bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resolution of natural groups using iterative assignment tests: an example from two species of Australian native rats (Rattus)
Authors: VÁzquez‐Domínguez E. , Paetkau D. , Tucker N. , Hinten G. , Moritz C. 
Published: March 2003

AbstractSympatric individuals of Rattus fuscipes and Rattus leucopus, two Australian native rats from the tropical wet forests of north Queensland, are difficult to distinguish morphologically and are often confused in the field. When we started a study on fine‐scale movements of these species, using microsatellite markers, we found that the species as identified in the field did not form coherent genetic groups. In this study, we examined the potential of an iterative process of genetic assignment to separate specimens from distinct (e.g. species, populations) natural groups. Five loci with extensive overlap in allele distributions between species were used for the iterative process. Samples were randomly distributed into two starting groups of equal size and then subjected to the test. At each iteration, misassigned samples switched groups, and the output groups from a given round of assignment formed the input groups for the next round. All samples were assigned correctly on the 10th iteration, in which two genetic groups were clearly separated. Mitochondrial DNA sequences were obtained from samples from each genetic group identified by assignment, together with those of museum voucher specimens, to assess which species corresponded to which genetic group. The iterative procedure was also used to resolve groups within species, adequately separating the genetically identified R. leucopus from our two sampling sites. These results show that the iterative assignment process can correctly differentiate samples into their appropriate natural groups when diagnostic genetic markers are not available, which allowed us to resolve accurately the two R. leucopus and R. fuscipes species. Our approach provides an analytical tool that may be applicable to a broad variety of situations where genetic groups need to be resolved.
Idengification of the origin of an Atlantic salmon (Salmo salar L.) population in a recently recolonized river in the Baltic Sea
Authors: Vasemägi A. , Gross R. , Paaver T. , Kangur M. , Nilsson J. , Eriksson L.‐O. 
Published: March 2003

AbstractThe founder event in a recently recolonized salmon population in the Baltic Sea (Gulf of Finland) was investigated. To idengify the origin of the founders, four wild populations and two hatchery stocks were analysed using six microsatellite loci. The results of assignment tests and factorial correspondence analysis suggest that the initial recolonizers of the river Selja originated from the geographically nearest (7 km) wild population (river Kunda) but as the result of stocking activities, interbreeding between recolonizers and hatchery individuals has occurred in subsequent years. Although the hatchery releases are outnumbering the wild salmon recruitment in the Baltic Sea at present, our results suggest that the native populations may still have an important role in colonization processes of the former salmon rivers.
Evidence of low gene flow in a neotropical clustered tree species in two rainforest stands of French Guiana
Authors: Dutech C. , Seiter J. , Petronelli P. , Joly H. I. , Jarne P. 
Published: March 2003

AbstractThe spatial genetic structure of the neotropical, clustered tree speciesVouacapoua americana(Aublet) was studied in two natural forest stands (Paracou and Nouragues) in French Guiana. Using eight microsatellite loci,V. americanais characterized by a marked genetic structure at small spatial distances (under 30–60 m), in agreement with the limited seed dispersal by rodent species. Gene flow through pollen is also shown to be mainly restricted to less than 100 m. This result suggests that most pollination events (mediated through small insects) are probably limited to within‐patches of individuals, which might explain the high genetic differentiation among patches (FST = 0.11) separated by less than 2 km. We also assume that stronger genetic structure in Paracou is likely to be due to lower seed dispersal by rodents, large spatial distances separating patches, or a recent recolonization event.
The genetic structure of the rare lagoonal sea anemone,Nematostella vectensisStephenson (Cnidaria; Anthozoa) in the United Kingdom based on RAPD analysis
Authors: Pearson C. V. M. , Rogers A. D. , Sheader M. 
Published: March 2003

