The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081

The human enteropathogen, Yersinia enterocolitica, is a significant link in the range of Yersinia pathologies extending from mild gastroenteritis to bubonic plague. Comparison at the genomic level is a key step in our understanding of the genetic basis for this pathogenicity spectrum. Here we report the genome of Y. enterocolitica strain 8081 (serotype 0:8; biotype 1B) and extensive microarray data relating to the genetic diversity of the Y. enterocolitica species. Our analysis reveals that the genome of Y. enterocolitica strain 8081 is a patchwork of horizontally acquired genetic loci, including a plasticity zone of 199 kb containing an extraordinarily high density of virulence genes. Microarray analysis has provided insights into species-specific Y. enterocolitica gene functions and the intraspecies differences between the high, low, and nonpathogenic Y. enterocolitica biotypes. Through comparative genome sequence analysis we provide new information on the evolution of the Yersinia. We identify numerous loci that represent ancestral clusters of genes potentially important in enteric survival and pathogenesis, which have been lost or are in the process of being lost, in the other sequenced Yersinia lineages. Our analysis also highlights large metabolic operons in Y. enterocolitica that are absent in the related enteropathogen, Yersinia pseudotuberculosis, indicating major differences in niche and nutrients used within the mammalian gut. These include clusters directing, the production of hydrogenases, tetrathionate respiration, cobalamin synthesis, and propanediol utilisation. Along with ancestral gene clusters, the genome of Y. enterocolitica has revealed species-specific and enteropathogen-specific loci. This has provided important insights into the pathology of this bacterium and, more broadly, into the evolution of the genus. Moreover, wider investigations looking at the patterns of gene loss and gain in the Yersinia have highlighted common themes in the genome evolution of other human enteropathogens.     

Estimation of the correlation between nutrient intake measures under restricted sampling

Food frequency questionnaires (FFQs) are commonly used to assess dietary intake in epidemiologic research. To evaluate the FFQ reliability, the commonly used approach is to estimate the correlation coefficient between the data given in FFQ and those in food records (for example, 4-day food records [4DFR]) for nutrients of interest. However, in a dietary intervention study, a criterion for eligibility may be to select participants who have baseline FFQ-measured dietary intake of percent energy from fat above a prespecified quantity. Other instruments, such as the 4DFR, may be subsequently administrated only to eligible participants. Under these circumstances, analysis without adjusting for the restricted population will usually lead to biased estimation of correlation coefficients and other parameters of interest. In this paper, we apply likelihood-based and multiple imputation (MI) methods to accommodate such incomplete data obtained as a result of the study design. A simulation study is conducted to examine finite sample performance of various estimators. We note that both the MI estimate and the maximum likelihood (ML) estimate based on a bivariate-normal model are not sensitive to departures from this normality assumption. This led us to investigate robustness properties of the ML estimator analytically. We present some data analyses from a dietary assessment study from the Women's Health Initiative to illustrate the methods.     

Crystal structure of ADP-ribosylated ribosomal translocase from Saccharomyces cerevisiae

The crystal structure of ADP-ribosylated yeast elongation factor 2 in the presence of sordarin and GDP has been determined at 2.6 A resolution. The diphthamide at the tip of domain IV, which is the target for diphtheria toxin and Pseudomonas aeruginosa exotoxin A, contains a covalently attached ADP-ribose that functions as a very potent inhibitor of the factor. We have obtained an electron density map of ADP-ribosylated translation factor 2 revealing both the ADP-ribosylation and the diphthamide. This is the first structure showing the conformation of an ADP-ribosylated residue and confirms the inversion of configuration at the glycosidic linkage. Binding experiments show that the ADP-ribosylation has limited effect on nucleotide binding affinity, on ribosome binding, and on association with exotoxin A. These results provide insight to the inhibitory mechanism and suggest that inhibition may be caused by erroneous interaction of the translation factor with the codon-anticodon area in the P-site of the ribosome.     

BIOME 6000: reconstructing global mid-Holocene vegetation patterns from palaeoecological records

Global change research needs data sets describing past states of the Earth system. Vegetation distributions for specified 'time slices' (with known forcings, such as changes in insolation patterns due to the Earth's orbital variations, changes in the extent of ice-sheets, and changes in atmospheric trace-gas composition) should provide a benchmark for coupled climate-biosphere models. Pollen and macrofossil records from dated sediments give spatially extensive coverage of data on vegetation distribution changes. Applications of such data have been delayed by the lack of a global synthesis. The BIOME 6000 project of IGBP aims at a synthesis for 6000 years bp. Success depends on community-wide participation for data compilation and quality assurance, and on a robust methodology for assigning palaeorecords to biomes. In the method summarized here, taxa are assigned to one or more plant functional types (PFTs) and biomes reconstructed using PFT-based definitions. By involving regional experts in PFT assignments, one can combine data from different floras without compromising global consistency in biome assignments. This article introduces a series of articles that substantially extend the BIOME 6000 data set. The list of PFTs and the reconstruction procedure itself are evolving. Some compromises (for example, restricted taxon lists in some regions) limit the precision of biome assignments and will become obsolete as primary data are put into community data bases. This trend will facilitate biome mapping for other time slices. Co-evolution of climate-biosphere modelling and palaeodata synthesis and analysis will continue.     

Regression analysis of grouped survival data with application to breast cancer data

Use of the proportional hazards regression model (Cox 1972) substantially liberalized the analysis of censored survival data with covariates. Available procedures for estimation of the relative risk parameter, however, do not adequately handle grouped survival data, or large data sets with many tied failure times. The grouped data version of the proportional hazards model is proposed here for such estimation. Asymptotic likelihood results are given, both for the estimation of the regression coefficient and the survivor function. Some special results are given for testing the hypothesis of a zero regression coefficient which leads, for example, to a generalization of the log-rank test for the comparison of several survival curves. Application to breast cancer data, from the National Cancer Institute-sponsored End Results Group, indicates that previously noted race differences in breast cancer survival times are explained to a large extent by differences in disease extent and other demographic characteristics at diagnosis.     

Histone fractionation by high-performance liquid chromatography

A method for the rapid chromatography of histones by high-performance liquid chromatography (HPLC) using a reverse-phase μBondapak C₁₈ column containing a packing of octadecylsilane chemically bonded to silica and a linear elution gradient running from water to acetonitrile is described. Two conditions were found to be necessary to achieve histone fractionation: (i) silylation of the active groups of the silica solid support, and (ii) trifluoroacetic acid (TFA) in the eluting solvents. Greater than 90% of the total [³H]lysine-labeled protein applied to the column was eluted from the column. The fractionation of the histones appears to be based on the hydrophobic properties of the proteins. The HPLC histone fractions (identified by their electrophoretic mobilities) were eluted from the column in the following order: H1, H2B, (LHP)H2A, (MHP)H2A + H4, (LHP)H3, and (MHP)H3 (where LHP and MHP refer to the less hydrophobic and more hydrophobic histone variants). Phosphorylated histone species were not resolved from their unmodified parental species. The volatile nature of the water/acetonitrile/TFA eluting solvent facilitated the recovery of salt-free histones from the eluted HPLC fractions by simple lyophilization. This system is very useful for the rapid isolation of the lysine-rich histones, H1 and H2B, and the variants of histone H3. With further development, this system is expected to extend the advantages of HPLC to the fractionation of histone H4 and the variants of histone H2A as well.