bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evidence for a large‐scale population structure among accessions of Arabidopsis thaliana: possible causes and consequences for the distribution of linkage disequilibrium
Authors: OSTROWSKI MARIE‐FRANCE , DAVID JACQUES , SANTONI SYLVAIN , MCKHANN HEATHER , REBOUD XAVIER , LE CORRE VALERIE , CAMILLERI CHRISTINE , BRUNEL DOMINIQUE , BOUCHEZ DAVID , FAURE BENOIT , BATAILLON THOMAS 
Published: February 2006

AbstractThe existence of a large‐scale population structure was investigated in Arabidopsis thaliana by studying patterns of polymorphism in a set of 71 European accessions. We used sequence polymorphism surveyed in 10 fragments of ∼600 nucleotides and a set of nine microsatellite markers. Population structure was investigated using a model‐based inference framework. Among the accessions studied, the presence of four groups was inferred using genetic data, without using prior information on the geographical origin of the accessions. Significant genetic isolation by geographical distance was detected at the group level, together with a geographical gradient in allelic richness across groups. These results are discussed with respect to the previously proposed scenario of postglacial colonization of Europe from putative glacial refugia. Finally, the contribution of the inferred structure to linkage disequilibrium among 171 pairs of essentially unlinked markers was also investigated. Linkage disequilibrium analysis revealed that significant associations detected in the whole sample were mainly due to genetic differentiation among the inferred groups. We discuss the implication of this finding for future association studies in A. thaliana.
Phylogeographic structure and past history of the circum‐Mediterranean species Tomicus destruens Woll. (Coleoptera: Scolytinae)
Authors: HORN A. , ROUX‐MORABITO G. , LIEUTIER F. , KERDELHUE C. 
Published: February 2006

AbstractPhylogeographic studies are often focused on temperate European species with relict footholds in the Mediterranean region. Past climatic oscillations usually induced range contractions and expansions from refugial areas located in southern Europe, and spatial distribution of genetic diversity show that northward expansions were usually pioneer‐like. Actually, few studies have focused on circum‐Mediterranean species, which probably were not influenced in the same way by climatic oscillations. We present the phylogeography of the bark beetle Tomicus destruens, which is restricted to the whole Mediterranean basin and the Atlantic coasts of North Africa and Portugal. We systematically sequenced 617 bp of the mitochondrial genes COI and COII for 42 populations (N = 219). Analysis revealed 53 haplotypes geographically structured in two clades, namely eastern and western clades, that diverged during the Pleistocene. A contact zone was identified along the Adriatic coast of Italy. Interestingly, we found contrasting levels of genetic structure within each clade. The eastern group was characterized by a significant phylogeographic pattern and low levels of gene flow, whereas the western group barely showed a spatial structure in haplotype distribution. Moreover, the main pine hosts were different between groups, with the Aleppo‐brutia complex in the east and the maritime pine in the west. Potential roles of host species, climatic parameters and geographical barriers are discussed and the phylogeographic patterns are compared to classical models of postglacial recolonization in Europe.
Multifunctional analysis of Chlamydia‐specific genes in a yeast expression system
Authors: Sisko Jennifer L. , Spaeth Kris , Kumar Yadunanda , Valdivia Raphael H. 
Published: February 2006

SummaryOur understanding of how obligate intracellular pathogens co‐opt eukaryotic cellular functions has been limited by their intractability to genetic manipulation and by the abundance of pathogen‐specific genes with no known functional homologues. In this report we describe a gene expression system to characterize proteins of unknown function from the obligate intracellular bacterial pathogen Chlamydia trachomatis. We have devised a homologous recombination‐based cloning strategy to construct an ordered array of Saccharomyces cerevisiae strains expressing all Chlamydia‐specific genes. These strains were screened to identify chlamydial proteins that impaired various yeast cellular functions or that displayed tropism towards eukaryotic organelles. In addition, to identify bacterial factors that are secreted into the host cell, recombinant chlamydial proteins were screened for reactivity towards antisera raised against vacuolar membranes purified from infected mammalian cells. We report the identification of 34 C. trachomatis proteins that impact yeast cellular functions or are tropic for a range of eukaryotic organelles including mitochondria, nucleus and cytoplasmic lipid droplets, and a new family of Chlamydia‐specific proteins that are exported from the parasitopherous vacuole. The versatility of molecular manipulations and protein expression in yeast allows for the rapid construction of comprehensive protein expression arrays to explore the function of pathogen‐specific gene products from microorganisms that are difficult to genetically manipulate, grow in culture or too dangerous for routine analysis in the laboratory.
A gene involved in modifying transfer RNA is required for fungal pathogenicity and stress tolerance of Colletotrichum lagenarium
Authors: Takano Yoshitaka , Takayanagi Naoyuki , Hori Hiroyuki , Ikeuchi Yoshiho , Suzuki Tsutomu , Kimura Akiko , Okuno Tetsuro 
Published: February 2006

