bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microsatellite analysis of genetic divergence among populations of giant Galápagos tortoises
Authors: Ciofi Claudio , Milinkovitch Michel C. , Gibbs James P. , Caccone Adalgisa , Powell Jeffrey R. 
Published: March 2003

AbstractGiant Galápagos tortoises represent an interesting model for the study of patterns of genetic divergence and adaptive differentiation related to island colonization events. Recent mitochondrial DNA work elucidated the evolutionary history of the species and helped to clarify aspects of nomenclature. We used 10 microsatellite loci to assess levels of genetic divergence among and within island populations. In particular, we described the genetic structure of tortoises on the island of Isabela, where discrimination of different taxa is still subject of debate. Individual island populations were all genetically distinct. The island of Santa Cruz harboured two distinct populations. On Isabela, populations of Volcan Wolf, Darwin and Alcedo were significantly different from each other. On the other hand, Volcan Wolf showed allelic similarity with the island of Santiago. On Southern Isabela, lower genetic divergence was found between Northeast Sierra Negra and Volcan Alcedo, while patterns of gene flow were recorded among tortoises of Cerro Azul and Southeast Sierra Negra. These tortoises have endured heavy exploitation during the last three centuries and recently attracted much concern due to the current number of stochastic and deterministic threats to extant populations. Our study complements previous investigation based on mtDNA diversity and provides further information that may help devising tortoise management plans.
First synthesize new viruses then regulate their release? The case of the wild rabbit
Authors: Angulo E. , Cooke B. 
Published: March 2003

AbstractEuropean wild rabbits originated in southwestern Europe but have been introduced into many other countries world‐wide, becoming serious pests in many instances. As a consequence of rabbits being regarded so differently, applied research for their management often has opposing goals, namely their conservation or their control. Furthermore, modern gene technology has led to the concept of using genetically modified myxoma viruses for rabbit management, again with quite contrary aims in mind. In this paper we explain the possible ecological and economic consequences of using these genetically modified viruses inappropriately and we consider whether national and international regulations are sufficient to prevent improper use. If international regulations are inadequate, molecular biologists and ecologists must consider the consequences of their research and advice beyond their own country to avoid unwanted impacts.
Genetic structure and reproduction dynamics of Salix reinii during primary succession on Mount Fuji, as revealed by nuclear and chloroplast microsatellite analysis
Authors: Lian Chunlan , Oishi Ryuya , Miyashita Naoya , Nara Kazuhide , Nakaya Hironobu , Wu Bingyun , Zhou Zhihua , Hogetsu Taizo 
Published: March 2003

AbstractThe early stage of volcanic desert succession is underway on the southeastern slope of Mount Fuji. We used markers of nuclear microsatellites (simple sequence repeats; SSR) and chloroplast microsatellites (cpSSR) to investigate the population genetic structure and reproduction dynamics of Salix reinii, one of the dominant pioneer shrubs in this area. The number of S. reinii genets in a patch and the area of the largest genet within the patch increased with patch area, suggesting that both clonal growth and seedling recruitment are involved in the reproduction dynamics of S. reinii. Five polymorphic cpSSR markers were developed for S. reinii by sequencing the noncoding regions between universal sequences in the chloroplast genome. Nineteen different cpSSR haplotypes were identified, indicating that S. reinii pioneer genets were created by the long‐distance dispersal of seeds originating from different mother genets around the study site, where all vegetation was destroyed during the last eruption. Furthermore, the clustered distributions of different haplotypes within each patch or plot suggested that newly colonized genets tended to be generated from seeds dispersed near the initially established mother genets. These results revealed that the establishment of the S. reinii population on the southeastern slope of Mount Fuji involved two sequential modes of seed dispersal: long‐distance dispersal followed by short‐distance dispersal.
Bayesian inferences on the recent island colonization history by the bird Zosterops lateralis lateralis
Authors: Estoup A. , Clegg S. M. 
Published: March 2003

