bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical correlates of the biological variation of sperm DNA fragmentation in infertile men attending an andrology outpatient clinic
Authors: Smit M. , Dohle G. R. , Hop W. C. J. , Wildhagen M. F. , Weber R. F. A. , Romijn J. C.
Published: November 2006

Determination of sperm DNA fragmentation, as assessed by the sperm chromatin structure assay (SCSA), has become an important tool for the evaluation of semen quality. The aim of the present study was to describe the biological variation of sperm DNA fragmentation in men attending an andrology clinic and to identify clinical correlates of the biological variation of sperm DNA fragmentation. For this study, two consecutive semen samples from 100 patients attending our andrology outpatient clinic were subjected to semen analysis, performed in parallel according to WHO guidelines and by SCSA. A good agreement between pairs of samples was found for SCSA‐derived variables, as indicated by a significantly lower median coefficient of variation (CV) of the DNA Fragmentation Index (DFI) and the high DNA stainability (HDS) compared with WHO semen parameters. In half of the men attending our andrology clinic, however, the individual biological variation of DFI and HDS, expressed as CV of two samples, exceeded 10%. Dysregulation of spermatogenesis, as seen as testicular insufficiency or varicocele, was not associated with increased variability of DFI or HDS. A backward multiple linear regression analysis, however, indicated that the biological variation of DFI may be more profound in men with characteristics of normal spermatogenesis. In conclusion, we confirm previous reports that sperm DNA fragmentation has a lower biological variability than classical semen parameters. We hypothesize that the sperm chromatin structure may be more influenced in patients with normal spermatogenesis, whereas in men with disturbed spermatogenesis, the chromatin structure may be already so impaired that the effect of unidentified factors leading to variability of sperm DNA fragmentation in time may not be as profound.
Vigilance and fitness in grey partridges Perdix perdix: the effects of group size and foraging‐vigilance trade‐offs on predation mortality
Authors: WATSON MARK , AEBISCHER NICHOLAS J. , CRESSWELL WILL
Published: November 2006

Vigilance increases fitness by improving predator detection but at the expense of increasing starvation risk. We related variation in vigilance among 122 radio‐tagged overwintering grey partridges Perdix perdix (L.) across 20 independent farmland sites in England to predation risk (sparrowhawk Accipiter nisus L., kill rate), use of alternative antipredation behaviours (grouping and use of cover) and survival.

Vigilance was significantly higher when individuals fed in smaller groups and in taller vegetation. In the covey period (in early winter when partridges are in flocks), vigilance and use of taller vegetation was significantly higher at sites with higher sparrowhawk predation risk, but tall vegetation was used less by larger groups. Individuals were constrained in reducing individual vigilance by group size and habitat choice because maximum group size was determined by overall density in the area during the covey period and by the formation of pairs at the end of the winter (pair period), when there was also a significant twofold increase in the use of tall cover.

Over the whole winter individual survival was higher in larger groups and was lower in the pair period. However, when controlling for group size, mean survival decreased as vigilance increased in the covey period. This result, along with vigilance being higher at sites with increasing with raptor risk, suggests individual vigilance increases arose to reduce short‐term predation risk from raptors but led to long‐term fitness decreases probably because high individual vigilance increased starvation risk or indicated longer exposure to predation. The effect of raptors on survival was less when there were large groups in open habitats, where individual partridges can probably both detect predators and feed efficiently.

Our study suggests that increasing partridge density and modifying habitat to remove the need for high individual vigilance may decrease partridge mortality. It demonstrates the general principle that antipredation behaviours may reduce fitness long‐term via their effects on the starvation–predation risk trade‐off, even though they decrease predation risk short‐term, and that it may be ecological constraints, such as poor habitat (that lead to an antipredation behaviour compromising foraging), that cause mortality, rather than the proximate effect of an antipredation behaviour such as vigilance.
Long‐term enhancement of agricultural production by restoration of biodiversity
Authors: BULLOCK JAMES M. , PYWELL RICHARD F. , WALKER KEVIN J.
Published: November 2006

Experimental manipulations have shown positive impacts of increased species richness on ecosystem productivity, but there remain some questions about this relationship. First, most studies last < 4 years, which raises issues about whether diversity–productivity relationships are maintained in mature communities. Secondly, the conservation relevance of many studies is debatable. We addressed both issues using long‐term experimental studies of the agriculturally relevant hay yield of recreated species‐rich grasslands.

