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

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

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

Coupling carbon nanotube mechanics to a superconducting circuit

The quantum behaviour of mechanical resonators is a new and emerging field driven by recent experiments reaching the quantum ground state. The high frequency, small mass, and large quality-factor of carbon nanotube resonators make them attractive for quantum nanomechanical applications. A common element in experiments achieving the resonator ground state is a second quantum system, such as coherent photons or superconducting device, coupled to the resonators motion. For nanotubes, however, this is a challenge due to their small size. Here, we couple a carbon nanoelectromechanical (NEMS) device to a superconducting circuit. Suspended carbon nanotubes act as both superconducting junctions and moving elements in a Superconducting Quantum Interference Device (SQUID). We observe a strong modulation of the flux through the SQUID from displacements of the nanotube. Incorporating this SQUID into superconducting resonators and qubits should enable the detection and manipulation of nanotube mechanical quantum states at the single-phonon level

Heterogeneous models place the root of the placental mammal phylogeny

Heterogeneity among life traits in mammals has resulted in considerable phylogenetic conflict, particularly concerning the position of the placental root. Layered upon this are gene- and lineage-specific variation in amino acid substitution rates and compositional biases. Life trait variations that may impact upon mutational rates are longevity, metabolic rate, body size, and germ line generation time. Over the past 12 years, three main conflicting hypotheses have emerged for the placement of the placental root. These hypotheses place the Atlantogenata (common ancestor of Xenarthra plus Afrotheria), the Afrotheria, or the Xenarthra as the sister group to all other placental mammals. Model adequacy is critical for accurate tree reconstruction and by failing to account for these compositional and character exchange heterogeneities across the tree and data set, previous studies have not provided a strongly supported hypothesis for the placental root. For the first time, models that accommodate both tree and data set heterogeneity have been applied to mammal data. Here, we show the impact of accurate model assignment and the importance of data sets in accommodating model parameters while maintaining the power to reject competing hypotheses. Through these sophisticated methods, we demonstrate the importance of model adequacy, data set power and provide strong support for the Atlantogenata over other competing hypotheses for the position of the placental root

Microbiology: Mind the gaps in cellular evolution

Eukaryotic cells, with complex features such as membrane-bound nuclei, evolved from prokaryotic cells that lack these components. A newly identified prokaryotic group reveals intermediate steps in eukaryotic-cell evolution

A General Theory of Phase-Space Quasiprobability Distributions

We present a general theory of quasiprobability distributions on phase spaces of quantum systems whose dynamical symmetry groups are (finite-dimensional) Lie groups. The family of distributions on a phase space is postulated to satisfy the Stratonovich-Weyl correspondence with a generalized traciality condition. The corresponding family of the Stratonovich-Weyl kernels is constructed explicitly. In the presented theory we use the concept of the generalized coherent states, that brings physical insight into the mathematical formalism.Comment: REVTeX, 4 pages. More information on http://www.technion.ac.il/~brif/science.htm

Effectiveness of pre-entry active tuberculosis and post-entry latent tuberculosis screening in new entrants to the UK: a retrospective, population-based cohort study

BACKGROUND: Evaluating interventions that might lead to a reduction in tuberculosis in high-income countries with a low incidence of the disease is key to accelerate progress towards its elimination. In such countries, migrants are known to contribute a large proportion of tuberculosis cases to the burden. We assessed the effectiveness of screening for active tuberculosis before entry to the UK and for latent tuberculosis infection (LTBI) post-entry for reduction of tuberculosis in new-entrant migrants to the UK. Additionally, we investigated the effect of access to primary care on tuberculosis incidence in this population. METHODS: We did a retrospective, population-based cohort study of migrants from 66 countries who were negative for active tuberculosis at pre-entry screening between Jan 1, 2011, and Dec 31, 2014, and eligible for LTBI screening. We used record linkage to track their first contact with primary care, uptake of LTBI screening, and development of active tuberculosis in England, Wales, and Northern Ireland. To assess the effectiveness of the pre-entry screening programme, we identified a control group of migrants who were not screened for active tuberculosis using the specific code for new entrants to the UK registering in primary care within the National Health Service patient registration data system. Our primary outcome was development of active tuberculosis notified to the National Enhanced Tuberculosis Surveillance System. FINDINGS: Our cohort comprised 224 234 migrants who were screened for active tuberculosis before entry to the UK and a control group of 118 738 migrants who were not. 103 990 (50%) migrants who were screened for active tuberculosis registered in primary care; all individuals in the control group were registered in primary care. 1828 tuberculosis cases were identified during the cohort time, of which 31 were prevalent. There were 26 incident active tuberculosis cases in migrants with no evidence of primary care registration, and 1771 cases in the entire cohort of migrants who registered in primary care (n=222 728), giving an incidence rate of 174 (95% CI 166-182) per 100 000 person-years. 672 (1%) of 103 990 migrants who were screened for active tuberculosis went on to develop tuberculosis compared with 1099 (1%) of 118 738 not screened for active tuberculosis (incidence rate ratio [IRR] 1·49, 95% CI 1·33-1·67; p<0·0001). 2451 (1%) of the 222 728 migrants registered in primary care were screened for LTBI, of whom 421 (17%) tested positive and 1961 (80%) tested negative; none developed active tuberculosis within the observed time period. Migrants settling in the least deprived areas had a decreased risk of developing tuberculosis (IRR 0·74, 95% CI 0·62-0·89; p=0·002), and time from UK arrival to primary care registration of 1 year or longer was associated with increased risk of active tuberculosis (2·96, 2·59-3·38; p<0·0001). INTERPRETATION: Pre-entry tuberculosis screening, early primary care registration, and LTBI screening are strongly and independently associated with a lower tuberculosis incidence in new-entrant migrants. FUNDING: National Institute for Health Research (NIHR) Health Protection Research Unit in Respiratory Infections and NIHR Imperial Biomedical Research Centre