Molecular analysis of the distribution and phylogeny of the soxB gene among sulfur-oxidizing bacteria - evolution of the Sox sulfur-oxidizing enzyme system

The soxB gene encodes the SoxB component of the periplasmic thiosulfate-oxidizing Sox enzyme complex, which has been proposed to be widespread among the various phylogenetic groups of sulfur-oxidizing bacteria (SOB) that convert thiosulfate to sulfate with and without the formation of sulfur globules as intermediate. Indeed, the comprehensive genetic and genomic analyses presented in the present study identified the soxB gene in 121 phylogenetically and physiologically divergent SOB, including several species for which thiosulfate utilization has not been reported yet. In first support of the previously postulated general involvement of components of the Sox enzyme complex in the thiosulfate oxidation process of sulfur-storing SOB, the soxB gene was detected in all investigated photo- and chemotrophic species that form sulfur globules during thiosulfate oxidation (Chromatiaceae, Chlorobiaceae, Ectothiorhodospiraceae, Thiothrix, Beggiatoa, Thiobacillus, invertebrate symbionts and free-living relatives). The SoxB phylogeny reflected the major 16S rRNA gene-based phylogenetic lineages of the investigated SOB, although topological discrepancies indicated several events of lateral soxB gene transfer among the SOB, e.g. its independent acquisition by the anaerobic anoxygenic phototrophic lineages from different chemotrophic donor lineages. A putative scenario for the proteobacterial origin and evolution of the Sox enzyme system in SOB is presented considering the phylogenetic, genomic (sox gene cluster composition) and geochemical data

Size Doesn't Matter: Towards a More Inclusive Philosophy of Biology

notes: As the primary author, O’Malley drafted the paper, and gathered and analysed data (scientific papers and talks). Conceptual analysis was conducted by both authors.publication-status: Publishedtypes: ArticlePhilosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations

Circular dichroism of green bacterial chlorosomes.

Positive and negative bands in previously measured circular dichroism (CD) spectra of Chlorobium limicola chlorosomes appeared to be sign-reversed relative to those of Chloroflexus aurantiacus chlorosomes in the 740-750 nm spectral region where bacteriochlorophyll (BChl) c absorbs maximally. It was not clear, however, whether this difference was intrinsic to the chlorosomes or was due to differences in the procedures used to prepare them. We therefore repeated the CD measurements using chlorosomes isolated from both Cb. limicola f. thiosulfatophilum and Cf. aurantiacus using the method of Gerola and Olson (1986, Biochim. Biophys. Acta 848: 69-76). Contrary to the earlier results, both types of chlorosomes had very similar CD spectra, suggesting that both have similar arrangements of BChl c molecules. The previously reported difference between the CD spectra of Chlorobium and Chloroflexus chlorosomes is due to the instability of Chlorobium chlorosomes, which can undergo a hypsochromic shift in their near infrared absorption maximum accompanied by an apparent inversion in their near infrared CD spectrum during isolation. Treating isolated chlorosomes with the strong ionic detergent sodium dodecylsulfate, which removes BChl a, does not alter the arrangement of BChl c molecules in either Chlorofiexus or Chlorobium chlorosomes, as indicated by the lack of an effect on their CD spectra

The Breakup Cross Section of the D+D Reaction at 6.94 MeV

The D+D reactions are well known and widely used for a variety of purposes, mainly because of the use of the D(d, n)3He reaction as a mono-energetic neutron source. The least studied of the D+D reactions is the D(d, n)pD reaction known as the deuteron breakup reaction, which produces a continuum of neutrons at energies below the monoenergetic peak. The neutron energy distribution as a function of angle for the cross section, ${{{d^2}\sigma } \over {d\Omega dE}}$, of the D(d,n)pD reaction has been measured using a 6.94-MeV pulsed deuteron beam incident upon a D2 gas target. The time-of-flight technique was used to determine the energy of the neutrons detected in an array of two lithium glass scintillators and one NE-213 scintillator. The breakup cross section was determined as low as 225-keV neutron energy in the lithium glass detectors

The Breakup Cross Section of the D+D Reaction at 6.94 MeV

The D+D reactions are well known and widely used for a variety of purposes, mainly because of the use of the D(d, n)3He reaction as a mono-energetic neutron source. The least studied of the D+D reactions is the D(d, n)pD reaction known as the deuteron breakup reaction, which produces a continuum of neutrons at energies below the monoenergetic peak. The neutron energy distribution as a function of angle for the cross section, d2σdΩdE${{{d^2}\sigma } \over {d\Omega dE}}$, of the D(d,n)pD reaction has been measured using a 6.94-MeV pulsed deuteron beam incident upon a D2 gas target. The time-of-flight technique was used to determine the energy of the neutrons detected in an array of two lithium glass scintillators and one NE-213 scintillator. The breakup cross section was determined as low as 225-keV neutron energy in the lithium glass detectors

Stratigraphy of the Archean western Superior Province from P- and S-wave receiver functions: Further evidence for tectonic accretion?

The Archean western Superior Province in Canada represents the nucleus of the North American continent whose origin has been speculated to be the result of widespread crustal accretion some 2.7 Ga ago. In this paper, crustal and upper-mantle seismic discontinuities beneath the western Superior Province of the Canadian shield are imaged with teleseismic P-to-S and S-to-P converted phases using the receiver function method. Three crustal discontinuities are observed: the Moho, ranging in depth between 38 and 47 km and dipping to the south; and two intra-crustal discontinuities having depths of approximately 15 and 30 km. The crustal discontinuities undulate laterally and often lose continuity, possibly indicating an imbricated structure and/or regions of velocity gradients. In the shallow lithosphere, a positive discontinuity is imaged at approximately 65 km depth and is consistent with earlier refraction and wide-angle reflection results. Additionally, two zones of negative receiver function amplitudes at 55 km depth are observed and are coincident with a region of anomalous tomographic low P- and S-wave velocities as well as a zone of high electrical conductivity. The images for the crust and shallow upper-mantle, when integrated with previous geophysical studies, are consistent with ideas of continental root formation due to imbrication of Archean subducted material and accretion of island arcs observed in surface geology