AbstractThe sea anemoneNematostella vectensisoccurs in lagoons in the United States and along the southern and eastern coasts of the United Kingdom. In the United Kingdom it is considered rare and is threatened, principally through the destruction of lagoonal habitat. Random amplified polymorphic DNA (RAPD) data from populations across most of the rane ofN. vectensisin the United Kingdom revealed that 61% of individuals had an identical genotype, the frequency of which varied from 0.01 to 1.00. These data provide strong evidence for predominantly clonal reproduction and for the existence of a ‘general‐purpose genotype’ in the UK populations. Alternatively, the low levels of genetic variation observed in someN. vectensispopulations may have resulted if they were founded from very few successful individuals from the United States. Analysis of molecular variance (amova) showed significant genetic differentiation between lagoons with no large‐scale pattern of geographical variation. This result is consistent with occasional passive or anthropogenic dispersal of low numbers of individuals between lagoons followed by asexual proliferation of immigrants. Transplantation of individuals of the predominant (general‐purpose) genotype, for conservation purposes, will probably stand a good chance of survival given its prevalence throughout the United Kingdom.
Nestmate relatedness and population genetic structure of the Australian social crab spiderDiaea ergandros(Araneae: Thomisidae)
Authors: Evans Theodore A. , Goodisman Michael A. D. 
Published: March 2003

AbstractWe characterized the population genetic structure of the Australian social spiderDiaea ergandrosusing polymorphic allozyme markers. Our main objectives were to understand the social organization ofD. ergandrosand discern patterns of gene flow across distantly separated geographical areas. Spiders were sampled from nests located within 100 m wide locales, which were distributed within larger 50 km wide regions. Our results indicated that nestmates could have been produced by a single mother and father in 88.9% ofD. ergandrosnests. The remainder of nests contained spiders that were probably produced by polyandrous females or were immigrants from foreign nests. Nestmate relatedness was relatively high (r = 0.44) and did not differ significantly between the sexes or among juvenile, subadult and adult life stages. We also discovered thatD. ergandrospopulations were highly structured, with significant differentiation detected among locales (FLR = 0.23) and regions (FRT = 0.081). Spiders within locales were also substantially inbred (FIL = 0.15). Overall, our data show that significant population subdivision exists inD. ergandrospopulations, and we suggest that the poor dispersal ability ofDiaeaspiders can account for the observed genetic structure.
Population genetics of wolf spiders of fragmented habitat in the wheat belt of New South Wales
Authors: Colgan D. J. , Brown S. , Major R. E. , Christie F. , Gray M. R. , Cassis G. 
Published: March 2003

AbstractPossible effects of habitat fragmentation on the population genetics of a species of wolf spider (Lycosidae) from remnantCallitriswoodland in the wheat belt of central western New South Wales in Australia are examined. Single‐strand conformational analysis of mitochondrial cytochrome oxidase (subunit 1) was used to characterize the haplotypes of 295 spiders in six blocks each of four woodland sites. DNA sequences were collected from 119 of these spiders to confirm haplotype scoring, allow phylogeny estimation and permit calculation of sequence‐based statistics. Intra‐block tests do not suggest widespread effects of fragmentation. Genetic diversity is high in all blocks, with 25 haplotypes being identified. Nucleotide diversity is relatively low, as all of the haplotypes are closely related. One block had a significantly low value for the Ewens/Watterson test of neutrality and one block's value was nearly significantly high. Two blocks had nearly significant values of the Harpending Raggedness Index testing for recent population bottlenecks. No other intrablock tests approach significance. Interpopulation comparisons show significant nonhomogeneity of haplotype frequencies globally and in all pairwise comparisons. Relationships between woodland blocks based on haplotype frequencies are discordant with geographical proximity. Haplotype distribution patterns suggest that population structuring existed prior to fragmentation. We develop two measures of genetic distinctiveness to identify subpopulations of interest for conserving evolutionary processes in a species’ regional population. One is based on the sum of pairwiseFSTvalues and one on the spatial distribution of genetic variation. High values of the measure suggest a subpopulation might have been recently perturbed and low values that it is relatively undisturbed. The two measures identify different blocks as being of particular interest.
Polymerase chain reaction–single strand conformation polymorphism analyses of nuclear and chloroplast DNA provide evidence for recombination, multiple introductions and nascent speciation in the Caulerpa taxifolia complex
Authors: Meusnier I. , Valero M. , Destombe C. , Godé C. , Desmarais E. , Bonhomme F. , Stam W. T. , Olsen J. L. 
Published: March 2003

