light‐footed clapper rail populations and a representative for the single Yuma clapper rail population. Of the 1338 amplified bands (loci) surveyed in these five representative birds, approximately 1% were polymorphic, indicating the level of differentiation across all loci is quite low. Nine primers yielding these 16 polymorphic bands were used to analyse 48 individuals from five populations. Five of these bands were polymorphic in both subspecies, six were polymorphic only within the light‐footed clapper rails, and five were polymorphic only within the Yuma clapper rail samples. Considering the few bands that were polymorphic among the light‐footed clapper rail populations, a surprisingly high level of population differentiation (GST= 0.28) was found. This is in accord with the results of AMOVA analyses which show that a fairly high percentage of the limited variability among the rails is due to either differences between subspecies or differences between the light‐footed rail populations. Because inbreeding depression is suspected and overall genetic distances between populations are low, movement of light‐footed clapper rails from larger populations into smaller ones might be considered as a management strategy. Employing RAPDs as one of a series of assays is useful in revealing the population structure of genetically depauperate species.
Glacial survival does not matter: RAPD phylogeography of Nordic Saxifraga oppositifolia
Authors: GABRIELSEN T. M. , BACHMANN K. , JAKOBSEN K. S. , BROCHMANN C. 
Published: November 2003

AbstractThe arctic‐alpine Saxifraga oppositifolia has recently been suggested to have survived the last glaciation in high‐arctic refugia, based on a finding of more genetic (RFLP) variation in Svalbard compared with more southern areas. To elucidate the migration history of this allogamous species, we analysed 18 populations from Norway, Svalbard and Novaya Zemlya using random amplified polymorphic DNAs (RAPDs). There was no more RAPD variation in the high Arctic than further south. In an analysis of molecular variance (AMOV A), most of the RAPD variation was found within populations (64%). There was less intrapopulational variation in Svalbard (65%) than in northern Norway (78%) and southern Norway (86%), suggesting that there is more inbreeding towards the north, probably because of lower pollinator activity. Twenty‐eight per cent of the RAPD variation was found among populations within these geographical regions, and only 9% was found among the regions. In PCO and UPGMA analyses, plants and populations of different geographical origins were to a large extent intermingled. There was, however, a distinct, south‐north clinal geographical structuring of the RAPD variation both in the PCO analysis and in a spatial autocorrelation (Mantel) analysis. These results suggest that there has been extensive gene flow among more or less continuously distributed populations of S. oppositifolia during the Weichselian, and that the extant Nordic populations were established after massive, centripetal immigration from these genetically variable, periglacial populations. The postglacial period may not have been sufficiently long for the subsequently isolated populations of this long‐lived, allogamous perennial to diverge. Given the high levels of migration inferred from this study, genetic differentiation of glacial survivor populations, if any existed, would most likely have been swamped in the postglacial period. Thus, our molecular data support recent conclusions based on palaeobotanical and biogeographical data that the glacial survival hypothesis is superfluous.
Species‐specific primers discriminate schistosome intermediate hosts: unambiguous PCR diagnosis of Bulinus forskalii group taxa (Gastropoda: Planorbidae)
Authors: JONES C. S. , NOBLE L. R. , LOCKyER A. E. , BROWN D. S. , ROLLINSON D. 
Published: November 2003

AbstractThe morphological definition of taxa has proved difficult within the Bulinus forskalii group, which includes intermediate hosts of medically important Schistosoma species in West Africa. Although B. forskalii and B. senegalensis transmit different schistosome species they are conchologically similar and their distributions overlap. Randomly amplified polymorphic DNA (RAPD) allows differentiation of sibling species in the genus Bulinus, but RAPDs are difficult to standardize, impairing their value as a taxonomic tool. Hence, RAPD products diagnostic for either B. senegalensis or B. forskalii from West Africa were cloned, sequenced and a panel of species‐specific primers designed. Sequencing of RAPD products identified a homology in two apparently independent RAPD loci, a problem where RAPDs are indiscriminately scored for phylogenetic analyses. Specificity of primers was confirmed by widespread sampling throughout each species' range. This approach produced a simple, robust, unambiguous PCR‐based species identification strategy for this difficult group.
A hierarchical quorum‐sensing cascade in Pseudomonas aeruginosa links the transcriptional activators LasR and RhIR (VsmR) to expression of the stationary‐phase sigma factor RpoS
Authors: Latifi A. , Foglino M. , Tanaka K. , Williams P. , Lazdunski A. 
Published: November 2003

