Genome-wide meta-analysis for rheumatoid arthritis

Meta-analysis is being increasingly used as a tool for integrating data from different studies of complex phenotypes, because the power of any one study to identify causal loci is limited. We applied a novel meta-analytical approach (Loesgen et al. in Genet Epidemiol 21(Suppl 1):S142–S147, 2001) in compiling results from four studies of rheumatoid arthritis in Caucasians including two studies from NARAC (Jawaheer et al. in Am J Hum Genet 68:927–936, 2001; Jawaheer et al. in Arthritis Rheum 48:906–916, 2003), one study from the UK (MacKay et al. in Arthritis Rheum 46:632–639, 2001) and one from France (Cornelis et al. in Proc Natl Acad Sci USA 95:10746–10750, 1998). For each study, we obtained NPL scores by performing interval mapping (2 cM intervals) using GeneHunter2 (Kruglyak et al. in Am J Hum Genet 58:1347–1363, 1996; Markianos et al. in Am J Hum Genet 68:963–977, 2001). The marker maps differed among the three consortium groups, therefore, the marker maps were aligned after the interval mapping was completed and the NPL scores that were within 1 cM of each other were combined using the method of Loesgen et al. (Genet Epidemiol 21(Suppl 1):S142–S147, 2001) by calculating the weighted average of the NPL score. This approach avoids some problems in analysis encountered by using GeneHunter2 when some markers in the sample are not genotyped. This procedure provided marginal evidence (P<0.05) of linkage on chromosome 1, 2, 5 and 18, strong evidence (P<0.01) on chromosomes 8 and 16, and overwhelming evidence in the HLA region of chromosome 6.     

Phytophthora polonica, a new species isolated from declining Alnus glutinosa stands in Poland

In a survey of Phytophthora associated with alder decline in Poland, several isolates of a homothallic Phytophthora sp., which could not be assigned to other taxa including Phytophthora alni subspecies, were consistently recovered from rhizosphere soil samples. Their morphology and pathogenicity, as well as sequence data for three nuclear regions (internal transcribed spacer rDNA, elongation factor-1alpha and beta-tubulin) and a coding mitochondrial DNA region (nadh1), were examined. The new Phytophthora species is characterized by the moderate to slow growth rate of its colony in carrot agar at 20 degrees C, high optimal (c. 30 degrees C) and maximum (c. 38 degrees C) growth temperatures, formation of catenulate, often lateral, hyphal swellings, large chlamydospores in agar media and in soil extract, persistent, ovoid to ellipsoid nonpapillate sporangia and large oogonia with paragynous and sometimes amphigynous antheridia. Phytophthora polonica was slightly pathogenic to alder twigs and not pathogenic to trunks of several tree species. In a phylogenetic analysis using either Bayesian inference or maximum likelihood methods, P. polonica falls in clade 8 'sensu Kroon et al. (2004)' of Phytophthora.     

云南横坑切梢小蠹生物学研究

横坑切梢小蠹Tomicus minor (Hartig)是云南松Pinus yunnanensis Franchet的主要次期性害虫之一。1980年以来,该虫与纵坑切梢小蠹T. piniperda（L.）一起在中国西南部大量发生,导致数十万公顷云南松林受害。本文报道了横坑切梢小蠹在云南地区的生活史、生长、发育、繁殖等生物学特征。横坑切梢小蠹年生活史为一代,前后两代在冬春季有部分重叠。成虫羽化于4月下旬开始陆续,5 月下旬结束。成虫羽化后即飞到树冠上蛀食枝梢,直到11月发育成熟,开始繁殖。在此期间,每头成虫可以蛀食4～6个枝梢。横坑切梢小蠹在云南没有越冬习性。繁殖期从11月至次年3月。成虫主要在已经受到纵坑切梢小蠹危害的树木的中、下部产卵。繁殖期较纵坑切梢小蠹约迟1周。由于横坑切梢小蠹从枝梢到树干对云南松持续危害,对树木的危害性较在其它地区更为严重。横坑切梢小蠹利用受到纵坑切梢小蠹蛀害的树木繁殖产卵,加强了蠹虫对云南松树的危害,加速了受害树木的死亡进程。横坑切梢小蠹的上述生物生态学特征是该虫对云南松造成严重危害的重要原因。从横坑切梢小蠹虫体和虫坑中检测到伴生真菌云南半帚孢Leptographium yunnanensis。横坑切梢小蠹对该菌的带菌率在蛀梢期为11.5%;在蛀干中期约为10%～26%。     

Rapid and high-throughput genotyping of Staphylococcus epidermidis isolates by automated multilocus variable-number of tandem repeats: a tool for real-time epidemiology

Fast and reliable genotyping methods allowing real-time epidemiology would be instrumental to discriminate Staphylococcus epidermidis isolates, in order to evaluate potential cross-infections or to follow genome content of infecting strains of this important opportunistic pathogen. We describe an automated multilocus variable-number tandem repeat-based assay (MLVA) for the rapid genotyping of S. epidermidis. Multiplex PCR amplifications using 6 primer pairs targeting gene-regions containing variable numbers of tandem repeats and the mecA gene are resolved by micro-capillary electrophoresis and automatically assessed by cluster analysis. This genotyping technique was evaluated for discriminatory power and reproducibility on 2 sequenced strains, on a collection of 21 strains previously characterized using genotyping reference methods and finally on 65 clinical isolates identified in two different institutions. All steps of this new procedure were developed to ensure rapid turn-around time and moderate costs. Our results suggest that this rapid approach is a valuable epidemiological tool to genotype S. epidermidis isolates in real-time. The rapid analysis of a limited number of evolutionary markers showed a power of discrimination similar to that of pulse-field gel electrophoresis (PFGE) or multilocus sequence type (MLST). This type of rapid and high-throughput methodology opens the possibility to rapidly assess long-term nosocomial transmission or to characterize infecting strains in the general procedure of routine laboratories, in real-time.     

