bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predictive modelling and spatial mapping of freshwater fish and decapod assemblages using GIS and neural networks
Authors: Joy Michael K. , Death Russell G. 
Published: July 2004

Summary1. We used stream fish and decapod spatial occurrence data extracted from a national database and recent surveys with geospatial landuse data, geomorphologic, climatic, and spatial data in a geographical information system (GIS) to model fish and decapod occurrence in the Wellington Region, New Zealand.2. To predict the occurrence of each species at a site from a common set of predictor variables we used a multi‐response, artificial neural network (ANN), to produce a single model that predicted the entire fish and decapod assemblage in one procedure.3. The predictions from the ANN using this landscape scale data proved very accurate based on evaluation metrics that are independent of species abundance or probability thresholds. The important variables contributing to the predictions included the latitudinal and elevational position of the site reach, catchment area, average air temperature, the vegetation type, landuse proportions of the catchment, and catchment geology.4. Geospatial data available for the entire regional river network were then used to create a habitat‐suitability map for all 14 species over the regional river network using a GIS. This prediction map has many potential uses including: monitoring and predicting temporal changes in fish communities caused by human activities and shifts in climate, identifying areas in need of protection, biodiversity hotspots, and areas suitable for the reintroduction of endangered or rare species.
Phylogeography of Trochodendron aralioides (Trochodendraceae) in Taiwan and its adjacent areas
Authors: Huang Shing‐Fan , Hwang Shih‐Ying , Wang Jenn‐Che , Lin Tsan‐Piao 
Published: July 2004

AbstractAim  This paper described current phylogeographical patterns of chloroplastic DNA variation of Trochodendron aralioides, a temperate tree species, and inferred its possible refugium in Taiwan. This information was compared with the known phylogeographical pattern of subtropical tree species.Location  A total of 24 populations were sampled including 20 from Taiwan, two each from the Ryukyus and Japan.Methods  A haplotype network was constructed by computer program TCS, various parameters of genetic diversity were calculated and neutrality was tested by computer program DnaSP. To examine the similarity of genetic structure among populations, a maximum parsimony tree was reconstructed by computer program PAUP*. The results of isozyme of T. aralioides from a previous publication were incorporated into this study to infer the phylogeographical history.Results  Nine haplotypes according to six substitutions, two indels and one inversion of the two cpDNA intergenic spacer fragments (petG‐trnP and petA‐psbJ) of T. aralioides were recognized. Genetic structure of the population of Japan is totally different from those of Taiwan and the Ryukyus. In Taiwan, the genetic structure was differentiated among populations revealed by Gst = 0.700 and Nst = 0.542, and the population genetics was clearly spatially structured. Two population groups were recognized. The first group was distributed islandwide and extended to the Ryukyus. The second group contained five of the seven known haplotypes, and was restricted to the area between latitude 24°46′ and 24°06′ N.Conclusions  In Taiwan, north‐central area between latitude 24°46′ and 24°06′ N is potentially a refugium during the last glaciations. This finding is contradicted to subtropical species as Cyclobalanopsis glauca.
Austro‐boreal disjunctions: a remarkable biogeographical pattern illustrated by Nan Ao Island, Guangdong, China
Authors: Lazell James 
Published: July 2004

