bluuebunny/crossref_metadata_2025 huggingface dataset:
QTL architecture of resistance and tolerance traits in Arabidopsis thaliana in natural environments
Authors: Weinig Cynthia , Stinchcombe John R. , Schmitt Johanna
Published: December 2004

Quantitative‐genetic approaches have offered significant insights into phenotypic evolution. However, quantitative‐genetic analyses fail to provide information about the evolutionary relevance of specific loci. One complex and ecologically relevant trait for plants is their resistance to herbivory because natural enemies can impose significant damage. To illustrate the insights of combined molecular and ecological research, we present the results of a field study mapping quantitative trait loci (QTL) for resistance and tolerance to natural rabbit herbivory in the genetic model, Arabidopsis thaliana. Replicates of the Ler × Col recombinant inbred lines were planted into field sites simulating natural autumn and spring seasonal germination cohorts. Shortly after flowering, herbivores removed the main flowering inflorescence (apical meristem). We found several main‐effect QTL for resistance within each seasonal cohort and significant QTL–season interactions, demonstrating that the loci underlying resistance to a single herbivore differ across seasonal environments. The presence of QTL × environment also shows that variation at specific loci is only available to selection in some environments. Despite significant among‐line variance components, no QTL for tolerance were detected. The combined results of the quantitative‐genetic and QTL analyses demonstrate that many loci of small effect underlie tolerance to damage by rabbits, and counter the hypothesis of locus‐specific tradeoffs between resistance and tolerance. The results also provide insights as to the locus‐specific nature of evolutionary constraints, i.e. some loci influence flowering time and resistance in both seasonal cohorts. Our results show how linking molecular‐genetic tools with field studies in ecologically relevant settings can clarify the role of specific loci in the evolution of quantitative traits.
Analysis of molecular data of Arabidopsis thaliana (L.) Heynh. (Brassicaceae) with Geographical Information Systems (GIS)
Authors: Hoffmann Matthias H. , GLAß Anne S. , Tomiuk Jürgen , Schmuths Heike , Fritsch Reinhard M. , Bachmann Konrad
Published: December 2004

A Geographical Information System (GIS) is used to analyse allelic information of 13 sequenced loci of natural populations of Arabidopsis thaliana and to identify geographical structures. GIS provides tools for visualization and analysis of geographical population structures using molecular data. The geographical distribution of the number of variable positions in the alignments, the distribution of recombinant sequence blocks, and the distribution of a newly defined measure, the differentiation index, are studied. The differentiation index is introduced to measure the sequence divergence among individual plants sampled from various geographical localities. The numbers of variable positions and the differentiation index are also used for a metadata analysis covering about 26 kb of the genome. This analysis reveals, for the first time, differences in DNA sequence structures of geographically different populations of A. thaliana. The broadly defined west Mediterranean region consists of accessions with the highest numbers of polymorphic positions followed by the west European region. The GIS technology Kriging is used to define Arabidopsis specific diversity zones in Europe. The highest genetic variability is observed along the Atlantic coast from the western Iberian Peninsula to southern Great Britain, while lowest variability is found in central Europe.
Wolbachia infection complexity among insects in the tropical rice‐field community
Authors: Kittayapong P. , Jamnongluk W. , Thipaksorn A. , Milne J. R. , Sindhusake C.
Published: December 2004

Wolbachia are a group of intracellular bacteria that cause reproductive alterations in their arthropod hosts. Widely discordant host and Wolbachia phylogenies indicate that horizontal transmission of these bacteria among species sometimes occurs. A likely means of horizontal transfer is through the feeding relations of organisms within communities. Feeding interactions among insects within the rice‐field insect community have been well documented in the past. Here, we present the results of a polymerase chain reaction‐based survey and phylogenetic analysis of Wolbachia strains in the rice‐field insect community of Thailand. Our field survey indicated that 49 of 209 (23.4%) rice‐field insect species were infected with Wolbachia. Of the 49 infected species, 27 were members of two feeding complexes: (i) a group of 13 hoppers preyed on by 2 mirid species and parasitized by a fly species, and (ii) 2 lepidopteran pests parasitized by 9 wasp species. Wolbachia strains found in three hoppers, Recilia dorsalis, Nephotettix malayanus and Nisia nervosa, the two mirid predators, Cyrtorhinus lividipennis and Tytthus chinensis, and the fly parasitoid, Tomosvaryella subvirescens, were all in the same Wolbachia clade. In the second complex, the two lepidopteran pests, Cnaphalocrocis medinalis and Scirpophaga incertulas, were both infected with Wolbachia from the same clade, as was the parasitoid Tropobracon schoenobii. However, none of the other infected parasitoid species in this feeding complex was infected by Wolbachia from this clade. Mean (± SD) genetic distance of Wolbachia wsp sequences among interacting species pairs of the hopper feeding complex (0.118 ± 0.091 nucleotide sequence differences), but not for the other two complexes, was significantly smaller than that between noninteracting species pairs (0.162 ± 0.079 nucleotide sequence differences). Our results suggest that some feeding complexes, such as the hopper complex described here, could be an important means by which Wolbachia spreads among species within arthropod communities.
Phylogeography of the common vole (Microtus arvalis) with particular emphasis on the colonization of the Orkney archipelago
Authors: Haynes Susan , Jaarola Maarit , Searle Jeremy B.
Published: December 2004