Grasslands were recreated within replicated experiments in ex‐arable fields at two sites in southern England by using either species‐poor or species‐rich seed mixtures. The species‐poor mixture comprised seven grasses as recommended for grassland creation in English agri‐environment schemes. The species‐rich mixture comprised 11 grasses and 28 forbs and was designed to recreate a typical southern English hay meadow.

After 8 years the plots sown with species‐rich mixtures resembled target diverse community types. The plots sown with species‐poor mixtures had been colonized by a number of forbs but had lower numbers of grasses, legumes and other forbs than the species‐rich plots. Increased hay yield of the species‐rich plots in the first years of the experiments have been described in an earlier paper, and these differences were maintained after 8 years.

In the eighth year the species‐rich plots had an average 43% higher hay yield than the species‐poor plots. Regression analysis showed that the variation in hay yield was related to differences in the number of non‐leguminous forbs and showed no relation to grass or legume numbers. This suggests increased hay yield is an effect of the greater range of life forms exhibited by forbs rather than a simple fertilizing effect of legumes.

The nitrogen content and phosphorus content of the hay showed complex treatment effects over time. However, the nutritional value of the hay was above the minimum requirements for livestock.

Synthesis and applications. The aims of conservationists and farmers can often be in conflict. This study has shown that the recreation of diverse grasslands of conservation value can have a positive impact on hay yield, which benefits the farm business, and this is repeated across differing sites. Because the effect is maintained over time, farm income will be increased in the long term.
Amassing diversity in an ancient lake: evolution of a morphologically diverse parthenogenetic gastropod assemblage in Lake Malawi
Authors: GENNER MARTIN J. , TODD JONATHAN A. , MICHEL ELLINOR , ERPENBECK DIRK , JIMOH ABAYOMI , JOYCE DOMINO A. , PIECHOCKI ANDRZEJ , POINTIER JEAN‐PIERRE
Published: November 2006

Exceptional ecological niche diversity, clear waters and unique divergent selection pressures have often been invoked to explain high morphological and genetic diversity of taxa within ancient lakes. However, it is possible that in some ancient lake taxa high diversity has arisen because these historically stable environments have allowed accumulation of lineages over evolutionary timescales, a process impossible in neighbouring aquatic habitats undergoing desiccation and reflooding. Here we examined the evolution of a unique morphologically diverse assemblage of thiarid gastropods belonging to the Melanoides polymorpha‘complex’ in Lake Malawi. Using mitochondrial DNA sequences, we found this Lake Malawi complex was not monophyletic, instead sharing common ancestry with Melanoides anomala and Melanoides mweruensis from the Congo Basin. Fossil calibrations of molecular divergence placed the origins of this complex to within the last 4 million years. Nuclear amplified fragment length polymorphism markers revealed sympatric M. polymorpha morphs to be strongly genetically differentiated lineages, and males were absent from our samples indicating that reproduction is predominantly parthenogenetic. These results imply the presence of Lake Malawi as a standing water body over the last million years or more has facilitated accumulation of clonal morphological diversity, a process that has not taken place in more transient freshwater habitats. As such, the historical stability of aquatic environments may have been critical in determining present spatial distributions of biodiversity.
Reproductive isolation among deep‐water cichlid fishes of Lake Malawi differing in monochromatic male breeding dress
Authors: GENNER MARTIN J. , NICHOLS PAUL , CARVALHO GARY R. , ROBINSON ROSANNA L. , SHAW PAUL W. , TURNER GEORGE F.
Published: November 2006

Male nuptial colour hues are important for the maintenance of reproductive isolation among cichlid fish species, and environmental changes that lead to narrower light spectra can lead to hybridization. However, cichlid species can naturally co‐occur in narrow light spectrum habitats, such as turbid shallow lakes and the deep benthic zones of African rift lakes. Closely related species from narrow light spectrum habitats tend to differ little in the palette of male nuptial colours, thus for these taxa differences in colour patterns may be more important than differences in colour hue for species recognition. To investigate this hypothesis we examined morphometric and genetic differentiation among males of four sympatric putative species within the deep‐water genus Diplotaxodon. These taxa live in a narrow‐light spectrum environment where only blue light is present, and males differ primarily in ‘monochromatic’ black, white and silver patterning of the body and fins. Significant genetic differentiation was present among taxa in both microsatellite DNA and mitochondrial DNA, including one pair with no significant morphometric differentiation. Thus, these taxa represent reproductively isolated biological species, a result consistent with male nuptial patterning being important for species recognition and assortative mating. As such, we suggest that narrow‐light spectra need not always represent barriers to effective visually mediated mate recognition.
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

