bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deterministic paternity exclusion using RAPD markers
Authors: LEWIS P. O. , SNOW A. A. 
Published: April 2008

SummaryThe Random Amplified Polymorphic DNA (RAPD) technique can potentially provide hundreds of polymorphic markers for use by ecologists studying mating systems in natural populations. We consider here the implications of the dominance displayed by RAPD markers for deterministic paternity assignment. Our goal was to provide a means for assessing the costs associated with such a study for ecologists who might be considering the use of RAPD markers for paternity analysis. The theoretical expected proportion of offspring for which all males except the true father can be excluded (PET) is calculated for both dominant and codominant marker systems. The ability to assign paternity unambiguously generally increases with the number of loci and the frequency of the recessive allele (but only up to a point), and decreases with increasing sample size (number of individuals surveyed). The gain in PET with decreasing sample size is unexpectedly slight. Not surprisingly, the performance of dominant markers at paternity exclusion is, in general, greatly exceeded by codominant markers, with the exception of the case in which the frequency of the recessive allele is high at all loci. In this case, codominant markers perform only slightly better than do dominant markers. Thus, a researcher should expect to score more than 50 RAPD loci for each offspring for most applications of paternity exclusion analysis. While this may at first seem too costly, ameliorating factors include (i) more than one locus can often be scored from one primer, (ii) one can ‘pick‐andchoose’ the loci of greatest value from among those identified in a preliminary survey, (iii) a considerable degree of automation of the technique is possible, and (iv) some applications may be less stringent in the degree of exclusion required (i.e. fractional paternity assignment).
Influence of DNA supercoiling on the loss of culturability of Escherichia coli cells incubated in seawater
Authors: GAUTHIER M.J. , LABEDAN B. , BREITTMAYER V.A. 
Published: April 2008

AbstractThe relationship between the loss of culturability of Escherichia coli cells in seawater and the DNA supercoiling level of a reporter plasmid (pUC8) have been studied under different experimental conditions. Transfer to seawater of cells grown at low osmolarity decreased their ability to grow without apparent modification of the plasmid supercoiling. We found that E. coli cells could be protected against seawater‐induced loss of culturability by increasing their DNA‐negative supercoiling in response to environmental factors: either a growth at high osmolarity before the transfer to seawater, or addition of organic matter (50‐mg/l peptone) in seawater. We further found conditions where a DNAinduced relaxation was accompanied by an increase in seawater sensitivity. Indeed, inactivation of either one of the subunits A and B of DNA gyrase, which leads to important DNA relaxation, was accompanied in both cases by an increased loss of culturability of conditional mutants after transfer to seawater which could not be explained uniquely by the increase in the temperature required to inactivate the gyrase. Similarly, a strain harbouring a mutation in topoisomerase I, compensated by another mutation in subunit B of the gyrase, was more sensitive to seawater than the isogenic wild‐type cell and this greater sensitivity was correlated to a relaxation of plasmid DNA. Again, in these different cases, a previous growth at high osmolarity protected against this seawater sensitivity. We thus propose that the ability of E. coli cells to survive in seawater and maintain their ability to grow on culture media could be linked, at least in part, to the topological state of their DNA. This latter state might govern expression of genes whose products could allow restoration of cellular homeostasis in this medium.
The identification of sex in the starling Sturnus vulgaris using a molecular DNA technique
Authors: GRIFFITHS R. , TIWARI B. , BECHER S. A. 
Published: April 2008

AbstractFemale birds can be identified through the presence of a W‐chromosome. We describe a procedure for amplifying a W‐linked DNA marker in the starling (Sturnus vulgaris) by the polymerase chain reaction (PCR) so allowing the diagnosis of sex in this species. The technique is sensitive, allowing even the smallest chicks to be sexed from a blood sample. The method possesses a positive internal control to ensure accuracy. It is also applicable to the spotless starling (S. unicolor) but not to two bird species outside the genus. The nucleotide sequence of the female‐specific PCR product is given.
Survival and detection of an introduced Escherichia coli containing the porcine somatotropin gene from a waste treatment microcosm
Authors: GEALT M. D. , SELVARATNAM S. , ABRAMS L. , SYNENKI R. M. 
Published: April 2008