Summary In Pseudomonas aeruginosa, the production of many virulence factors and secondary metabolites is regulated in concert with cell density through quorum sensing. Two quorum‐sensing regulons have been identified in which the LuxR homologues LasR and RhIR are activated by N‐(3‐oxododecanoyl)‐l‐homo‐serine lactone (OdDHL) and N‐butanoyl‐l‐homoserine lactone (BHL) respectively. The lasR and rhIR genes are linked to the luxl homologues last and rhll, which are responsible for synthesis of OdDHL and BHL, respectively. As lasRI and rhlRI are both involved in regulating synthesis of exoenzymes such as elastase, we sought to determine the nature of their interrelationship. By using lacZ transcriptional fusions in both homologous (P. aeruginosa) and heterologous (Escherichia coli) genetic backgrounds we provide evidence that (i) lasR is expressed constitutively throughout the growth cycle, (ii) rhIR expression is regulated by LasR/OdDHL, and (iii) that RhIR/BHL regulates rhll. We also show that expression of the stationary‐phase sigma factor gene rpoS is abolished in a P. aeruginosa lasR mutant and in the pleiotropic BHL‐negative mutant PAN067. Furthermore, our data reveal that in E. coli, an rpoS‐lacZ fusion is regulated directly by RhIR/BHL. Taken together, these results indicate that P. aeruginosa employs a multilayered hierarchical quorum‐sensing cascade involving RhIR/BHL and LasR/OdDHL, interlinked via RpoS, to integrate the regulation of virulence determinants and secondary metabolites with adaptation and survival in the stationary phase.
Carbon catabolite repression of xylanase I (xyn1) gene expression in Trichoderma reesei
Authors: Mach Robert L. , Strauss Joseph , Zeilinger Susanne , Schindler Martin , Kubicek Christian P. 
Published: November 2003

SummaryThe filamentous fungus Trichoderma reesei forms two specific, xylan‐inducible xylanases encoded by xyn1 and xyn2 to degrade the β‐1,4‐d‐xylan backbone of hemicelluloses. This enzyme system is formed in the presence of xylan, but not glucose. The molecular basis of the absence of xylanase I formation on glucose was the purpose of this study. Northern blotting of the xyn1 transcript as well as the use of the Escherichia coli hygromycin B phosphotransferase‐encoding gene (hph) as a reporter consistently showed that the basal expression of xyn1 was affected by glucose, whereas its induction by xylan remained uninfluenced. The repression of basal xyn1 transcription is mediated by the carbon catabolite repressor protein Cre1, which in vivo binds to two of four consensus sites (5‐SYG‐GRG‐3) in the xyn1 promoter, which occurred in the form of an inverted repeat. T. reesei strains, bearing a xynlv. hph reporter construct, in which four nucleotides from the middle of the inverted repeat had been removed, expressed hph on glucose at a level comparable to that observed during growth on a carbon catabolite derepressing carbon source. Northern analysis of xynl expression in a T. reesei mutant strain (RUT C‐30), which contains a truncated, non‐functional crel gene, also confirmed basal transcription of xyn1. In this strain, xyn1 transcription was still inducible by xylose or xylan to an even higher degree than in the wild‐type strain, suggesting that induction overcomes glucose repression at the level of xynl expression. Based on these data, we postulate that basal transcription of xyn1 is repressed by glucose and mediated by an inverted repeat of the consensus motif for Cre1‐mediated carbon catabolite repression.
Expression of the tolQRA genes of Escherichia coli K‐12 is controlled by the RcsC sensor protein involved in capsule synthesis
Authors: Clavel Thierry , Lazzaroni Jean Claude , Vianney Anne , Portalier Raymond 
Published: November 2003

SummaryThe tolQRABpal cluster of Escherichia coli K‐12 encodes proteins involved in the maintenance of cell‐envelope integrity. In addition, toi/pal mutations result in a mucoid colony phenotype at low temperature. The synthesis of capsular polysaccharides by the cps genes is controlled by the positive regulator RcsA and the two‐component RcsC/RcsB system. It was shown that the mucoid phenotype of the tol/pal mutants was due to an rcsCB‐dependent activation of the cps genes. Furthermore, we have identified a mutation in the rcsC gene that decreased the activity of a tolA‐lac operon fusion independently of RcsA and partially independently of RcsB activators. The corresponding rcsC338 mutation resulted in a Glu to Lys substitution at residue 338 of RcsC. This mutation induced mucoidy even at high temperature. We propose that RcsC modulates the phosphorylated forms of RcsB and an uncharacterized regulatory protein involved in the control of the tolQRA genes in an opposite manner. Moreover, our findings strengthen the previous suggestion that RcsC senses some alterations in the cell surface such as those induced by tol, pal or rfa mutations, and activates capsule synthesis to protect the cell against deleterious agents.
Involvement of σ54 in exponential silencing of the Pseudomonas putida TOL plasmid Pu promoter
Authors: Cases IIdefonso , de Lorenzo Victor , Pérez‐Martín José 
Published: November 2003

