bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chloroplast DNA supports a hypothesis of glacial refugia over postglacial recolonization in disjunct populations of black pine (Pinus nigra) in western Europe
Authors: AFZAL‐RAFII ZARA , DODD RICHARD S. 
Published: November 2006

AbstractEuropean black pine (Pinus nigraArn.) is a widely distributed Mediterranean conifer. To test the hypothesis that fragmented populations in western Europe survivedin situduring the last glacial rather than having been re‐colonized in the postglacial period, genetic variation was assessed using a suite of 10 chloroplast DNA microsatellites. Among 311 individuals analysed, 235 haplotypes were detected revealing high levels of chloroplast haplotype diversity in most populations. Bayesian analysis using a model of linked loci, with no prior assumption of population structure, assigned individuals to 10 clusters that corresponded well with the six predefined sampling regions, while an analysis carried out at the population level and assuming unlinked loci, recovered the original six sampling regions. This regional structure was supported by a biogeographical analysis that detected five barriers, with the two most significant separating Alps from Corsica and southern Italy, and southern Spain from the Pyrenees. No signals of demographic expansion were detected, and comparisons ofRSTwithpRSTsuggested that a stepwise mutational model was important in regional differentiation, but not in population‐within‐region differentiation. These tests support long‐term persistence of the species within the six regions. The temporal depth estimate, assuming a high mutation rate in coalescent modelling, placed the deepest split between the Alps and the other regions at about 150 000 years ago, and the most recent split of Pyrenees from southern France at about 30 000 years ago. Taken together, the data suggest that chloroplast DNA is structured in black pine and disjunct populations in western Europe are likely to have been present during the Last Glacial Maximum.
Hierarchical components of genetic variation at a species boundary: population structure in two sympatric varieties ofLupinus microcarpus(Leguminosae)
Authors: DRUMMOND CHRISTOPHER S. , HAMILTON MATTHEW B. 
Published: November 2006

AbstractLupinus microcarpusis a self‐compatible annual plant that forms a species complex of morphologically variable but indeterminate varieties. In order to examine the hypothesis that varieties ofL. microcarpuscomprise genetically differentiated and reproductively isolated species, populations ofL. microcarpusvar.horizontalisand var.densifloruswere sampled from an area of sympatry in central California and genotyped using six microsatellite loci. Bayesian clustering divided the total sample into two groups corresponding to the named varieties with extremely low levels of inferred coancestry. Similarly, maximum likelihood and distance methods for genetic assignment placed individuals in two nonoverlapping groups. Evidence for isolation by distance (IBD) within each variety was found at shorter distance classes, but varieties remained differentiated in sympatry. Furthermore, coalescent estimates of divergence time indicate separation within the past 950–5050 generations, with minimal gene flow after divergence. A four‐level hierarchical analysis of molecular variance (amova) found significant levels of genetic differentiation among varieties (θP = 0.292), populations within varieties (θS = 0.449), subpopulations within populations (θSS = 0.623), and individuals within subpopulations (f = 0.421); but the greatest degree of differentiation was at the subpopulation level. Although it is sometimes assumed that the magnitude of genetic differences (e.g.FST) should be greater between species than among populations or subpopulations of the same species, shared ancestral polymorphism may lead to relatively low levels of differentiation at the species level, even as the stochastic effects of genetic drift generate higher levels of differentiation at lower hierarchical levels. These results suggest thatL. microcarpusvar.horizontalisand var.densiflorusare recently diverged yet reproductively isolated species, with high levels of inbreeding resulting from the combined effects of limited gene flow, demographic bottlenecks, and partial selfing in finite, geographically structured populations.
Divergent selection as revealed byPSTand QTL‐basedFSTin three‐spined stickleback (Gasterosteus aculeatus) populations along a coastal‐inland gradient
Authors: RAEYMAEKERS JOOST A. M. , VAN HOUDT JEROEN K. J. , LARMUSEAU MAARTEN H. D. , GELDOF SARAH , VOLCKAERT FILIP A. M. 
Published: November 2006