AbstractThe number Escherichia coli containing the porcine somatotropin (pST) gene cloned into plasmid pBR322 recovered from a laboratory‐scale waste treatment microcosm decreased over a period of several days following their introduction. The pST gene was detected by hybridization analysis in these bacteria when recovered from authentic wastewater at 72 h after introduction, but the gene was not detected in bacteria recovered at 144 h. No significant difference in recovery, as judged by auxotrophic and antibiotic‐resistance markers, was noted between the pST‐containing strain and an isogenic E. coli without pST, indicating that presence of the pST gene confers no survival advantage or disadvantage on the bacterial host.
The structure and interrelationship of fungal populations in native and cultivated soils
Authors: GORDON T. R. , OKAMOTO D. , MILGROOM M. G. 
Published: April 2008

AbstractMitochondrial DNA haplotypes have been characterized for 120 isolates of the asexual fungus Fusarium oxysporum. Sixty of these isolates were obtained from soil in a native grassland in the San Joaquin Valley of California, including 20 isolates from each of six different sampling locations. The same sampling strategy was used to obtain 60 additional isolates from an agricultural field of the same soil type directly adjacent to the native soil. Twenty‐three different mitochondrial DNA haplotypes were identified among the 120 isolates, including 11 haplotypes represented by two or more isolates and 12 that were unique. The five most common mitochondrial DNA haplotypes accounted for 93 (78%) of the 120 isolates. Isolates representing each of these five mitochondrial DNA haplotypes were found both in the cultivated and in the native soil. Seventy‐two per cent of the isolates found in the cultivated soil were associated with the same mitochondrial DNA haplotype as one or more isolates in the native soil. The remaining isolates in the cultivated soil were associated with comparatively rare mitochondrial DNA haplotypes, most of which showed a close relationship to one of the haplotypes found in the native soil. Hierarchial gene diversity analysis indicated that a significant proportion of the mitochondrial DNA haplotype diversity was attributable to differences between sampling sites in the native soil but not in the cultivated soil. This may reflect significant spatial structuring of genetic diversity in populations of F. oxysporum in a native soil. The proportion of mtDNA haplotype diversity attributable to differences between populations in the native and cultivated soils was not significant. This suggests that our entire collection, encompassing strains from both native and cultivated soils, is representative of a single population of F. oxysporum.
Discriminate suckling in pipistrelle bats is supported by DNA fingerprinting
Authors: BISHOP C. M. , JONES G. , LAZARUS C. M. , RACEY P. A. 
Published: April 2008

AbstractDNA fingerprints were obtained by using Jeffreys' probes 33.6 and 33.15 with DNA extracted from nine mother‐young pairs of pipistrelle bats Pipistrellus pipistrellns to investigate the feasibility of this technique for determining relatedness in this species. The bats had mated in the wild and gave birth in captivity. All of nine pairs in which infants were found attached showed band‐sharing coefficients higher than those for individuals presumed to be unrelated but run in adjacent lanes of the gels. We therefore conclude that all attached infants were probably true offspring.
Molecular phylogeographic evidence for multiple shifts in habitat preference in the diversification of an amphipod species
Authors: STANHOPE M. J. , HARTWICK B. , BAILLIE D. 
Published: April 2008