AbstractAim  To document disjunct, insular populations of animals separated from similar conspecifics distributed to the north, inland and upland, and compare this pattern with that historically described for northern Florida and the Florida Keys islands.Location  Nan Ao Island is on the Tropic of Cancer 117° E in the South China Sea, eastern Guangdong Province, China. There are archipelagos of islets extending south‐east, and several coastal islets around Nan Ao.Methods  Five field surveys were made in 1999–2001. Voucher specimens were tagged, catalogued, and deposited in major museum collections. The comparable Floridian disjunct pattern was researched and described in overview.Results  Five species – a toad, two lizards and two snakes – collected on Nan Ao and three satellite islands were added to the two previously documented species – a lizard and a snake – that fit the austro‐boreal disjunct pattern. One lizard and one snake are minor range extensions of a hundred or few km. One snake's Nan Ao population is disjunct by about 450 km and one lizard's by about 550 km. The small, semi‐fossorial, short‐legged toad is the most notable, separated from the main area of its range by about 800 km. This is similar to the greatest distance between north Floridian and Keys disjunct populations.Main conclusions  (1) Seven Nan Ao species of terrestrial vertebrates are isolated and disjunct from conspecifics found to the north, upland and inland; this compares to five species showing a similar north Florida to Florida Keys pattern. (2) The Nan Ao species have no conspecifics known from the intervening area whereas four of the five Floridian species have conspecific, but dissimilar, populations in the gap. (3) Nan Ao and its satellite islets were high points on a large coastal plain at glacial maximum. (4) Holocene sea level rise and concomitant global warming may have isolated the Nan Ao relicts that had continuous distributions at glacial maximum. (5) The intervening mainland conspecific populations may have been replaced by tropical species that moved north along the mainland but failed to colonize the islands. (6) If so, significant adaptation to a warmer climate must have occurred to enable survival of the Nan Ao relicts to the present.
Should we use proportional sampling for species–area studies?
Authors: Schoereder José H. , Galbiati Carla , Ribas Carla R. , Sobrinho Tathiana G. , Sperber Carlos F. , DeSouza Og , Lopes‐Andrade Cristiano 
Published: July 2004

AbstractAim  In this paper we aim to show that proportional sampling can detect species–area relationships (SARs) more effectively than uniform sampling. We tested the contribution of alpha and beta diversity in ant communities as explanations for the SAR.Location  Tropical forest remnants in Viçosa, Minas Gerais, Brazil (20 °45′ S, 42 °50′ W).Methods  We sampled 17 forest remnants with proportional sampling. To disentangle sampling effects from other mechanisms, species richness was fitted in a model with remnant size, number of samples (sampling effects) and an interaction term.Results  A SAR was observed independent of the number of samples, discarding sampling effects. Alpha diversity was not influenced by remnant size, and beta diversity increased with remnant size; evidence to the fact that habitat diversity within remnants could be the dominant cause of the SAR. Such a relationship between beta diversity and remnant area may have also arisen due to the combined effects of territoriality and aggregation of ant species.Main conclusions  The proposed model, together with proportional sampling, allowed the distinction between sampling effects and other mechanisms.
Relative effects of climate change, isolation and competition on body‐size evolution in the Japanese field mouse, Apodemus argenteus
Authors: Millien Virginie 
Published: July 2004

AbstractAim  This paper examines body size variation in both recent and Quaternary populations of the Japanese field mouse Apodemus argenteus in order to assess the relative effects on body size of climate change, isolation and competitive interactions with its congeneric A. speciosus. Both temporal (since the Last Glacial Maximum, LGM) and spatial (over the Japanese archipelago) scales are considered.Location  The small field mouse is widespread in Japan, and the specimens examined were collected from 10 localities on islands of widely differing area (from 4 km2 to 230,510 km2) and at latitudes ranging from 30.3° N to 45.1° N.Methods  The effects of geographical factors such as latitude and island area on the size variation of A. argenteus were investigated, using the lower incisor size. In addition, the size of some specimens from two Quaternary localities was compared with the size of the extant specimens. Evolutionary rates of size change since the LGM were calculated in darwins. Hutchinson size ratios were used to examine the pattern of variation of the size segregation between the two Japanese field mice, A. argenteus and A. speciosus, in relation to time and space.Results  There was a negative relationship between size and latitude among living A. argenteus populations. In addition, there was no effect of island area on body size, especially at higher latitudes. At lower latitudes, A. argenteus were larger on smaller islands, although this trend was not statistically significant. Quaternary specimens of A. argenteus were smaller in size than their living representatives. The interspecific size ratio between the two Japanese Apodemus was larger on smaller islands and at higher latitudes, and there has been a decrease in the size ratio between the two Apodemus since the LGM. Lastly, in accordance with the theory of character displacement, the small A. argenteus was larger in allopatry than in sympatry, whereas the large A. speciosus was smaller in allopatry than in sympatry.Main conclusions  These results indicate that A. argenteus does not conform to Bergmann's rule or to the island rule. The variation in size for the small Japanese field mouse at both spatial and temporal scales may be related to climate change, with an additional effect of competition with the large field mouse, especially on smaller islands. The size convergence between the two Japanese Apodemus observed over the last 21,000 years may be explained by the diminution of available food resources due to the reduction of land mass areas following the LGM. It may also be the result of an evolution towards an optimal body size; a hypothesis previously proposed to explain the evolution of body size in island mammals. Lastly, the evolutionary rates of body size calculated for A. argenteus since the LGM are typical of rates calculated for other Quaternary mainland mammals, thus suggesting that the evolution in this species was not particularly rapid, as is often thought for island mammals.
Investigating the role of secA2 in secretion and glycosylation of a fimbrial adhesin in Streptococcus parasanguis FW213
Authors: Chen Qiang , Wu Hui , Fives‐Taylor Paula M. 
Published: July 2004