Summary7‐Methylguanosine (m7G) modification of tRNA occurs widely in prokaryotes and eukaryotes, although information about its biological roles is limited. Here, we report that a gene involved in m7G modification of tRNA is required for infection by the phytopathogenic fungus Colletotrichum lagenarium. Analysis of the infection‐deficient mutant of C. lagenarium, produced by plasmid insertional mutagenesis, identified a tagged gene that is designated APH1. The aph1 mutants, generated by targeted gene disruption, exhibit significant reduction in pathogenicity on the host plants. We conclude that APH1 is required for fungal infection in C. lagenarium. Aph1 showed a strong similarity to Saccharomyces cerevisiae Trm8 involved in m7G modification of tRNA. The m7G content of tRNA from the aph1 deletion mutant was severely reduced compared with that from the wild type, indicating that APH1 is required for m7G methyltransferase activity. Appressoria formed by the aph1 mutants developed penetration hyphae into cellophane, suggesting that appressoria of the mutants retain basic function for penetration. However, the aph1 mutants failed to develop intracellular penetration hyphae into epidermis of the host plants, suggesting a specific requirement of APH1 for appressorium‐mediated host invasion. The mutants also had increased sensitivity to salinity and H2O2 stresses. Interestingly, a heat shock treatment on the host plants enabled the aph1 mutant to penetrate them. These data suggest that the APH1 is required for the plant invasion, probably to overcome environmental stresses derived from basal preinvasion (penetration) defence of the host plants.
An unusual pattern of protein expression and localization of yeast alanyl‐tRNA synthetase isoforms
Authors: Huang Hsiao‐Yun , Tang Huei‐Lin , Chao Hen‐Yi , Yeh Lu‐Shu , Wang Chien‐Chia 
Published: February 2006

SummaryPrevious studies have shown that in Saccharomyces cerevisiae the mitochondrial and cytoplasmic forms of alanyl‐tRNA synthetase are encoded by a single nuclear gene, ALA1, through alternative use of in‐frame successive ACG triplets and a downstream AUG triplet. Here we show that despite the obvious participation of the non‐AUG‐initiated leader peptide in mitochondrial localization, the leader peptide per se cannot target a cytoplasmic passenger protein into mitochondria under normal conditions. Functional mapping further shows that an efficient targeting signal is composed of the leader peptide and an 18‐residue sequence downstream of Met1. Consistent to this observation, overexpression of the cytoplasmic form enables it to overcome the compartmental barrier and function in the mitochondria as well, but deletion of as few as eight amino acid residues from its amino‐terminus eliminates such a potential. Thus, the sequence upstream of the first in‐frame AUG initiator not only carries an unusual initiation site, but also contributes to a novel pattern of protein expression and localization.
Inhibition of Lon‐dependent degradation of the Escherichia coli transcription activator SoxS by interaction with ‘soxbox’ DNA or RNA polymerase
Authors: Shah Ishita M. , Wolf Richard E. 
Published: February 2006

Summary Escherichia coli SoxS, the direct transcription activator of the SoxRS (superoxide) regulon, is intrinsically unstable with an in vivo half‐life of ∼2 min. Overexpression of SoxS is lethal, but mutations interfering with DNA binding relieve the toxicity. Here, we determined the effects on the half‐life of SoxS of alanine substitutions that confer defects in positive control, i.e. transcription activation, or in specific DNA binding. We found that both types of mutations render SoxS more unstable than the wild‐type protein, as if ‘soxbox’ DNA and RNA polymerase serve as stabilizing ligands in vivo that protect SoxS from degradation by Lon, the protease shown previously to be primarily responsible for its turnover. Indeed, we found that the addition of soxbox DNA or RNA polymerase to an in vitro degradation system decreases the rate of SoxS proteolysis by Lon protease. To the best of our knowledge, these are the first examples of target DNA and RNA polymerase serving as ligands that inhibit the turnover of an unstable transcription activator.
The impact of sequence divergence and DNA mismatch repair on homeologous recombination in Arabidopsis
Authors: Li Liangliang , Jean Martine , Belzile François 
Published: February 2006