AbstractAn earlier study of ours demonstrated polygenic control of habitat preference between sympatric populations of an estuarine amphipod (Stanhope et al. 1992). Knowledge of the ecological history in this estuary suggested that two new and distinct habitat types (wood debris andFucus) had been formed immediately adjacent to each other, in an area which was previously the habitat type common to the rest of the estuary (bank). This suggested the possibility that the ancestral population had been split into two resource specialists (disruptive selection on habitat preference). The genetic relatedness of these three populations (the proposed ancestor and the two proposed descendants) and six others occupying the same three habitat types were investigated on a regional geographic scale, using an extensive set of genomic DNA RFLPs. These data were combined with measures of habitat preference (including genetic tests) in the additional populations. A very strongly supported phylogeographic tree, unequivocally supported a shift in habitat preference in the wood‐debris population of this estuary. The data did not, however, support the hypothesis of disruptive selection on the ancestor (bank) with a consequent split into two resource specialists. Instead, it clearly indicated that the occupants of theFucushabitat type were members of a habitat specific race, and thus their presence in this estuary reflected the expansion of an old resource base. Furthermore, the combined RFLP and habitat preference data, for all nine populations, indicated that the same polygenically based shift in habitat preference that had occurred in the original estuary had occurred independently, in another estuary, 700 km removed, that had similar environmental circumstances.
ITS primers with enhanced specificity for basidiomycetes ‐ application to the identification of mycorrhizae and rusts
Authors: GARDES M. , BRUNS T. D. 
Published: April 2008

AbstractWe have designed two taxon‐selective primers for the internal transcribed spacer (ITS) region in the nuclear ribosomal repeat unit. These primers, ITS1‐F and ITS4‐B, were intended to be specific to fungi and basidiomycetes, respectively. We have tested the specificity of these primers against 13 species of ascomycetes, 14 of basidiomycetes, and 15 of plants. Our results showed that ITS4‐B, when paired with either a ‘universal’ primer ITS1 or the fungal‐specific primer ITS1‐F, efficiently amplified DNA from all basidiomycetes and discriminated against ascomycete DNAs. The results with plants were not as clearcut. The ITS1‐F/ITS4‐B primer pair produced a small amount of PCR product for certain plant species, but the quantity was in most cases less than that produced by the ‘universal’ ITS primers. However, under conditions where both plant and fungal DNAs were present, the fungal DNA was amplified to the apparent exclusion of plant DNA. ITS1‐F/ITS4‐B preferential amplification was shown to be particularly useful for detection and analysis of the basidiomycete component in ectomycorrhizae and in rust‐infected tissues. These primers can be used to study the structure of ectomycorrhizal communities or the distribution of rusts on alternate hosts.
Molecular tools for the identification of ectomycorrhizal fungi — taxon‐specific oligonucleotide probes for suilloid fungi
Authors: BRUNS T. D. , GARDES M. 
Published: April 2008

AbstractFive taxon‐specific oligonucleotide probes are described that can be used to help identify the fungal components of ectomycorrhizae. Comparisons among partial sequence from the mitochondrial large subunit rRNA gene (mt‐LrRNA) were used to select the probes, which were intended to be specific to several taxa within the suilloid group of the Boletales (Basidiomycota). Probes S1, R1, and G1 were targeted at the genera Suillus, Rhizopogon and Gomphidius; probe G2 was designed to recognize the family, Gomphidiaceae, and probe US1 was designed to recognize all of these taxa and any other members of the suilloid group. The specificity of each probe was determined empirically by testing their ability to hybridize to PCR amplified fragments derived from 84 species of basidiomycetes. Although none of the probes exhibited their intended specificity, all specifically hybridized to useful subsets of taxa, and collectively they can be used to identify many suilloid taxa to the generic level or below. The probes were also tested for their ability to identify field collected mycorrhizae and were found to perform well.
Use of random amplified polymorphic DNA (RAPD) for generating specific DNA probes for microorganisms
Authors: FANI R. , DAMIANI G. , SERIO C. DI , GALLORI E. , GRIFONI A. , BAZZICALUPO M. 
Published: April 2008

AbstractWe report the rapid generation of DNA probes for several Azospirillum strains. This method does not require any knowledge of the genetics and/or the molecular biology of the organism (genome) to be investigated. The procedure is based on the generation of random amplified polymorphic DNA (RAPD) fingerprints using primers with an embedded restriction site. The amplification product(s) peculiar to one strain or common to two or more strains can be purified, cloned, sequenced and used as molecular probes in hybridization experiments for the detection and identification of microorganisms. We have tested this methodology in the nitrogen‐fixing bacterium Azospirillum by amplyfing the total DNA extracted from several Azospirillum strains. We have used amplification bands with different specificity as molecular probes in hybridization experiments performed on amplified DNA. Results obtained have demonstrated the usefulness of this methodology for Azospirillum. Its use in microbial ecology studies as a general strategy to generate specific DNA probes is also discussed.
Genetic consequences of an invasion through a patchy environment — the cynipid gallwasp Andricus quercuscalicis (Hymenoptera: Cynipidae)
Authors: STONE G.N. , SUNNUCKS P. 
Published: April 2008

