Adaptive evolution of the human fatty acid synthase gene: Support for the cancer selection and fat utilization hypotheses?

Cancer may act as the etiological agent for natural selection in some genes. This selective pressure would act to reduce the success of neoplastic lineages over normal cell lineages in individuals of reproductive age. In addition, humanâs relatively larger brain and longer lifespan may have also acted as a selective force requiring new genotypes. One of the most important proteins in both processes is the fatty acid synthase (FAS) gene involved in fatty acid biosynthesis. Avariety of other proteins, including PTEN, MAPK1, SREBP1, SREBP2 and PI are also involved in the regulation of fatty acid biosynthesis. We have specifically analysed variability in selective pressure across all these genes in human, mouse and other vertebrates.We have found that the FAS gene alone has signatures indicative of adaptive evolution.We did not find any signatures of adaptive evolution in any of the other proteins. In the FAS gene, we have detected an excess of non-synonymous over synonymous substitutions in approximately 6% of sites in the human lineage. Contrastingly, the substitution process at these sites in other available vertebrates and mammals indicates strong purifying selection. This is likely to reflect a functional shift in human FAS and correlates well with previously observed changes in FAS biochemical activities. We speculate that the role played by FAS either in cancer development or in human brain development has created this selective pressure, although we cannot rule out the various other functions of FAS

A Note on Frame Dragging

The measurement of spin effects in general relativity has recently taken centre stage with the successfully launched Gravity Probe B experiment coming toward an end, coupled with recently reported measurements using laser ranging. Many accounts of these experiments have been in terms of frame-dragging. We point out that this terminology has given rise to much confusion and that a better description is in terms of spin-orbit and spin-spin effects. In particular, we point out that the de Sitter precession (which has been mesured to a high accuracy) is also a frame-dragging effect and provides an accurate benchmark measurement of spin-orbit effects which GPB needs to emulate

Building capacity in waterbird and wetland monitoring in eastern Africa

The wetlands of eastern Africa support internationally important assemblages of plants and animals, and are a vital source of livelihood and water for many societies. The combined human population of Burundi, Djibouti, Eritrea, Ethiopia, Kenya, Rwanda, Sudan, Tanzania and Uganda is estimated to be about 200 million. The region has an area of about 5.6 million km2 of which only 4.5% is open water/wetlands. Wetland conversion to agriculture often provides only short-term benefits and can pose long-term problems. The ever-increasing human population density coupled with the scarce water resources in Africa have put African governments under increasing pressure to allow further exploitation and drainage of wetlands. Lack of sufficient up-to-date information to guide policy and development programmes for the respective Africa governments is considered as one of the causes for the continued loss and degradation of wetlands. To fill this information gap, it was recognized that a standardized system for monitoring wetland biodiversity and making the data and information available to governments and other stakeholders was required. In 2002, a project was implemented to build and maintain capacity in the monitoring of wetland biodiversity in eastern Africa and to provide the necessary information required for wetland conservation. This paper describes the capacity building process leading to: (1) the development of a wetlands database with query tools; (2) the provision of training in the use of the wetland monitoring database; (3) the launch of the Wetland Biodiversity Monitoring Scheme (WBMS) to provide data for use in wetland conservation and development of site management plans; and (4) training in the development of a wetland site management plan in each of the nine partner countries

Universality of Mixed Action Extrapolation Formulae

Mixed action theories with chirally symmetric valence fermions exhibit very desirable features both at the level of the lattice calculations as well as in the construction and implementation of the low energy mixed action effective field theory. In this work we show that when such a mixed action effective field theory is projected onto the valence sector, both the Lagrangian and the extrapolation formulae become universal in form through next to leading order, for all variants of discretization methods used for the sea fermions. Our conclusion relies on the chiral nature of the valence quarks. The result implies that for all sea quark methods which are in the same universality class as QCD, the numerical values of the physical coefficients in the various mixed action chiral Lagrangians will be the same up to lattice spacing dependent corrections. This allows us to construct a prescription to determine the mixed action extrapolation formulae for a large class of hadronic correlation functions computed in partially quenched chiral perturbation theory at the one-loop level. For specific examples, we apply this prescription to the nucleon twist--2 matrix elements and the nucleon--nucleon system. In addition, we determine the mixed action extrapolation formula for the neutron EDM as this provides a nice example of a theta-dependent observable; these observables are exceptions to our prescription.Comment: 36 pages, appendix on twisted mass sea fermions added, expanded discussion of NLO operators, version published in JHEP; typographical errors corrected in Eqs. (68) and (69

