bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeography of western PacificLeucetta ‘chagosensis’(Porifera: Calcarea) from ribosomal DNA sequences: implications for population history and conservation of the Great Barrier Reef World Heritage Area (Australia)
Authors: Wörheide Gert , Hooper John N. A. , Degnan Bernard M. 
Published: March 2003

AbstractLeucetta ‘chagosensis’is a widespread calcareous sponge, occurring in shaded habitats of Indo‐Pacific coral reefs. In this study we explore relationships among 19 ribosomal DNA sequence types (the ITS1‐5.8S–ITS2 region plus flanking gene sequences) found among 54 individuals from 28 locations throughout the western Pacific, with focus on the Great Barrier Reef (GBR). Maximum parsimony analysis revealed phylogeographical structuring into four major clades (although not highly supported by bootstrap analysis) corresponding to the northern/central GBR with Guam and Taiwan, the southern GBR and subtropical regions south to Brisbane, Vanuatu and Indonesia. Subsequent nested clade analysis (NCA) confirmed this structure with a probability of > 95%. After NCA of geographical distances, a pattern of range expansion from the internal Indonesian clade was inferred at the total cladogram level, as the Indonesian clade was found to be the internal and therefore oldest clade. Two distinct clades were found on the GBR, which narrowly overlap geographically in a line approximately from the Whitsunday Islands to the northern Swain Reefs. At various clade levels, NCA inferred that the northern GBR clade was influenced by past fragmentation and contiguous range expansion events, presumably during/after sea level low stands in the Pleistocene, after which the northern GBR might have been recolonized from the Queensland Plateau in the Coral Sea. The southern GBR clade is most closely related to subtropicalL. ‘chagosensis’, and we infer that the southern GBR probably was recolonized from there after sea level low stands, based on our NCA results and supported by oceanographic data. Our results have important implications for conservation and management of the GBR, as they highlight the importance of marginal transition zones in the generation and maintenance of species rich zones, such as the Great Barrier Reef World Heritage Area.
The role of ecologic diversification in sibling speciation ofEmpidonaxflycatchers (Tyrannidae): multigene evidence from mtDNA
Authors: Johnson N. K. , Cicero C. 
Published: March 2003

AbstractAvian genera characterized by sibling species with distinctive habitat preferences present an evolutionary enigma in view of the more commonplace occurrence of syntopic congeners that differ strikingly in colour and pattern. No existing theory has explained the evolutionary background that led to these differences. Here we propose that great phenotypic similarity among some groups of sibling species limits their coexistence and that clues to their radiation can be seen in patterns of geographical occurrence. To illustrate our thesis we focused on the New World flycatcher genusEmpidonax, a group of 15 species notorious for their great phenotypic similarity. Using 3069 base pairs of mitochondrial DNA from four genes, we produced a complete molecular phylogeny that identified four clades, three of which represent close relatives. The fourth clade includes onlyE. virescens, which apparently has no close living relatives. The majority of species, including many distant relatives, are completely (58.1%) or essentially (6.7%) allopatric in breeding distribution and exhibit striking ecological segregation into distinctive climate–vegetation zones. Even where ranges overlap, occupancy of the same habitat by different species is rare. Phylogenetic and distributional patterns inEmpidonaxsuggest a peripatric model of stepwise colonization and then range expansion of small groups of pioneers during glacial periods into initially enlarging, distinctive habitats destined to be widespread during interglacials. Vicariance is not indicated in the absence of barriers of appropriate age and geographical position. Rapoport's rule that northern species have larger ranges than southern species is strongly supported.
Population genetic structure and male‐biased dispersal in the queenless antDiacamma cyaneiventre
Authors: Doums Claudie , Cabrera Humberto , Peeters Christian 
Published: March 2003