To investigate the human introduction of the common vole Microtus arvalis onto the Orkney islands, the complete cytochrome b gene was sequenced in 41 specimens from both Orkney (four localities) and elsewhere in their range (26 localities). Orkney voles belonged to the same phylogenetic lineage, ‘Western’, as individuals from France and Spain indicating southwestern Europe as the most likely source area for the islands. This result is of interest with respect to the movement and trading links of the Neolithic people who likely transported the voles. As well as the Western lineage, our phylogenetic trees revealed three other purely European lineages: the ‘Italian’ (single specimen from N. Italy), the ‘Central’ (Germany, Netherlands, Denmark) and the ‘Eastern’ (Hungary, Slovakia, Poland, Ukraine, Finland, European Russia). Individuals from European Russia, W. Siberia, Georgia, Ukraine and Armenia formed a fifth distinct lineage coinciding with the distribution of the ‘obscurus’ chromosomal form of M. arvalis. These phylogeographical data suggest that M. arvalis occupied multiple refugia during the last glaciation.
Holarctic phylogeography of the root vole (Microtus oeconomus): implications for late Quaternary biogeography of high latitudes
Authors: Brunhoff C. , Galbreath K. E. , Fedorov V. B. , Cook J. A. , Jaarola M.
Published: December 2004

A species‐wide phylogeographical study of the root vole (Microtus oeconomus) was performed using the whole 1140 base pair mitochondrial (mt) cytochromebgene. We examined 83 specimens from 52 localities resulting in 65 unique haplotypes. Our results demonstrate that the root vole is divided into four main mtDNA phylogenetic lineages that seem to have largely allopatric distributions. Net divergence estimates (2.0–3.5%) between phylogroups, as well as relatively high nucleotide diversity estimates within phylogroups, indicate that the distinct phylogeographical structure was initiated by historical events that predated the latest glaciation. European root voles are divided into a Northern and a Central mtDNA phylogroup. The mtDNA data in concert with fossil records imply that root voles remained north of the classical refugial areas in southern Europe during the last glacial period. The currently fragmented populations in central Europe belong to a single mtDNA phylogroup. The Central Asian and the North European lineages are separated by the Ural Mountains, a phylogeographical split also found in collared lemmings (Dicrostonyx) and the common vole (M. arvalis). The Beringian lineage occurs from eastern Russia through Alaska to northwestern Canada. This distribution is congruent with the traditional boundaries of the Beringian refugium and with phylogeographical work on other organisms. In conclusion, similarities between the phylogeographical patterns in the root vole and other rodents, such as Arctic and subarctic lemmings, as well as more temperate vole species, indicate that late Quaternary geological and climatic events played a strong role in structuring northern biotic communities.
Phylogeography of Ponto‐Caspian crustaceans: a benthic–planktonic comparison
Authors: Cristescu Melania E. A. , Hebert Paul D. N. , Onciu Teodora M.
Published: December 2004

The Black, Azov, Caspian and Aral Seas, remnants of the intracontinental Paratethys basin, are home to a spectacular diversity of crustaceans. This study examines the past history of the Ponto‐Caspian fauna through comparative phylogeographical studies on both benthic and planktonic taxa, based on an examination of nucleotide diversity in the mitochondrial, cytochrome c oxidase subunit 1 (COI) gene. The COI data reveal a striking example of phylogeographical concordance. All species analysed, three amphipods and three cladocerans, are characterized by two monophyletic clades corresponding to the Black and Caspian regions. However, this phylogeographical partition is, on average, four times deeper for the benthic amphipods than for the planktonic cladocerans. Based on standard molecular clocks, the Black and Caspian lineages of benthic crustaceans diverged at varied intervals from 1 to 8 million years ago. By contrast, planktonic lineages are more recent with their divergence occurring in the last million years. Levels of intraspecific polymorphisms are variable and generally lower in planktonic than benthic taxa. The mechanisms responsible for the high diversity of crustaceans in the Ponto‐Caspian region are discussed on the basis of these results.
Molecular evolution and quantitative variation for chemosensory behaviour in the nematode genus Caenorhabditis
Authors: Jovelin R. , Ajie B. C. , Phillips P. C.
Published: December 2004

Caenorhabditis elegans is a model organism in biology, yet despite the tremendous information generated from genetic, genomic and functional analyses, C. elegans has rarely been used to address questions in ecological genetics. Here, we analyse genetic variation for chemosensory behaviour, an ecologically important trait that is also genetically well characterized, at both the phenotypic and molecular levels within three species of the genus Caenorhabditis. We show that the G‐protein ODR‐3 plays an important role in chemosensory avoidance behaviour and identify orthologues of odr‐3 in C. briggsae and C. remanei. Both quantitative genetic analysis of chemosensory behaviour and molecular population genetic analysis of odr‐3 show that there is little genetic variation among a worldwide collection of isolates of the primarily selfing C. elegans, whereas there is substantially more variation within a single population of the outcrossing C. remanei. Although there are a large number of substitutions at silent sites within odr‐3 among the three species, molecular evolution at the protein level is extremely conserved, suggesting that odr‐3 plays an important role in cell signalling during chemosensation and/or neuronal cilia development in C. remanei and in C. briggsae as it does in C. elegans. Our results suggest that C. remanei may be a more suitable subject for ecological and evolutionary genetic studies than C. elegans.
Candidate gene analysis of metamorphic timing in ambystomatid salamanders
Authors: Voss S. R. , Prudic K. L. , Oliver J. C. , Shaffer H. B.
Published: December 2004