SummaryAdhesion of Streptococcus parasanguis FW213, a primary colonizer, to the tooth surface is mediated mainly by peritrichous long fimbriae. The fimbrial structural unit, Fap1, is indispensable for fimbriae biogenesis, adhesion to an in vitro tooth model and biofilm formation. Mature Fap1 is a glycoprotein with an apparent molecular mass of 200 kDa. Glycosylated Fap1 is not present in some mutants screened from a transposon mutant library. Localization of the transposition sites revealed a gene determined to be secA2, which is distinct from the canonical secA gene. In FW213, glycosylated Fap1 was present in all the subcellular fractions including the cytoplasm. In VT1574, a non‐polar mutant of secA2 generated by in frame deletion, Fap1 was not secreted. Glycosylated Fap1 was present in the membrane and cytoplasm of the mutant, although in greatly reduced amounts. Fap1 secretion and abundance were restored when VT1574 was complemented by a plasmid‐borne secA2. The secretion defect of the secA2 mutation appears to be limited to a small group of proteins such as Fap1 and FimA. These data suggested that Fap1 secretion rather than glycosylation was the major effect of the deletion of secA2; however, this deletion also had an impact on Fap1 abundance. Two more secA2 mutants with different regions deleted were tested for their ability to secrete Fap1. One mutant was completely unable to secrete Fap1 while the other was able to secrete, but in a decreased amount. These data suggest that the region deleted in the latter mutant (nucleotides 2032–2337) is dispensable for Fap1 secretion.
Cyclic diguanylate (c‐di‐GMP) regulates Vibrio cholerae biofilm formation
Authors: Tischler Anna D. , Camilli Andrew 
Published: July 2004

SummaryWhile studying virulence gene regulation in Vibrio cholerae during infection of the host small intestine, we identified VieA as a two‐component response regulator that contributes to activating expression of cholera toxin. Here we report that VieA represses transcription of Vibrio exopolysaccharide synthesis (vps) genes involved in biofilm formation by a mechanism independent of its phosphorelay and DNA‐binding activities. VieA controls the intracellular concentration of the cyclic nucleotide second messenger cyclic diguanylate (c‐di‐GMP) using an EAL domain that functions as a c‐di‐GMP phosphodiesterase. Two‐dimensional thin layer chromatography of nucleotide extracts confirmed that VieA reduces the concentration of c‐di‐GMP, opposing the action of  c‐di‐GMP synthetase proteins. Expression of unrelated V. cholerae c‐di‐GMP synthetase or phosphodiesterae proteins also modulated c‐di‐GMP concentration and vps gene expression. We propose that c‐di‐GMP synthetase and phosphodiesterase domain‐containing proteins contribute to regulating biofilm formation by controlling c‐di‐GMP concentration.
Light matters: phototaxis and signal transduction in unicellular cyanobacteria
Authors: Bhaya Devaki 
Published: July 2004