AbstractThe founding of new populations by small numbers of colonists has been considered a potentially important mechanism promoting evolutionary change in island populations. Colonizing species, such as members of the avian species complex Zosterops lateralis, have been used to support this idea. A large amount of background information on recent colonization history is available for one Zosterops subspecies, Z. lateralis lateralis, providing the opportunity to reconstruct the population dynamics of its colonization sequence. We used a Bayesian approach to combine historical and demographic information available on Z. l. lateralis with genotypic data from six microsatellite loci, and a rejection algorithm to make simultaneous inferences on the demographic parameters describing the recent colonization history of this subspecies in four southwest Pacific islands. Demographic models assuming mutation–drift equilibrium or a large number of founders were better supported than models assuming founder events for three of four recently colonized island populations. Posterior distributions of demographic parameters supported (i) a large stable effective population size of several thousands individuals with point estimates around 4000–5000; (ii) a founder event of very low intensity with a large effective number of founders around 150–200 individuals for each island in three of four islands, suggesting the colonization of those islands by one flock of large size or several flocks of average size; and (iii) a founder event of higher intensity on Norfolk Island with an effective number of founders around 20 individuals, suggesting colonization by a single flock of moderate size. Our inferences on demographic parameters, especially those on the number of founders, were relatively insensitive to the precise choice of prior distributions for microsatellite mutation processes and demographic parameters, suggesting that our analysis provides a robust description of the recent colonization history of the subspecies.
Mitochondrial markers in the antLeptothorax rugatulusreveal the population genetic consequences of female philopatry at different hierarchical levels
Authors: Rüppell Olav , Strätz Michaela , Baier Bernd , Heinze Jürgen 
Published: March 2003

AbstractLeptothorax rugatulus, an abundant North American ant, displays a conspicuous queen size polymorphism that is related to alternative reproductive tactics. Large queens participate mainly in mating flights and found new colonies independent of their mother colony. In contrast, small queens do not found new colonies independently, but seek readoption into their natal nest which results in multiple‐queen colonies (polygyny). Populations differ strongly in the ratio of small to large queens, the prevalent reproductive tactic and colony social structure, according to ecological parameters such as nest site stability and population density. This study compares the genetic structure of two strongly differing populations within the same mountain range. Data from microsatellites and mitochondrial DNA give no evidence for alien reproductives in polygynous colonies. The incidence of alien workers in colonies (as determined by mitochondrial haplotype) was low and did not differ between monogynous and polygynous colonies. We found significant population viscosity (isolation‐by‐distance) at the mitochondrial level in only the predominantly polygynous population, which supports the theoretical prediction that female philopatry leads to mtDNA‐specific population structure. Nuclear and mitochondrial genetic diversity was similar in both populations. The genetic differentiation between the two investigated populations was moderate at the mitochondrial level, but not significantly different from zero when measured with microsatellites, which corroborates limited dispersal of females (but not males) at a larger scale.
Identification of a non‐haem catalase in Salmonella and its regulation by RpoS (σS)
Authors: Robbe‐Saule Véronique , Coynault Colette , Ibanez‐Ruiz Magdalena , Hermant Daniel , Norel Françoise 
Published: March 2003

We report the identification and functional analysis of katN, a gene encoding a non‐haem catalase of Salmonella enterica serotype Typhimurium. katN, which is not present in Escherichia coli, is located between the yciGFE and yciD E. coli homologues in the Salmonella genome. Its predicted protein product has a molecular weight of 31 826 Da and is similar to the Mn‐catalases of Lactobacillus plantarum and Thermus spp. Its product, KatN, was visualized as a 37 kDa protein in E. coli maxicells. A KatN recombinant protein, containing six histidine residues at its C‐terminus, was purified, and its catalase activity was observed on a non‐denaturing polyacrylamide gel. KatN was also visualized by catalase activity gel staining of bacterial cell extracts. Its expression was shown to be regulated by growth phase and rpoS. Northern blotting indicated that kat forms an operon with the upstream yciGFE genes. A putative rpoS‐regulated promoter was identified upstream of yciG. Southern blotting revealed that katN is conserved within Salmonella serovars. katN homologues were found in Pseudomonas aeruginosa, Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloacae and Serratia marcescens. A katN mutation did not appear to affect the hydrogen peroxide (H2O2) response of Salmonella. However, the expression of katN increased the H2O2 resistance of unadapted cells in the exponential phase and of rpoS mutants in stationary phase. Thus, KatN may contribute to hydrogen peroxide resistance in Salmonella in certain environmental conditions.
The Neisseria gonorrhoeae lpxLII gene encodes for a late‐functioning lauroyl acyl transferase, and a null mutation within the gene has a significant effect on the induction of acute inflammatory responses
Authors: Ellis Charles D. , Lindner Buko , Khan C. M. Anjam , Zähringer Ulrich , De Hormaeche Raquel Demarco 
Published: March 2003