Baboon endogenous virus genome: Molecular cloning and structural characterization of nondefective viral genomes from DNA of a baboon cell strain

Several heterogeneities in the baboon endogenous virus (BaEV) genomes that are present in the DNA of normal baboon tissues and the baboon cell strain BEF-3 have been described previously. To study these genomes, we cloned BaEV proviruses from BEF-3 cellular DNA into the vector Charon 4A. Of the four full-length clones isolated, one was nondefective as determined by transfection. The sequence of a portion of this clone was found to code for amino acids 61-91 in the p30 region of the gag gene. This identification allowed us to align the restriction map with the BaEV genetic map. One heterogeneity, a BamHI site 2.4 kilobases (kb) from the proviral 5' end, was located close to the gag-pol junction; another, a BamHI site 1.4 kb from the 5' end of the genome, corresponded to the gag p30 coding sequence for amino acids 32-34; and a third, a Xho I site, was near the 3' end of the pol gene. To select the nondefective BaEV genomes from BEF-3 cells, we infected permissive cells with virus produced by BEF-3 cells and also transfected BEF-3 cellular DNA into permissive cells. The BaEV genomes in the permissive recipient cultures were then analyzed by restriction enzyme analysis. These nondefective genomes were found to be heterogeneous with respect to the gag-pol BamHI site and the Xho I site, but all were found to contain the BamHI site 1.4 kb from the 5' end of the genome

The public goods hypothesis for the evolution of life on Earth

It is becoming increasingly difficult to reconcile the observed extent of horizontal gene transfers with the central metaphor of a great tree uniting all evolving entities on the planet. In this manuscript we describe the Public Goods Hypothesis and show that it is appropriate in order to describe biological evolution on the planet. According to this hypothesis, nucleotide sequences (genes, promoters, exons, etc.) are simply seen as goods, passed from organism to organism through both vertical and horizontal transfer. Public goods sequences are defined by having the properties of being largely non-excludable (no organism can be effectively prevented from accessing these sequences) and non-rival (while such a sequence is being used by one organism it is also available for use by another organism). The universal nature of genetic systems ensures that such non-excludable sequences exist and non-excludability explains why we see a myriad of genes in different combinations in sequenced genomes. There are three features of the public goods hypothesis. Firstly, segments of DNA are seen as public goods, available for all organisms to integrate into their genomes. Secondly, we expect the evolution of mechanisms for DNA sharing and of defense mechanisms against DNA intrusion in genomes. Thirdly, we expect that we do not see a global tree-like pattern. Instead, we expect local tree-like patterns to emerge from the combination of a commonage of genes and vertical inheritance of genomes by cell division. Indeed, while genes are theoretically public goods, in reality, some genes are excludable, particularly, though not only, when they have variant genetic codes or behave as coalition or club goods, available for all organisms of a coalition to integrate into their genomes, and non-rival within the club. We view the Tree of Life hypothesis as a regionalized instance of the Public Goods hypothesis, just like classical mechanics and euclidean geometry are seen as regionalized instances of quantum mechanics and Riemannian geometry respectively. We argue for this change using an axiomatic approach that shows that the Public Goods hypothesis is a better accommodation of the observed data than the Tree of Life hypothesis

The Magnetized Electron Gas in terms of Hurwitz Zeta Functions

We obtain explicit expressions for thermodynamic quantities of a relativistic degenerate free electron gas in a magnetic field in terms of Hurwitz Zeta functions. The formulation allows for systematic expansion in all regimes. Three energy scales appear naturally in the degenerate relativistic gas: the Fermi energy Ef, the temperature T and an energy related to the magnetic field or Landau level spacing, eB/Ef. We study the cold and warm scenarios, T << eB/Ef and eB/Ef << T, respectively. We reproduce the oscillations of the magnetization as a function of the field in the cold regime and the dilution of them in the warm regime.Comment: 33 pages, 6 figures, LaTeX 2e, uses epsf. v2: References added, minor additions to content