AbstractIn this study we investigated the population genetic structure of the queenless antDiacamma cyaneiventre. This species, lacking winged queens, is likely to have a restricted female dispersal. We used both mitochondrial and microsatellite markers to assess the consequence of such restricted female dispersal at three geographical scales: within a given locality (< 1 km), between localities within a given region (< 10 km) and between regions (> 36 km). Within a locality, a strong population structure was observed for mitochondrial DNA (mtDNA) whereas weak or nonexistent population genetic structure was observed for the microsatellites (around 5% of the value for mtDNA). Male gene flow was estimated to be about 20–30 times higher than female gene flow at this scale. At a larger spatial scale, very strong genetic differentiation for both markers was observed between localities — even within a single region. Female dispersal is nonexistent at these scales and male dispersal is very restricted, especially between regions. The phylogeographical structure of the mtDNA haplotypes as well as the very low genetic diversity of mtDNA within localities indicate that new sites are colonized by a single migration event from adjacent localities, followed by successive colony fissions. These patterns of genetic variability and differentiation agree with what is theoretically expected when colonization events are kin‐structured and when, following colonization, dispersion is mainly performed by males.
The clonal structure of Quercus geminata revealed by conserved microsatellite loci
Authors: Ainsworth E. A. , Tranel P. J. , Drake B. G. , Long S. P. 
Published: March 2003

AbstractThe scrub oak communities of the southeastern USA may have existed at their present locations for thousands of years. These oaks form suckers, and excavations of root systems suggest that clones may occupy very large areas. Resolution of the clonal nature of scrub oaks is important both to manage the tracts of this ecosystem that remain, and in conducting long‐term ecological studies, where the study area must substantially exceed the area occupied by any single clone. Microsatellites were used to determine the genetic diversity of a dominant oak species within a 2‐ha long‐term experimental site on Merritt Island at the Kennedy Space Center. This area contains a long‐term study of the effects of elevated CO2 on the ecosystem. Conservation of seven microsatellite loci, previously identified in the sessile oak, Quercus petraea, was tested in two Florida scrub oak species, Q. geminata and Q. myrtifolia. Sequence analysis revealed that all seven microsatellite loci were conserved in Q. geminata and five loci were conserved in Q. myrtifolia. Six microsatellite loci were polymorphic in Q. geminata and these were subsequently used to investigate the clonal structure of the Q. geminata population. Twenty‐one unique combinations of microsatellites, or haplotypes, occurred only once, whereas the remaining 26 individuals belonged to a total of seven different haplotypes. Trees with identical haplotypes were in close proximity, supporting the interpretation that they were clones. The results showed that there is significant genetic diversity within the 2‐ha experimental site. Microsatellites provided a powerful and noninvasive tool for distinguishing individual genotypes and determining an adequate area for long‐term ecosystem studies.
Phylogeography and conservation genetics of Eld's deer (Cervus eldi)
Authors: Balakrishnan Christopher N. , Monfort Steven L. , Gaur Ajay , Singh Lalji , Sorenson Michael D. 
Published: March 2003

AbstractEld's deer (Cervus eldi) is a highly endangered cervid, distributed historically throughout much of South Asia and Indochina. We analysed variation in the mitochondrial DNA (mtDNA) control region for representatives of all three Eld's deer subspecies to gain a better understanding of the genetic population structure and evolutionary history of this species. A phylogeny of mtDNA haplotypes indicates that the critically endangered and ecologically divergentC. eldi eldiis related more closely toC. e. thaminthan toC. e. siamensis, a result that is consistent with biogeographic considerations. The results also suggest a strong degree of phylogeographic structure both between subspecies and among populations within subspecies, suggesting that dispersal of individuals between populations has been very limited historically. Haplotype diversity was relatively high for two of the three subspecies (thaminandsiamensis), indicating that recent population declines have not yet substantially eroded genetic diversity. In contrast, we found no haplotype variation withinC. eldi eldior the Hainan Island population ofC. eldi siamensis, two populations which are known to have suffered severe population bottlenecks. We also compared levels of haplotype and nucleotide diversity in an unmanaged captive population, a managed captive population and a relatively healthy wild population. Diversity indices were higher in the latter two, suggesting the efficacy of well‐designed breeding programmes for maintaining genetic diversity in captivity. Based on significant genetic differentiation among Eld's deer subspecies, we recommend the continued management of this species in three distinct evolutionarily significant units (ESUs). Where possible, it may be advisable to translocate individuals between isolated populations within a subspecies to maintain levels of genetic variation in remaining Eld's deer populations.
Analysis of mRNA decay and rRNA processing in Escherichia coli in the absence of RNase E‐based degradosome assembly
Authors: Ow Maria C. , Liu Qi , Kushner Sidney R. 
Published: March 2003