SummaryMany photosynthetic microorganisms have evolved the ability to sense light quality and/or quantity and can steer themselves into optimal conditions within the environment. Phototaxis and gliding motility in unicellular cyanobacteria require type IV pili, which are multifunctional cell surface appendages. Screens for cells exhibiting aberrant motility uncovered several non‐motile mutants as well as some that had lost positive phototaxis (consequently, they were negatively phototactic). Several negatively phototactic mutants mapped to the tax1 locus, which contains five chemotaxis‐like genes. This locus includes a gene that encodes a putative photoreceptor (TaxD1) for positive phototaxis. A second chemotaxis‐like cluster (tax3 locus) appears to be involved in pilus biogenesis. The biosynthesis and regulation of type IV pilus‐based motility as well as the communication between the pilus motor and photosensory molecules appear to be complex and tightly regulated. Furthermore, the discovery that cyclic AMP and novel gene products are necessary for phototaxis/motility suggests that there might be additional levels of communication and signal processing.
Identification of activating region (AR) of Escherichia coli LysR‐type transcription factor CysB and CysB contact site on RNA polymerase alpha subunit at the cysP promoter
Authors: Lochowska Anna , Iwanicka‐Nowicka Roksana , Zaim Jolanta , Witkowska‐Zimny Malgorzata , Bolewska Krystyna , Hryniewicz Monika M. 
Published: July 2004

SummaryCysB is a LysR‐type transcriptional regulator (LTTR) controlling the expression of numerous genes involved in bacterial sulphur assimilation via cysteine biosynthesis. Our previous mutational analysis of CysB identified several residues within the N‐terminal domain crucial for DNA‐binding function. Here, we focus on the functional significance of CysB residues localized in the turn between the α2 and α3 helices forming an N‐terminal helix–turn–helix motif. On the basis of the characteristics of alanine‐substituted mutants, we propose that CysB residues Y27, T28 and S29, lying in this turn region, comprise an ‘activating region’ (AR) that is crucial for positive control of the cysP promoter, but not for DNA binding and inducer response activities of CysB. Using a library of alanine substitutions in the C‐terminal domain of the RNAP α subunit (α‐CTD), we identify several residues in α‐CTD that are important for CysB‐dependent transcription from the cysP promoter. After probing potential protein–protein contacts in vivo with a LexA‐based two‐hybrid system, we propose that the ‘273 determinant’ on α‐CTD, including residues K271 and E273, represents a target for interaction with CysB at the cysP promoter.
Molecular analysis of the psa permease complex of Streptococcus pneumoniae
Authors: McAllister Lauren J. , Tseng Hsing‐Ju , Ogunniyi A. David , Jennings Michael P. , McEwan Alastair G. , Paton James C. 
Published: July 2004

SummaryThe psaBCA locus of Streptococcus pneumoniae encodes a putative ABC Mn2+‐permease complex. Downstream of the operon is psaD, which may be co‐transcribed and encodes a thiol peroxidase. Previously, there has been discordance concerning the phenotypic impact of mutations in the psa locus, resolution of which has been complicated by differences in mutant construction and the possibility of polar effects. Here, we constructed unmarked, in frame deletion mutants ΔpsaB, ΔpsaC, ΔpsaA, ΔpsaD, ΔpsaBC, ΔpsaBCA and ΔpsaBCAD in S. pneumoniae D39 to examine the role of each gene within the locus in Mn2+ uptake, susceptibility to oxidative stress, virulence, nasopharyngeal colonization and chain morphology. The requirement for Mn2+ for growth and transformation was also investigated for all mutants. Inductively coupled plasma mass spectrometry (ICP‐MS) analysis provided the first direct evidence that PsaBCA is indeed a Mn2+ transporter. However, this study did not substantiate previous reports that the locus plays a role in choline‐binding protein pro‐duction or chain morphology. We also confirmed the importance of the Psa permease in systemic virulence and resistance to superoxide and hydrogen peroxide, as well as demonstrating a role in nasopharyngeal colonization for the first time. Further evi‐dence is provided to support the requirement for Mn2+ supplementation for growth and transformation of ΔpsaB, ΔpsaC, ΔpsaA, ΔpsaBC, ΔpsaBCA and ΔpsaBCAD mutants. However, transformation, as well as growth, of the ΔpsaD mutant was not dependent upon Mn2+ supplementation. We also show that, apart from sensitivity to hydrogen peroxide, the ΔpsaD mutant exhibited essentially similar phenotypes to those of the wild type. Western blot analysis with a PsaD antiserum showed that deleting any of the genes upstream of psaD did not affect its expression. However, we found that deleting psaB resulted in decreased expression of PsaA relative to that in D39, whereas deleting both psaB and psaC resulted in at least wild‐type levels of PsaA.
Analysis in vitro and in vivo of the transcriptional regulator CrgA of Neisseria meningitidis upon contact with target cells
Authors: Deghmane Ala‐Eddine , Giorgini Dario , Maigre Laure , Taha Muhamed‐Kheir 
Published: July 2004

