Comparative Genomic Evidence for a Complete Nuclear Pore Complex in the Last Eukaryotic Common Ancestor

BackgroundThe Nuclear Pore Complex (NPC) facilitates molecular trafficking between nucleus and cytoplasm and is an integral feature of the eukaryote cell. It exhibits eight-fold rotational symmetry and is comprised of approximately 30 nucleoporins (Nups) in different stoichiometries. Nups are broadly conserved between yeast, vertebrates and plants, but few have been identified among other major eukaryotic groups. Methodology/Principal FindingsWe screened for Nups across 60 eukaryote genomes and report that 19 Nups (spanning all major protein subcomplexes) are found in all eukaryote supergroups represented in our study (Opisthokonts, Amoebozoa, Viridiplantae, Chromalveolates and Excavates). Based on parsimony, between 23 and 26 of 31 Nups can be placed in LECA. Notably, they include central components of the anchoring system (Ndc1 and Gp210) indicating that the anchoring system did not evolve by convergence, as has previously been suggested. These results significantly extend earlier results and, importantly, unambiguously place a fully-fledged NPC in LECA. We also test the proposal that transmembrane Pom proteins in vertebrates and yeasts may account for their variant forms of mitosis (open mitoses in vertebrates, closed among yeasts). The distribution of homologues of vertebrate Pom121 and yeast Pom152 is not consistent with this suggestion, but the distribution of fungal Pom34 fits a scenario wherein it was integral to the evolution of closed mitosis in ascomycetes. We also report an updated screen for vesicle coating complexes, which share a common evolutionary origin with Nups, and can be traced back to LECA. Surprisingly, we find only three supergroup-level differences (one gain and two losses) between the constituents of COPI, COPII and Clathrin complexes. Conclusions/SignificanceOur results indicate that all major protein subcomplexes in the Nuclear Pore Complex are traceable to the Last Eukaryotic Common Ancestor (LECA). In contrast to previous screens, we demonstrate that our conclusions hold regardless of the position of the root of the eukaryote tree

08091 Abstracts Collection -- Logic and Probability for Scene Interpretation

From 25.2.2008 to Friday 29.2.2008, the Dagstuhl Seminar 08091 ``Logic and Probability for Scene Interpretation\u27\u27 was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper

Locating the LCROSS Impact Craters

The Lunar CRater Observations and Sensing Satellite (LCROSS) mission impacted a spent Centaur rocket stage into a permanently shadowed region near the lunar south pole. The Sheperding Spacecraft (SSC) separated \sim9 hours before impact and performed a small braking maneuver in order to observe the Centaur impact plume, looking for evidence of water and other volatiles, before impacting itself. This paper describes the registration of imagery of the LCROSS impact region from the mid- and near-infrared cameras onboard the SSC, as well as from the Goldstone radar. We compare the Centaur impact features, positively identified in the first two, and with a consistent feature in the third, which are interpreted as a 20 m diameter crater surrounded by a 160 m diameter ejecta region. The images are registered to Lunar Reconnaisance Orbiter (LRO) topographical data which allows determination of the impact location. This location is compared with the impact location derived from ground-based tracking and propagation of the spacecraft's trajectory and with locations derived from two hybrid imagery/trajectory methods. The four methods give a weighted average Centaur impact location of -84.6796\circ, -48.7093\circ, with a 1{\sigma} un- certainty of 115 m along latitude, and 44 m along longitude, just 146 m from the target impact site. Meanwhile, the trajectory-derived SSC impact location is -84.719\circ, -49.61\circ, with a 1{\sigma} uncertainty of 3 m along the Earth vector and 75 m orthogonal to that, 766 m from the target location and 2.803 km south-west of the Centaur impact. We also detail the Centaur impact angle and SSC instrument pointing errors. Six high-level LCROSS mission requirements are shown to be met by wide margins. We hope that these results facilitate further analyses of the LCROSS experiment data and follow-up observations of the impact region.Comment: Accepted for publication in Space Science Review. 24 pages, 9 figure

In-Flight Performance of the Mercury Laser Altimeter Laser Transmitter

The Mercury Laser Altimeter (MLA) is one of the payload instruments on the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft, which was launched on August 3, 2004. MLA maps Mercury's shape and topographic landforms and other surface characteristics using a diode-pumped solid-state laser transmitter and a silicon avalanche photodiode receiver that measures the round-trip time of individual laser pulses. The laser transmitter has been operating nominally during planetary flyby measurements and in orbit about Mercury since March 2011. In this paper, we review the MLA laser transmitter telemetry data and evaluate the performance of solid-state lasers under extended operation in a space environment