We demonstrate here that the assembly of the RNase E‐based degradosome of Escherichia coli is not required for normal mRNA decay in vivo. In contrast, deletion of the arginine‐rich RNA binding site (ARRBS) from the RNase E protein slightly impairs mRNA decay. When both the degradosome scaffold region and the ARRBS are missing, mRNA decay is dramatically slowed, but 9S rRNA processing is almost normal. An extensive RNase E truncation mutation (rneδ610) had a more pronounced mRNA decay defect at 37°C than the temperature‐sensitive rne‐1 allele at 44°C. Taken together, these data suggest that the inviability associated with inactivation of RNase E is not related to defects in either mRNA decay or rRNA processing.
Evidence for non‐enzymatic glycosylation in Escherichia coli
Authors: Mironova Roumyana , Niwa Toshimitsu , Hayashi Hideki , Dimitrova Rositsa , Ivanov Ivan 
Published: March 2003

Non‐enzymatic glycosylation (glycation) is a chain of chemical reactions affecting free amino groups in proteins of long‐living eukaryotes. It proceeds in several steps leading to the consecutive formation of Schiff bases, Amadori products and advanced glycation end‐products (AGEs). To our knowledge, this process has not been observed in prokaryotes so far. However, the present study provides clear‐cut evidence that glycation takes place in bacteria despite their short life span. We have detected AGEs in recombinant human interferon gamma (rhIFN‐γ) produced in Escherichia coli as well as in total protein of the same bacterium using three different approaches: (i) Western blotting using two monoclonal antibodies raised against AGEs; (ii) fluorescent spectroscopy; and (iii) investigation of the effect of known AGE inhibitors (such as acetyl salicylic acid and thiamine) on the glycation reaction. Our study shows that non‐enzymatic glycosylation is initiated during the normal growth of E. coli and results in AGE formation even after isolation of proteins. This process seems to be tightly associated with some post‐translational modifications observed in the cysteineless rhIFN‐γ, such as covalent dimerization and truncation.
Pph1 from Myxococcus xanthus is a protein phosphatase involved in vegetative growth and development
Authors: Treuner‐Lange Anke , Ward Mandy J. , Zusman David R. 
Published: March 2003

Myxococcus xanthus is a Gram‐negative bacterium with a complex life cycle that includes vegetative swarming on rich medium and, upon starvation, aggregation to form fruiting bodies containing spores. Both of these behaviours require multiple Ser/Thr protein kinases. In this paper, we report the first Ser/Thr protein phosphatase gene, pph1, from M. xanthus. DNA sequence analysis of pph1 indicates that it encodes a protein of 254 residues (Mr = 28 308) with strong homology to eukaryotic PP2C phosphatases and that it belongs to a new group of bacterial protein phosphatases that are distinct from bacterial PP2C phosphatases such as RsbU, RsbX and SpoIIE. Recombinant His‐tagged Pph1 was purified from Escherichia coli and shown to have Mn2+ or Mg2+ dependent, okadaic acid‐resistant phosphatase activity on a synthetic phosphorylated peptide, RRA(pT)VA, indicating that Pph1 is a PP2C phosphatase. Pph1‐expression was observed under both vegetative and developmental conditions, but peaked during early aggregation. A pph1 null mutant showed defects during late vegetative growth, swarming and glycerol spore formation. Under starvation‐induced developmental conditions, the mutant showed reduced aggregation and failure to form fruiting bodies with viable spores. Using the yeast two‐hybrid system, we have observed a strong interaction between Pph1 and the M. xanthus protein kinase Pkn5, a negative effector of development. These results suggest a functional link between a Pkn2‐type protein kinase and a PP2C phosphatase.
Oligopeptide permease is required for expression of the Bacillus thuringiensis plcR regulon and for virulence
Authors: Gominet Myriam , Slamti Leyla , Gilois Nathalie , Rose Matthias , Lereclus Didier 
Published: March 2003

