bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population genetics of shortnose sturgeon Acipenser brevirostrum based on mitochondrial DNA control region sequences
Authors: Grunwald C. , Stabile J. , Waldman J. R. , Gross R. , Wirgin I. 
Published: March 2003

AbstractShortnose sturgeon is an anadromous North American acipenserid that since 1973 has been designated as federally endangered in US waters. Historically, shortnose sturgeon occurred in as many as 19 rivers from the St. John River, NB, to the St. Johns River, FL, and these populations ranged in census size from 101 to 104, but little is known of their population structure or levels of gene flow. We used the polymerase chain reaction (PCR) and direct sequence analysis of a 440 bp portion of the mitochondrial DNA (mtDNA) control region to address these issues and to compare haplotype diversity with population size. Twenty‐nine mtDNA nucleotide‐substitution haplotypes were revealed among 275 specimens from 11 rivers and estuaries. Additionally, mtDNA length variation (6 haplotypes) and heteroplasmy (2–5 haplotypes for some individuals) were found. Significant genetic differentiation (P < 0.05) of mtDNA nucleotide‐substitution haplotypes and length‐variant haplotypes was observed among populations from all rivers and estuaries surveyed with the exception of the Delaware River and Chesapeake Bay collections. Significant haplotype differentiation was even observed between samples from two rivers (Kennebec and Androscoggin) within the Kennebec River drainage. The absence of haplotype frequency differences between samples from the Delaware River and Chesapeake Bay reflects a probable current absence of spawning within the Chesapeake Bay system and immigration of fish from the adjoining Delaware River. Haplotypic diversity indices ranged between 0.817 and 0.641; no relationship (P > 0.05) was found between haplotype diversity and census size. Gene flow estimates among populations were often low (< 2.0), but were generally higher at the latitudinal extremes of their distribution. A moderate level of haplotype diversity and a high percentage (37.9%) of haplotypes unique to the northern, once‐glaciated region suggests that northern populations survived the Pleistocene in a northern refugium. Analysis of molecular variance best supported a five‐region hierarchical grouping of populations, but our results indicate that in almost all cases populations of shortnose sturgeon should be managed as separate units.
Extreme genetic differentiation among the remnant populations of marble trout (Salmo marmoratus) in Slovenia
Authors: Fumagalli L. , Snoj A. , Jesenšek D. , Balloux F. , Jug T. , Duron O. , Brossier F. , Crivelli A. J. , Berrebi P. 
Published: March 2003

AbstractPopulations of the marble trout (Salmo marmoratus) have declined critically due to introgression by brown trout (Salmo trutta) strains. In order to define strategies for long‐term conservation, we examined the genetic structure of the 8 known pure populations using 15 microsatellite loci. The analyses reveal extraordinarily strong genetic differentiation among populations separated by < 15 km, and extremely low levels of intrapopulation genetic variability. As natural recolonization seems highly unlikely, appropriate management and conservation strategies should comprise the reintroduction of pure populations from mixed stocks (translocation) to avoid further loss of genetic diversity.
A simulated annealing approach to define the genetic structure of populations
Authors: Dupanloup I. , Schneider S. , Excoffier L. 
Published: March 2003

AbstractWe present a new approach for defining groups of populations that are geographically homogeneous and maximally differentiated from each other. As a by‐product, it also leads to the identification of genetic barriers between these groups. The method is based on a simulated annealing procedure that aims to maximize the proportion of total genetic variance due to differences between groups of populations (spatial analysis of molecular variance;samova). Monte Carlo simulations were used to study the performance of our approach and, for comparison, the behaviour of the Monmonier algorithm, a procedure commonly used to identify zones of sharp genetic changes in a geographical area. Simulations showed that thesamovaalgorithm indeed finds maximally differentiated groups, which do not always correspond to the simulated group structure in the presence of isolation by distance, especially when data from a single locus are available. In this case, the Monmonier algorithm seems slightly better at finding predefined genetic barriers, but can often lead to the definition of groups of populations not differentiated genetically. Thesamovaalgorithm was then applied to a set of European roe deer populations examined for their mitochondrial DNA (mtDNA) HVRI diversity. The inferred genetic structure seemed to confirm the hypothesis that some Italian populations were recently reintroduced from a Balkanic stock, as well as the differentiation of groups of populations possibly due to the postglacial recolonization of Europe or the action of a specific barrier to gene flow.
Genetic mating system and the significance of harem associations in the bat Saccopteryx bilineata
Authors: Heckel Gerald , Von Helversen Otto 
Published: March 2003