European 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

Lupinus 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

Three 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

Interest 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

Genomics 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.
Transient expression of gfp in the obligate biotrophic oomycete Plasmopara halstedii using electroporation and a mechanoperforation method
Authors: Hammer T. R. , Thines M. , Spring O.
Published: November 2006

Studying plant biotrophic oomycetes is difficult, because they depend on living plant cells for nutrition, which necessitates investigations in planta. Internal optical labelling is a powerful tool for analysing intra‐ and interspecific interactions. Different approaches are described for establishing a gfp‐transformation system for Plasmopara halstedii, the causal agent of sunflower downy mildew. A vector containing gfp and the oomycete‐specific ham34 regulators from Bremia lactucae was constructed for transformation experiments. Particle bombardment of infected sunflower cotyledons during different developmental stages of the pathogen did not result in successful transformation. In contrast, transient gfp expression in sporangia was achieved using electroporation. However, gfp expression was lost during the subsequent round of infection. A novel transformation method for biotrophic organisms in planta employing mechanoperforation – so‐called Löchern–resulted in sporangiophores of P. halstedii transiently expressing gfp and emerging distant from the site of transformation. The new technique is advantageous compared with others as the transformed hyphae can recover during their vegetative growth, before reproductive structures occur. This first step lays an important foundation for further investigations of obligate biotrophic organisms.
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.
Incidence‐density relationship of pear scab (Venturia nashicola) on fruits and leaves
Authors: Li B.‐H. , Yang J.‐R. , Li B.‐D. , Xu X.‐M.
Published: November 2006

Lesion‐count data on fruits/leaves from two regions of China and on leaves from controlled‐environment studies were used to investigate incidence‐density [incidence of leaves/fruits with lesion(s) and average number of lesions per leaf/fruit] and incidence‐incidence [incidences of leaves and shoots with lesion(s)] relationships. Few of the datasets for the number of lesions per fruit/leaf could be fitted satisfactorily by a Poisson distribution. Three two‐parameter distributions (negative binominal, Neyman type A and Polya‐Aeppli) provided significantly better fit than the Poisson distribution, indicating a degree of aggregation in the number of lesions on a single leaf/fruit. However, many datasets could still not satisfactorily be fitted by these distributions. The dynamics of aggregation of lesions on leaves/fruits was well described by Taylor's power‐law model. Regression models provided accurate predictions of the average number of lesions per leaf/fruit from the incidence of leaves or fruits with lesion(s). Nevertheless, the incidence‐density relationship varied considerably between regions and between leaf and fruit scab. Field data also indicated that the number of scabbed leaves per shoot showed some degree of aggregation. The incidence of leaves with scab could be predicted accurately from the incidence of shoots with scab. The incidence‐density relationships developed in this study could be used in making practical disease‐management decisions when incidence of leaves with scab is less than 35%.
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

Antibodies 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

Based 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

Human 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

In 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.
Nucleotide sequence diversity of the 5S rDNA spacer in the simple blade kelp genera Laminaria, Cymathaere and Kjellmaniella (Laminariales, Phaeophyceae) from northern Japan
Authors: Yotsukura Norishige , Kawai Tadashi , Kawashima Shoji , Ebata Hiroki , Ichimura Terunobu
Published: November 2006