PlcR is a pleiotropic regulator of virulence factors in the insect pathogen Bacillus thuringiensis and in the opportunistic human pathogen Bacillus cereus. It activates the transcription of at least 15 genes encoding extracellular proteins, including phospholipases C, proteases and enterotoxins. Expression of the plcR gene is autoregulated and activated at the onset of stationary phase. Here, we used mini‐Tn10 transposition to generate a library of B. thuringiensis mutants, with the goal of characterizing genes involved in the expression of the plcR gene. Three mutant strains were identified carrying distinct mini‐Tn10 insertions. The mutations impaired plcR expression and caused a deficient haemolytic phenotype, similar to the phenotype of a B. thuringiensis strain in which the plcR gene had been disrupted. The insertion sites of the three mini‐Tn10 transposons mapped in a five‐gene operon encoding polypeptides homologous to the components of the oligopeptide permease (Opp) system of Bacillus subtilis, and with a similar structural organization. By analogy, the five B. thuringiensis genes were designated oppA, B, C, D and F. In vitro disruption of the B. thuringiensis oppB gene reproduced the effect of the mini‐Tn10 insertions (i.e. the loss of haemolytic activity) and reduced the virulence of the strain against insects. These phenotypes are similar to those of a ΔplcR mutant. Opp is required for the import of small peptides into the cell. Therefore, plcR expression might be activated at the onset of stationary phase by the uptake of a signalling peptide acting as a quorum‐sensing effector. The opp mutations impaired the sporulation efficiency of B. thuringiensis when the cells were cultured in LB medium. Thus, Opp is on the pathway that ultimately regulates Spo0A phosphorylation, as is the case in B. subtilis. However, analysis of plcR expression in ΔoppB, Δspo0A and ΔoppBΔspo0A mutants indicates that Opp is required for plcR expression via a Spo0A‐independent mechanism.
The chromosome partitioning protein, ParB, is required for cytokinesis in Caulobacter crescentus
Authors: Mohl Dane A. , Easter Jesse , Gober James W. 
Published: March 2003

In Caulobacter crescentus, the genes encoding the chromosome partitioning proteins, ParA and ParB, are essential. Depletion of ParB resulted in smooth filamentous cells in which DNA replication continued. Immunofluorescence microscopy revealed that the formation of FtsZ rings at the mid‐cell, the earliest molecular event in the initiation of bacterial cell division, was blocked in cells lacking ParB. ParB binds sequences near the C. crescentus origin of replication. Cell cycle experiments show that the formation of bipolarly localized ParB foci, and presumably localization of the origin of replication to the cell poles, preceded the formation of FtsZ rings at the mid‐cell by 20 min. These results suggest that one major function of ParA and ParB may be to regulate the initiation of cytokinesis in C. crescentus.
Plasmid transfer from Streptomyces to Mycobacterium smegmatis by spontaneous transformation
Authors: Bhatt Apoorva , Melton Rachel E. , Kieser Tobias 
Published: March 2003

SummaryHybrids of the Streptomyces coelicolor conjugative plasmid SCP2* and the
Mycobacterium plasmid pAL5000 were transferred from Streptomyces coelicolor
or Streptomyces lividans to Mycobacterium smegmatis mc2155
in plate crosses. Inactivation of the SCP2* transfer function did not prevent or
reduce plasmid transfer. This transfer was DNase I sensitive and thus involved release
of DNA from Streptomyces, followed by transformation of M. smegmatis.
M. smegmatis growing on specific solid media was also transformed by pure
CCC and linear plasmid DNA. Small plasmids were taken up intact but large plasmids
suffered deletions. Competence developed within 24 h of incubation at 30°C or
37°C, and up to 400 transformants were obtained per μg of CCC plasmid
DNA. Transformation frequencies were higher when M. smegmatis was co‐cultivated
with plasmid‐free Streptomyces, but unaffected by resident homologous sequences
or inactivation of recA in M. smegmatis. Spontaneous transformation
was also observed with a circular Streptomyces transposable element which
inserted into chromosomal sites. Transformative plasmid transfer was also shown to
occur between M. smegmatis strains. This is the first report of non‐artificially
induced, spontaneous plasmid transformation in Mycobacterium.
RNase E levels in Escherichia coli are controlled by a complex regulatory system that involves transcription of the rne gene from three promoters
Authors: Ow Maria C. , Liu Qi , Mohanty Bijoy K. , Andrew Margaret E. , Maples Valerie F. , Kushner Sidney R. 
Published: March 2003

SummaryThe rne gene of Escherichia coli encodes RNase E, an essential endoribonuclease
that is involved in both mRNA decay and rRNA processing. Here we present evidence
that the gene is transcribed from three promoters: p1, p2 and p3. The p2 and p3 promoters
map 34 and 145 nt upstream from the previously characterized rne promoter,
p1, generating unusually long 5′ UTRs of 395 and 506 nt respectively.
Based on promoter–lacZ transcriptional fusions, p1 is a more efficient
promoter than either p2 or p3. Low copy number or single copy number vectors carrying
rne transcribed from either p1, p2 or p3 alone complement the rneΔ1018::bla
deletion mutation at 30°C, 37°C and 44°C. However,
normal autoregulation requires the presence of all three promoters. A comparison
among intracellular levels of RNase E, the half‐lives of the rpsO, rpsT
and rne mRNAs, and growth rates, indicates that the cell contains a considerable
excess of RNase E protein. In addition, when the rne transcript is stabilized at low RNase E levels, it is not efficiently translated.
Interactions of haemoglobin with the Neisseria meningitidis receptor HpuAB: the role of TonB and an intact proton motive force
Authors: Rohde K. H. , Gillaspy A. F. , Hatfield M. D. , Lewis L. A. , Dyer D. W. 
Published: March 2003

