Genome Analysis of Minibacterium massiliensis Highlights the Convergent Evolution of Water-Living Bacteria

Filtration usually eliminates water-living bacteria. Here, we report on the complete genome sequence of Minibacterium massiliensis, a β-proteobacteria that was recovered from 0.22-μm filtered water used for patients in the hospital. The unexpectedly large 4,110,251-nucleotide genome sequence of M. massiliensis was determined using the traditional shotgun sequencing approach. Bioinformatic analyses shows that the M. massiliensis genome sequence illustrates characteristic features of water-living bacteria, including overrepresentation of genes encoding transporters and transcription regulators. Phylogenomic analysis based on the gene content of available bacterial genome sequences displays a congruent evolution of water-living bacteria from various taxonomic origins, principally for genes involved in energy production and conversion, cell division, chromosome partitioning, and lipid metabolism. This phylogenomic clustering partially results from lateral gene transfer, which appears to be more frequent in water than in other environments. The M. massiliensis genome analyses strongly suggest that water-living bacteria are a common source for genes involved in heavy-metal resistance, antibiotics resistance, and virulence factors

Nanobacteria Are Mineralo Fetuin Complexes

“Nanobacteria” are nanometer-scale spherical and ovoid particles which have spurred one of the biggest controversies in modern microbiology. Their biological nature has been severely challenged by both geologists and microbiologists, with opinions ranging from considering them crystal structures to new life forms. Although the nature of these autonomously replicating particles is still under debate, their role in several calcification-related diseases has been reported. In order to gain better insights on this calciferous agent, we performed a large-scale project, including the analysis of “nanobacteria” susceptibility to physical and chemical compounds as well as the comprehensive nucleotide, biochemical, proteomic, and antigenic analysis of these particles. Our results definitively ruled out the existence of “nanobacteria” as living organisms and pointed out the paradoxical role of fetuin (an anti-mineralization protein) in the formation of these self-propagating mineral complexes which we propose to call “nanons.” The presence of fetuin within renal calculi was also evidenced, suggesting its role as a hydroxyapatite nucleating factor

IMBeR into the future Science Plan and Implementation Strategy 2016-2025

The Integrated Marine Biosphere Research (IMBeR) project, formerly the Integrated Marine Biogeochemistry and Ecosystem Research (IMBER1) project, is a global environmental change research initiative. Since its start in 2005, IMBeR has advanced understanding about potential marine environmental effects of global change, and the impacts and linkages to human systems at multiple scales. It is apparent that complex environmental issues and associated societal/sustainability choices operate at and across the interfaces of natural and social sciences and the humanities, and require both basic, curiosity-driven research and problem-driven, policy-relevant research. Collaborative, disciplinary, interdisciplinary, transdisciplinary and integrated research that addresses key ocean science issues generated by and/or impacting society is required to provide evidence-based knowledge and guidance, along with options for policy-makers, managers and marine-related communities, to help achieve sustainability of the marine realm under global change. This recognition underlies a new vision, “Ocean sustainability under global change for the benefit of society”, to guide IMBeR research for the next decade (2016-2025). This vision recognises that the evolution of marine ecosystems (including biogeochemical cycles and human systems) is linked to natural and anthropogenic drivers and stressors, as articulated in the new IMBeR research goal to, “Understand, quantify and compare historic and present structure and functioning of linked ocean and human systems to predict and project changes including developing scenarios and options for securing or transitioning towards ocean sustainability”. To implement its new vision and goal in the next decade, IMBeR’s mission is to, “Promote integrated marine research and enable capabilities for developing and implementing ocean sustainability options within and across the natural and social sciences, and communicate relevant information and knowledge needed by society to secure sustainable, productive and healthy oceans”. This Science Plan and Implementation Strategy provides a 10-year (2016-2025) marine research agenda for IMBeR. It is developed around three Grand Challenges (GC, see Graphical Executive Summary) focusing on climate variability, global change and drivers and stressors. The qualitative and quantitative understanding of historic and present ocean variability and change (Grand Challenge I) are the basis for scenarios, projections and predictions of the future (Grand Challenge II). These are linked in Grand Challenge III to understand how humans are causing the variability and changes, and how they, in turn, are impacted by these changes, including feedbacks between the human and ocean systems. Priority research areas with overarching and specific research questions are identified for each Grand Challenge. The Grand Challenges are supplemented with Innovation Challenges (IC, see graphical executive summary) that focus on new topics for IMBeR where research is needed and where it is believed that major achievements can be made within three to five years. The Innovation Challenges also provide a means for IMBeR to adjust its focus as major science discoveries are made and new priorities arise, especially regarding scientific innovations

Measurement of the branching fraction and CP content for the decay B(0) -> D(*+)D(*-)

This is the pre-print version of the Article. The official published version can be accessed from the links below. Copyright @ 2002 APS.We report a measurement of the branching fraction of the decay B0→D*+D*- and of the CP-odd component of its final state using the BABAR detector. With data corresponding to an integrated luminosity of 20.4  fb-1 collected at the Υ(4S) resonance during 1999–2000, we have reconstructed 38 candidate signal events in the mode B0→D*+D*- with an estimated background of 6.2±0.5 events. From these events, we determine the branching fraction to be B(B0→D*+D*-)=[8.3±1.6(stat)±1.2(syst)]×10-4. The measured CP-odd fraction of the final state is 0.22±0.18(stat)±0.03(syst).This work is supported by DOE and NSF (USA), NSERC (Canada), IHEP (China), CEA and CNRS-IN2P3 (France), BMBF (Germany), INFN (Italy), NFR (Norway), MIST (Russia), and PPARC (United Kingdom). Individuals have received support from the A.P. Sloan Foundation, Research Corporation, and Alexander von Humboldt Foundation

A Study of Time-Dependent CP-Violating Asymmetries and Flavor Oscillations in Neutral B Decays at the Upsilon(4S)

We present a measurement of time-dependent CP-violating asymmetries in neutral B meson decays collected with the BABAR detector at the PEP-II asymmetric-energy B Factory at the Stanford Linear Accelerator Center. The data sample consists of 29.7 ${\rm fb}^{-1}$ recorded at the $\Upsilon(4S)$ resonance and 3.9 ${\rm fb}^{-1}$ off-resonance. One of the neutral B mesons, which are produced in pairs at the $\Upsilon(4S)$, is fully reconstructed in the CP decay modes $J/\psi K^0_S$, $\psi(2S) K^0_S$, $\chi_{c1} K^0_S$, $J/\psi K^{*0}$ ($K^{*0}\to K^0_S\pi^0$) and $J/\psi K^0_L$, or in flavor-eigenstate modes involving $D^{(*)}\pi/\rho/a_1$ and $J/\psi K^{*0}$ ($K^{*0}\to K^+\pi^-$). The flavor of the other neutral B meson is tagged at the time of its decay, mainly with the charge of identified leptons and kaons. The proper time elapsed between the decays is determined by measuring the distance between the decay vertices. A maximum-likelihood fit to this flavor eigenstate sample finds $\Delta m_d = 0.516\pm 0.016 {\rm (stat)} \pm 0.010 {\rm (syst)} {\rm ps}^{-1}$. The value of the asymmetry amplitude $\sin2\beta$ is determined from a simultaneous maximum-likelihood fit to the time-difference distribution of the flavor-eigenstate sample and about 642 tagged $B^0$ decays in the CP-eigenstate modes. We find $\sin2\beta=0.59\pm 0.14 {\rm (stat)} \pm 0.05 {\rm (syst)}$, demonstrating that CP violation exists in the neutral B meson system. (abridged)Comment: 58 pages, 35 figures, submitted to Physical Review