AbstractWe analysed the polygynous mating system of the bat Saccopteryx bilineata using behaviour observations and genetic data on 11 microsatellite DNA loci. Basic social units in S. bilineata are harem groups that consist of single males and up to eight females. Colonies comprise several harem groups, and the composition of colonies and harems is often stable over several reproductive seasons. The combination of parentage exclusion and likelihood‐based parentage assignment in this study produced detailed parentage information for a large colony of S. bilineata. Reproduction occurred mostly within the colony (17% extra‐colony paternity), but social associations in harems within the colony did not represent reproductive units (70% extra‐harem paternity). The latter finding was consistent over three reproductive seasons. Spatial association of the roosting sites of males and females could not explain parentage patterns in the colony. Even though intra‐harem paternity was less frequent than expected, it contributed significantly to reproduction of harem males. On average, the number of offspring sired by a male with females in his harem territory increased significantly with harem size, which corresponds to the higher energetic investment that is related to the maintenance of large harems. However, extra‐harem paternity was not correlated with a male's harem size or intra‐harem reproductive success. This suggests that individual preferences of females rather than male traits associated with the ability to defend large harems are most likely to cause the detected differences between social association and genetic mating system.
Impact of oilseed rape expressing the insecticidal cysteine protease inhibitor oryzacystatin on the beneficial predator Harmonia axyridis (multicoloured Asian ladybeetle)
Authors: Ferry N. , Raemaekers R. J. M. , Majerus M. E. N. , Jouanin L. , Port G. , Gatehouse J. A. , Gatehouse A. M. R. 
Published: March 2003

AbstractInsect‐resistant transgenic plants have been suggested to have deleterious effects on beneficial predators through transmission of the transgene product by the pest to the predator. To test this hypothesis, effects of oilseed rape expressing the cysteine protease inhibitor oryzacystatin‐1 (OC‐1) on the predatory ladybird Harmonia axyridis were investigated using diamondback moth Plutella xylostella as the pest species. As expected, oilseed rape expressing OC‐1 had no effects on either development or survival of the pest, which utilizes serine digestive proteases. Immunoassays confirmed accumulation of the transgene product in pest larval tissues at levels of up to 3 ng per gut. Characterization of proteolytic digestive enzymes of H. axyridis demonstrated that larvae and adults utilize cysteine and aspartic proteases; the former activity was completely inhibited by oryzacystatin in vitro. However, when H. axyridis larvae consumed prey reared on OC‐1 expressing plants over their entire life cycle, no significant effects upon survival or overall development were observed. The inhibitor initially stimulated development, with a shortening of the developmental period of the second instar by 27% (P < 0.0001) accompanied by a 36% increase in weight of second instar larvae (P = 0.007). OC‐1 had no detrimental effects on reproductive fitness of adult H. axyridis. Interestingly there was a significant increase in consumption of OC‐1 dosed prey. The results show that prey reared on transgenic plants expressing a protein which inhibited ladybird digestive enzymes in vitro had no effects in vivo; the ladybird was able to up‐regulate digestive proteases in response to the inhibitor.
Glacial refugia, haplotype distributions, and clonal richness of the Daphnia pulex complex in arctic Canada
Authors: Weider L. J. , Hobæk A. 
Published: March 2003

AbstractAs part of a large international Arctic biodiversity expedition (Tundra Northwest ′99), we examined the distribution of members of the arctic Daphnia pulex complex (Cladocera, Anomopoda) from 121 tundra ponds, spread across 16 sites spanning a large portion of arctic Canada (i.e. from 62°22′ N to 79°01′ N; 66°45′ W to 139°37′ W). Using allozyme electrophoresis and mitochondrial (mt)DNA analyses, we examined the population genetic (clonal) structure of these populations. The following taxa were detected in this complex: Daphnia pulicaria, D. middendorffiana and D. tenebrosa. Clear geographical differences in mean clonal richness and diversity were observed, with most western sites exhibiting higher clonal richness and diversity, than sites in the eastern Canadian Arctic. For both the pulicaria group (i.e. D. pulicaria and D. middendorffiana) and D. tenebrosa, the highest mean regional clonal richness was detected from the southern section of Banks Island, an unglaciated site situated on the edge or directly in the eastern fringe of the Beringian glacial refuge. A significant negative correlation was found between geographical distance from the Beringian edge, and overall regional clonal richness (i.e. sites closer to the edge harboured greater clonal richness). These results clearly indicate that more recently deglaciated regions (i.e. eastern Canadian Arctic) harbour lower levels of clonal richness than western regions nearer Beringia. We discuss the role that glacial refugia have played in influencing both biotic and genetic diversity in arctic taxa.
Identification and characterization of spdR mutations that bypass the BsgA protease‐dependent regulation of developmental gene expression in Myxococcus xanthus
Authors: Hager Elizabeth , Tse Hubert , Gill Ronald E. 
Published: March 2003