SummaryWe have characterized the interaction of the Neis‐seria meningitidis TonB‐dependent receptor HpuAB with haemoglobin (Hb). Protease accessibility assays indicated that HpuA and HpuB are surface exposed, HpuB interacts physically with HpuA, and TonB energization affects the conformation of HpuAB. Binding assays using [125I]‐Hb revealed that the bipartite receptor has a single binding site for Hb (Kd≈ 150 nM). Competitive binding assays using heterologous Hbs revealed that HpuAB Hb recognition was not species specific. The binding kinetics of Hb to HpuAB were dramatically altered in a TonB– mutant and in wild‐type meningococci treated with the protonophore carbonylcyanide m‐chlorophenylhydrazone (CCCP), indicating that TonB and an intact proton motive force are required for normal Hb binding and release from HpuAB. Our results support a model in which both HpuA and HpuB are required to form a receptor complex in the outer membrane with a single binding site, whose structure and ligand interactions are significantly affected by the TonB‐mediated energy state of the receptor.
Identification and characterization of phage‐resistance genes in temperate lactococcal bacteriophages
Authors: McGrath Stephen , Fitzgerald Gerald F. , Sinderen Douwe van 
Published: March 2003

SummaryThe sie2009 gene, which is situated between the genes encoding the repressor and integrase, on the lysogeny module of the temperate lactococcal bacteriophage Tuc2009, was shown to mediate a phage‐resistance phenotype in Lactococcus lactis against a number of bacteriophages. The Sie2009 protein is associated with the cell membrane and its expression leaves phage adsorption, transfection and plasmid transformation unaffected, but interferes with plasmid transduction, as well as phage replication. These observations indicate that this resistance is as a result of DNA injection blocking, thus representing a novel superinfection exclusion system. A polymerase chain reaction (PCR)‐based strategy was used to screen a number of lactococcal strains for the presence of other prophage‐encoded phage‐resistance systems. This screening resulted in the identification of two such systems, without homology to sie2009, which were shown to mediate a phage‐resistance phenotype similar to that conferred by sie2009. To our knowledge, this is the first description of a phage‐encoded superinfection exclusion/injection blocking mechanism in the genus Lactococcus.
Molecular analysis of KTI12/TOT4, a Saccharomyces cerevisiae gene required for Kluyveromyces lactis zymocin action
Authors: Fichtner Lars , Frohloff Frank , Bürkner Konstanze , Larsen Michael , Breunig Karin D. , Schaffrath Raffael 
Published: March 2003

SummaryTOT, the putative Kluyveromyces lactis zymocin target complex from Saccharomyces cerevisiae, is encoded by TOT1–7, six loci of which are isoallelic to RNA polymerase II (RNAPII) Elongator genes (ELP1–6). Unlike TOT1–3 (ELP1–3) and TOT5–7 (ELP5, ELP6 and ELP4 respectively), which display zymocin resistance when deleted, TOT4 (KTI12) also renders cells refractory to zymocin when maintained in multicopy or overexpressed from the GAL10 promoter. Elevated TOT4 copy number results in an intermediate tot phenotype, which includes mild sensitivities towards caffeine, Calcofluor white and elevated growth temperature, suggesting that TOT4 influences TOT/Elongator function. Tot4p interacts with Elongator, as shown by co‐immunoprecipitation, and cell fractionation studies demonstrate partial co‐migration with RNAPII and Elongator. As Elongator subunit interaction is not affected by either deletion of TOT4 or multicopy TOT4, Tot4p may not be a structural Elongator subunit but, rather, may regulate TOT/Elongator in a fashion that requires transient physical contact with TOT/Elongator. Consistent with a regulatory role, the presence of a potential P‐loop motif conserved between yeast and human TOT4 homologues suggests capability of ATP or GTP binding and P‐loop deletion renders Tot4p biologically inactive.