Although much is known about the ecological significance of metamorphosis and metamorphic timing, few studies have examined the underlying genetic architecture of these traits, and no study has attempted to associate phenotypic variation to molecular variation in specific genes. Here we report on a candidate gene approach (CGA) to test specific loci for a statistical contribution to variation in metamorphic timing. Three segregating populations (SP1, SP2 and SP3) were constructed utilizing three species of paedomorphic Mexican ambystomatid salamander, including the axolotl,Ambystoma mexicanum. We used these replicated species to test the hypothesis that inheritance of alternate genotypes at two thyroid hormone receptor loci (TRα, TRβ) affects metamorphic timing in ambystomatid salamanders. A significantTRα*SP effect indicated that variation in metamorphic timing may be influenced byTRαgenotype, however, the effect was not a simple one, as both the magnitude and direction of the phenotypic effect depended upon the genetic background. These are the first data to implicate a specific gene in contributing to variation in metamorphic timing. In general, candidate gene approaches can be extended to any number of loci and to any organism where simple genetic crosses can be performed to create segregating populations. The approach is thus of particular value in ecological studies where target genes have been identified but the study organism is not one of the few well‐characterized model systems that dominate genetic research.
A ‘fair go’* for coral hybridization
Authors: Miller David J. , Van Oppen Madeleine J. H.
Published: December 2004

Hybridisation between coral species clearly occurs in vitro, but the evolutionary significance of this cross‐fertility is still the subject of much debate. Compelling genetic and reproductive evidence support introgressive hybridization amongst Indo‐Pacific members of the scleractinian genus Acropora. Although population genetic analyses indicate that interspecific hybridization events are relatively rare, they are likely be important on evolutionary time scales, creating the capacity for adaptive evolution by increasing genomic diversity and heterozygosity. However, in a recent paper based exclusively on the three endemic Caribbean Acropora species, Vollmer and Palumbi (2002) dispute the occurrence of reticulation in corals. Here we use data from both the Vollmer and Palumbi study and our earlier paper on the same species (van Oppen et al., 2000) to show that reticulation has occurred amongst the Caribbean Acropora species. Furthermore, conclusions based on the limited Caribbean Acropora fauna cannot simply be extrapolated to Indo‐Pacific corals, and it is inappropriate to view some coral species as ‘immortal mules’.
Patterns of nucleotide variation in homoeologous regulatory genes in the allotetraploid Hawaiian silversword alliance (Asteraceae)
Authors: Lawton‐Rauh Amy , Robichaux Robert H. , Purugganan Michael D.
Published: December 2004

Genome‐wide duplication (polyploidization) is prevalent in a large number of eukaryotic organisms and is particularly widespread in flowering plants. Polyploid species appear to vary from their diploid progenitors in a variety of ecologically important traits, suggesting that genome duplications provide a mechanism for ecological diversification. Studies of nucleotide variation at duplicate genes that arise via polyploidization allow us to infer the evolutionary forces that act on these polyploid loci. In an effort to examine the evolutionary dynamics of homoeologous loci, molecular population genetic analyses were undertaken for duplicate regulatory genes in the allopolyploid Hawaiian silversword alliance, a premier example of adaptive radiation. The levels and patterns of nucleotide variation for the floral homeotic genes ASAPETALA1 (ASAP1) and ASAPETALA3/TM6 (ASAP3/TM6) were studied in two species representing different lineages within the Hawaiian silversword alliance: Argyroxiphium sandwicense ssp. macrocephalum and Dubautia ciliolata ssp. glutinosa. Homoeologueous copies of ASAP1 and ASAP3/TM6 show differing levels and patterns of nucleotide polymorphism. Duplicate ASAP1 copies have similar levels of nucleotide diversity and haplotype structure in both species; by contrast, duplicate ASAP3/TM6 genes display different levels and patterns of variation in D. ciliolata ssp. glutinosa. Additionally, D. ciliolata ssp. glutinosa appears to be segregating for a moderate frequency null allele in one ASAP3/TM6 homoeologue. These results suggest that differing evolutionary forces can affect duplicate loci arising from allopolyploidization.
Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite‐island model
Authors: Excoffier Laurent
Published: December 2004

It has been long recognized that population demographic expansions lead to distinctive features in the molecular diversity of populations. However, recent simulation results have suggested that a distinction could be made between a pure demographic expansion in an unsubdivided population, and a range expansion in a subdivided population, both leading to a large increase in the total number of the individuals. In order to better characterize the effect of a range expansion, I introduce a simple model of instantaneous expansion under an infinite‐island model, under which I derive the distribution of the number of mutation differences between pairs of genes (the mismatch distribution), the heterozygosity, the average number of pairwise difference, and the fixation index FST. These derivations are checked against simulations, and are shown to lead to results qualitatively similar to those one would obtain after a range expansion in a 2‐dimensional stepping‐stone model. I then apply these results to estimate immigration rates in hunter‐gather and post‐Neolithic human populations from patterns of mitochondrial (mtDNA) diversity. Potential problems with this estimation procedure are also discussed.
Combining demographic, environmental and genetic data to test hypotheses about colonization events in metapopulations
Authors: Gaggiotti O. E. , Brooks S. P. , Amos W. , Harwood J.
Published: December 2004