The BsgA protease of Myxococcus xanthus is an intracellular protease closely related to the Lon protease of Escherichia coli. BsgA is required for normal levels of developmentally induced gene expression. In this report, we describe the identification of mutations that suppress the developmental defect of bsgA mutants. These mutations localized to the spdR gene (suppressor protease deficiency regulator) that appears to play a role in the regulation of early developmental gene expression. Mutations in spdR fully restored the ability of a bsgA mutant to form fruiting bodies and spores and, with one exception, restored the expression of several development‐specific lacZ fusions. spdR mutants exhibited characteristic phenotypic properties including increased expression of the development‐specific tps gene during vegetative growth, formation of fruiting bodies and spores on semi‐rich nutrient medium and completion of starvation‐induced development in a shorter time period than wild‐type strains. The spdR locus was cloned and sequenced and found to encode a member of the NtrC family of two‐component transcriptional regulators. One interpretation of these data is that SpdR acts, directly or otherwise, to regulate developmental gene expression negatively and that the BsgA protease is required to relieve this inhibitory effect at the onset of development. However, Western immunoblot analysis indicated that SpdR is present at a relatively constant level during growth and early development in both wild‐type and BsgA protease‐deficient cells. This finding suggests that BsgA does not function to degrade SpdR at the onset of development.
CspD, a novel DNA replication inhibitor induced during the stationary phase in Escherichia coli
Authors: Yamanaka Kunitoshi , Zheng Weidong , Crooke Elliott , Wang Yuh‐Hwa , Inouye Masayori 
Published: March 2003

CspD is a stationary phase‐induced, stress response protein in the CspA family of Escherichia coli. Here, we demonstrate that overproduction of CspD is lethal, with the cells displaying a morphology typical of cells with impaired DNA replication. CspD consists mainly of β‐strands, and the purified protein exists exclusively as a dimer and binds to single‐stranded (ss)DNA and RNA in a dose‐dependent manner without apparent sequence specificity. CsdD effectively inhibits both the initiation and the elongation steps of minichromosome replication in vitro. Electron microscopic studies revealed that CspD tightly packs ssDNA, resulting in structures distinctly different from those of SSB‐coated DNA. We propose that CspD dimers, with two independent β‐sheets interacting with ssDNA, function as a novel inhibitor of DNA replication and play a regulatory role in chromosomal replication in nutrient‐depleted cells.
Large‐scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid‐associated protein, H‐NS
Authors: Hommais Florence , Krin Evelyne , Laurent‐Winter Christine , Soutourina Olga , Malpertuy Alain , Le Caer Jean‐Pierre , Danchin Antoine , Bertin Philippe 
Published: March 2003

Despite many years of intense work investigating the function of nucleoid‐associated proteins in prokaryotes, their role in bacterial physiology remains largely unknown. The two‐dimensional protein patterns were compared and expression profiling was carried out on H‐NS‐deficient and wild‐type strains of Escherichia coli K‐12. The expression of approximately 5% of the genes and/or the accumulation of their protein was directly or indirectly altered in the hns mutant strain. About one‐fifth of these genes encode proteins that are involved in transcription or translation and one‐third are known to or were in silico predicted to encode cell envelope components or proteins that are usually involved in bacterial adaptation to changes in environmental conditions. The increased expression of several genes in the mutant resulted in a better ability of this strain to survive at low pH and high osmolarity than the wild‐type strain. In particular, the putative regulator, YhiX, plays a central role in the H‐NS control of genes required in the glutamate‐dependent acid stress response. These results suggest that there is a strong relationship between the H‐NS regulon and the maintenance of intracellular homeostasis.
Escherichia coli P fimbriae utilize the Toll‐like receptor 4 pathway for cell activation
Authors: Frendéus Björn , Wachtler Caroline , Hedlund Maria , Fischer Hans , Samuelsson Patrik , Svensson Majlis , Svanborg Catharina 
Published: March 2003

