Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative fenomics of six Geobacteraceae species

<p>Abstract</p> <p>Background</p> <p>The anaerobic degradation of organic matter in natural environments, and the biotechnical use of anaerobes in energy production and remediation of subsurface environments, both require the cooperative activity of a diversity of microorganisms in different metabolic niches. The <it>Geobacteraceae </it>family contains members with three important anaerobic metabolisms: fermentation, syntrophic degradation of fermentation intermediates, and anaerobic respiration.</p> <p>Results</p> <p>In order to learn more about the evolution of anaerobic microbial communities, the genome sequences of six <it>Geobacteraceae </it>species were analyzed. The results indicate that the last common <it>Geobacteraceae </it>ancestor contained sufficient genes for anaerobic respiration, completely oxidizing organic compounds with the reduction of external electron acceptors, features that are still retained in modern <it>Geobacter </it>and <it>Desulfuromonas </it>species. Evolution of specialization for fermentative growth arose twice, via distinct lateral gene transfer events, in <it>Pelobacter carbinolicus </it>and <it>Pelobacter propionicus</it>. Furthermore, <it>P. carbinolicus </it>gained hydrogenase genes and genes for ferredoxin reduction that appear to permit syntrophic growth via hydrogen production. The gain of new physiological capabilities in the <it>Pelobacter </it>species were accompanied by the loss of several key genes necessary for the complete oxidation of organic compounds and the genes for the <it>c</it>-type cytochromes required for extracellular electron transfer.</p> <p>Conclusion</p> <p>The results suggest that <it>Pelobacter </it>species evolved parallel strategies to enhance their ability to compete in environments in which electron acceptors for anaerobic respiration were limiting. More generally, these results demonstrate how relatively few gene changes can dramatically transform metabolic capabilities and expand the range of environments in which microorganisms can compete.</p

Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes

Background: Geobacter species grow by transferring electrons out of the cell - either to Fe(III)-oxides or to manmade substances like energy-harvesting electrodes. Study of Geobacter sulfurreducens has shown that TCA cycle enzymes, inner-membrane respiratory enzymes, and periplasmic and outer-membrane cytochromes are required. Here we present comparative analysis of six Geobacter genomes, including species from the clade that predominates in the subsurface. Conservation of proteins across the genomes was determined to better understand the evolution of Geobacter species and to create a metabolic model applicable to subsurface environments. Results: The results showed that enzymes for acetate transport and oxidation, and for proton transport across the inner membrane were well conserved. An NADH dehydrogenase, the ATP synthase, and several TCA cycle enzymes were among the best conserved in the genomes. However, most of the cytochromes required for Fe(III)-reduction were not, including many of the outer-membrane cytochromes. While conservation of cytochromes was poor, an abundance and diversity of cytochromes were found in every genome, with duplications apparent in several species. Conclusions: These results indicate there is a common pathway for acetate oxidation and energy generation across the family and in the last common ancestor. They also suggest that while cytochromes are important for extracellular electron transport, the path of electrons across the periplasm and outer membrane is variable. This combination of abundant cytochromes with weak sequence conservation suggests they may not be specific terminal reductases, but rather may be important in their heme-bearing capacity, as sinks for electrons between the inner-membrane electron transport chain and the extracellular acceptor

Chiral Corrections to Lattice Calculations of Charge Radii

Logarithmic divergences in pion and proton charge radii associated with chiral loops are investigated to assess systematic uncertainties in current lattice determinations of charge radii. The chiral corrections offer a possible solution to the long standing problem of why present lattice calculations yield proton and pion radii which are similar in size.Comment: PostScript file only. Ten pages. Figures included. U. of MD Preprint #92-19

De Novo Assembly of the Complete Genome of an Enhanced Electricity-Producing Variant of Geobacter sulfurreducens Using Only Short Reads

State-of-the-art DNA sequencing technologies are transforming the life sciences due to their ability to generate nucleotide sequence information with a speed and quantity that is unapproachable with traditional Sanger sequencing. Genome sequencing is a principal application of this technology, where the ultimate goal is the full and complete sequence of the organism of interest. Due to the nature of the raw data produced by these technologies, a full genomic sequence attained without the aid of Sanger sequencing has yet to be demonstrated

CLINICAL AND BIOMECHANICAL COMPARISONS BETWEEN YOUTH PITCHERS WITH AND WITHOUT A HISTORY OF THROWING ARM PAIN OR INJUR

This study aimed to determine if there are clinical and kinematic differences in youth pitchers with a self-reported history of throwing arm pain or injury (PI) to those without (NPI). Forty male baseball pitchers ages 9 to 14 years old were divided into a PI group (n=20) and a NPI group (n=20). Injury history, pitching exposure, subject demographics, range of motion, and strength measurements were collected, along with throwing arm kinematics via a motion capture system. When comparing PI and NPI, significant physical differences were observed, with a greater presence of axillary hair, increased forearm length and decreased shoulder internal rotation strength in PI. No significant differences of upper limb motion during pitching were reported. When considering youth pitchers, evidence of physical maturity, arm length, and strength could be important factors in developing pain or injury

