bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the validity of habitat as a predictor of genetic structure in aquatic systems: a comparative study using California water beetles
Authors: SHORT A. E. Z , CATERINO M. S. 
Published: January 2009

AbstractAmong freshwater organisms, water flow is frequently considered to be one of the most important environmental variables affecting life‐history traits such as dispersal abilities and therefore genetic structure. Recent studies have suggested that habitat type alone as defined by water flow is predictive of genetic population differentiation, while others have advocated against broad generalizations in favour of more conservative, species‐specific conclusions. If aquatic habitat type is predictive of population differentiation, then one would expect sympatric taxa that occupy the same aquatic habitat to converge on a similar genetic structure. We tested this prediction by examining the haplotype diversity, phylogeographical concordance, population connectivity and population isolation of three lotic water beetle species in southern California:Anacaena signaticollis,Eubrianax edwardsiiandStictotarsus striatellus. In addition to coarse habitat and geography, we also controlled for the potentially confounding factors of range size, method of dispersal and clade independence. Together, the species spanned extremes of genetic and phylogeographical structure in all measures examined, suggesting that a coarse dichotomy of aquatic habitat type is not predictive of genetic structure. While there is little question that water flow plays a major role in shaping the life‐history traits of freshwater organisms, it is perilous to confer predictive properties to an artificially simplistic dichotomy or use it as a surrogate for other unmeasured variables.
Hybridization between mouse lemurs in an ecological transition zone in southern Madagascar
Authors: GLIGOR M. , GANZHORN J. U. , RAKOTONDRAVONY D. , RAMILIJAONA O. R. , RAZAFIMAHATRATRA E. , ZISCHLER H. , HAPKE A. 
Published: January 2009

AbstractHybrid zones in ecotones can be useful model systems for the study of evolutionary processes that shape the distribution and discreteness of species. Such studies could be important for an improved understanding of the complex biogeography of Madagascar, which is renowned for its outstanding degree of small‐scale endemism. Certain forest remnants in central Madagascar indicate that transitional corridors across the island could have connected microendemics in different forest types in the past. Evolutionary processes in such corridors are difficult to study because most of these corridors have disappeared due to deforestation in central Madagascar. We studied a hybrid zone in one of the few remaining ecotonal corridors between dry and humid forests in Madagascar, which connects two species of mouse lemurs,Microcebus griseorufusin dry spiny forest andMicrocebus murinusin humid littoral forest. We sampled 162 mouse lemurs at nine sites across this boundary. Morphometric analyses revealed intermediate morphotypes of many individuals in transitional habitat. Bayesian clustering of microsatellite genotypes and assignment tests yielded evidence for a mixed ancestry of mouse lemurs in the ecotone, where we also observed significant linkage disequilibria and heterozygote deficiency. In contrast to these observations, mitochondrial haplotypes displayed a sharply delimited boundary at the eastern edge of spiny forest, which was noncoincident with the signals from microsatellite data. Among several alternative scenarios, we propose asymmetric nuclear introgression due to male‐biased dispersal, divergent environmental selection, and an expansion of dry spiny forest in the course of aridification as a probable explanation of our observations.
Proteomic and phenotypic profiling of the amphibian pathogen Batrachochytrium dendrobatidis shows that genotype is linked to virulence
Authors: FISHER MATTHEW C. , BOSCH JAIME , YIN ZHIKANG , STEAD DAVID A. , WALKER JANET , SELWAY LAURA , BROWN ALISTAIR J. P. , WALKER LOUISE A. , GOW NEIL A. R. , STAJICH JASON E. , GARNER TRENTON W. J. 
Published: January 2009