AbstractIndependent lines of evidence support an Australian origin for the Mediterranean populations of the tropical alga Caulerpa taxifolia. To complement previous biogeographical studies based on nuclear rDNA internal transcribed spacer (ITS), a new chloroplast marker was developed — the cp 16S rDNA intron‐2. Sequence variability for both nuclear and chloroplast markers were assessed in 110 individuals using single strand conformation polymorphism. Comparison of intrapopulation genetic diversity between invasive Mediterranean and ‘native’ Australian populations revealed the occurrence of two divergent and widespread clades. The first clade grouped nontropical invasive populations with inshore‐mainland populations from Australia, while the second clustered all offshore‐island populations studied so far. Despite our finding of nine distinct nuclear and five distinct chloroplast profiles, a single nucleocytoplasmic combination was characteristic of the invasive populations and sexual reproduction was found to be very rare. C. taxifolia is clearly a complex of genetically and ecologically differentiated sibling species or subspecies.
DNA sequence variation in BpMADS2 gene in two populations of Betula pendula
Authors: Järvinen Pia , Lemmetyinen Juha , Savolainen Outi , Sopanen Tuomas 
Published: March 2003

AbstractThe PISTILLATA (PI) homologue, BpMADS2, was isolated from silver birch (Betula pendula Roth) and used to study nucleotide polymorphism. Two regions (together about 2450 bp) comprising mainly untranslated sequences were sequenced from 10 individuals from each of two populations in Finland. The nucleotide polymorphism was low in the BpMADS2 locus, especially in the coding region. The synonymous site overall nucleotide diversity (πs) was 0.0043 and the nonsynonymous nucleotide diversity (πa) was only 0.000052. For the whole region, the π values for the two populations were 0.0039 and 0.0045, and for the coding regions, the π values were only 0 and 0.00066 (for the corresponding coding regions of Arabidopsis thaliana PI world‐wide π was 0.0021). Estimates of π or θ did not differ significantly between the two populations, and the two populations were not diverged from each other. Two classes of BpMADS2 alleles were present in both populations, suggesting that this gene exhibits allelic dimorphism. In addition to the nucleotide site variation, two microsatellites were also associated within the haplotypes. This allelic dimorphism might be the result of postglacial re‐colonization partly from northwestern, partly from southeastern/eastern refugia. The sequence comparison detected five recombination events in the regions studied. The large number of microsatellites in all of the three introns studied suggests that BpMADS2 is a hotspot for microsatellite formation.
Degradation of the Cry1Ab protein within transgenic Bacillus thuringiensis corn tissue in the field
Authors: Zwahlen C. , Hilbeck A. , Gugerli P. , Nentwig W. 
Published: March 2003

AbstractLarge quantities of Bacillus thuringiensis (Bt) corn plant residue are left in the field after harvest, which may have implications for the soil ecosystem. Potential impacts on soil organisms will also depend on the persistence of the Bt toxin in plant residues. Therefore, it is important to know how long the toxin persists in plant residues. In two field studies in the temperate corn‐growing region of Switzerland we investigated degradation of the Cry1Ab toxin in transgenic Bt corn leaves during autumn, winter and spring using an enzyme‐linked immunosorbent assay (ELISA). In the first field trial, representing a tillage system, no degradation of the Cry1Ab toxin was observed during the first month. During the second month, Cry1Ab toxin concentrations decreased to ≈ 20% of their initial values. During winter, there was no further degradation. When temperatures again increased in spring, the toxin continued to degrade slowly, but could still be detected in June. In the second field trial, representing a no‐tillage system, Cry1Ab toxin concentrations decreased without initial delay as for soil‐incorporated Bt plants, to 38% of the initial concentration during the first 40 days. They then continued to decrease until the end of the trial after 200 days in June, when 0.3% of the initial amount of Cry1Ab toxin was detected. Our results suggest that extended pre‐ and post‐commercial monitoring are necessary to assess the long‐term impact of Bt toxin in transgenic plant residues on soil organisms.
Physiological consequences of blocked Caulobacter crescentus dnaA expression, an essential DNA replication gene
Authors: Gorbatyuk Boris , Marczynski Gregory T. 
Published: March 2003