Nuclear export competence of pre-40S subunits in fission yeast requires the ribosomal protein Rps2

Ribosome biogenesis is an evolutionarily conserved pathway that requires ribosomal and nonribosomal proteins. Here, we investigated the role of the ribosomal protein S2 (Rps2) in fission yeast ribosome synthesis. As for many budding yeast ribosomal proteins, Rps2 was essential for cell viability in fission yeast and the genetic depletion of Rps2 caused a complete inhibition of 40S ribosomal subunit production. The pattern of pre-rRNA processing upon depletion of Rps2 revealed a reduction of 27SA₂ pre-rRNAs and the concomitant production of 21S rRNA precursors, consistent with a role for Rps2 in efficient cleavage at site A₂ within the 32S pre-rRNA. Importantly, kinetics of pre-rRNA accumulation as determined by rRNA pulse-chases assays indicated that a small fraction of 35S precursors matured into 20S-containing particles, suggesting that most 40S precursors were rapidly degraded in the absence of Rps2. Analysis of steady-state RNA levels revealed that some pre-40S particles were produced in Rps2-depleted cells, but that these precursors were retained in the nucleolus. Our findings suggest a role for Rps2 in a mechanism that monitors pre-40S export competence.     

Temporal changes in kin structure through a population cycle in a territorial bird, the red grouse Lagopus lagopus scoticus

Populations of red grouse ( Lagopus lagopus scoticus ) undergo regular multiannual cycles in abundance. The 'kinship hypothesis' posits that such cycles are caused by changes in kin structure among territorial males producing delayed density-dependent changes in aggressiveness, which in turn influence recruitment and regulate density. The kinship hypothesis makes several specific predictions about the levels of kinship, aggressiveness and recruitment through a population cycle: (i) kin structure will build up during the increase phase of a cycle, but break down prior to peak density; (ii) kin structure influences aggressiveness, such that there will be a negative relationship between kinship and aggressiveness over the years; (iii) as aggressiveness regulates recruitment and density, there will be a negative relationship between aggressiveness in one year and both recruitment and density in the next; (iv) as kin structure influences recruitment via an affect on aggressiveness, there will be a positive relationship between kinship in one year and recruitment the next. Here we test these predictions through the course of an 8-year cycle in a natural population of red grouse in northeast Scotland, using microsatellite DNA markers to resolve changing patterns of kin structure, and supra-orbital comb height of grouse as an index of aggressiveness. Both kin structure and aggressiveness were dynamic through the course of the cycle, and changing patterns were entirely consistent with the expectations of the kinship hypothesis. Results are discussed in relation to potential drivers of population regulation and implications of dynamic kin structure for population genetics.     

An improved method for quantitative trait loci detection and identification of within-line segregation in F2 intercross designs

We present a new flexible, simple, and powerful genome-scan method (flexible intercross analysis, FIA) for detecting quantitative trait loci (QTL) in experimental line crosses. The method is based on a pure random-effects model that simultaneously models between- and within-line QTL variation for single as well as epistatic QTL. It utilizes the score statistic and thereby facilitates computationally efficient significance testing based on empirical significance thresholds obtained by means of permutations. The properties of the method are explored using simulations and analyses of experimental data. The simulations showed that the power of FIA was as good as, or better than, Haley-Knott regression and that FIA was rather insensitive to the level of allelic fixation in the founders, especially for pedigrees with few founders. A chromosome scan was conducted for a meat quality trait in an F(2) intercross in pigs where a mutation in the halothane (Ryanodine receptor, RYR1) gene with a large effect on meat quality was known to segregate in one founder line. FIA obtained significant support for the halothane-associated QTL and identified the base generation allele with the mutated allele. A genome scan was also performed in a previously analyzed chicken F(2) intercross. In the chicken intercross analysis, four previously detected QTL were confirmed at a 5% genomewide significance level, and FIA gave strong evidence (P < 0.01) for two of these QTL to be segregating within the founder lines. FIA was also extended to account for epistasis and using simulations we show that the method provides good estimates of epistatic QTL variance even for segregating QTL. Extensions of FIA and its applications on other intercross populations including backcrosses, advanced intercross lines, and heterogeneous stocks are also discussed.     

Filtering and interpreting location errors in satellite telemetry of marine animals

Argos telemetry offers a powerful means of tracking wild animals in their habitat, yet the delivered locations are subject to complex errors and random coverage. Bayesian filters and statistical models allow for objective trajectory estimates and inference on movement rates. As an alternative to Monte-Carlo methods, we investigate here how classic time series technique, such as the Kalman Filter, can be made robust to uncover patterns in the data. Our approach relies on a composite measurement model to account for outliers, and makes use of all the Location Classes to smooth observations and regularize the track to a regular time grid. Two application examples are presented. Using data from freely-swimming leatherback turtles, we confirm that locations of class A (LCA) are more accurate on average than class 0, and we recommend their use in tracking studies. We further show how measurement errors (and their geometry) interact with the assumed movement model, further modulating the final location error and the discriminating ability of the filter. The choice of the movement model appears important, since a model with no velocity constraint may fit observational errors at the expense of trajectory smoothness, while a speed-based model is better behaved but less forgiving for data fitting and outlier identification. Varying sea surface temperatures also appear to degrade the quality of locations and increase the occurrence of outliers, possibly in relation to thermal stratification and depth behavior. These results have important implications when inferring changes in behavior from long-term movements.