AbstractPopulation genetics of the amphibian pathogen Batrachochytrium dendrobatidis (Bd) show that isolates are highly related and globally homogenous, data that are consistent with the recent epidemic spread of a previously endemic organism. Highly related isolates are predicted to be functionally similar due to low levels of heritable genetic diversity. To test this hypothesis, we took a global panel of Bd isolates and measured (i) the genetic relatedness among isolates, (ii) proteomic profiles of isolates, (iii) the susceptibility of isolates to the antifungal drug caspofungin, (iv) the variation among isolates in growth and phenotypic characteristics, and (v) the virulence of isolates against the European common toad Bufo bufo. Our results show (i) genotypic differentiation among isolates, (ii) proteomic differentiation among isolates, (iii) no significant differences in susceptibility to caspofungin, (iv) differentiation in growth and phenotypic/morphological characters, and (v) differential virulence in B. bufo. Specifically, our data show that Bd isolates can be profiled by their genotypic and proteomic characteristics, as well as by the size of their sporangia. Bd genotypic and phenotypic distance matrices are significantly correlated, showing that less‐related isolates are more biologically unique. Mass spectrometry has identified a set of candidate genes associated with inter‐isolate variation. Our data show that, despite its rapid global emergence, Bd isolates are not identical and differ in several important characters that are linked to virulence. We argue that future studies need to clarify the mechanism(s) and rate at which Bd is evolving, and the impact that such variation has on the host–pathogen dynamic.
Inferring the past to predict the future: climate modelling predictions and phylogeography for the freshwater gastropod Radix balthica (Pulmonata, Basommatophora)
Authors: CORDELLIER M. , PFENNINGER M. 
Published: January 2009

AbstractUnderstanding the impact of past climatic events on species may facilitate predictions of how species will respond to future climate change. To this end, we sampled populations of the common pond snail Radix balthica over the entire species range (northwestern Europe). Using a recently developed analytical framework that employs ecological niche modelling to obtain hypotheses that are subsequently tested with statistical phylogeography, we inferred the range dynamics of R. balthica over time. A Maxent modelling for present‐day conditions was performed to infer the climate envelope for the species, and the modelled niche was used to hindcast climatically suitable range at the last glacial maximum (LGM) c. 21 000 years ago. Ecological niche modelling predicted two suitable areas at the LGM within the present species range. Phylogeographic model selection on a COI mitochondrial DNA data set confirmed that R. balthica most likely spread from these two disjunct refuges after the LGM. The match observed between the potential range of the species at the LGM given its present climatic requirements and the phylogeographically inferred refugial areas was a clear argument in favour of niche conservatism in R. balthica, thus allowing to predict the future range. The subsequent projection of the potential range under a global change scenario predicts a moderate pole‐ward shift of the northern range limits, but a dramatic loss of areas currently occupied in France, western Great Britain and southern Germany.
Effects of dynamic landscape elements on fish dispersal: the example of creek chub (Semotilus atromaculatus)
Authors: BOIZARD J. , MAGNAN P. , ANGERS B. 
Published: January 2009

AbstractBarriers along a watercourse and interconnections between drainage systems are dynamic landscape elements that are expected to play major roles in the dispersal and genetic structure of fish species. The objective of this study was to assess the role of these elements using creek chub (Semotilus atromaculatus) in the Mastigouche Wildlife Reserve (Québec, Canada) as model. Numerous impassable waterfalls and interconnections among drainage systems were inferred with geographic information systems and confirmed de visu. The analysis of 32 populations using seven nuclear microsatellites revealed the presence of three genetically distinct groups. Some groups were found upstream of impassable barriers and in adjacent portions of distinct drainage systems. Admixture among groups was also detected in some populations. Constraining phylogenetic procedures as well as Mantel correlation tests confirmed that the genetic structure is more likely to result from interconnections between the drainage systems than from the permanent network. This study indicates that landscape elements such as interconnections are of major importance for circumventing impassable barriers and colonizing lakes that are otherwise inaccessible. Such an approach could be relevant for determining the origins of fish species (i.e. native vs. introduced) in the context of conservation.
Fine‐ and regional‐scale genetic structure of the exotic ascidian Styela clava (Tunicata) in southwest England, 50 years after its introduction
Authors: DUPONT L. , VIARD F. , DOWELL M. J. , WOOD C. , BISHOP J. D. D. 
Published: January 2009