We describe a method for making inferences about the factors that influence colonization processes in natural populations. We consider the general situation where we have genetic data from a newly colonized population and also fromIsource populations that may have contributed individuals to the founding group that established the new population. The model assumes thatp(biotic/abiotic) factors,G1, … ,Gpmay have influenced some individuals in some of the source populations to find a new habitat patch where they could establish a new population. The aim of the method is to determine the composition of the founding group and to ascertain if the aforementioned factors have indeed played a role in the colonization event. We investigate the performance of our method using simulated data sets and illustrate its application with data from the grey sealHalichoerus grypus. These applications demonstrate that the method can identify accurately those factors that are most important for the founding of new populations. This is the case even when genetic differentiation among source populations is low. The estimates of the contribution that each source population makes to the founding groups is somewhat sensitive to the degree of genetic differentiation but it is still possible to identify the sources that are the main contributors to the founding group, even when genetic differentiation is low (FST = 0.01).
Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid species
Authors: Hey Jody , Won Yong‐Jin , Sivasundar Arjun , Nielsen Rasmus , Markert Jeffrey A.
Published: December 2004

When populations or species have recently separated they often share genetic variation. However, it can be difficult to determine whether shared polymorphisms are the result of gene flow, the result of the persistence of variation in both populations since the time of common ancestry, or both of these factors. We have developed an empirical protocol for using loci that include unique nuclear DNA sequence haplotypes together with linked microsatellites or short tandem repeats (STRs). These ‘HapSTRs’ offer the potentially high resolution associated with the high mutation rate of STRs, together with the advantages of low homoplasy of unique sequence DNA. We also describe a new procedure for estimating the likelihood of HapSTR data under an Isolation with Migration model. An example using Cichlid fishes from Lake Malawi is described. The analysis suggests that the species have been exchanging genes since the time they began to diverge.
Evidence of genetic distinction and long‐term population decline in wolves (Canis lupus) in the Italian Apennines
Authors: Lucchini V. , Galov A. , Randi E.
Published: December 2004

Historical information suggests the occurrence of an extensive human‐caused contraction in the distribution range of wolves (Canis lupus) during the last few centuries in Europe. Wolves disappeared from the Alps in the 1920s, and thereafter continued to decline in peninsular Italy until the 1970s, when approximately 100 individuals survived, isolated in the central Apennines. In this study we performed a coalescent analysis of multilocus DNA markers to infer patterns and timing of historical population changes in wolves surviving in the Apennines. This population showed a unique mitochondrial DNA control‐region haplotype, the absence of private alleles and lower heterozygosity at microsatellite loci, as compared to other wolf populations. Multivariate, clustering and Bayesian assignment procedures consistently assigned all the wolf genotypes sampled in Italy to a single group, supporting their genetic distinction. Bottleneck tests showed evidences of population decline in the Italian wolves, but not in other populations. Results of a Bayesian coalescent model indicate that wolves in Italy underwent a 100‐ to 1000‐fold population contraction over the past 2000–10 000 years. The population decline was stronger and longer in peninsular Italy than elsewhere in Europe, suggesting that wolves have apparently been genetically isolated for thousands of generations south of the Alps. Ice caps covering the Alps at the Last Glacial Maximum (c. 18 000 years before present), and the wide expansion of the Po River, which cut the alluvial plains throughout the Holocene, might have provided effective geographical barriers to wolf dispersal. More recently, the admixture of Alpine and Apennine wolf populations could have been prevented by deforestation, which was already widespread in the fifteenth century in northern Italy. This study suggests that, despite the high potential rates of dispersal and gene flow, local wolf populations may not have mixed for long periods of time.
Multitrophic interactions involving genetically modified potatoes, nontarget aphids, natural enemies and hyperparasitoids
Authors: Cowgill S. E. , Danks C. , Atkinson H. J.
Published: December 2004

Genetically modified (GM) potatoes expressing a cysteine proteinase inhibitor (cystatin) have been developed as an option for the management of plant parasitic nematodes. The relative impact of such plants on predators and parasitoids (natural enemies) of nontarget insects was determined in a field trial. The trial consisted of GM plants, control plants grown in soil treated with a nematicide and untreated control plants. The quantity of nontarget aphids and their quality as hosts for natural enemies were studied. Aphid density was significantly reduced by nematicide treatment and few natural enemies were recorded from treated potatoes during the study. In contrast, similar numbers of aphids and their more adundant predators were recorded from the untreated control and the GM potatoes. The size of aphids on GM and control plants was recorded twice during the study. During the first sampling period (2–9 July) aphids clip‐caged on GM plants were smaller than those on control plants. During the second sampling period (23–30 July) there was no difference in aphid size between those from the GM and control plants. Host size is an important component of host quality. It can affect the size and fecundity of parasitoid females and the sex ratio of their offspring. However, neither the fitness of females of Aphidius ervi, the most prevalent primary parasitoid, nor the sex ratio of their progeny, were affected when the parasitoids developed on aphids feeding on GM plants. Two guilds of secondary parasitoid were also recorded during the study. The fitness of the most abundant species, Aspahes vulgaris, was not affected when it developed on hosts from GM plants. The transgene product, OC IΔD86, was not detected in aphids that had fed on GM plants in the field, suggesting that there is minimal secondary exposure of natural enemies to the inhibitor. The results indicate that transgenic nematode resistance is potentially more compatible with aphid biological control than is current nematicide use.
Tandem constructs to mitigate transgene persistence: tobacco as a model
Authors: Al‐Ahmad Hani , Galili Shmuel , Gressel Jonathan
Published: December 2004