AbstractThree measures of divergence, estimated at nine putatively neutral microsatellite markers, 14 quantitative traits, and seven quantitative trait loci (QTL) were compared in eight populations of the three‐spined stickleback (Gasterosteus aculeatusL.) living in the Scheldt river basin (Belgium). Lowland estuarine and polder populations were polymorphic for the number of lateral plates, whereas upland freshwater populations were low‐plated. The number of short gill rakers and the length of dorsal and pelvic spines gradually declined along a coastal‐inland gradient. Plate number, short gill rakers and spine length showed moderate to strong signals of divergent selection between lowland and upland populations in comparison betweenPST(a phenotypic alternative forQST) and neutralFST. However, such comparisons rely on the unrealistic assumption that phenotypic variance equals additive genetic variance, and that nonadditive genetic effects and environmental effects can be minimized. In order to verify this assumption and to confirm the phenotypic signals of divergence, we tested for divergent selection at the underlying QTL. For plate number, strong genetic evidence for divergent selection between lowland and upland populations was obtained based on an intron marker of theEdagene, of which the genotype was highly congruent with plate morph. Genetic evidence for divergent selection on short gill rakers was limited to some population pairs whereFSTat only one of two QTL was detected as an outlier, althoughFSTat both loci correlated significantly withPST. No genetic confirmation was obtained for divergent selection on dorsal spine length, as no outlierFSTs were detected at dorsal spine QTL, and no significant correlations withPSTwere observed.
Determining the outcome of field‐based competition between two Rhizopogon species using real‐time PCR
Authors: KENNEDY PETER G. , BERGEMANN SARAH E. , HORTAL SARA , BRUNS THOMAS D. 
Published: November 2006

AbstractInterest in the ecology of ectomycorrhizal (ECM) fungi has increased considerably, but little is known about interspecific interactions among ECM species. We examined competitive interactions between Rhizopogon occidentalis and R. salebrosus at Point Reyes National Seashore, California, USA. At three field sites, species abundances were compared in single‐ and two‐species treatments on Pinus muricata seedlings inoculated with spores. Competition for root tips was assessed using real‐time polymerase chain reaction (PCR) of internal transcribed spacer rDNA. In general, we found strong competitive exclusion of R. salebrosus by R. occidentalis, with ≥ 75% of the seedlings in the two‐species treatment colonized exclusively by R. occidentalis after 5 and 10 months. However, on the seedlings that were co‐colonized, we observed no significant difference in the abundances of R. salebrosus and R. occidentalis, suggesting that once R. salebrosus was established, it was no longer competitively inferior. There were no significant differences in survival, growth, or percentage leaf nitrogen of seedlings colonized with either Rhizopogon species, but both growth and percentage leaf nitrogen were significantly higher for ECM than non‐ECM seedlings. We also observed strong positive correlations between actual ECM root tip weight and that inferred from real‐time PCR for both species, indicating that this method provided an accurate assessment of root tip occupation and hence ECM competitive dynamics. In conjunction with a previous experiment, our results indicate that competition between these two Rhizopogon species occurs similarly in both field and laboratory settings and that when colonizing from spore, timing largely determines the outcome of initial competitive interactions.
The molecular ecologist's guide to expressed sequence tags
Authors: BOUCK AMY , VISION TODD 
Published: November 2006

AbstractGenomics and bioinformatics have great potential to help address numerous topics in ecology and evolution. Expressed sequence tags (ESTs) can bridge genomics and molecular ecology because they can provide a means of accessing the gene space of almost any organism. We review how ESTs have been used in molecular ecology research in the last several years by providing sequence data for the design of molecular markers, genome‐wide studies of gene expression and selection, the identification of candidate genes underlying adaptation, and the basis for studies of gene family and genome evolution. Given the tremendous recent advances in inexpensive sequencing technologies, we predict that molecular ecologists will increasingly be developing and using EST collections in the years to come. With this in mind, we close our review by discussing aspects of EST resource development of particular relevance for molecular ecologists.
Persistent virulence associations in sexual populations of Puccinia coronata
Authors: Leonard K. J. 
Published: November 2006