SummaryContact between CrgA, a LysR‐like regulatory protein in Neisseria meningitidis, and DNA is involved in the repression of several bacterial genes upon contact with epithelial cells. We used a defined in vitro system containing crgA promoter, purified RNA polymerase (RNAP) and purified CrgA protein to demonstrate that CrgA was directly responsible for this transcriptional repression. Interaction between the C‐terminal domain of CrgA and the RNAP led to the production of short abortive transcripts, suggesting that CrgA may act by preventing RNAP from clearing the promoter. We probed the regulation by CrgA of its own production by analysing CrgA–DNA contacts during cell–bacteria interaction by assaying in vivo protection against dimethyl sulphate (DMS) methylation. Comparison of DMS footprints in vitro and in vivo suggested that CrgA repressed transcription through specific base contacts, probably in the major groove of the DNA double helix, resulting in DNA looping. Upon contact with target cells, CrgA was released from the DNA, allowing transcription of the target gene to proceed to elongation and facilitating tight control of the expression of genes regulated by CrgA.
Neisseria meningitidis accelerates ferritin degradation in host epithelial cells to yield an essential iron source
Authors: Larson Jason A. , Howie Heather L. , So Magdalene 
Published: July 2004

SummaryIn order to colonize humans and cause disease, pathogenic bacteria must assimilate iron from their host. The vast majority of non‐haem iron in humans is localized intracellularly, within the storage molecule ferritin. Despite the vast reserves of iron within ferritin, no pathogen has been demonstrated previously to exploit this molecule as an iron source. Here, we show that the Gram‐negative diplococcus Neisseria meningitidis can trigger rapid redistribution and degradation of cytosolic ferritin within infected epithelial cells. Indirect immunofluorescence microscopy revealed that cytosolic ferritin is aggregated and recruited to intracellular meningococci (MC). The half‐life of ferritin within cultured epithelial cells was found to decrease from 20.1 to 5.3 h upon infection with MC. Supplementation of infected epithelial cells with ascorbic acid abolished ferritin redistribution and degradation and prevented intracellular MC from replicating. The lysosomal protease inhibitor leupeptin slowed ferritin turnover and also retarded MC replication. Our laboratory has shown recently that MC can interfere with transferrin uptake by infected cells (Bonnah R.A., et al., 2000, Cell Microbiol 2: 207–218) and that, perhaps as a result, the infected cells have a transcriptional profile indicative of iron starvation (Bonnah, R.A., et al., 2004, Cell Microbiol 6: 473–484). In view of these findings, we suggest that accelerated ferritin degradation occurs as a response to an iron starvation state induced by MC infection and that ferritin degradation provides intracellular MC with a critical source of iron.
Translation repression by an RNA polymerase elongation complex
Authors: Wilson Helen R. , Zhou Jian‐guang , Yu Daiguan , Court Donald L. 
Published: July 2004

SummaryBacteriophage λ N and bacterial Nus proteins together with a unique site NUT in the leader of the early viral N gene transcript bind RNA polymerase (RNAP) and form a highly processive antitermination complex; N bound at NUT also represses N translation. In this study, we investigate whether N and NUT cause N translation repression as part of the antitermination complex by testing conditions that inhibit the formation of the N‐modified transcription complex for their effect on N‐mediated translation repression. We show that nus and nut mutations that in combination destabilize multiple interactions in the antitermination complex prevent N‐mediated translation repression. Likewise, transcription of the nut‐N region by T7 RNAP, which does not lead to the assembly of an effective antitermination complex when N is supplied, eliminates translation repression. We also demonstrate that a unique mutant β subunit of RNAP reduces N‐mediated translation repression, and that overexpression of transcription factor NusA suppresses this defect. We conclude that the N‐modified RNAP transcription complex is necessary to repress N translation.