Segmentally Variable Genes: A New Perspective on Adaptation

Genomic sequence variation is the hallmark of life and is key to understanding diversity and adaptation among the numerous microorganisms on earth. Analysis of the sequenced microbial genomes suggests that genes are evolving at many different rates. We have attempted to derive a new classification of genes into three broad categories: lineage-specific genes that evolve rapidly and appear unique to individual species or strains; highly conserved genes that frequently perform housekeeping functions; and partially variable genes that contain highly variable regions, at least 70 amino acids long, interspersed among well-conserved regions. The latter we term segmentally variable genes (SVGs), and we suggest that they are especially interesting targets for biochemical studies. Among these genes are ones necessary to deal with the environment, including genes involved in host–pathogen interactions, defense mechanisms, and intracellular responses to internal and environmental changes. For the most part, the detailed function of these variable regions remains unknown. We propose that they are likely to perform important binding functions responsible for protein–protein, protein–nucleic acid, or protein–small molecule interactions. Discerning their function and identifying their binding partners may offer biologists new insights into the basic mechanisms of adaptation, context-dependent evolution, and the interaction between microbes and their environment. Segmentally variable genes show a mosaic pattern of one or more rapidly evolving, variable regions. Discerning their function may provide new insights into the forces that shape genome diversity and adaptationNational Science Foundation (998088, 0239435

Semileptonic Decays of Heavy Omega Baryons in a Quark Model

The semileptonic decays of $\Omega_c$ and $\Omega_b$ are treated in the framework of a constituent quark model developed in a previous paper on the semileptonic decays of heavy $\Lambda$ baryons. Analytic results for the form factors for the decays to ground states and a number of excited states are evaluated. For $\Omega_b$ to $\Omega_c$ the form factors obtained are shown to satisfy the relations predicted at leading order in the heavy-quark effective theory at the non-recoil point. A modified fit of nonrelativistic and semirelativistic Hamiltonians generates configuration-mixed baryon wave functions from the known masses and the measured \lcle rate, with wave functions expanded in both harmonic oscillator and Sturmian bases. Decay rates of \ob to pairs of ground and excited \omc states related by heavy-quark symmetry calculated using these configuration-mixed wave functions are in the ratios expected from heavy-quark effective theory, to a good approximation. Our predictions for the semileptonic elastic branching fraction of $\Omega_Q$ vary minimally within the models we use. We obtain an average value of (84$\pm$ 2%) for the fraction of $\Omega_c\to \Xi^{(*)}$ decays to ground states, and 91% for the fraction of $\Omega_c\to \Omega^{(*)}$ decays to the ground state $\Omega$. The elastic fraction of \ob \to \omc ranges from about 50% calculated with the two harmonic-oscillator models, to about 67% calculated with the two Sturmian models.Comment: 52 pages, 8 figure

Wilson Line Picture of Levin-Wen Partition Functions

Levin and Wen [Phys. Rev. B 71, 045110 (2005)] have recently given a lattice Hamiltonian description of doubled Chern-Simons theories. We relate the partition function of these theories to an expectation of Wilson loops that form a link in 2+1 dimensional spacetime known in the mathematical literature as Chain-Mail. This geometric construction gives physical interpretation of the Levin-Wen Hilbert space and Hamiltonian, its topological invariance, exactness under coarse-graining, and how two opposite chirality sectors of the doubled theory arise.Comment: Final published version; Appendix adde

Relationship between starting and finishing position in World Cup BMX racing

The BMX start is one of the most important aspects of BMX racing and has been deemed by coaches as one of the strongest determining factors of finish line placing. The present study analysed the correlation between elite BMX riders and their relative position at the start of a BMX race in relation to finish line placing. Data from 348 riders results in 175 elite races in the four 2012 Union Cycliste Internationale (UCI) world cup events were analysed. Time gates were placed in four positions around each BMX track and the data sets were analysed using Kendall's tau-b bivariante correlation. A strong correlation was established at the second time gate for both males (t=0.581, P<0.01) and females (t=0.571, P<0.01). The correlation between riders' final placing was greater in positions 1st to 3rd (t=0.586, P <0.01. 4th to 8th t=0.249, P <0.01) compared to riders placed 4th to 8th (t=0.519, P <0.01. 4th to 8th t=0.372, P <0.01.) for both male and female riders respectively. In conclusion, a strong correlation exists between riders position 8-10 s into a race. Therefore, focusing on a riders' ability to gain placings at the start of a race will have an effect on their finish line position.N/