From 1992 to 1999, 18 sets of aecial or uredinial isolates of Puccinia coronata were collected from two sites in Minnesota for analysis of virulence associations. In addition, one set of aecial isolates was collected in Ontario and one in New York. Also, aecial isolates and uredinial isolates collected from scattered locations in Minnesota in 1994 and again in 1995 were bulked for comparison with populations from discrete sites. Isolates were tested for virulence on 26 single‐Pc gene oat lines. Virulences to 14 pairs of differential lines were found to be significantly (P < 0·05) associated in linkage disequilibrium in at least six of the 24 site × year populations. The significant virulence associations were found among both uredinial and aecial isolates. Linkage disequilibria normally dissipate with repeated generations of sexual reproduction. Finding the same virulence associations repeatedly over years and locations for sexual populations of P. coronata indicates that certain pairs of virulence genes (or avirulence genes) contribute to increased fitness when they occur together, even in the absence of the corresponding resistance genes in the host. Mean virulence complexity did not differ significantly between a site with no known Pc genes in the host population and a site with low frequencies of Pc genes, suggesting little or no selection pressure against unnecessary virulence per se. Means and standard deviations of virulence complexity were similar for aecial and uredinial isolates within sites, which suggests that selection did not strongly favour either heterozygotes or intermediate virulence complexity during uredinial generations.
Exploiting host resistance to reduce the use of fungicides to control potato late blight
Authors: Nærstad R. , Hermansen A. , Bjor T. 
Published: November 2006

Field trials in 1996, 1997 and 1998 with six potato cultivars differing in levels of foliar and tuber race‐nonspecific resistance to late blight were treated with 100, 50 and 33% of the recommended dose of the fungicide fluazinam at application intervals of 7, 14 and 21 days. Using a mixed inoculum of six or seven indigenous isolates of Phytophthora infestans small potato plots were inoculated via infector plants. A foliar blight model for the relationship between the effects of resistance, fungicide application and disease pressure was developed using multiple regression analysis. Cultivars with a high level of quantitative resistance offered the greatest potential for fungicide reduction. The model showed that the effect of resistance on integrated control increased exponentially with increasing cultivar resistance. Reducing fungicide input by lowering the dose resulted in less foliar disease than extending application intervals. The higher the disease pressure, the greater the risk associated with reducing fungicide input by extension of application intervals. The field resistance of cultivars to tuber blight mainly determined the frequency of tuber infection. Exploiting high foliar resistance to reduce fungicide input carried a high risk when cultivar resistance to tuber blight was low. When field resistance to tuber blight was high, a medium level of resistance in the foliage could be exploited to reduce fungicide dose to c. 50%, provided application was at the right time. At a high level of field resistance to both foliar and tuber blight, application intervals could be extended.
Gene‐for‐gene relationships between rice and diverse avrBs3/pthA avirulence genes in Xanthomonas oryzae pv. oryzae
Authors: Wu X. M. , Li Y. R. , Zou L. F. , Chen G. Y. 
Published: November 2006

The interactions between Xanthomonas oryzae pv. oryzae (Xoo) and rice are controlled in a gene‐for‐gene manner. In this study, a 359 bp DNA fragment of the avrXa3 gene containing three nuclear localization signal (NLS) motifs present in all members of the avrBs3/pthA family was used as a probe to screen a genomic library of the JXOIII strain of Xoo. The results demonstrated that diverse members of the family exist in the pathogen genome. The avrBs3/pthA genes occurred at isolated individual portions or in clusters. The positive avr gene clones were transferred into the virulent recipient PXO99A. Pathogenicity tests in near isogenic lines of rice confirmed that four resistance (R) genes (Xa2, Xa3, xa5 and xa8) matched the four avr genes (avrXa2, avrXa3, avrxa5 and avrxa8) in the genome of Xoo strain JXOIII. The avrBs3/PthA‐like gene (1·7 kb) present in cosmid p54, may specifically interact with the Xa3 gene present in IRBB3, and is designated avr/pthA3. Sequencing indicated that there are only 1·5 copies of the 102 bp repeat unit in avr/pthA3. Alignment of the twelfth and thirteenth amino acids in the repetitive units encoded by this gene with those in other representatives of the AvrBs3 family revealed a unique repeat arrangement which might contribute to variation in the avirulence genes in Xoo. The parental rice line IR24 was found to contain several R genes for resistance to Xoo bacterial blight.
In vitro antifungal activity of brassinin, camalexin and two isothiocyanates against the crucifer pathogens Alternaria brassicicola and Alternaria brassicae
Authors: Sellam A. , Iacomi‐Vasilescu B. , Hudhomme P. , Simoneau P. 
Published: November 2006