Some transgenic crops can introgress genes into other varieties of the crop, to related weeds or themselves remain as ‘volunteer’ weeds, potentially enhancing the invasiveness or weediness of the resulting offspring. The presently suggested mechanisms for transgene containment allow low frequency of gene release (leakage), requiring the mitigation of continued spread. Transgenic mitigation (TM), where a desired primary gene is tandemly coupled with mitigating genes that are positive or neutral to the crop but deleterious to hybrids and their progeny, was tested as a mechanism to mitigate transgene introgression. Dwarfism, which typically increases crop yield while decreasing the ability to compete, was used as a mitigator. A construct of a dominant ahasR (acetohydroxy acid synthase) gene conferring herbicide resistance in tandem with the semidominant mitigator dwarfing Δgai (gibberellic acid‐insensitive) gene was transformed into tobacco (Nicotiana tabacum). The integration and the phenotypic stability of the tandemly linked ahasR and Δgai genomic inserts in later generations were confirmed by polymerase chain reaction. The hemizygous semidwarf imazapyr‐resistant TM T1 (= BC1) transgenic plants were weak competitors when cocultivated with wild type segregants under greenhouse conditions and without using the herbicide. The competition was most intense at close spacings typical of weed offspring. Most dwarf plants interspersed with wild type died at 1‐cm, > 70% at 2.5‐cm and 45% at 5‐cm spacing, and the dwarf survivors formed no flowers. At 10‐cm spacing, where few TM plants died, only those TM plants growing at the periphery of the large cultivation containers formed flowers, after the wild type plants terminated growth. The highest reproductive TM fitness relative to the wild type was 17%. The results demonstrate the suppression of crop–weed hybrids when competing with wild type weeds, or such crops as volunteer weeds, in seasons when the selector (herbicide) is not used. The linked unfitness would be continuously manifested in future generations, keeping the transgene at a low frequency.
Genetic effects of chronic habitat fragmentation on tree species: the case of Sorbus aucuparia in a deforested Scottish landscape
Authors: Bacles C. F. E. , Lowe A. J. , Ennos R. A.
Published: December 2004

Sustainable forest restoration and management practices require a thorough understanding of the influence that habitat fragmentation has on the processes shaping genetic variation and its distribution in tree populations. We quantified genetic variation at isozyme markers and chloroplast DNA (cpDNA), analysed by polymerase chain reaction–restriction fragment length polymorphism (PCR‐RFLP) in severely fragmented populations of Sorbus aucuparia (Rosaceae) in a single catchment (Moffat) in southern Scotland. Remnants maintain surprisingly high levels of gene diversity (HE) for isozymes (HE = 0.195) and cpDNA markers (HE = 0.490). Estimates are very similar to those from non‐fragmented populations in continental Europe, even though the latter were sampled over a much larger spatial scale. Overall, no genetic bottleneck or departures from random mating were detected in the Moffat fragments. However, genetic differentiation among remnants was detected for both types of marker (isozymes Θn = 0.043, cpDNA Θc = 0.131; G‐test, P‐value < 0.001). In this self‐incompatible, insect‐pollinated, bird‐dispersed tree species, the estimated ratio of pollen flow to seed flow between fragments is close to 1 (r = 1.36). Reduced pollen‐mediated gene flow is a likely consequence of habitat fragmentation, but effective seed dispersal by birds is probably helping to maintain high levels of genetic diversity within remnants and reduce genetic differentiation between them.
Population differentiation and recombination in wheat scab populations of Gibberella zeae from the United States
Authors: Zeller Kurt A. , Bowden Robert L. , Leslie John F.
Published: December 2004

In limited previous studies of the Ascomycete fungus Gibberella zeae in North America, the populations examined were genetically and phenotypically diverse and could be viewed as subsamples of a larger population. Our objective in this study was to test the hypothesis that a homogeneous, randomly mating population of G. zeae is contiguous throughout the central and eastern United States across a span of several years. We analysed presence/absence alleles based on amplified fragment length polymorphisms (AFLPs) at 30 loci, 24 of which are defined genetically on a linkage map of G. zeae, from > 500 isolates in eight field populations from seven states collected during the 1998, 1999 and 2000 cropping seasons. All these strains had AFLP profiles similar to those of standard isolates of G. zeae phylogenetic lineage 7. All the populations are genetically similar, have high genotypic diversity and little or no detectable genetic disequilibrium, and show evidence of extensive interpopulation genetic exchange. Allele frequencies in some of the populations examined are not statistically different from one another, but others are. Thus, the populations examined are not mere subsamples from a single, large, randomly mating population. Geographic distance and genetic distance between populations are correlated significantly. The observed differences are relatively small, however, indicating that while genetic isolation by distance may occur, genetic exchange has occurred at a relatively high frequency among US populations of G. zeae. We think that these differences reflect the time required for the alleles to diffuse across the distances that separate them, because relatively little linkage disequilibrium is detected either in the population as a whole or in any of the individual subpopulations.
Multiple paternity in clutches of common lizard Lacerta vivipara: data from microsatellite markers
Authors: Laloi D. , Richard M. , Lecomte J. , Massot M. , Clobert J.
Published: December 2004