SummaryWe examined the effects of substrate divergence and DNA mismatch repair (MMR) on recombination in Arabidopsis thaliana. Relative to the frequency observed in plants with a homologous construct (0% divergence), recombination was decreased 4.1‐, 9.6‐, 11.7‐ or 20.3‐fold, respectively, in lines with constructs containing 0.5%, 2%, 4% or 9% divergence between the recombination substrates. To evaluate the contribution of the MMR system in this decrease, 12 independent reporter lines (two or three lines per reporter construct) were crossed to an AtMSH2 T‐DNA insertional mutant. We examined the recombination frequency in progeny homozygous for a reporter T‐DNA and homozygous either for the wild type or the mutant allele of AtMSH2. The loss of MMR activity led to a two‐ to ninefold increase in homeologous recombination and the size of the increase did not seem to correlate with the amount of divergence. Inversely, complementation of the insertional mutant with a wild‐type cDNA of AtMSH2 reduced recombination. Our results demonstrate clearly that sequence divergence can dramatically reduce the recombination frequency in plants and that the MMR system plays a part in this decrease.
The Agrobacterium vitis T‐6b oncoprotein induces auxin‐independent cell expansion in tobacco
Authors: Clément Bernadette , Pollmann Stephan , Weiler Elmar , Urbanczyk‐Wochniak Ewa , Otten Léon 
Published: February 2006

SummaryAmong the Agrobacterium T‐DNA genes, rolB, rolC, orf13, orf8, lso, 6b and several other genes encode weakly homologous proteins with remarkable effects on plant growth. The 6b oncogene induces tumors and enations. In order to study its properties we have used transgenic tobacco plants that carry a dexamethasone‐inducible 6b gene, dex‐T‐6b. Upon induction, dex‐T‐6b plants develop a large array of morphological modifications, some of which involve abnormal cell expansion. In the present investigation, dex‐T‐6b‐induced expansion was studied in intact leaves and an in vitro leaf disc system. Although T‐6b and indole‐3‐acetic acid (IAA) both induced expansion and were non‐additive, T‐6b expression did not increase IAA levels, nor did it induce an IAA‐responsive gene. Fusicoccin (FC) is known to stimulate expansion by increasing cell wall plasticity. T‐6b‐ and FC‐induced expansion were additive at saturating FC concentrations, indicating that T‐6b does not act by a similar mechanism to FC. T‐6b expression led to higher leaf osmolality values, in contrast to FC, suggesting that the T‐6b gene induces expansion by increasing osmolyte concentrations. Metabolite profiling showed that glucose and fructose played a major role in this increase. We infer that T‐6b disrupts the osmoregulatory controls that govern cell expansion during development and wound healing.
Peroxiredoxin Q of Arabidopsis thaliana is attached to the thylakoids and functions in context of photosynthesis†
Authors: Lamkemeyer Petra , Laxa Miriam , Collin Valérie , Li Wenxue , Finkemeier Iris , Schöttler Mark A. , Holtkamp Volker , Tognetti Vanesa B. , Issakidis‐Bourguet Emmanuelle , Kandlbinder Andrea , Weis Engelbert , Miginiac‐Maslow Myroslawa , Dietz Karl‐Josef 
Published: February 2006