Physics of a microsystem starting from non-equilibrium quantum statistical mechanics

In this paper we address the problem to give a concrete support to the idea, originally stemming from Niels Bohr, that quantum mechanics must be rooted inside the physics of macroscopic systems. It is shown that, starting from the formalism of the non-equilibrium statistical operator, which is now a consolidated part of quantum statistical mechanics, particular correlations between two isolated systems can be singled out and interpreted as microsystems. In this way also a new framework is established in which questions of decoherence can be naturally addressed.Comment: 14 pages, latex, no figures, contribution to the Proceedings of the XXXIII Symposium on Mathematical Physics (Torun, Poland

Spitzer spectral line mapping of the HH211 outflow

Aims: We employ archival Spitzer slit-scan observations of the HH211 outflow in order to investigate its warm gas content, assess the jet mass flux in the form of H2 and probe for the existence of an embedded atomic jet. Methods: Detected molecular and atomic lines are interpreted by means of emission line diagnostics and an existing grid of molecular shock models. The physical properties of the warm gas are compared against other molecular jet tracers and to the results of a similar study towards the L1448-C outflow. Results: We have detected and mapped the v=0-0 S(0) - S(7) H2 lines and fine-structure lines of S, Fe+, and Si+. H2 is detected down to 5" from the source and is characterized by a "cool" T~300K and a "warm" T~1000 K component, with an extinction Av ~ 8 mag. The amount of cool H2 towards the jet agrees with that estimated from CO assuming fully molecular gas. The warm component is well fitted by C-type shocks with a low beam filling factor ~ 0.01-0.04 and a mass-flux similar to the cool H2. The fine-structure line emission arises from dense gas with ionization fraction ~0.5 - 5 x 10e-3, suggestive of dissociative shocks. Line ratios to sulfur indicate that iron and silicon are depleted compared to solar abundances by a factor ~10-50. Conclusions: Spitzer spectral mapping observations reveal for the first time a cool H$_2$ component towards the CO jet of HH211 consistent with the CO material being fully molecular and warm at ~ 300 K. The maps also reveal for the first time the existence of an embedded atomic jet in the HH211 outflow that can be traced down to the central source position. Its significant iron and silicon depletion excludes an origin from within the dust sublimation zone around the protostar. The momentum-flux seems insufficient to entrain the CO jet, although current uncertainties on jet speed and shock conditions are too large for a definite conclusion.Comment: 13 pages, 10 figures, accepted for publication in A&

Building capacity in waterbird and wetland monitoring in eastern Africa

The wetlands of eastern Africa support internationally important assemblages of plants and animals, and are a vital source of livelihood and water for many societies. The combined human population of Burundi, Djibouti, Eritrea, Ethiopia, Kenya, Rwanda, Sudan, Tanzania and Uganda is estimated to be about 200 million. The region has an area of about 5.6 million km2 of which only 4.5% is open water/wetlands. Wetland conversion to agriculture often provides only short-term benefits and can pose long-term problems. The ever-increasing human population density coupled with the scarce water resources in Africa have put African governments under increasing pressure to allow further exploitation and drainage of wetlands. Lack of sufficient up-to-date information to guide policy and development programmes for the respective Africa governments is considered as one of the causes for the continued loss and degradation of wetlands. To fill this information gap, it was recognized that a standardized system for monitoring wetland biodiversity and making the data and information available to governments and other stakeholders was required. In 2002, a project was implemented to build and maintain capacity in the monitoring of wetland biodiversity in eastern Africa and to provide the necessary information required for wetland conservation. This paper describes the capacity building process leading to: (1) the development of a wetlands database with query tools; (2) the provision of training in the use of the wetland monitoring database; (3) the launch of the Wetland Biodiversity Monitoring Scheme (WBMS) to provide data for use in wetland conservation and development of site management plans; and (4) training in the development of a wetland site management plan in each of the nine partner countries