Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction

Variably present genes and pseudogenes in Rickettsia species tend to have been acquired more recently and to be more divergent from the genes conserved across all specie

CO adsorption on Cu(111) and Cu(001) surfaces: improving site preference in DFT calculations

CO adsorption on Cu(111) and Cu(001) surfaces has been studied within ab-initio density functional theory (DFT). The structural, vibrational and thermodynamic properties of the adsorbate-substrate complex have been calculated. Calculations within the generalized gradient approximation (GGA) predict adsorption in the threefold hollow on Cu(111) and in the bridge-site on Cu(001), instead of on-top as found experimentally. It is demonstrated that the correct site preference is achieved if the underestimation of the HOMO-LUMO gap of CO characteristic for DFT is correct by applying a molecular DFT+U approach. The DFT+U approach also produces good agreement with the experimentally measured adsorption energies, while introducing only small changes in the calculated geometrical and vibrational properties further improving agreement with experiment which is fair already at the GGA level.Comment: 15 pages, 3 figures, submitted to Surf. Sci., WWW: http://cms.mpi.univie.ac.at/mgajdos

Genome dynamics of Bartonella grahamii in micro-populations of woodland rodents

<p>Abstract</p> <p>Background</p> <p>Rodents represent a high-risk reservoir for the emergence of new human pathogens. The recent completion of the 2.3 Mb genome of <it>Bartonella grahamii</it>, one of the most prevalent blood-borne bacteria in wild rodents, revealed a higher abundance of genes for host-cell interaction systems than in the genomes of closely related human pathogens. The sequence variability within the global <it>B. grahamii </it>population was recently investigated by multi locus sequence typing, but no study on the variability of putative host-cell interaction systems has been performed.</p> <p>Results</p> <p>To study the population dynamics of <it>B. grahamii</it>, we analyzed the genomic diversity on a whole-genome scale of 27 <it>B. grahamii </it>strains isolated from four different species of wild rodents in three geographic locations separated by less than 30 km. Even using highly variable spacer regions, only 3 sequence types were identified. This low sequence diversity contrasted with a high variability in genome content. Microarray comparative genome hybridizations identified genes for outer surface proteins, including a repeated region containing the <it>fha </it>gene for filamentous hemaggluttinin and a plasmid that encodes a type IV secretion system, as the most variable. The estimated generation times in liquid culture medium for a subset of strains ranged from 5 to 22 hours, but did not correlate with sequence type or presence/absence patterns of the <it>fha </it>gene or the plasmid.</p> <p>Conclusion</p> <p>Our study has revealed a geographic microstructure of <it>B. grahamii </it>in wild rodents. Despite near-identity in nucleotide sequence, major differences were observed in gene presence/absence patterns that did not segregate with host species. This suggests that genetically similar strains can infect a range of different hosts.</p

Genotyping Rickettsia prowazekii Isolates

We developed a typing method that can differentiate 8 strains of Rickettsia prowazekii into 7 genotypes. This method can be used to type and trace the origin of R. prowazekii isolated from samples collected during epidemics after a bioterrorism attack

Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade

Zaremba-Niedzwiedzka K, Viklund J, Zhao W, et al. Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade. Genome biology. 2013;14(11): R130.BACKGROUND: The SAR11 group of Alphaproteobacteria is highly abundant in the oceans. It contains a recently diverged freshwater clade, which offers the opportunity to compare adaptations to salt- and freshwaters in a monophyletic bacterial group. However, there are no cultivated members of the freshwater SAR11 group and no genomes have been sequenced yet. RESULTS: We isolated ten single SAR11 cells from three freshwater lakes and sequenced and assembled their genomes. A phylogeny based on 57 proteins indicates that the cells are organized into distinct microclusters. We show that the freshwater genomes have evolved primarily by the accumulation of nucleotide substitutions and that they have among the lowest ratio of recombination to mutation estimated for bacteria. In contrast, members of the marine SAR11 clade have one of the highest ratios. Additional metagenome reads from six lakes confirm low recombination frequencies for the genome overall and reveal lake-specific variations in microcluster abundances. We identify hypervariable regions with gene contents broadly similar to those in the hypervariable regions of the marine isolates, containing genes putatively coding for cell surface molecules. CONCLUSIONS: We conclude that recombination rates differ dramatically in phylogenetic sister groups of the SAR11 clade adapted to freshwater and marine ecosystems. The results suggest that the transition from marine to freshwater systems has purged diversity and resulted in reduced opportunities for recombination with divergent members of the clade. The low recombination frequencies of the LD12 clade resemble the low genetic divergence of host-restricted pathogens that have recently shifted to a new host

Disruption of Parasite hmgb2 Gene Attenuates Plasmodium berghei ANKA Pathogenicity