Abstract Styela clava, an ascidian native to the northwest Pacific, was first recorded in the Atlantic at Plymouth, southwest England, in 1953. It now ranges in the northeast Atlantic from Portugal to northern Denmark, and has colonized the east coast of North America. Within the region of first introduction, we aimed to characterize current genetic diversity in the species, elucidate the respective roles of human‐aided vs. natural dispersal, and assess the extent of larval dispersal by looking for genetic differentiation at very small scales. Eight sites, mostly marinas, were studied along c. 200 km of coast in southwest England encompassing Plymouth. Five microsatellite loci were genotyped in 303 individuals to analyse gene flow at regional (among sites) and fine (within sites) scales. F‐statistics and assignment tests were used to investigate regional genetic structure. At the fine scale, deviation from mutation–drift equilibrium was tested, and isolation by distance and genetic clustering analyses were undertaken. Significant genetic differentiation existed between sites, unrelated to geographical separation; migration between geographically distant marinas was inferred, highlighting the likely importance of human‐mediated dispersal in range expansion and occupancy by S. clava. Fine‐scale population structure was present within at least four sites, which may be explained by the limited dispersal ability of this ascidian and recruitment from differentiated pools of larvae. Populations in enclosed marinas had higher self‐recruitment rates than those in open sites. Some marinas might therefore function as reservoirs of propagules for subsequent spread, whereas others might be sinks for migrants.
Antigenic protein modifications in Ehrlichia
Authors: THOMAS S. , THIRUMALAPURA N. , CROSSLEY E. C. , ISMAIL N. , WALKER D. H 
Published: January 2009

SUMMARY To develop effective vaccination strategies against Ehrlichia, we have previously reported developing an animal model of cross‐protection in which C57BL/6 mice primed with E. muris were resistant to lethal infection with Ixodes ovatus ehrlichia (IOE). Polyclonal antibody produced in mice after priming with E. muris and later injected with IOE‐detected antigenic proteins in E. muris and IOE cell lysates. Cross‐reaction of antigenic proteins was observed when we probed both the E. muris and IOE cell lysates with IOE and E. muris‐specific polyclonal antibody. Analysis of the total proteins of E. muris and IOE by two dimensional electrophoresis showed that both E. muris and IOE have the same antigenic proteins. Finally, studies on post‐translational protein modifications using a novel technique, Eastern blotting, showed that E. muris proteins are more lipoylated and glycosylated than those of IOE.
Neogene exhumation of the Marrakech High Atlas (Morocco) recorded by apatite fission‐track analysis
Authors: Balestrieri Maria Laura , Moratti Giovanna , Bigazzi Giulio , Algouti Ahmed 
Published: January 2009

AbstractApatite fission‐track (AFT) data have been obtained along a traverse across the Marrakech High Atlas to constrain its tectono‐thermal evolution. AFT ages vary between 212 ± 15 Ma and 20 ± 4 Ma. An Early Miocene AFT age accompanied by long mean track length from the central part of the chain has been interpreted as the timing of the main inversion of this region with the creation of relief because of the shortening induced by the interplay between the African and Eurasian plates. Thermal modelling of samples collected south of the South Atlas Fault Zone indicates a Middle‐Late Miocene or even later cooling that has been attributed to the component of the uplift of the chain related to the thermal anomaly present beneath the Atlas Mountains.
Identification of the novel protein QQS as a component of the starch metabolic network in Arabidopsis leaves
Authors: Li Ling , Foster Carol M. , Gan Qinglei , Nettleton Dan , James Martha G. , Myers Alan M. , Wurtele Eve Syrkin 
Published: January 2009

SummaryLittle is known about the role of proteins that lack primary sequence homology with any known motifs (proteins with unknown functions, PUFs); these comprise more than 10% of all proteins. This paper offers a generalized experimental strategy for identifying the functions of such proteins, particularly in relation to metabolism. Using this strategy, we have identified a novel regulatory function for Arabidopsis locus At3g30720 (which we term QQS for qua‐quine starch). QQS expression, revealed through global mRNA profiling, is up‐regulated in an Arabidopsis Atss3 mutant that lacks starch synthase III and has increased leaf starch content. Analysis of public microarray data using MetaOmGraph (metnetdb.org), in combination with transgenic Arabidopsis lines containing QQS promoter–GUS transgenes, indicated that QQS expression responds to a variety of developmental/genetic/environmental perturbations. In addition to the increase in the Atss3 mutant, QQS is up‐regulated in the carbohydrate mutants mex1 and sis8. A 586 nt sequence for the QQS mRNA was identified by 5′ and 3′ RACE experiments. The QQS transcript is predicted to encode a protein of 59 amino acids, whose expression was confirmed by immunological Western blot analysis. The QQS gene is recognizable in sequenced Arabidopsis ecotypes, but is not identifiable in any other sequenced species, including the closely related Brassica napus. Transgenic RNA interference lines in which QQS expression is reduced show excess leaf starch content at the end of the illumination phase of a diurnal cycle. Taken together, the data identify QQS as a potential novel regulator of starch biosynthesis.
The ABC transporter BcatrB from Botrytis cinerea exports camalexin and is a virulence factor on Arabidopsis thaliana
Authors: Stefanato Francesca L. , Abou‐Mansour Eliane , Buchala Antony , Kretschmer Matthias , Mosbach Andreas , Hahn Matthias , Bochet Christian G. , Métraux Jean‐Pierre , Schoonbeek Henk‐jan 
Published: January 2009