Tandem repeats of the 5S ribosomal RNA gene (rDNA) were confirmed for almost all laminarian, cymathaerean and kjellmaniellan species distributed in northern Japan. The nucleotide sequence of the spacer region between tandemly repeated 5S rDNA was investigated for 79 samples from 31 sites. Phylogenetic analysis of the 29 different sequences detected revealed two lineages: (1) Laminaria coriacea group, including Laminaria coriacea Miyabe, Laminaria cichorioides Miyabe, Laminaria sachalinensis (Miyabe) Miyabe, Laminaria yendoana Miyabe, Cymathaere japonica Miyabe et Nagai, Kjellmaniella gyrata (Kjellman) Miyabe and Kjellmaniella crassifolia Miyabe; (2) Laminaria japonica group including Laminaria japonica Areschoug, Laminaria religiosa Miyabe, Laminaria ochotensis Miyabe, Laminaria diabolica Miyabe, Laminaria longipedalis Okamura, Laminaria angustata Kjellman and Laminaria longissima Miyabe. In addition, the latter group was divided into two: subgroup (2a) including L. angustata and L. longissima and subgroup (2b) including L. japonica, L. religiosa, L. ochotensis, L. diabolica and L. longipedalis. Members of the three groups differ from each other in the appearance of ornaments (bullation, gyration and folds) on the surface of the blade. These are absent in group (2a), only present in the early stages of the lifespan of group (2b), and present for the duration of the lifespan in group (1). Genetic distances among samples were extremely small within group (2a). Together with previous crossing studies and data on ocean currents and distribution, these findings suggest that gene flow occurs within group (2b).
Seasonal variations in the diel vertical distribution of phytoplankton and zooplankton in a shallow pond
Authors: Yamamoto Yoshimasa , Nakahara Hiroyuki
Published: November 2006

The seasonal succession of phytoplankton diversity, and the variations in the diel vertical distribution of phyto‐ and zooplankton were investigated in a small shallow pond (1.7 m water depth) in 2003. It was inferred that the water tended to stratify weakly in the daytime from February to June. In February and April, the green alga Golenkinia radiata Chodat dominated the phytoplankton assemblage. The cell density of G. radiata greatly decreased in April, when rotifers increased near the bottom. The vertical mixing was attenuated in June, large populations of the euglenoids (Lepocinclis salina Fritsch, Phacus acuminatus Stokes, Trachelomonas hispida (Perty) Stein et Deflandre) developed, and the cyanobacterium Aphanizomenon flos‐aquae var. klebahnii Elenk. appeared at low density. Euglenoids and A. flos‐aquae were mostly distributed in the bottom layer. In late September, when the water was mixed throughout the day, euglenoids and A. flos‐aquae were distributed evenly throughout the water column. The zooplankton (cyclopoid copepods and rotifers) densities in September were the lowest throughout the year. The vertical mixing increased in November, and the phytoplankton community was composed of A. flos‐aquae, P. acuminatus, T. hispida and the green alga Ankistrodesmus falcatus (Corda) Ralfs. In November, at the final stage of water bloom of A. flos‐aquae, its population density decreased with depth. The two euglenoids exhibited similar cell distributions at 0.8 m and 1.6 m during 1–3 November. A. falcatus was distributed evenly throughout the water column; however, when the vertical mixing lessened, the cells at the surface started to sink. Copepod nauplii and rotifers appeared at high densities in November. Seasonal variation in the phytoplankton community structure in the pond seemed to be related to the vertical mixing of the water. In addition, zooplankton, especially rotifers, might play an important role in initiating a spring clear‐water phase and in the bloom collapse of A. flos‐aquae.
Stephanodiscus kusuensis, sp. nov a new Pleistocene diatom from Southern Japan
Authors: Julius Matthew L. , Curtin Michael , Tanaka Hiroyuki
Published: November 2006

A new fossil diatom, Stephanodiscus kusuensis sp. nov., is described from a diatomite deposit from the Kusu Basin, Oita Prefecture Japan. Radiometric age estimates of the strata in which the taxon occurs are 400–500 kyr. The new species is distinct from all other known species of Stephanodiscus because it possesses a highly pronounced double concentric undulation and two distinct arrangements of central strutted processes. Cladistic analysis is used to identify the phylogenetic position of this taxon with respect to other Stephanodiscus species.
Reproductive morphology and taxonomic reappraisal ofExophyllum wentiiWeber‐van Bosse (Rhodomelaceae, Rhodophyta) from Bali Island, Indonesia
Authors: Indy Jeane R. , N’Yeurt Antoine D. R. , Yasui Hajime
Published: November 2006