Caulobacter crescentus chromosome replication is precisely coupled to a developmental cell cycle. Like most eubacteria, C. crescentus has a DnaA homologue that is presumed to initiate chromosome replication. However, the C. crescentus replication origin (Cori) lacks perfect consensus Escherichia coli DnaA boxes. Instead, the Cori strong transcription promoter (Ps) may regulate chromosome replication through the CtrA cell cycle response regulator. We therefore created a conditional dnaA C. crescentus strain. Blocking dnaA expression immediately decreased DNA synthesis, which stopped after approximately one doubling period. Fluorescent flow cytometry confirmed that DNA synthesis is blocked at the initiation stage. Cell division also stopped, but not swarmer to stalked cell differentiation. All cells became stalked cells that grew as long filaments. Therefore, general transcription and protein synthesis continued, whereas DNA synthesis stopped. However, transcription was selectively blocked from the flagellar fliQ and fliL and methyltransferase ccrM promoters, which require CtrA and are blocked by different DNA synthesis inhibitors. Interestingly, transcription from Cori Ps continued unaltered. Therefore, Ps transcription is not sufficient for chromosome replication. Approximately 6–8 h after blocked dnaA expression, cells lost viability exponentially. Coincidentally, β‐galactosidase was induced from one transcription reporter, suggesting an altered physiology. We conclude that C. crescentus DnaA is essential for chromosome replication initiation, and perhaps also has a wider role in cell homeostasis.
In vitro transcription of PrfA‐dependent and  ‐independent genes of Listeria monocytogenes
Authors: Lalic‐Mülthaler M. , Bohne J. , Goebel W. 
Published: March 2003

In vitro transcription starting from the promoters of the Listeria monocytogenes genes hly, plcA, actA, mpl, prfA and iap has been studied. Whereas transcription from Phly, PplcA and PactA is strictly PrfA‐dependent, that from Piap, PprfA1/2 and, unexpectedly, also from Pmpl is independent. Initiation of in vitro transcription at all tested promoters except PprfA requires high concentrations of ATP but not GTP. The nucleotides required in higher concentrations for efficient in vitro transcription are always included in the first three nucleotides of the corresponding transcript. RNA polymerase prepared from L. monocytogenes cultured either in rich culture medium (RNAPBHI), exposed to heat shock conditions (RNAP48) or conditioned in minimal essential medium (RNAPMEM) shows significant differences in the transcription efficiencies when transcription is initiated at these promoters. Transcription starting from the PrfA‐dependent promoters PactA and Phly is enhanced with RNAP48 and RNAPMEM (in relation to Piap–mediated transcription), while transcription from the other promoters is reduced when compared with RNAPBHI. These data suggest that in vivo transcription of the genes actA and hly may not function optimally with RNA polymerase loaded with the vegetative sigma factor 43, but may require a modified RNA polymerase, possibly loaded with an alternative sigma factor.
The parAB gene products of Pseudomonas putida exhibit partition activity in both P. putida and Escherichia coli
Authors: Godfrin‐Estevenon Anne‐Marie , Pasta Franck , Lane David 
Published: March 2003

SummaryThe bacteria for which there is evidence that proteins of the ParAB family act in chromosome segregation also undergo developmental transitions that involve the ParAB homologues, raising the question of whether the partition activity is equivalent to that of plasmid partition systems. We have investigated the role in partition of the parAB locus of a free‐living bacterium, Pseudomonas putida, not known to pass through developmental phases. A parAB deletion mutant, compared with wild type, showed slightly higher frequencies of anucleate cells in exponen‐tially growing cultures but much higher frequencies in deceleration phase. This increase was growth medium dependent. Oversupply of ParA and ParB proteins also raised anucleate cell levels, specifically in the deceleration phase, in wild‐type and mutant strains and regardless of medium, as well as generating abnormal cell morphologies. Absence or oversupply of ParAB function had either slight or considerable effects on growth rate, depending on temperature and medium. The need for the Par proteins in chromosome partition thus appears to be subject to the cell’s physiological state. Three sequences similar to cis‐acting stabilization sites of Bacillus subtilis are present in the P. putida oriC–parAB region. One was inserted into an unstable mini‐F and shown to stabilize it in E. coli in a ParAB‐dependent manner.
Identification of binding sites for the group A streptococcal global regulator CovR
Authors: Federle Michael J. , Scott June R. 
Published: March 2003