SummaryPeroxiredoxin Q (Prx Q) is one out of 10 peroxiredoxins encoded in the genome of Arabidopsis thaliana, and one out of four that are targeted to plastids. Peroxiredoxin Q functions as a monomeric protein and represents about 0.3% of chloroplast proteins. It attaches to the thylakoid membrane and is detected in preparations enriched in photosystem II complexes. Peroxiredoxin Q decomposes peroxides using thioredoxin as an electron donor with a substrate preference of H2O2 > cumene hydroperoxide ≫ butyl hydroperoxide ≫ linoleoyl hydroperoxide and insignificant affinity towards complex phospholipid hydroperoxide. Plants with decreased levels of Prx Q did not have an apparently different phenotype from wildtype at the plant level. However, similar to antisense 2‐cysteine (2‐Cys) Prx plants [Baier, M. et al. (2000)Plant Physiol., 124, 823–832], Prx Q‐deficient plants had a decreased sensitivity to oxidants in a leaf slice test as indicated by chlorophyll a fluorescence measurements. Increased fluorescence ratios of photosystem II to I at 77 K and modified transcript levels of plastid‐ and nuclear‐encoded proteins show that regulatory mechanisms are at work to compensate for the lack of Prx Q. Apparently Prx Q attaches to photosystem II and has a specific function distinct from 2‐Cys peroxiredoxin in protecting photosynthesis. Its absence causes metabolic changes that are sensed and trigger appropriate compensatory responses.
Stream communities across a rural–urban landscape gradient
Authors: Urban Mark C. , Skelly David K. , Burchsted Denise , Price William , Lowry Sarah 
Published: February 2006

ABSTRACTRapid urbanization throughout the world is expected to cause extensive loss of biodiversity in the upcoming decades. Disturbances associated with urbanization frequently operate over multiple spatial scales such that local species extirpations have been attributed both to localized habitat degradation and to regional changes in land use. Urbanization also may shape stream communities by restricting species dispersal within and among stream reaches. In this patch‐dynamics view, anthropogenic disturbances and isolation jointly reduce stream biodiversity in urbanizing landscapes. We evaluated predictions of stream invertebrate community composition and abundance based on variation in environmental conditions at five distinct spatial scales: stream habitats, reaches, riparian corridors and watersheds and their spatial location within the larger three‐river basin. Despite strong associations between biodiversity loss and human density in this study, local stream habitat and stream reach conditions were poor predictors of community patterns. Instead, local community diversity and abundance were more accurately predicted by riparian vegetation and watershed landscape structure. Spatial coordinates associated with instream distances provided better predictions of stream communities than any of the environmental data sets. Together, results suggest that urbanization in the study region was associated with reduced stream invertebrate diversity through the alteration of landscape vegetation structure and patch connectivity. These findings suggest that maintaining and restoring watershed vegetation corridors in urban landscapes will aid efforts to conserve freshwater biodiversity.
Detection and quantification of herpesviruses in Kostmann syndrome periodontitis using real‐time polymerase chain reaction: a case report
Authors: Yildirim S. , Yapar M. , Kubar A. 
Published: February 2006

Background/aims:  Kostmann syndrome, or severe congenital neutropenia, is an autosomal recessive disease of neutrophil production and is associated with severe periodontal pathology. The aim of this study was to determine whether human cytomegalovirus (HCMV) and Epstein‐Barr virus (EBV) contribute to the pathogenesis of Kostmann syndrome periodontitis.Methods:  Supragingival plaque and saliva samples were taken from a 6‐year‐old boy and his 3‐year‐old sister suffering from Kostmann syndrome, and from two age‐ and gender‐matched healthy children serving as controls. The samples were taken before and 24 months after periodontal treatment. Real‐time polymerase chain reaction (TaqMan Real‐Time PCR) assay was used to quantify HCMV and EBV DNA.Results:  EBV was detected in baseline samples from the Kostmann syndrome patients but not in samples from the healthy control subjects. HCMV was only detected in the saliva of the boy with Kostman syndrome at baseline. Herpesviruses numbers decreased dramatically in the post‐treatment samples.Conclusion:  EBV and HCMV were detected in the two subjects with Kostmann syndrome periodontitis. The results of the study indicate that nonsurgical treatment of Kostmann syndrome periodontitis can reduce supragingival and salivary herpes viral loads.
Serum IgG1 and IgG2 antibody responses to Porphyromonas gingivalis in patients with periodontitis
Authors: Booth V. , Solakoglu Ö. , Bavisha N. , Curtis M. A. 
Published: February 2006