The little‐known and rarely collected algaExophyllum wentiiWeber‐van Bosse is re‐described in detail from the type material, as well as from new collections from Indonesia, which for the first time reveal in detail the structure of cystocarpic and spermatangial plants and the development of tetrasporangial stichidia under culture conditions. New morphological reproductive information confirms placement of the genusExophyllumwithin the Rhodomelaceae.Exophyllumis distinguished from other related genera within the Rhodomelaceae by its cartilaginous, non‐trichoblastic decumbent thallus with multiple holdfasts and its discoid spermatangial organs. Some Pacific material earlier attributed toE. wentiiwas found to be misidentified and re‐assigned to the Dasyaceae.
A further phylogenetic study of the heterotrophic dinoflagellate genus, Protoperidinium (Dinophyceae) based on small and large subunit ribosomal RNA gene sequences
Authors: Yamaguchi Aika , Kawamura Hiroshi , Horiguchi Takeo
Published: November 2006

The heterotrophic marine dinoflagellate genus Protoperidinium is the largest genus in the Dinophyceae. Previously, we reported on the intrageneric and intergeneric phylogenetic relationships of 10 species of Protoperidinium, from four sections, based on small subunit (SSU) rDNA sequences. The present paper reports on the impact of data from an additional 5 species and, therefore, an additional two sections, using the SSU rDNA data, but now also incorporating sequence data from the large subunit (LSU) rDNA. These sequences, in isolation and in combination, were used to reconstruct the evolutionary history of the genus. The LSU rDNA trees support a monophyletic genus, but the phylogenetic position within the Dinophyceae remains ambiguous. The SSU, LSU and SSU + LSU rDNA phylogenies support monophyly in the sections Avellana, Divergentia, Oceanica and Protoperidinium, but the section Conica is paraphyletic. Therefore, the concept of discrete taxonomic sections based on the shape of 1′ plate and 2a plate is upheld by molecular phylogeny. Furthermore, the section Oceanica is indicated as having an early divergence from other groups within the genus. The sections Avellana and Excentrica and a clade combining the sections Divergentia/Protoperidinium derived from Conica‐type dinoflagellates independently. Analysis of the LSU rDNA data resulted in the same phylogeny as that obtained using SSU rDNA data and, with increased taxon sampling, including members of new sections, a clearer idea of the evolution of morphological features within the genus Protoperidinium was obtained. Intraspecific variation was found in Protoperidinium conicum (Gran) Balech, Protoperidinium excentricum (Paulsen) Balech and Protoperidinium pellucidum Bergh based on SSU rDNA data and also in Protoperidinium claudicans (Paulsen) Balech, P. conicum and Protoperidinium denticulatum (Gran et Braarud) Balech based on LSU rDNA sequences. The common occurrence of base pair substitutions in P. conicum is indicative of the presence of cryptic species.
Phenology of the rhodomelarian algae Neorhodomela aculeata and Ceramium kondoi and their survival strategies against herbivorous snails
Authors: Choi Han Gil , Lee Ji Hee , Choo Young‐Kug , Chai Kyu‐Yun , Kim Young Sik , Han Jung‐Soo , Prathep Anchana , Nam Ki Wan
Published: November 2006

The seasonal growth and reproductive phenology of Neorhodomela aculeata (Perestenko) Masuda and Ceramium kondoi Yendo, and the food preferences of herbivorous snails were examined to elucidate (i) why snails select the fronds of N. aculeata for their habitat; and (ii) the survival strategies of the two red algae under grazing pressures. The maximal lengths and weights of both algal species were recorded for each season over a 12‐month period beginning with the spring of 2003. C. kondoi grew in length at a faster rate than N. aculeate, whereas the turf alga N. aculeata produced new branches from the tips of broken branches. The reproductive period of C. kondoi was between the spring and summer but the reproductive organs of N. aculeata were observed throughout the year. The algal loss rate of fresh N. aculeata to snails was low but snails had a food preference for N. aculeata when compared to C. kondoi in an artificial food experiment. These results indicate that snails may adapt to chemical compounds characteristic of N. aculeata and that the alga further reduces predation damage by its structural resistance. In conclusion, the survival strategies of C. kondoi appear to be rapid growth, seasonal sexual reproduction, and a delicately branched frond morphology that reduces stable feeding patterns of its predators plus high tissue nitrogen content, whereas the survival strategy of N. aculeata includes regenerative growth responses, structural toughness and chemical defenses while under the grazing pressure of herbivorous snails.