In vitro assays investigated the responses of Alternaria brassicicola and A. brassicae isolates towards two crucifer phytoalexins and two isothiocyanates (ITC) by evaluating their potential toxic effects on different fungal growth parameters. Although variable responses towards each compound was observed within the species A. brassicicola, the results obtained confirmed the antifungal effects of camalexin, brassinin, allyl‐ (AlITC) and benzyl‐ (BzITC) isothiocyanates, at different developmental stages of both Alternaria species. Irrespective of the tested isolate, the phytoalexin camalexin exhibited the greater inhibitory effect with mean EC50 values ranging from 34 µm (germ‐tube elongation) to 183 µm (mycelial growth). Germ‐tube elongation was more sensitive compared to conidial germination and mycelial growth, with mean EC50 values of the former of 81 µm, 520 µm and 870 µm for brassinin, BzITC and AlITC, respectively.
Development of a PCR test to detect the downy mildew causal agent Plasmopara halstedii in sunflower seeds
Authors: Ioos R. , Laugustin L. , Rose S. , Tourvieille J. , Tourvieille de Labrouhe D. 
Published: November 2006

Plasmopara halstedii, the causal agent of downy mildew of sunflower, is an obligate parasite but viable sporangia and oospores of the pathogen may be found in a quiescent state in seeds of sunflower and therefore may be transported with sunflower seeds in international commercial exchanges. In order to prevent the spread of this pathogen, especially the introduction of potentially new races, an efficient method to analyse sunflower seed samples is required. In this study, a P. halstedii‐specific polymerase chain reaction (PCR) test was developed based on the ribosomal large sub unit (LSU) DNA. The forward (PHAL‐F) and reverse (PHAL‐R) PCR primers were designed from two polymorphic regions of LSU. After screening 22 isolates of P. halstedii corresponding to different races and countries and 32 other oomycete, deuteromycete and ascomycete isolates, the PHAL‐F/R primers amplified only a single PCR band of c. 310 bp from P. halstedii. The PHAL‐F/R PCR test could detect as little as 3 pg of P. halstedii genomic DNA per 20 µL reaction volume and enabled the direct detection of P. halstedii in 35 g sunflower seed samples without the need for any prior biological baiting step. An internal amplification control (IAC) was developed to help discriminate against false negative samples due to the potential presence of inhibitory compounds in DNA extracts. The test was successfully used on samples of naturally contaminated seeds. These new molecular tools should be of great interest for quarantine seed testing purposes.
Size, shape and intensity of aggregation of take‐all disease during natural epidemics in second wheat crops
Authors: Gosme M. , Willocquet L. , Lucas P. 
Published: November 2006

Point pattern analysis (fitting of the beta‐binomial distribution and binary form of power law) was used to describe the spatial pattern of natural take‐all epidemics (caused byGaeumannomyces graminisvar.tritici) on a second consecutive crop of winter wheat in plots under different cropping practices that could have an impact on the quantity and spatial distribution of primary inoculum, and on the spread of the disease. The spatial pattern of take‐all was aggregated in 48% of the datasets when disease incidence was assessed at the plant level and in 83% when it was assessed at the root level. Clusters of diseased roots were in general less than 1 m in diameter for crown roots and 1–1·5 m for seminal roots; when present, clusters of diseased plants were 2–2·5 m in diameter. Anisotropy of the spatial pattern was detected and could be linked to soil cultivation. Clusters did not increase in size over the cropping season, but increased spatial heterogeneity of the disease level was observed, corresponding to local disease amplification within clusters. The relative influences of autonomous spread and inoculum dispersal on the size and shape of clusters are discussed.
Antibody responses to xenogenic antigens—a study in the mouse‐to‐rat system
Authors: Bersztel A. , Lorant T. , Björkland A. , Johnsson C. , Tufveson G. 
Published: November 2006