SummaryThe σ54‐dependent Pu promoter of the TOL plasmid pWWO of Pseudomonas putida becomes activated by the prokaryotic enhancer‐binding XyIR protein when cells encounter m‐xylene in the medium. However, even in the presence of the aromatic inducer, Pu activity is silenced in vivo during rapid exponential growth of the cells in rich medium. Various elements known to be involved in the control of the transcriptional activity of the promoter were examined to ascertain the mechanism by which expression of Pu is limited during the exponential phase of growth. A truncated and fully constitutive XyIR derivative deleted of its signal reception N‐terminal domain was found to be subjected to the same exponential silencing as the wild‐type XyIR when exposed to m‐xylene. This indicated that the phenomenon is not due to a late activation of XyIR by the aromatic effector. A Pu variant in which the integration host factor (IHF)‐binding site had been functionally replaced by a statically curved DNA segment showed the same induction pattern, thus ruling out variations in the intracellular levels of IHF changes during growth as the element responsible for the inactivity of Pu in rapidly growing cells. On the contrary, overproduction of the σ54 factor allowed Pu expression during exponential phase. As σ54 protein levels remained approximately constant during growth, the exponential silencing of Pu could be caused ultimately by changes in the activity of the factor itself. This effect may not be exclusive to Pu, but could be a general co‐regulation mechanism in σ54‐dependent promoters that connects transcription of a specific set of genes with the general physiological status of the cells.
Use of chimeric recombinant polypeptides to analyse conformational, surface epitopes on trypanosome variant surface glycoproteins
Authors: Hsia Ru‐ching , Beals Thomas , Boothroyd John C. 
Published: November 2003

SummaryIdentification of surface‐exposed epitopes on the variant surface glycoproteins (VSGs) of African trypanosomes has been complicated by the observation that most such epitopes are highly conformational. As a result, whenever the molecule is broken down for analysis, the epitope is generally lost. We have exploited the existence of closely related gene families to create chimeric molecules in which particular segments of one VSG are placed in the analogous position of a related but antigenically distinct VSG. The process is used in both a positive and negative manner, so that the epitope can be specifically added or destroyed in a given chimera. As an example, we have used this approach to identify the regions involved in reactivity to a monoclonal antibody specific for VSG117 on the surface of live trypanosomes. We show that while deletion of almost any region of VSG117 results in loss of reactivity to this monoclonal antibody, substituting particular regions with the corresponding segment of the structurally related but antigenically distinct VSG FM8.5 restores reactivity in most but not all cases, thereby delimiting the antigenically key regions. Likewise, substituting key regions from VSG117 into FM8.5 confers reactivity on the resulting chimeras. This approach circumvents some of the problems that result from the highly conformational nature of VSG and should allow further elucidation of the biologically relevant antigenic topology of VSGs.
The katE gene, which encodes the catalase HPII of Mycobacterium avium
Authors: Milano A. , De Rossi E. , Gusberti L. , Heym B. , Marone P. , Riccardi G. 
Published: November 2003

SummaryDisseminated Mycobacterium avium‐Mycobacterium intracellular disease is a prevalent opportunistic infection in patients with acquired immune deficiency syndrome (AIDS). These pathogens are generally resistant to isoniazid (INH), a powerful antituberculosis drug. It is now generally accepted that the INH susceptibility of Mycobacterium tuberculosis results from the transformation of the drug into a toxic derivative, as a result of the action of the enzyme catalase‐peroxidase (HPI), encoded by the katG gene. It has been speculated that the presence of a second catalase (HPII) in some mycobacterial species, but lacking in M. tuberculosis, may impair the action of INH. In this report, the nucleotide sequence of the M. avium katE gene, encoding catalase HPII, is described. This enzyme shows strong similarity to Escherichia coli catalase HPII and eukaryotic catalases. All amino acids previously postulated as participating directly in catalysis by liver catalase and most of the amino acids binding the prosthetic group are conserved in M. avium catalase HPII. The enzyme is expressed in E. coli and is inhibited by 3‐amino ‐l,2,4 triazole (AT). Furthermore, Southern blot hybridizations and polymerase chain reaction experiments demonstrate the distribution of katE gene in several mycobacterial species.To evaluate the potentially antagonistic effect of HPII catalase on INH susceptibility, the katE gene was transformed into M. tuberculosis H37Rv and the minimum inhibitory concentration (MIC) for INH was determined. Despite strong expression of the katEgene, no change in MIC was observed, thus ruling out a possible contribution of this enzyme to the natural resistance of M. avium to the drug.The availability of the gene probe, encoding the second mycobacterial catalase HPII, should open the way for the development of new drugs and diagnostic tests to combat drug‐resistant pathogen strains.
The local repressor AcrR plays a modulating role in the regulation of acrAB genes of Escherichia coli by global stress signals
Authors: Ma Dzwokai , Alberti Marie , Lynch Christy , Nikaido Hiroshi , Hearst John E. 
Published: November 2003