Eukaryotic high-mobility-group-box (HMGB) proteins are nuclear factors involved in chromatin remodeling and transcription regulation. When released into the extracellular milieu, HMGB1 acts as a proinflammatory cytokine that plays a central role in the pathogenesis of several immune-mediated inflammatory diseases. We found that the Plasmodium genome encodes two genuine HMGB factors, Plasmodium HMGB1 and HMGB2, that encompass, like their human counterparts, a proinflammatory domain. Given that these proteins are released from parasitized red blood cells, we then hypothesized that Plasmodium HMGB might contribute to the pathogenesis of experimental cerebral malaria (ECM), a lethal neuroinflammatory syndrome that develops in C57BL/6 (susceptible) mice infected with Plasmodium berghei ANKA and that in many aspects resembles human cerebral malaria elicited by P. falciparum infection. The pathogenesis of experimental cerebral malaria was suppressed in C57BL/6 mice infected with P. berghei ANKA lacking the hmgb2 gene (Δhmgb2 ANKA), an effect associated with a reduction of histological brain lesions and with lower expression levels of several proinflammatory genes. The incidence of ECM in pbhmgb2-deficient mice was restored by the administration of recombinant PbHMGB2. Protection from experimental cerebral malaria in Δhmgb2 ANKA-infected mice was associated with reduced sequestration in the brain of CD4(+) and CD8(+) T cells, including CD8(+) granzyme B(+) and CD8(+) IFN-γ(+) cells, and, to some extent, neutrophils. This was consistent with a reduced parasite sequestration in the brain, lungs, and spleen, though to a lesser extent than in wild-type P. berghei ANKA-infected mice. In summary, Plasmodium HMGB2 acts as an alarmin that contributes to the pathogenesis of cerebral malaria.Pitié-Salpêtrière, Institut Pasteur (Paris)

The GATA1s isoform is normally down-regulated during terminal haematopoietic differentiation and over-expression leads to failure to repress MYB, CCND2 and SKI during erythroid differentiation of K562 cells

Background: Although GATA1 is one of the most extensively studied haematopoietic transcription factors little is currently known about the physiological functions of its naturally occurring isoforms GATA1s and GATA1FL in humans—particularly whether the isoforms have distinct roles in different lineages and whether they have non-redundant roles in haematopoietic differentiation. As well as being of general interest to understanding of haematopoiesis, GATA1 isoform biology is important for children with Down syndrome associated acute megakaryoblastic leukaemia (DS-AMKL) where GATA1FL mutations are an essential driver for disease pathogenesis. &lt;p/&gt;Methods: Human primary cells and cell lines were analyzed using GATA1 isoform specific PCR. K562 cells expressing GATA1s or GATA1FL transgenes were used to model the effects of the two isoforms on in vitro haematopoietic differentiation. &lt;p/&gt;Results: We found no evidence for lineage specific use of GATA1 isoforms; however GATA1s transcripts, but not GATA1FL transcripts, are down-regulated during in vitro induction of terminal megakaryocytic and erythroid differentiation in the cell line K562. In addition, transgenic K562-GATA1s and K562-GATA1FL cells have distinct gene expression profiles both in steady state and during terminal erythroid differentiation, with GATA1s expression characterised by lack of repression of MYB, CCND2 and SKI. &lt;p/&gt;Conclusions: These findings support the theory that the GATA1s isoform plays a role in the maintenance of proliferative multipotent megakaryocyte-erythroid precursor cells and must be down-regulated prior to terminal differentiation. In addition our data suggest that SKI may be a potential therapeutic target for the treatment of children with DS-AMKL

Do female association preferences predict the likelihood of reproduction?

Sexual selection acting on male traits through female mate choice is commonly inferred from female association preferences in dichotomous mate choice experiments. However, there are surprisingly few empirical demonstrations that such association preferences predict the likelihood of females reproducing with a particular male. This information is essential to confirm association preferences as good predictors of mate choice. We used green swordtails (&lt;i&gt;Xiphophorus helleri&lt;/i&gt;) to test whether association preferences predict the likelihood of a female reproducing with a male. Females were tested for a preference for long- or short-sworded males in a standard dichotomous choice experiment and then allowed free access to either their preferred or non-preferred male. If females subsequently failed to produce fry, they were provided a second unfamiliar male with similar sword length to the first male. Females were more likely to reproduce with preferred than non-preferred males, but for those that reproduced, neither the status (preferred/non-preferred) nor the sword length (long/short) of the male had an effect on brood size or relative investment in growth by the female. There was no overall preference based on sword length in this study, but male sword length did affect likelihood of reproduction, with females more likely to reproduce with long- than short-sworded males (independent of preference for such males in earlier choice tests). These results suggest that female association preferences are good indicators of female mate choice but that ornament characteristics of the male are also important

Multichannel response analysis on 2D projection views for detection of clustered microcalcifications in digital breast tomosynthesis

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134871/1/mp8694.pd

Deformation of Codimension-2 Surface and Horizon Thermodynamics

The deformation equation of a spacelike submanifold with an arbitrary codimension is given by a general construction without using local frames. In the case of codimension-1, this equation reduces to the evolution equation of the extrinsic curvature of a spacelike hypersurface. In the more interesting case of codimension-2, after selecting a local null frame, this deformation equation reduces to the well known (cross) focusing equations. We show how the thermodynamics of trapping horizons is related to these deformation equations in two different formalisms: with and without introducing quasilocal energy. In the formalism with the quasilocal energy, the Hawking mass in four dimension is generalized to higher dimension, and it is found that the deformation of this energy inside a marginal surface can be also decomposed into the contributions from matter fields and gravitational radiation as in the four dimension. In the formalism without the quasilocal energy, we generalize the definition of slowly evolving future outer trapping horizons proposed by Booth to past trapping horizons. The dynamics of the trapping horizons in FLRW universe is given as an example. Especially, the slowly evolving past trapping horizon in the FLRW universe has close relation to the scenario of slow-roll inflation. Up to the second order of the slowly evolving parameter in this generalization, the temperature (surface gravity) associated with the slowly evolving trapping horizon in the FLRW universe is essentially the same as the one defined by using the quasilocal energy.Comment: Latex, 61 pages, no figures; v2, type errors corrected; v3, references and comments are added, English is improved, to appear in JHE