Fimbriae mediate bacterial attachment to host cells and provide a mechanism for tissue attack. They activate a host response by delivery of microbial products such as lipopolysaccharide (LPS) or through direct fimbriae‐dependent signalling mechanisms. By coupling to glycosphingolipid (GSL) receptors, P fimbriae trigger cytokine responses in CD14 negative host cells. Here we show that P fimbriae utilize the Toll‐like receptor 4 (TLR4)‐dependent pathway to trigger mucosal inflammation. Escherichia coli strains expressing P fimbriae as their only virulence factor stimulated chemokine and neutrophil responses in the urinary tract of TLR4 proficient mice, but TLR4 defective mice failed to respond to infection. Mucosal cells were CD14 negative but expressed several TLR species including TLR4, and TLR4 protein was detected. Infection with P fimbriated bacteria stimulated an increase in TLR4 mRNA levels. The activation signal did not involve the LPS‐CD14 pathway and was independent of lipid A myristoylation, as shown by mutational inactivation of the msbB gene. Co‐staining experiments revealed that TLR4 and the GSL receptors for P fimbriae co‐localized in the cell membrane. The results demonstrate that P fimbriae activate epithelial cells by means of a TLR4‐dependent signalling pathway, and suggest that GSL receptors for P fimbriae can recruit TLR4 as co‐receptors.
The adhesive property of the type IV pilus‐associated component PilC1 of pathogenic Neisseria is supported by the conformational structure of the N‐terminal part of the molecule
Authors: Morand Philippe C. , Tattevin Pierre , Eugene Emmanuel , Beretti Jean‐Luc , Nassif Xavier 
Published: March 2003

Neisserial PilC proteins are key elements in type IV pili biogenesis and adhesion. Two pilC alleles are usually present in Neisseria meningitidis. At least one of the PilC proteins is required for pilus assembly and competence for transformation. In addition, meningococcal PilC1, but not PilC2, modulates adhesiveness, whereas, in N. gonorrhoeae, both alleles are adhesive. The meningococcal pilC genes are differently regulated, and it was shown that the expression of pilC1, but not that of pilC2, is transiently induced by bacteria–cell contact. The aim of this work was to determine whether, besides regulation, PilC1‐mediated adhesion was conferred by some specific protein pattern not present in the meningococcal PilC2 protein. We demonstrate first that differences within the primary sequence of the meningococcal PilC1 and PilC2 are responsible for different adhesion phenotypes, thus eliminating the regulation of transcription being solely responsible for the adhesive phenotype of PilC1. To identify the regions of PilC1 responsible for adhesion, we engineered meningococcal strains expressing various PilC1–PilC2 hybrids at the pilC1 locus. Our data demonstrate that the specific PilC1 adhesion‐promoting regions are located in the amino‐terminal part of the molecule and that several domains within this region probably interact with each other to promote adhesion to human cells.
Light‐induced carotenogenesis inMyxococcus xanthus: evidence that CarS acts as an anti‐repressor of CarA
Authors: Whitworth David E. , Hodgson David A. 
Published: March 2003

In the bacteriumMyxococcus xanthus, carotenoids are produced in response to illumination, as a result of expression of thecrtcarotenoid biosynthesis genes. The majority ofcrtgenes are clustered in thecrtEBDCoperon, which is repressed in the dark by CarA. Genetic data suggest that, in the light, CarS is synthesized and achieves activation of thecrtEBDCoperon by removing the repressive action of CarA. As CarS contains no known DNA‐binding motif, the relief of CarA‐mediated repression was postulated to result from a direct interaction between these two proteins. Use of the yeast two‐hybrid system demonstrated direct interaction between CarA and CarS. The two‐hybrid system also implied that CarA and, possibly, CarS are capable of homodimerization. Direct evidence for CarS anti‐repressor action was providedin vitro. A glutathioneS‐transferase (GST)–CarA protein fusion was shown to bind specifically to a palindromic operator sequence within thecrtEBDCpromoter. CarA was prevented from binding to its operator, and prebound CarA was removed by the addition of purified CarS. CarS is therefore an anti‐repressor.
Clostridial VirR/VirS regulon involves a regulatory RNA molecule for expression of toxins
Authors: Shimizu Tohru , Yaguchi Harumi , Ohtani Kaori , Banu Sayera , Hayashi Hideo 
Published: March 2003