The common lizard (Lacerta vivipara) is a small live‐bearing lacertid that reproduces once a year. In order to document the poorly known mating system of this species, we present here an assessment of multiple paternity using microsatellite markers. Paternities were established within 122 clutches belonging to two wild populations from contrasted areas and to four seminatural enclosed populations. The proportion of multiply sired clutches was found to be very high (between 50.0% and 68.2%) and similar among populations, which suggests that the mating system of this species may be insensitive to environmental and population conditions.
Glucose metabolism in Chlamydia trachomatis: the ‘energy parasite’ hypothesis revisited
Authors: Iliffe‐Lee Emma R. , McClarty Grant
Published: December 2004

Chlamydia trachomatis is an obligate intracellular eubacteria that is dependent on a eukaryotic host cell for a variety of metabolites. For years, it has been speculated that chlamydiae are energy parasites, totally dependent on their host cell for ATP and other high‐energy intermediates. To determine whether C. trachomatis contains functional enzymes that produce energy or reducing power, four enzymes involved in glycolysis or the pentose phosphate pathway, specifically pyruvate kinase, phosphoglycerate kinase, glyceraldehyde‐3‐phosphate dehydrogenase and glucose‐6‐phosphate dehydrogenase, were cloned, sequenced and expressed as recombinant proteins in Escherichia coli. The deduced amino acid sequences obtained show high homology to other pyruvate kinase, phosphoglycerate kinase, glyceraldehyde‐3‐phosphate dehydrogenase and glucose‐6‐phosphate dehydrogenase enzymes. In contrast to numerous other bacterial species, chlamydial glycolytic genes are not arranged in an operon, but are dispersed throughout the genome. Results from reverse transcriptase–polymerase chain reaction (RT–PCR) analysis indicate that all four genes are maximally expressed in the middle of the chlamydial developmental cycle. The chlamydial genes are capable of complementing mutant E. coli strains lacking the respective enzyme activities. In vitro enzyme analysis indicates that recombinant chlamydial enzymes expressed in E. coli are active and, interestingly, recombinant chlamydial pyruvate kinase is not regulated allosterically by fructose 1,6 bisphosphate or AMP, as found with other bacterial pyruvate kinases. In summary, identification and characterization of these glucose‐catabolizing enzymes indicate that chlamydia contains the functional capacity to produce its own ATP and reducing power.
Conditional senescence in bacteria: death of the immortals
Authors: Nyström Thomas
Published: December 2004

Like ageing insects, worms and mammals, growth‐arrested Escherichia coli cells accumulate oxidatively damaged proteins. In the early stages of the E. coli stationary phase, this oxidation is caused by an increased production of aberrant proteins, which are especially susceptible to oxidative attack. This route of oxidation appears to elude the classical oxidative defence proteins. The failure of growth‐arrested cells fully to combat oxidative damage may also be linked to a trade‐off between proliferation activities (primarily directed by the housekeeping sigma factor, σ70) and maintenance (primarily directed by σS). This trade‐off is regulated by the alarmone ppGpp such that elevated ppGpp levels allow σS, and other alternative sigma factors, to work in concert with σ70 by shifting their relative competitiveness for RNA polymerase binding. However, even during elevated ppGpp levels and stasis, E. coli cells maintain a basal transcription of housekeeping σ70‐dependent genes, and resources are thus partly diverted from maintenance and stress defences to activities relating to proliferation. An alternative view argues for ppGpp being involved in programmed cell death upon growth arrest by regulating chromosomally located toxin–antitoxin loci. Thus, models of bacterial senescence, like those dealing with ageing in higher organisms, encompass both stochastic deterioration theories and programming theories. This review summarizes and evaluates these models.
Soluble sugar permeases of the phosphotransferase system in Escherichia coli: evidence for two physically distinct forms of the proteins in vivo
Authors: Aboulwafa Mohammad , H. Saier Milton
Published: December 2004