AbstractAntibodies play a crucial role in the rejection of an organ that has been transplanted between different animal species, i.e. xenotransplantation. In previous work, we have induced a state of humoral tolerance where mouse‐to‐rat heart grafts continued to beat under ciclosporine A monotherapy. Initially, a combined treatment with ciclosporine A and 15‐deoxyspergualin was given. This state of tolerance could not be reproduced when the vascularised heart graft was replaced with a free tissue graft or xenogeneic blood transfusions. To gain further insight into the humoral response against mouse antigens, we studied the antibody production in naive rats and rats challenged with heart transplants, heart cells, mononuclear cells (MNC) and erythrocytes from mice. Rats not challenged with any mouse cells or organs had a moderate amount of antibodies targeted against mouse MNC as well as rosette‐forming cells in the spleen targeted against mouse erythrocytes. A challenge with either mouse MNC or erythrocytes lead to immunisation with antibodies of both IgM and IgG subtype directed against both MNC and erythrocytes. Antibody titres against mouse erythrocytes in animals challenged with MNC were not detectable until day 7, whereas antibody titres against mouse MNC in animals challenged with erythrocytes were detected on day 1. Immunisation with mouse erythrocytes raised the titre of rosette‐forming cells in the spleen compared with naive rats (P < 0.05). Our data indicate that different xenogeneic antigens in the mouse‐to‐rat system are shared between heart cells, MNC and erythrocytes; however, the immunisation patterns differ regarding the time when antibodies are first detected.
Identification of nine new HLA class I alleles in volunteers from the Singapore stem cell donor registries
Authors: Tang T. F. , Hou L. , Tu B. , Hwang W. Y. K. , Yeoh A. E. J. , Ng J. , Hurley C. K. 
Published: November 2006

AbstractBased on unusual probe hybridization patterns, two human leukocyte antigen (HLA)‐A, five HLA‐B, and two HLA‐C alleles (A*240208, A*3211Q; B*1822, B*3938Q, B*4606, B*4607N, B*5139; Cw*0321, Cw*0734) were identified in individuals from the Singapore Bone Marrow Donor Program and Singapore Cord Blood Bank. Eight of the nine alleles encode amino acid substitutions altering the antigen‐binding region including three alleles with changes altering a cysteine at codon 164 (A*3211Q, B*3938Q, B*4607N). This substitution either eliminates a key disulfide bond or results in a stop codon, both likely affecting the expression of the HLA molecules. Only one allele (A*240208) carries a synonymous substitution.
Association of the maternal 14‐bp insertion polymorphism in the HLA‐G gene in women with recurrent spontaneous abortions
Authors: Yan W. H. , Lin A. , Chen X. J. , Dai M. Z. , Gan L. H. , Zhou M. Y. , Zhu M. , Shi W. W. , Liu J. M. 
Published: November 2006

AbstractHuman leukocyte antigen (HLA)‐G has been postulated as an important immunotolerant molecule in maintaining fetal–maternal relationship. Recent reports indicated that the 14‐bp deletion/insertion polymorphism in exon 8 of HLA‐G gene influences HLA‐G mRNA stability and isoform splicing patterns, thus modulating the levels of HLA‐G expression. This might play an immunomodulatory role of HLA‐G during implantation and pregnancy. In the present study, 109 unrelated fertile control women and 79 women who had experienced recurrent spontaneous abortion (RSA) were genotyped for the 14‐bp insertion/deletion polymorphism. No significant difference was observed in the distribution of 14‐bp insertion/deletion genotype between controls and the RSA group. However, a greater number of 14‐bp insertion alleles exist in the RSA group than in the controls.
Effects of temperature and pH on growth and photosynthesis of the thermophilic cyanobacterium Synechococcus lividus as measured by pulse‐amplitude modulated fluorometry
Authors: Liao Chung‐Ching , Liu Shao‐Lun , Wang Wei‐Lung 
Published: November 2006

SUMMARYIn this study, the effects of five different temperatures and pH conditions on growth and photosynthetic performance of Synechococcus lividus Copeland from Taiwan were monitored in the field and the laboratory by using an underwater pulse‐amplitude modulated (Diving‐PAM) fluorometer. In the field, the optimal growth temperature of S. lividus was found to be 57°C. Such a finding was congruent with the growth rate in the laboratory culture, in which the optimal growth temperatures ranged from 45 to 60°C. In photosynthetic performance, the light‐saturated maximum relative electron transport rate (ETRmax) and the light‐limited slope (αETR) exhibited highest values at 50°C. At five different pH conditions, higher ETRmax and αETR were observed from pH 7 to 9. In addition, regression analysis demonstrated a significant positive relationship between the growth rate and the ETRmax values (R2 = 0.9527), indicating that the growth of S. lividus was largely restricted to its photosynthetic performance. In conclusion, the photosynthetic performance and growth of the thermophilic cyanobacterium S. lividus were sensitive to fluctuations in temperature but not in pH. The present investigation offers a better understanding of the photosynthetic physiology.