Summary Arabidopsis thaliana is known to produce the phytoalexin camalexin in response to abiotic and biotic stress. Here we studied the mechanisms of tolerance to camalexin in the fungus Botrytis cinerea, a necrotrophic pathogen of A. thaliana. Exposure of B. cinerea to camalexin induces expression of BcatrB, an ABC transporter that functions in the efflux of fungitoxic compounds. B. cinerea inoculated on wild‐type A. thaliana plants yields smaller lesions than on camalexin‐deficient A. thaliana mutants. A B. cinerea strain lacking functional BcatrB is more sensitive to camalexin in vitro and less virulent on wild‐type plants, but is still fully virulent on camalexin‐deficient mutants. Pre‐treatment of A. thaliana with UV‐C leads to increased camalexin accumulation and substantial resistance to B. cinerea. UV‐C‐induced resistance was not seen in the camalexin‐deficient mutants cyp79B2/B3, cyp71A13, pad3 or pad2, and was strongly reduced in ups1. Here we demonstrate that an ABC transporter is a virulence factor that increases tolerance of the pathogen towards a phytoalexin, and the complete restoration of virulence on host plants lacking this phytoalexin.
A microRNA–transcription factor module regulates lateral organ size and patterning in Arabidopsis
Authors: Larue Clayton T. , Wen Jiangqi , Walker John C. 
Published: January 2009

SummaryPrecise regulatory mechanisms are necessary to properly control the enlargement and patterning of plant lateral organs. However, our understanding of the regulatory modules that govern both of these processes is limited. An emerging theme in plant development is microRNA (miRNA)‐mediated gene regulation of transcription factors, including several NAC domain family members such as CUP‐SHAPED COTYLEDON2 (CUC2). We uncovered a novel allele of CUC2, cuc2‐1D, that revealed important functions of miRNAs and CUC2 in a regulatory module governing lateral organ enlargement and patterning. cuc2‐1D carried a single point mutation in the CUC2 miRNA target site, disrupting miRNA targeting. Disruption of the tight balance between CUC2 and its targeting miRNA, miRNA164, led to over‐accumulation of CUC2 mRNA and expansion of the CUC2 expression domain. cuc2‐1D plants had enlarged vegetative and reproductive lateral organs relative to wild‐type plants. Mechanistically, these enlarged organs resulted from an increase in cell proliferation that occurred over a longer developmental time frame relative to wild‐type. This organ enlargement was dependent on the receptor‐like kinase, ERECTA (ER). This and lateral organ patterning phenotypes in cuc2‐1D suggest that miRNA164 and CUC2 are critical regulators of both processes. Therefore, we propose that miRNA164 and CUC2 form a central regulatory module that acts as a governor of lateral organ patterning and expansion.
The vacuolar processing enzyme OsVPE1 is required for efficient glutelin processing in rice
Authors: Wang Yihua , Zhu Susong , Liu Shijia , Jiang Ling , Chen Liangming , Ren Yulong , Han Xiaohua , Liu Feng , Ji Sulan , Liu Xi , Wan Jianmin 
Published: January 2009