The bacterial phosphoenolpyruvate‐dependent phosphotransferase system (PTS) consists of a set of cytoplasmic energy‐coupling proteins and various integral membrane permeases/sugar phosphotransferases, each specific for a different sugar. We have conducted biochemical analyses of three PTS permeases (enzymes II), the glucose permease (IIGlc), the mannitol permease (IIMtl) and the mannose permease (IIMan). These enzymes each catalyse two vectorial/chemical reactions, sugar phosphorylation using phosphoenolpyruvate (PEP) as the phosphoryl donor, dependent on enzyme I, HPr and IIA as well as IIBC (the PEP reaction), and transphosphorylation using a sugar phosphate (glucose‐6‐P for IIGlc and IIMan; mannitol‐1‐P for IIMtl) as the phosphoryl donor, dependent only on IIBC (the TP reaction). When crude extracts of French‐pressed or osmotically shocked Escherichia coli cells are centrifuged in an ultracentrifuge at high speed, 5–20% of the enzyme II activity remains in the high‐speed supernatant, and passage through a gel filtration column gives two activity peaks, one in the void volume exhibiting high PEP‐dependent and TP activities, and a second included peak with high PEP‐dependent activity and high (IIMan), moderate (IIGlc) or negligible (IIMtl) TP activities. Both log and stationary phase cells exhibit comparable relative amounts of pelletable and soluble enzyme II activities, but long‐term exposure of cells to chloramphenicol results in selective loss of the soluble fraction with retention of much of the pelleted activity concomitant with extensive protein degradation. Short‐term exposure of cells to chloramphenicol results in increased activities in both fractions, possibly because of increased lipid association, with more activation in the soluble fraction than in the pelleted fraction. Western blot analyses show that the soluble IIGlc exhibits a subunit size of about 45 kDa, and all three soluble enzymes II elute from the gel filtration column with apparent molecular weights of 40–50 kDa. We propose that enzymes II of the PTS exist in two physically distinct forms in the E. coli cell, one tightly integrated into the membrane and one either soluble or loosely associated with the membrane. We also propose that the membrane‐integrated enzymes II are largely dimeric, whereas the soluble enzymes II, retarded during passage through a gel filtration column, are largely monomeric.
The archaeal cell cycle: current issues
Authors: Bernander Rolf
Published: December 2004

The recently discovered structural similarities between the archaeal Orc1/Cdc6 and bacterial DnaA initiator proteins for chromosome replication have exciting implications for cell cycle regulation. Together with current attempts to identify archaeal chromosome replication origins, the information is likely to yield fundamental insights into replication control in both archaea and eukaryotes within the near future. Several proteins that affect, or are likely to affect, chromatin structure and genome segregation in archaea have been described recently, including Sph1 and 2, ScpA and B, Sir2, Alba and Rio1p. Important insights into the properties of the MinD and FtsZ cell division proteins, and of putative cytoskeletal elements, have recently been gained in bacteria. As these proteins also are present among archaea, it is likely that the new information will also be essential for understanding archaeal genome segregation and cell division. A series of interesting cell cycle issues has been brought to light through the discovery of the novel Nanoarchaeota phylum, and these are outlined briefly. Exciting areas for extended cell cycle investigations of archaea are identified, including termination of chromosome replication, application of in situ cytological techniques for localization of cell cycle proteins and the regulatory roles of GTP‐binding proteins and small RNAs.
A C‐terminal EGF‐like domain governs BAD1 localization to the yeast surface and fungal adherence to phagocytes, but is dispensable in immune modulation and pathogenicity of Blastomyces dermatitidis
Authors: Brandhorst Tristan , Wüthrich Marcel , Finkel‐Jimenez Beatriz , Klein Bruce
Published: December 2004

BAD1, an adhesin and immune modulator of Blastomyces dermatitidis, is an essential virulence factor that is released extracellularly before association with the yeast surface. Here, deletion of the C‐terminal EGF‐like domain profoundly affected BAD1 function, leading to non‐association with yeast, extracellular accumulation and impaired yeast adherence to macrophages. In equilibrium binding assays, ΔC‐term BAD1, lacking an EGF‐like domain, bound poorly to BAD1 null yeast, yielding a low affinity (Kd, 3 × 10−7 M versus 5 × 10−8 M) and Bmax (1.9 × 105 versus 7.9 × 105) compared with BAD1. Similar protein binding profiles were observed using chitin particles, reinforcing the notion that chitin fibrils are a receptor for BAD1, and that the EGF‐like domain is critical for BAD1 interactions with chitin on yeast. ΔC‐term strains bound poorly to macrophages, compared with parental or BAD1‐reconstituted null strains. However, ΔC‐term strains and the purified protein itself sharply suppressed tumour necrosis factor (TNF)‐α release by phagocytes in vitro and in lung in vivo, and the strains retained pathogenicity in a murine model of blastomycosis. Our results illustrate the previously undefined role of the EGF‐like domain for BAD1 localization to yeast surfaces during cell wall biogenesis. They also demonstrate that the requirements for host cell binding and immune modulation by BAD1 can be dissociated from one another, and that the former is unexpectedly dispensable in the requisite role of BAD1 in pathogenesis.
The composition, structure and stability of a group II chaperonin are temperature regulated in a hyperthermophilic archaeon
Authors: Kagawa Hiromi K. , Yaoi Takuro , Brocchieri Luciano , McMillan R. Andrew , Alton Thomas , Trent Jonathan D.
Published: December 2004