SummaryThe CovRS two‐component system (also called CsrRS) of the group A streptococcus (GAS) acts as a global regulator, influencing the transcription of at least six virulence factors. The synthesis of the hyaluronic acid capsule, a virulence factor encoded by the hasABC operon, is negatively regulated by CovRS. We confirmed that

phosphorylation of CovR increases its binding to a DNA fragment containing the hasA

promoter. Using DNase I footprinting, we identified five binding sites surrounding

the hasA promoter from bases –79 to +73 (where +1 is

the start of transcription). One pair of thymines within each binding site appears

to be necessary for CovR binding in vitro, as shown by uracil interference

analysis. When each of these thymine pairs was altered by site‐directed mutagenesis,

CovR binding was reduced in vitro, confirming the role of each thymine pair

in binding. Using a transcriptional reporter system with a single chromosomal copy

of PhasA–gusA, we demonstrated the importance of each of four of these

binding sites for CovR repression of the hasA promoter. Based on this information, we propose a consensus sequence for CovR binding to DNA.
The roles of the polytopic membrane proteins NarK, NarU and NirC in Escherichia coli K‐12: two nitrate and three nitrite transporters
Authors: Clegg Stephanie , Yu Feng , Griffiths Lesley , Cole Jeffrey A. 
Published: March 2003

SummaryTwo polytopic membrane proteins, NarK and NarU, are assumed to transport nitrite out of the Escherichia coli cytoplasm, but how nitrate enters enteric bacteria

is unknown. We report the construction and use of four isogenic strains that lack

nitrate reductase Z and the periplasmic nitrate reductase, but express all combinations

of narK and narU. The active site of the only functional nitrate reductase,

nitrate reductase A, is located in the cytoplasm, so nitrate reduction by these four

strains is totally dependent upon a mechanism for importing nitrate. These strains

were exploited to determine the roles of NarK and NarU in both nitrate and nitrite

transport. Single mutants that lack either NarK or NarU were competent for nitrate‐dependent

anaerobic growth on a non‐fermentable carbon source, glycerol. They transported and

reduced nitrate almost as rapidly as the parental strain. In contrast, the narK–narU

double mutant was defective in nitrate‐dependent growth unless nitrate transport

was facilitated by the nitrate ionophore, reduced benzyl viologen (BV). It was also

unable to catalyse nitrate reduction in the presence of physiological electron donors.

Synthesis of active nitrate reductase A and the cytoplasmic, NADH‐dependent nitrite

reductase were unaffected by the narK and narU mutations. The rate

of nitrite reduction catalysed by the cytoplasmic, NADH‐dependent nitrite reductase

by the double mutant was almost as rapid as that of the NarK+‐NarU+

strain, indicating that there is a mechanism for nitrite uptake by E. coli

that is in‐dependent of either NarK or NarU. The nir operon encodes a soluble,

cytoplasmic nitrite reductase that catalyses NADH‐dependent reduction of nitrite

to ammonia. One additional component that contributes to nitrite uptake was shown

to be NirC, the hydrophobic product of the third gene of the nir operon, which

is predicted to be a polytopic membrane protein with six membrane‐spanning helices.

Deletion of both NarK and NirC decreased nitrite uptake and reduction to a basal

rate that was fully restored by a single chromosomal copy of either narK or

nirC. A multicopy plasmid encoding NarU complemented a narK mutation for nitrite excretion, but not for nitrite uptake. We conclude that, in contrast to NirC, which transports only nitrite, NarK and NarU provide alternative mechanisms for both nitrate and nitrite transport. However, NarU might selectively promote nitrite ex‐cretion, not nitrite uptake.