SummaryGenes acrAB encode a multidrug efflux pump in Escherichia coli. We have previously reported that transcription of acrAB is increased under general stress conditions (i.e. 4% ethanol, 0.5 M NaCl, and the stationary phase in Luria‐Bertanl medium). In this study, lacZ transcriptional fusions and an in vitro gel mobility shift assay have been utilized to study the mechanisms governing the regulation of acrAB. We found that a closely linked gene, acrR, encoded a repressor of acrAB. Nevertheless, the general stress conditions increased transcription of acrAB in the absence of functional AcrR, and such conditions surprisingly increased the transcription of acrR even more strongly than that of acrAB. These results suggest that the general‐stress‐induced transcription of acrAB is primarily mediated by global regulatory pathway(s), and that one major role of AcrR is to function as a specific secondary modulator to fine tune the level of acrAB transcription and to prevent the unwanted overexpression of acrAB. To our knowledge, this represents a novel mechanism of regulating gene expression in E. coli. Evidence also suggests that the up‐regulation of acrAB expression under general stress conditions is not likely to be mediated by the known global regulators, such as MarA or SoxS, although elevated levels of these proteins were shown to increase the transcription of acrAB.
Molecular characterization of hybrid Tbp2 proteins from Neisseria meningitides
Authors: Legrain Michèle , Findeli Annie , Villeval Dominique , Quentin‐Millet Marie‐José , Jacobs Eric 
Published: November 2003

SummaryTransferrin‐binding protein 2 (Tbp2) from Neisseria is an outer membrane‐associated extracellular lipoprotein that is involved in iron capture within the infected host. The analysis of tbp2 clones isolated from various bacterial strains revealed extensive divergences throughout the open reading frame (ORF), with predicted amino acid (aa) sequences displaying 47% to 83% identity. Such a variability is likely to have resulted from the selective pressure exerted by the host immune system, but raises questions regarding the existing constraints for conservation of protein function. Indeed, the neisserial Tbp2s include a large structured domain, extending throughout the N‐terminal half of the protein (∼270–290 aa), which is extremely stable and whose conformational integrity is required for efficient binding to human transferrin (hTf). In this work, a functional study of Tbp2s encoded by hybrid genes constructed by reassorting highly divergent tbp2 sequences in the region of the ORF encoding this structured domain was performed. The data demonstrate that the determinant intramolecular interactions allowing formation of a stable Tbp2 structure able to interact efficiently with hTf or/and that the Tbp2 residues involved in the interaction with hTf are not well conserved. However, a number of rearrangements appeared to generate genes encoding proteins which have retained structural stability and hTf‐binding capacity. This suggested that despite the extreme aa sequence divergence and the conformational constraints, horizontal genetic exchanges, which are known to occur in neisserial populations, may have contributed significantly to the generation of sequence variation within tbp2 ORFs. The analysis of two tbp2clones characterized in this work supports this hypothesis.
Identification of an essential core element and stimulatory sequences in a Kluyveromyces lactis ARS element, KARS101
Authors: Fabiani Lucia , Frontali Laura , Newlon Carol S. 
Published: November 2003

A Kluyveromyces lactis chromosomal sequence of 913 bp is sufficient for replication in Saccharomyces cerevisiae and K. lactis. This fragment contains a 12 bp sequence 5′‐ATTTATTGTTTT‐3′ that is related to the S. cerevisiae ACS (ARS consensus sequence). This dodecamer was removed by site‐directed mutagenesis and the effect on K. lactis and S. cerevisiae ARS (autonomous replicating sequence) activity was determined. The dodecamer is essential for S. cerevisiae ARS function but only contributes to K. lactis ARS activity; therefore, its role in K. lactis is unlikely to be the same as that of the essential S. cerevisiae ACS.A 103 bp subclone was found to retain ARS activity in both yeasts, but the plasmid was very unstable in S. cerevisiae. Deletion and linker substitution mutagenesis of this fragment was undertaken to define the DNA sequence required for K. lactis ARS function and to test whether the sequence required for ARS activity in K. lactis and S. cerevisiae coincide. We found a 39 bp core region essential for K. lactis ARS function flanked by sequences that contribute to ARS efficiency. The instability of the plasmid in S. cerevisiae made a fine‐structure analysis of the S. cerevisiae ARS element impossible. However, the sequences that promote high‐frequency transformation in S. cerevisiae overlap the essential core of the K. lactis ARS element but have different end‐points.