LPS is a fundamental constituent of the outer membrane of all Gram‐negative bacteria, and the lipid A domain plays a central role in the induction of inflammatory responses. We identified genes of the Neisseria gonorrhoeae lipid A biosynthetic pathway by searching the complete gonococcal genome sequence with sequences of known enzymes from other species. The lpxLII gene was disrupted by an insertion–deletion in an attenuated aroA mutant of the gonococcal strain MS11. Lipopolysaccharide (LPS) and lipid A analysis demonstrated that the lpxLII mutant had synthesized an altered LPS molecule lacking a single lauric fatty acid residue in the GlcN II of the lipid A backbone. LPS of the lpxLII mutant had a markedly reduced ability to induce the proinflammatory cytokines tumour necrosis factor (TNF)‐α, interleukin (IL)‐1β, IL‐6 and IL‐8 from human macrophages and IL‐8 from polymorphonuclear cells. This study demonstrates that the lpxLII gene in gonococci encodes for a late‐functioning lauroyl acyl transferase that adds a lauric acid at position 2′ in the lipid A backbone. The presence of lauric acid at such a position appears to be crucial for the induction of full inflammatory responses by N. gonorrhoeae LPS.
Cryptic plasmids of Mycobacterium avium: Tn552 to the rescue
Authors: Kirby Carolyn , Waring Al , Griffin Thomas J. , Falkinham Joseph O. , Grindley Nigel D. F. , Derbyshire Keith M. 
Published: March 2003

SummaryPlasmids have been described in almost all bacterial species analysed and have proven to be essential genetic tools. In many bacteria these extrachro‐mosomal DNAs are cryptic with no known markers or function, which makes their characterization and genetic exploitation extremely difficult. Here we describe a system that will allow the rescue of any circular DNA (plasmid or phage) using an in vitro
transposition system to deliver both a selectable marker (kanamycin) and an Escherichia
coli plasmid origin of replication. In this study, we demonstrate the rescue
of four cryptic plasmids from the opportunistic pathogen Mycobacterium avium.
To evaluate the host range of the rescued plasmids, we have examined their ability
to be propagated in Mycobacterium smegmatis and Mycobacterium bovis BCG, and their compatibility with other mycobacterial plasmids. In addition, we use a library of transposon insertions to sequence one plasmid, pVT2, and to begin a genetic analysis of plasmid genes. Using this approach, we identified a putative conjugative relaxase, suggesting this myco‐bacterial plasmid is transferable, and three genes required for plasmid establishment and replication.
Functional complementation reveals the importance of intermolecular monomer interactions for Helicobacter pylori VacA vacuolating activity
Authors: Ye Dan , Blanke Steven R. 
Published: March 2003

SummaryThe Helicobacter pylori vacuolating cytotoxin (VacA) induces degenerative

vacuolation of sensitive mammalian cell lines. Although evidence is accumulating

that VacA enters cells and functions from an intracellular site of action, the biochemical

mechanism by which VacA mediates cellular vacuolation has not been established. In

this study, we used functional complementation and biochemical approaches to probe

the structure of VacA. VacA consists of two discrete fragments, p37 and p58, that

are both required for vacuolating activity. Using a transient transfection system,

we expressed genetically modified forms of VacA and identified mutations in either

p37 or p58 that inactivated the toxin. VacA with an inactivating single‐residue substitution

in the p37 domain [VacA (P9A)] functionally complemented a second mutant form of

VacA with an inactivating two‐residue deletion in the p58 domain [VacA Δ(346–347)].