Key issues in regional growth and integration in Southern Africa

Abstract: The decade to 2015 saw rapid growth in trade between Southern African Development Community (SADC) countries. Much of this growth reflected South African exports to its neighbours of diversified manufactured goods to meet growing urban consumption and to supply inputs to mining and infrastructure. While most SADC countries, aside from South Africa, grew quite rapidly over this period, their exports remained oriented to a narrow range of minerals and agricultural commodities destined to go outside the region. Drawing from a series of sectoral studies, we assess key regional issues including the investment and production decisions of firms whose operations stretch across borders, and consider the implications for a bottom-up integration agenda that could build productive capabilities across countries. Our evaluation highlights the importance of the spread of supermarkets, the need to address transport and logistics, and value chains whose competitive advantages are inherently regional, as in the cases of poultry and mining

Characterising the dynamics of placental glycogen stores in the mouse.

INTRODUCTION: The placenta performs a range of functions to support fetal growth. In addition to facilitating nutrient transport, the placenta also stores glucose as glycogen, which is thought to maintain fetal glucose supply during late gestation. However, evidence to support such a role is currently lacking. Similarly, our understanding of the dynamics of placental glycogen metabolism in normal mouse pregnancy is limited. METHODS: We quantified the placental glycogen content of wild type C57BL/6JOlaHsd mouse placentas from mid (E12.5) to late (E18.5) gestation, alongside characterising the temporal expression pattern of genes encoding glycogenesis and glycogenolysis pathway enzymes. To assess the potential of the placenta to produce glucose, we investigated the spatiotemporal expression of glucose 6-phosphatase by qPCR and in situ hybridisation. Separate analyses were undertaken for placentas of male and female conceptuses to account for potential sexual dimorphism. RESULTS: Placental glycogen stores peak at E15.5, having increased over 5-fold from E12.5, before declining by a similar extent by E18.5. Glycogen stores were 17% higher in male placentas than in females at E15.5. Expression of glycogen branching enzyme (Gbe1) was reduced ~40% towards term. Expression of the glucose 6-phosphatase isoform G6pc3 was enriched in glycogen trophoblast cells and increased towards term. DISCUSSION: Reduced expression of Gbe1 suggests a decline in glycogen branching towards term. Expression of G6pc3 by glycogen trophoblasts is consistent with an ability to produce and release glucose from glycogen stores. However, the ultimate destination of the glucose generated from placental glycogen remains to be elucidated.Centre for Trophoblast Researc

Multiwavelength Studies of PSR J1420-6048, a Young Pulsar in the Kookaburra

We present X-ray, radio, and infrared observations of the 68 ms pulsar PSR J1420-6048 and its surrounding nebula, a possible counterpart of the gamma-ray source GeV J1417-6100/3EG J1420-6038. Pulsed X-ray emission at the radio period is marginally detected by ASCA from a source embedded in the hard spectrum X-ray nebula AX J1420.1-6049. At radio wavelengths, the pulsar is found to be strongly linearly and circularly polarized, and the polarization sweep is measured. A comparison of high resolution ATCA radio imaging of the Kookaburra's upper wing (G313.6+0.3), which contains the pulsar and the X-ray nebula, with infrared images suggests the radio emission is partly non-thermal.Comment: 8 pages, 4 figures, to appear in Astrophysical Journal Letter

Genomic functional annotation using co-evolution profiles of gene clusters

BACKGROUND: The current speed of sequencing already exceeds the capability of annotation, creating a potential bottleneck. A large proportion of the genes in microbial genomes remains uncharacterized. Here we propose a new method for functional annotation using the conservation patterns of gene clusters. If several gene clusters show the same coevolution pattern across different genomes it is reasonable to infer they are functionally related. The gene cluster phylogenetic profile integrates chromosomal proximity information and phylogenetic profile information and allows us to infer functional dependences between the gene clusters even at great distance on the chromosome. RESULTS: As a proof of concept, we applied our method to the genome of Escherichia coli K12 strain. Our method establishes functional relationships among 176 gene clusters, comprising 738 E. coli genes. The accuracy of pair phylogenetic profiles was compared with the single-gene phylogenetic profile and was shown to be higher. As a result, we are able to suggest functional roles for several previously unknown genes or unknown genomic regions in E. coli. We also examined the robustness of coevolution signals across a larger set of genomes and suggest a possible upper limit of accuracy for the phylogenetic profile methods. CONCLUSIONS: The higher-order phylogenetic profiles, such as the gene-pair phylogenetic profiles, can detect functional dependences that are missed by using conventional single-gene phylogenetic profile or the chromosomal proximity method only. We show that the gene-pair phylogenetic profile is more accurate than the single-gene phylogenetic profiles