AbstractOver the last 300–400 years, the cynipid gallwasp Andricus quercuscalicis has invaded northern and western Europe following human introduction of an obligate host plant, the Turkey oak (Quercus cerris) from south‐eastern Europe. In the introduced range, distances between Turkey oak patches are greater and the numbers of oaks in each patch are far lower than in its native range. These changes in spatial distribution of Turkey oak are predicted to result in high genetic subdivision of A. quercuscalicis in invaded areas relative to its native range. Allozyme electrophoresis was used to examine genetic variation in 823 gall wasps from 39 populations of A. quercuscalicis. No new electrophoretic variants were found in the invaded range and both allelic diversity and mean heterozygosity decreased significantly with distance from the native range. Spatial autocorrelation analysis and values of Wright's Fst indicate that differences in allele frequences between populations were substantially greater in the invaded range than in the native range. Spatial autocorrelation analysis also suggests that changes in allele frequencies across Europe are unlikely to be the results of selection, but rather of strong directional migration followed by limited gene flow between populations. Patterns of genetic differentiation across Europe suggest that populations of A. quercuscalicis have been founded sequentially from the east through a process of random genetic subsampling and not by source‐sink colonization directly from the native range.
Comparison of geographically distant populations of Rhizobium isolated from root nodules of Phaseolus vulgaris
Authors: GENIAUX E. , LAGUERRE G. , AMARGER N. 
Published: April 2008

AbstractSeventy‐two rhizobial strains were isolated from the root nodules of french beans (Phaseolus vulgaris). They were sampled from two geographically distant field populations and 18 additional different sites in France. They were characterized by a) plasmid profiles, (b) RFLP analysis of total cellular DNA using various chromosomal and symbiotic gene probes (including nifH from Rhizobium etli bv. phaseoli) and c) their ability to nodulate a potential alternative host, L. leucocephala. Over half of the isolates were ascribed to Rhizobium leguminosarum bv. phaseoli on the basis of the hybridization analysis, the possession of multiple copies of nifH and their inability to nodulate L. leucocephala. The remaining isolates belonged to 2 groups which were shown to be genomically distinct from R. leguminosarum bv. phaseoli, R. etli bv. phaseoli and R. tropici. Most members of these two groups shared with R. tropici the ability to nodulate L. leucocephala and, for isolates of only one of these groups, the presence of one copy of nif H. Members of each of the 3 taxa were widely distributed in France and circumstantial evidence of pSym transfer between them was shown. R. leguminosarum bv. phaseoli and one of the two novel groups co‐occurred within the two geographically distant populations. Individual genotypes were conserved between them. The finding of a third taxon at various other locations indicated additional diversity among rhizobia nodulating beans.
Recombinant and wild‐type Pseudomonas aureofaciens strains in soil: survival, respiratory activity and effects on nodulation of whitebean Phaseolus vulgaris L. by Rhizobiutn species
Authors: ENGLAND L. S. , LEE H. , TREVORS J. T. 
Published: April 2008

AbstractSurvival and respiratory activity of a genetically engineered Pseudomonas aureofaciens Ps3732RNL11 were compared to the parental wild‐type P. aureofaciens Ps3732RN in loam and sandy loam soils over 17‐ and 28‐day periods. Survival and respiratory activity of P. aureofaciens Ps3732RNL11 was not statistically significantly different from that of P. aureofaciens Ps3732RN. Soil texture had an effect on respiratory activity; carbon dioxide evolution was significantly higher in the sandy loam soil. This effect was observed on days 2, 10 and 18 but not on day 24. The presence of P. aureofaciens Ps3732RNL11 and Ps3732RN did not significantly affect growth of whitebean (Phaseolus vulgaris L.) in vermiculite, loam, or sandy loam soils. There was no significant difference (95% level) in numbers of nodules produced in the presence of P. aureofaciens Ps3732RNL11 and Ps3732RN as a result of the symbiotic relationship between Rhizobium phaseoli and the whitebean roots in vermiculite. Enumeration of nodules on whitebean roots in loam and sandy loam soils was not conducted due to difficulties in removing intact roots from the soils.
Nontarget and ecological effects of transgenically altered disease resistance in crops ‐possible effects on the mycorrhizal symbiosis
Authors: MILLER R.M. 
Published: April 2008