VacA (P9A) and VacA Δ(346–347) also co‐immunoprecipitated from

vacuolated monolayers, supporting the hypothesis that these two inactive mutants

associate directly to function in trans. p37 and p58 interact directly when expressed as separate fragments within HeLa cells, suggesting that p37–p58 inter‐actions facilitate VacA monomer associations. Collectively, these results support a model in which the active form of VacA requires assembly into a complex of two or more monomers to elaborate toxin function.
The Sinorhizobium meliloti stringent response affects multiple aspects of symbiosis
Authors: Wells Derek H. , Long Sharon R. 
Published: March 2003

Summary Sinorhizobium meliloti and host legumes enter into a nitrogen‐fixing, symbiotic

relationship triggered by an exchange of signals between bacteria and plant. S.

meliloti produces Nod factor, which elicits the formation of nodules on plant

roots, and succinoglycan, an exopolysaccharide that allows for bacterial invasion

and colonization of the host. The biosynthesis of these molecules is well defined,

but the specific regu‐lation of these compounds is not completely understood. Bacteria

control complex regulatory networks by the production of ppGpp, the effector molecule

of the stringent response, which induces physiological change in response to adverse

growth conditions and can also control bacterial development and virulence. Through

detailed analysis of an S. meliloti mutant incapable of producing ppGpp, we

show that the stringent response is required for nodule formation and regulates the

production of succinoglycan. Although it remains unknown whether these phenotypes

are connected, we have isolated suppressor strains that restore both defects and

potentially identify key downstream regulatory genes. These results indicate that

the S. meliloti stringent response has roles in both succinoglycan production and nodule formation and, more importantly, that control of bacterial physiology in response to the plant and surrounding environment is critical to the establishment of a successful symbiosis.
Endonuclease cleavage of messenger RNA in Bacillus subtilis
Authors: Drider Djamel , DiChiara Jeanne M. , Wei Jin , Sharp Josh S. , Bechhofer David H. 
Published: March 2003

SummaryA deletion derivative of the ermC gene was constructed that expresses a

254‐nucleotide mRNA. The small size of this mRNA facilitated the detection of processing

products that did not differ greatly in size from the full‐length transcript. In

the presence of erythromycin, which induces ribosome stalling near the 5′

end of ermC mRNA, the 254‐nucleotide mRNA was cleaved endonucleolytically

at the site of ribosome stalling. Only the downstream product of this cleavage was

detectable; the upstream product was apparently too unstable to be detected. The

downstream cleavage product accumulated at times after rifampicin addition, suggesting

that the stalled ribosome at the 5′ end conferred stability to this

RNA fragment. Neither Bs‐RNase III nor RNase M5, the two known narrow‐specificity

endoribonucleases of Bacillus subtilis, was responsible for this cleavage.

These results indicate the presence in B. subtilis of another specific endoribonuclease, which may be ribosome associated.
HSF and Msn2/4p can exclusively or cooperatively activate the yeast HSP104 gene
Authors: Grably Melanie R. , Stanhill Ariel , Tell Osnat , Engelberg David 
Published: March 2003

SummaryIn an effort to understand how an accurate level of stress‐specific expression is obtained, we studied the promoter of the yeast HSP104 gene. Through 5′ deletions, we defined a 334 bp fragment upstream of the first coding AUG as sufficient and essential for maximal basal activity and a 260 bp fragment as sufficient and essential for heat shock responsiveness. These sequences contain heat shock elements (HSEs) and stress response elements (STREs) that cooperate to achieve maximal inducible expression. However, in the absence of one set of factors (e.g. in msn2Δmsn4Δ cells) proper induction is obtained exclusively through HSEs. We also show that HSP104 is constitutively derepressed in ras2Δ cells. This derepression is achieved exclusively through activation of STREs, with no role for HSEs. Strikingly, in ras2Δmsn2Δmsn4Δ cells the HSP104 promoter is also derepressed, but in this strain derepression is mediated through HSEs, showing the flexibility and adaptation of the promoter. Thus, appropriate transcription of HSP104 is usually obtained through cooperation between the Msn2/4/STRE and the HSF/ HSE systems, but each factor could activate the promoter alone, backing up the other. Transcription control of HSP104 is adaptive and robust, ensuring proper expression under extreme conditions and in various mutants.
Expression, mutagenesis and kinetic analysis of recombinant K1E endosialidase to define the site of proteolytic processing and requirements for catalysis
Authors: Leggate Daniel R. , Bryant J. Mark , Redpath Maria B. , Head Denise , Taylor Peter W. , Luzio J. Paul 
Published: March 2003