Background/aims:  Protein and carbohydrate antigens of Porphyromonas gingivalis interact with the host to produce antibody of different subclasses. IgG1 and IgG2 antibodies frequently account for approximately 90% of the total serum IgG. This work aimed to investigate serum IgG1 and IgG2 antibody responses of periodontitis patients to protein and carbohydrate‐rich antigens of P. gingivalis.Methods:  Sodium dodecyl sulphate‐polyacrylamide gel electrophoresis and Western blots of P. gingivalis antigens and proteinase K digested antigens rich in carbohydrates were used to investigate the molecular weight of antigen recognised by serum IgG1 and IgG2. Enzyme‐linked immunosorbent assay was used to measure levels of IgG1 and IgG2 antibody to P. gingivalis and radial immunodiffusion was used to estimate the total concentration of IgG1 and IgG2 in serum.Results:  Serum IgG antibodies bound to antigens of molecular weights 47, 39 and 32 kDa. Antigen most frequently recognised by both IgG1 and IgG2 antibody had a molecular weight of 47 kDa. Serum IgG2 antibody bound to carbohydrate antigen with a molecular weight of 32 kDa but there was no recognition of carbohydrate antigens by IgG1 antibodies. There was no correlation between the titre of anti‐P. gingivalis IgG1 or IgG2 antibody and the total concentration of serum IgG1 or IgG2 antibodies of all specificities.Conclusion:  Both IgG1 and IgG2 antibodies recognised a dominant antigen of 47 kDa, probably Arg‐gingipain. Much of the response to carbohydrate antigen is of the IgG2 subclass. Neither the level of IgG1 nor the IgG2 antibody specific to P. gingivalis was related to the total serum concentration of that antibody.
Human immunodeficiency virus test‐seeking motivation in blood donors, São Paulo, Brazil
Authors: Goncalez T. T. , Sabino E. C. , Murphy E. L. , Chen S. , Chamone D. A. F. , McFarland W. 
Published: February 2006

Background and Objective  Previous studies have shown that volunteer, community‐recruited donors have a higher prevalence of human immunodeficiency virus (HIV) infection in São Paulo, Brazil, than replacement donors. One hypothesis which may explain this unexpected finding is that some individuals donate blood because they are seeking HIV testing. The objective of this study was to characterize test‐seeking blood donors and to determine whether they are at higher risk for HIV infection compared with other donors.Materials and Methods  Subjects presenting for blood donation were asked to participate in a study assessing their motivations (including test seeking) to donate, as measured by perceiving donation as a means to obtain infectious disease test results. Participants completed the standard blood bank predonation screening questions plus our additional survey, and were tested for HIV, hepatitis B virus (HBV), hepatitis C virus (HCV), human T‐cell lymphocytotrophic virus (HTLV) I/II, syphilis and Chagas’ disease. As a result of anticipated low statistical power to directly measure the association between test‐seeking motivation and HIV infection, we tested for herpes simplex virus type 2 (HSV‐2) as a marker of sexual risk for HIV. Our survey includes accepted donors as well as persons whose risk‐behaviour histories would result in their exclusion from donation according to routine screening procedures.Results  Of 1720 potential blood donors randomly selected and approached, 1600 (93·0%) participated. Overall, 141 (8·8%) were classified as test seekers; 15·6% of these were HSV‐2 positive. The proportion of test seekers was the same among community‐recruited and replacement donors. Test seekers had a higher prevalence of HSV‐2 [adjusted odds ratio (AOR) 1·66; 95% confidence interval (CI): 1·06–2·59] adjusting for age, gender and prior donation. The association was significant among community‐recruited blood donors whose previous donation was more than 1 year ago (i.e. ‘lapsed donors’) (AOR 2·55; 95% CI: 1·20–5·44). Test seekers were not more likely to be rejected from blood donation as a result of health reasons, self‐reported HIV risk‐related behaviour, or by their own confidential unit exclusion. We found no difference in HSV‐2 prevalence between persons accepted for donation (15·7%) and those rejected because of self‐reported sexual risk (16·7%).Conclusions  We did not detect a difference in the proportion of test seekers across different types of blood donors; however, we did detect an association between HSV‐2 infection and test seeking, especially among community‐recruited lapsed blood donors. Of note, questions on test‐seeking behaviour detected donors with increased prevalence of HSV‐2, but the self‐reported sexual risk behaviours currently used for deferral criteria did not. Incentives to get tested at sites other than blood banks may decrease the residual risk of HIV in the blood supply.