AbstractThe ability to increase crop disease resistance by using transgenic (TG) means has recently been demonstrated for several crops. The current TG procedures alter the temporal expression of transgene pathogenesis‐related (PR) proteins, so that the usually inducible PR proteins are expressed constitutively in the foreign host. The constitutive expression of the transgene PR protein chitinase is believed to increase the host's nonspecific basic resistance to pathogens. A potential nontarget effect of constitutively expressing chitinase may be a decrease in the activity of beneficial microbes, especially vesicular‐arbuscular mycorrhizal fungi. The decrease in activity of mycorrhizal fungi is related to reduced susceptibility of TG plant roots to colonization by these fungi, which is in turn associated with lysis of fungal cell walls by the constitutively expressed chitinase. An argument is presented that use of TG means to alter the temporal expression of PR proteins ignores a legacy of past evolutionary trade‐offs in vascular plants. A major nontarget effect of expressing transgene chitinase is a reduction in the susceptibility of roots to colonization by mycorrhizal fungi. This reduction in mycorrhizal susceptibility occurs without alteration of the mycorrhizal dependence of the host on symbiont‐supplied nutrients. Data are presented in support of this contention that demonstrate a strong negative association between host pathogen resistance and mycorrhizal colonization. An ecological consequence of reducing mycorrhizal colonization is a decrease in the soil's mycorrhizal propagule reserve that diminishes the next crop's production, especially under low‐input cropping practices. A further consequence that has both ecological and evolutionary outcomes is the escape of the transgene for improved pathogen resistance into wild populations. By increasing a crop's disease resistance by TG means, we may inadvertently be creating a ‘super weed’ when the TG plant or the transgene escapes into wild relatives through hybridization. Hybridization of wild relatives with TG plants would be especially relevant for crops, such as sugar beet, rapeseed, and many modern cereal cultivars that have close relatives in the wild but have a relatively low requirement for symbiont supplied nutrients or are nondependent.
Using molecular and ecological data to diagnose endangered populations of the puritan tiger beetle Cicindela puritana
Authors: VOGLER A. P. , KNISLEY C. B. , GLUECK S. B. , HILL J. M. , DESALLE R. 
Published: April 2008

AbstractPopulations of the puritan tiger beetle Cicindela puritana in the eastern United States were found to be highly threatened at the Connecticut River, whereas several large populations on the western shore and newly discovered populations on the eastern shore of the Chesapeake Bay appeared to be less endangered. We assessed if the disjunct C. puritana subgroups are genetically distinct and therefore should be treated as separate units for conservation purposes. A total of 13 individuals from the Connecticut River and 27 individuals from the Chesapeake Bay were each analysed by sequencing of up to 837 base pairs of mitochondrial DNA per individual. Five different haplotypes could be distinguished. In a phylogenetic analysis of these DNA sequences that included four related Cicindela species as out‐groups, haplotypes from the Chesapeake Bay represent a distinct clade. The conservation status of these populations was evaluated using a phylogenetic approach based on cladistic analysis and the framework of the phylogenetic species concept. According to this analysis, beetles from the Connecticut River and the Chesapeake Bay have to be considered as independent units. Populations from the eastern and western shore of Chesapeake Bay are not split in more than one unit using the same criteria, although they exhibited some degree of genetic subdivision. The results from the mtDNA analysis were corroborated by ecological parameters in that the Chesapeake Bay populations can be distinguished from all congeners by their different tat association.