SummaryCatalytically active, recombinant fusion proteins of bacteriophage E endosialidase were expressed and purified fromEscherichia coli. Constructs with different fusion partners added to the amino terminus of the endosialidase were enzymatically active. A post‐translational proteolytic cleavage was shown to occur between serine 706 and aspartate 707 to generate the 76 kDa mature enzyme from the 90 kDa translation product. Endosialidase truncated at the C‐terminus from aspartate 707 was observed to have the same 76 kDa molecular weight as wild‐type enzyme using denaturing SDS–PAGE but, under native PAGE conditions, was not observed to form the≈250 kDa trimeric wild‐type enzyme, implying that the C‐terminus of the enzyme may be required for correct assembly of active trimer, rather than as part of the active site as has been previously suggested. Mutagenesis of aspartate 138 to alanine greatly reduced enzyme activity whereas conversion of other selected aspartate residues to alanine had less effect, consistent with similarities between the structure and cata‐lytic mechanism of bacteriophage E endosialidase and those of exosialidases.
Pyruvate kinase fromChlamydia trachomatisis activated by fructose‐2,6‐bisphosphate
Authors: Iliffe‐Lee Emma R. , McClarty Grant 
Published: March 2003

SummaryPyruvate kinase is the final regulatory point in the catabolic Embden–Meyerhoff–Parnas pathway, which controls the carbon flux of glycolytic intermediates and regulates the level of ATP in the cell. In a previous study, we identified, cloned and sequenced pyruvate kinase from the obligate intracellular bacteriumChlamydia trachomatisand demonstrated that the enzyme was active in crude extract. Here, we report the kinetic properties of highly purifiedC. tracho‐matispyruvate kinase. The results indicate thatC. trachomatispyruvate kinase is 53.5 kDa with a pH optima of 7.3. Kinetic studies show thatC. trachomatispyruvate kinase requires both K+and Mg2+ions for activity, exhibits sigmoidal kinetics with respect to phosphoenolpyruvate and Michaelis–Menten kinetics with respect to ADP. In addition,C. trachomatispyruvate kinase is able to use alternative nucleoside diphosphates as phosphate acceptors, although it shows the greatest activity with ADP. In contrast to other bacterial pyruvate kinases that are activated by AMP, our data show that AMP, in addition to ATP and GTP, inhibitsC. trachomatispyruvate kinase. Surprisingly, unlike any other known bacterial pyruvate kinase,C. trachomatispyruvate kinase was alloste‐rically activated by fructose‐2,6‐bisphosphate, an important regulatory metabolite that has only been reported in eukaryotes.
Bacterial conjugative transfer: visualization of successful mating pairs and plasmid establishment in live Escherichia coli
Authors: Lawley Trevor D. , Gordon G. Scott , Wright Andrew , Taylor Diane E. 
Published: March 2003

SummaryWe used the LacO/GFP–LacI system to label and visualize the IncPβ plasmid R751 fluorescently during conjugative transfer between live donor and recipient bacteria. Comparisons of R751 in conjugative and non‐conjugative conditions have allowed us to identify key localizations and movements associated with the initiation of conjugative transfer in the donor and the establishment of R751 in the recipient. A survey of successful mating pairs demonstrates that close physical contact between donor and recipient bacteria is required for DNA transfer and that regions of intimate contact can occur at any location on the donor or recipient cell membrane. The transferred DNA is positioned at the characteristic centre or quarter‐cell position after conversion to a double‐stranded molecule in the recipient cell. Initial duplication of plasmids often results in an asymmetric distribution of plasmid foci. Symmetric localization (either at centre or at 1/4 and 3/4 cell lengths) occurs only after a significant lag, presumably reflecting the time required to synthesize the plasmid‐encoded partitioning proteins.