SummaryWe analysed the region encoding VR‐RNA (VirR‐regulated RNA), which has been reported to be positively regulated by the two‐component VirR/VirS system in Clostridium perfringens. The VR‐RNA promoter identified by primer extension analysis was preceded by a probable VirR‐binding site (CCAGTTNNNCAC), which resembled a repeated sequence motif present in the promoter region of the theta‐toxin (pfoA) gene. A VR‐RNA‐null mutant, constructed by a homologous recombination, exhibited a reduced amount of transcription of the alpha‐ (plc) and kappa‐toxin (colA) genes, which was restored by the complementation of intact VR‐RNA, indicating that the VR‐RNA region plays an important role in the regulation of the plc and colA genes in C. perfringens. It was found that the regulatory effect was observed even when the hyp7 gene encoded on VR‐RNA was deleted or a nonsense mutation was introduced in the hyp7‐coding region. We found that the small 3′‐portion of VR‐RNA was sufficient for the activation of toxin genes, which suggested that VR‐RNA itself could act as an RNA regulatory molecule for the plc and colA genes mediating the regulatory information from the VirR/VirS system in C. perfringens.
Analysis of the kefA2 mutation suggests that KefA is a cation‐specific channel involved in osmotic adaptation in Escherichia coli
Authors: McLaggan Debra , Jones Michael A. , Gouesbet Gwenola , Levina Natasha , Lindey Susanna , Epstein Wolfgang , Booth Ian R. 
Published: March 2003

SummaryMechanosensitive channels play an essential role in the regulation of turgor pressure in bacteria. In Escherichia coli, there are multiple mechanosensitive channels that have been characterized genetically: MscL, YggB and KefA. In this report, we describe the cloning of the kefA gene, the organization of the KefA protein and the phenotype of a missense mutation, kefA, which affects the KefA mechanosensitive channel. The altered function of the channel is manifest through increased sensitivity to K+ during growth at low osmolarity and complete inhibition of growth in media containing high K+ concentrations (0.6 M) in the presence of betaine or proline. Growth in high Na+ medium (0.6 M NaCl plus 20 mM K+) is normal. Analysis of the cytoplasmic pools shows that the mutant cannot regulate the K+ content of the cytoplasm when grown in high K+ medium. However, regulation of pools of amino acids is essentially normal and the mutant can accumulate high pools of proline during growth inhibition. The mutant shows increased sensitivity to acid hypo‐osmotic shock (transition from neutral to acid pH combined with a reduction in osmolarity). The data are consistent with abnormal regulation of KefA in the presence of high K+ concentrations and either betaine or proline.
Functional genomics reveals the sole sulphate transporter of the Mycobacterium tuberculosis complex and its relevance to the acquisition of sulphur in vivo
Authors: Wooff Esen , Michell Stephen Ll. , Gordon Stephen V. , Chambers Mark A. , Bardarov Stoyan , Jacobs William R. , Hewinson R. Glyn , Wheeler Paul R. 
Published: March 2003

SummarySulphur is essential for some of the most vital biological activities such as translation initiation and redox maintenance, and genes involved in sulphur metabolism have been implicated in virulence. Mycobacterium tuberculosis has three predicted genes for the prototrophic acquisition of sulphur as sulphate: cysA, part of an ABC transporter, and cysA2 and A3, SseC sulphotransferases. Screening for amino acid auxotrophs of Mycobacterium bovis BCG, obtained by transposon mutagenesis, was used to select methionine auxotrophs requiring a sulphur‐containing amino acid for growth. We have characterized one of these auxotrophs as being disrupted in cysA. Both the cysA mutant and a previously identified mutant in an upstream gene, subI, were functionally characterized as being completely unable to take up sulphate. Complementation of the cysA mutant with the wild‐type gene from M. tuberculosis restored prototrophy and the ability to take up sulphate with the functional characteristics of an ABC transporter. Hence, it appears that this is the sole locus encoding inorganic sulphur transport in the M. tuberculosis complex