Testing QCD Sum Rule Techniques on the Lattice

Results for the first test of the ``crude'' QCD continuum model, commonly used in QCD Sum Rule analyses, are presented for baryon correlation functions. The QCD continuum model is found to effectively account for excited state contributions to the short-time regime of two-point correlation functions and allows the isolation of ground state properties. Confusion in the literature surrounding the physics represented in point-to-point correlation functions is also addressed. These results justify the use of the ``crude'' QCD continuum model and lend credence to the results of rigorous QCD Sum Rule analyses.Comment: Discussion of systematic uncertainties augmente

EpiCollect: Linking Smartphones to Web Applications for Epidemiology, Ecology and Community Data Collection

Epidemiologists and ecologists often collect data in the field and, on returning to their laboratory, enter their data into a database for further analysis. The recent introduction of mobile phones that utilise the open source Android operating system, and which include (among other features) both GPS and Google Maps, provide new opportunities for developing mobile phone applications, which in conjunction with web applications, allow two-way communication between field workers and their project databases.Here we describe a generic framework, consisting of mobile phone software, EpiCollect, and a web application located within www.spatialepidemiology.net. Data collected by multiple field workers can be submitted by phone, together with GPS data, to a common web database and can be displayed and analysed, along with previously collected data, using Google Maps (or Google Earth). Similarly, data from the web database can be requested and displayed on the mobile phone, again using Google Maps. Data filtering options allow the display of data submitted by the individual field workers or, for example, those data within certain values of a measured variable or a time period.Data collection frameworks utilising mobile phones with data submission to and from central databases are widely applicable and can give a field worker similar display and analysis tools on their mobile phone that they would have if viewing the data in their laboratory via the web. We demonstrate their utility for epidemiological data collection and display, and briefly discuss their application in ecological and community data collection. Furthermore, such frameworks offer great potential for recruiting 'citizen scientists' to contribute data easily to central databases through their mobile phone

The racist bodily imaginary: the image of the body-in-pieces in (post)apartheid culture

This paper outlines a reoccurring motif within the racist imaginary of (post)apartheid culture: the black body-in-pieces. This disturbing visual idiom is approached from three conceptual perspectives. By linking ideas prevalent in Frantz Fanon’s description of colonial racism with psychoanalytic concepts such as Lacan’s notion of the corps morcelé, the paper offers, firstly, an account of the black body-in-pieces as fantasmatic preoccupation of the (post)apartheid imaginary. The role of such images is approached, secondly, through the lens of affect theory which eschews a representational ‘reading’ of such images in favour of attention to their asignifying intensities and the role they play in effectively constituting such bodies. Lastly, Judith Butler’s discussion of war photography and the conditions of grievability introduces an ethical dimension to the discussion and helps draw attention to the unsavory relations of enjoyment occasioned by such images

Baryon Octet to Decuplet Electromagnetic Transitions

The electromagnetic transition moments of the $SU(3)$-flavor baryon octet to decuplet are examined within a lattice simulation of quenched QCD. The magnetic transition moment for the $N \; \gamma \to \Delta$ channel is found to be in agreement with recent experimental analyses. The lattice results indicate $\mu_{p \Delta} / \mu_p = 0.88(15)$. In terms of the Particle Data Group convention, $f_{M1} = 0.231(41)$ GeV${}^{-1/2}$ for $p \; \gamma \to \Delta^+$ transitions. Lattice predictions for the hyperon $M1$ transition moments agree with those of a simple quark model. However the manner in which the quarks contribute to the transition moments in the lattice simulation is different from that anticipated by quark model calculations. The scalar quadrupole form factor exhibits a behavior consistent with previous multipole analyses. The $E2/M1$ multipole transition moment ratios are also determined. The lattice results suggest $R_{EM} \equiv -{\cal G}_{E2}/{\cal G}_{M1} = +3\pm 8$ \% for $p \; \gamma \to \Delta^+$ transitions. Of particular interest are significant nonvanishing signals for the $E2/M1$ ratio in $\Xi^-$ and $\Sigma^-$ electromagnetic transitions.Comment: PostScript file, 37 pages including figures. U. MD PP #93-085, U. KY PP #UK/92-09, TRIUMF PP #TRI-PP-92-12

Unquenching the Rho Meson

Two-pion induced self-energy contributions to the $\rho$-meson mass are examined in relation to the quenched approximation of QCD, where the physics associated with two-pion intermediate states has been excluded from vector-isovector correlation functions. Corrections to quenched QCD calculations of the $\rho$-meson mass are estimated to be small at the order of a few percent of the $\rho$-meson mass. The two-pion contributions display nonanalytic behavior as a function of the pion mass as the two-pion cut is encountered. The implications of this nonanalytic behavior in extrapolations of full QCD calculations are also discussed. We note that for full QCD, the error made in making a linear extrapolation of the $\rho$ mass, neglecting nonanalytic behavior, increases as one approaches the two-pion cut.Comment: RevTeX 3.0 manuscript. UU-File is a single postscript file of paper including figures. 13 pages. (References and Intro. to Sec. II and III revised.) U. MD PP \#94-00