SummaryRice (Oryza sativa L.) accumulates prolamines and glutelins as its major storage proteins. Glutelins are synthesized on rough endoplasmic reticulum as 57‐kDa precursors; they are then sorted into protein storage vacuoles where they are processed into acidic and basic subunits. We report a novel rice glutelin mutant, W379, which accumulates higher levels of the 57‐kDa glutelin precursor. Genetic analysis revealed that the W379 phenotype is controlled by a single recessive nuclear gene. Using a map‐based cloning strategy, we identified this gene, OsVPE1, which is a homolog of the Arabidopsis βVPE gene. OsVPE1 encodes a 497‐amino‐acid polypeptide. Nucleotide sequence analysis revealed a missense mutation in W379 that changes Cys269 to Gly. Like the wild‐type protein, the mutant protein is sorted into vacuoles; however, the enzymatic activity of the mutant OsVPE1 is almost completely eliminated. Further, we show that OsVPE1 is incorrectly cleaved, resulting in a mature protein that is smaller than the wild‐type mature protein. Taken together, these results demonstrate that OsVPE1 is a cysteine protease that plays a crucial role in the maturation of rice glutelins. Further, OsVPE1 Cys269 is a key residue for maintaining the Asn‐specific cleavage activity of OsVPE1.
A soil bacterium regulates plant acquisition of iron via deficiency‐inducible mechanisms
Authors: Zhang Huiming , Sun Yan , Xie Xitao , Kim Mi‐Seong , Dowd Scot E. , Paré Paul W. 
Published: January 2009

SummaryDespite the abundance of iron in nature, it is the third most limiting nutrient for plants due to its minimal solubility in most soils. While certain soil microbes produce chelating agents that enhance the solubility of iron, the effectiveness of such siderophores in the assimilation of iron by plants is debated. With an increasing understanding that select soil microbes play a signaling role in activating growth and stress responses in plants, the question arises as to whether such symbionts regulate iron assimilation. Here we report a previously unidentified mechanism in which the growth‐promoting bacterium Bacillus subtilis GB03 activates the plant’s own iron acquisition machinery to increase assimilation of metal ions in Arabidopsis. Mechanistic studies reveal that GB03 transcriptionally up‐regulates the Fe‐deficiency‐induced transcription factor 1 (FIT1), which is necessary for GB03‐induction of ferric reductase FRO2 and the iron transporter IRT1. In addition, GB03 causes acidification of the rhizosphere by enhancing root proton release and by direct bacterial acidification, thereby facilitating iron mobility. As a result, GB03‐exposed plants have elevated endogenous iron levels as well as increased photosynthetic capacity compared with water‐treated controls. In contrast, loss‐of‐function fit1‐2 mutants are compromised in terms of enhanced iron assimilation and photosynthetic efficiency triggered by GB03. In all studies reported herein, a physical partition separating roots from bacterial media precludes non‐volatile microbial siderophores from contributing to GB03‐stimulated iron acquisition. These results demonstrate the potential of microbes to control iron acquisition in plants and emphasize the sophisticated integration of microbial signaling in photosynthetic regulation.
Community intervention to promote rational treatment of acute respiratory infection in rural Nepal
Authors: Holloway Kathleen A , Karkee Shiba B , Tamang Ashalal , Gurung Yam Bahadur , Kafle Kumud K , Pradhan Ramesh , Reeves Barnaby C 
Published: January 2009

SummaryObjective  To evaluate a community education program about treatment of acute respiratory infection (ARI).Methods  First, community case definitions for severe and mild ARI were developed. The intervention was then evaluated using a controlled before‐and‐after design. Household surveys collected data about ARI treatment in 20 clusters, each based around a school and health facility. Treatment indicators included percentages of cases attending health facilities and receiving antibiotics. The intervention consisted of an education program in schools culminating in street theater performances, discussions with mothers after performances and training for community leaders and drug retailers by paramedics. The intervention was conducted in mid‐2003. Indicators were measured before the intervention in Nov/Dec 2002 and again in Dec 2003/Jan 2004.Results  Two thousand and seven hundred and nineteen households were surveyed and 3654 under‐fives were identified, of whom 377 had severe ARI. After implementing the intervention, health post (HP) attendance rose by 13% in under‐fives with severe ARI and fell by 9% in under‐fives with mild ARI (test of interaction, P = 0.01). Use of prescribed antibiotics increased in under‐fives with severe ARI by 21% but only by 1% in under‐fives with mild ARI (test of interaction, P = 0.38). Irrespective of ARI severity, the use of non‐prescribed antibiotics dropped by 5% (P = 0.002), and consultation with female community health volunteers (FCHVs)and use of safe home remedies increased by 6.7% (P not estimated) and 5.7% (P = 0.008) respectively.Conclusion  The intervention was implemented using local structures and in difficult circumstances, yet had a moderate impact. Thus it has the potential to effect large scale changes in behaviour and merits replication elsewhere.