The hyperthermoacidophilic archaeonSulfolobus shibataecontains group II chaperonins, known as rosettasomes, which are two nine‐membered rings composed of three different 60 kDa subunits (TF55 alpha, beta and gamma). We sequenced the gene for the gamma subunit and studied the temperature‐dependent changes in alpha, beta and gamma expression, their association into rosettasomes and their phylogenetic relationships. Alpha and beta gene expression was increased by heat shock (30 min, 86°C) and decreased by cold shock (30 min, 60°C). Gamma expression was undetectable at heat shock temperatures and low at normal temperatures (75–79°C), but induced by cold shock. Polyacrylamide gel electrophoresis indicated thatin vitroalpha and beta subunits form homo‐oligomeric rosettasomes, and mixtures of alpha, beta and gamma form hetero‐oligomeric rosettasomes. Transmission electron microscopy revealed that beta homo‐oligomeric rosettasomes and all hetero‐oligomeric rosettasomes associate into filaments.In vivorosettasomes were hetero‐oligomeric with an average subunit ratio of 1α:1β:0.1γ in cultures grown at 75°C, a ratio of 1α:3β:1γ in cultures grown at 60°C and a ratio of 2α:3β:0γ after 86°C heat shock. Using differential scanning calorimetry, we determined denaturation temperatures (Tm) for alpha, beta and gamma subunits of 95.7°C, 96.7°C and 80.5°C, respectively, and observed that rosettasomes containing gamma were relatively less stable than those with alpha and/or beta only. We propose that,in vivo, the rosettasome structure is determined by the relative abundance of subunits and not by a fixed geometry. Furthermore, phylogenetic analyses indicate that archaeal chaperonin subunits underwent multiple duplication events within species (paralogy). The independent evolution of these paralogues raises the possibility that chaperonins have functionally diversified between species.
Interactions of the quorum sensing regulator QscR: interaction with itself and the other regulators of Pseudomonas aeruginosa LasR and RhlR
Authors: Ledgham Fouzia , Ventre Isabelle , Soscia Chantal , Foglino Maryline , Sturgis James N. , Lazdunski Andrée
Published: December 2004

Pseudomonas aeruginosa controls the production of many exoproteins and secondary metabolites via a hierarchical quorum sensing (QS) regulatory cascade involving the LuxR‐like proteins LasR, RhlR and their cognate signal molecules N‐(3‐oxododecanoyl)‐l‐homoserine lactone (3O‐C12‐HSL) and N‐(butanoyl)‐l‐homoserine lactone (C4‐HSL). The finding of a third LuxR‐type protein in P. aeruginosa, QscR, adds further complexity to this regulatory network. It has been shown previously that QscR represses transcription of three QS‐controlled gene clusters, phz (phenazine), hcn (hydrogen cyanide) and qsc105 (Chugani, Whiteley, Lee, D’Argenio, Manoil, and Greenberg, 2001, Proc Natl Acad Sci USA 98: 2752–2757). In this study, we identify two novel QscR targets these are lasB, encoding the extracellular elastase, and the second phenazine gene cluster, both of which are downregulated by QscR. In addition, we show that QscR synthesis is regulated by the two‐component response regulator GacA. Taking advantage of the in vivo fluorescence anisotropy technology that we have developed, we show that QscR can be found in several different types of association. Indeed, we identify QscR multimers in the absence of any acyl‐HSL, lower order QscR oligomers associated either with C4‐HSL or 3O‐C12‐HSL and QscR‐containing heterodimers with LasR or RhlR. The formation of heterodimers between QscR and LasR or RhlR, in the absence of acyl‐HSLs, is a very exciting, new result that should improve our understanding of the QscR network and its relationship to the production of P. aeruginosa virulence factors.
Genes required for mycobacterial growth defined by high density mutagenesis
Authors: Sassetti Christopher M. , Boyd Dana H. , Rubin Eric J.
Published: December 2004

Despite over a century of research, tuberculosis remains a leading cause of infectious death worldwide. Faced with increasing rates of drug resistance, the identification of genes that are required for the growth of this organism should provide new targets for the design of antimycobacterial agents. Here, we describe the use of transposon site hybridization (TraSH) to comprehensively identify the genes required by the causative agent, Mycobacterium tuberculosis, for optimal growth. These genes include those that can be assigned to essential pathways as well as many of unknown function. The genes important for the growth of M. tuberculosis are largely conserved in the degenerate genome of the leprosy bacillus, Mycobacterium leprae, indicating that non‐essential functions have been selectively lost since this bacterium diverged from other mycobacteria. In contrast, a surprisingly high proportion of these genes lack identifiable orthologues in other bacteria, suggesting that the minimal gene set required for survival varies greatly between organisms with different evolutionary histories.
Light‐induced carotenogenesis in Myxococcus xanthus: functional characterization of the ECF sigma factor CarQ and antisigma factor CarR
Authors: Browning Douglas F. , Whitworth David E. , Hodgson David A.
Published: December 2004

Illumination of dark‐grown Myxococcus xanthus with blue light leads to the induction of carotenoid synthesis. Central to this response is the activation of the light‐inducible promoter, PcarQRS, and the transcription of three downstream genes, carQ, carR and carS. Sequence analysis predicted that CarQ is a member of the ECF (extracytoplasmic function) subfamily of RNA polymerase sigma factors, and that CarR is an inner membrane protein. Genetic analysis strongly implied that CarR is an antisigma factor that sequesters CarQ in a transcriptionally inactive complex. Using in vitro transcription run‐off assays, we present biochemical evidence that CarQ functions as a bacterial sigma factor and is responsible for transcription initiation at PcarQRS. Similar experiments using the crtI promoter failed to implicate CarQ in direct transcription of the crtI gene. Experiments using the yeast two‐hybrid system demonstrated a protein–protein interaction betweefn CarQ and CarR, providing evidence of a CarQ–CarR complex. The yeast two‐hybrid system data also indicated that CarR is capable of oligomerization. Fractionation of M. xanthus membranes with the detergent sarkosyl showed that CarR was associated with the inner membrane. Furthermore, CarR was found to be unstable in illuminated stationary phase cells, providing a possible mechanism by which the CarR–CarQ complex is disrupted.