The Beta Problem: A Study of Abell 262

We present an investigation of the dynamical state of the cluster A262. Existing optical line of sight velocities for select cluster galaxies have been augmented by new data obtained with the Automated Multi-Object Spectrograph at Lick Observatory. We find evidence for a virialized early-type population distinct from a late-type population infalling from the Pisces-Perseus supercluster ridge. We also report on a tertiary population of low luminosity galaxies whose velocity dispersion distinguishes them from both the early and late-type galaxies. We supplement our investigation with an analysis of archival X-ray data. A temperature is determined using ASCA GIS data and a gas profile is derived from ROSAT HRI data. The increased statistics of our sample results in a picture of A262 with significant differences from earlier work. A previously proposed solution to the "beta-problem" in A262 in which the gas temperature is significantly higher than the galaxy temperature is shown to result from using too low a velocity dispersion for the early-type galaxies. Our data present a consistent picture of A262 in which there is no "beta-problem", and the gas and galaxy temperature are roughly comparable. There is no longer any requirement for extensive galaxy-gas feedback to drastically overheat the gas with respect to the galaxies. We also demonstrate that entropy-floor models can explain the recent discovery that the beta values determined by cluster gas and the cluster core radii are correlated.Comment: 31 pages, 14 figures, AAS LaTeX v5.0, Encapsulated Postscript figures, to be published in The Astrophysical Journa

Problems for MOND in Clusters and the Ly-alpha Forest

The observed dynamics of gas and stars on galactic and larger scales cannot be accounted for by self-gravity, indicating that there are large quantities of unseen matter, or that gravity is non-Newtonian in these regimes. Milgrom's MOdified Newtonian Dynamics (MOND) postulates that Newton's laws are modified at very low acceleration, and can account for the rotation curves of galaxies and some other astrophysical observations, without dark matter. Here we apply MOND to two independent physical systems: Ly-alpha absorbers and galaxy clusters. While physically distinct, both are simple hydrodynamical systems with characteristic accelerations in the MOND regime. We find that Ly-alpha absorbers are somewhat smaller than in Newtonian gravity with dark matter, but the result depends crucially on the (unknown) background acceleration field in which they are embedded. In clusters MOND appears to explain the observed (baryonic) mass-temperature relation. However, given observed gas density and enclosed mass profiles and the assumption of hydrostatic equilibrium, MOND predicts radial temperature profiles which disagree badly with observations. We show this explicitly for the Virgo, Abell 2199 and Coma clusters, but the results are general, and seem very difficult to avoid. If this discrepancy is to be resolved by positing additional (presumably baryonic) dark matter, then this dark matter must have ~1-3 times the cluster gas mass within 1 Mpc. This result strongly disfavors MOND as an alternative to dark matter (Abridged).Comment: Revised version. Important caveat in Ly-alpha calculation discussed; conclusions weakened. Coma cluster and calculation of dark matter mass required by MOND added; cluster conclusions strengthened. 11 EmulateApJ pages with 3 embedded figures. Accepted by Ap

Characterization and distribution of potentially avian pathogenic eschericia coli isolates from broilers in Peru

La colibacilosis aviar producida por infecciones de Escherichia coli es causa de elevados niveles de mortalidad y morbilidad en la industria avícola. El objetivo de este trabajo fue identificar las cepas patógenas de explotaciones avícolas en el Perú en base a la presencia de cinco genes codificadores de los factores de virulencia: iss, iucC, tsh, cvaC e irp2, mediante la técnica de Multiplex PCR. Se muestrearon 36 aves entre los 14 y 31 días de edad, provenientes de tres centros avícolas ubicados en el norte, centro y sur del país. Se hicieron aislados intestinales y se obtuvieron tres colonias sospechosas de E. coli por ave (n=108 colonias), que fueron evaluadas bioquímicamente con TSI, SIM, LIA y CITRATO, y adicionalmente con agar EMB para confirmación del diagnóstico. Las 41 colonias positivas a E. coli fueron analizadas mediante Multiplex PCR, resultando 65.9% de colonias potencialmente patógenas (portadoras de dos o más genes codificadores de virulencia); asimismo, se demostró que el 9.8% de los aislados contenían los cinco genes. Adicionalmente, los tres patotipos que contienen los genes irp2, iucC y tsh fueron encontrados en las zonas de La Libertad y Lima.Avian colibacillosis produced by Escherichia coli infections cause high mortality and morbidity in poultry farms. The objective of this study was to identify the pathogenic isolates of Peruvian broiler farms based in the presence of five genes encoding the virulence factors: iss, iucC, tsh, cvaC and irp2 by the Multiplex PCR. A total of 36 chicks between 14 and 31 days old from three poultry farms located in the north, centre, and south of Peru were sampled. Three colonies suspected to be E. coli were isolated from the intestine of each bird (n=108 colonies), and were biochemically tested with TSI, SIM, LIA, CITRATE and EMB mediums for the confirmation of the diagnostic. The 41 positive colonies to E. coli were analysed by Multiplex PCR, resulting 65.95% potentially pathogenic (carriers of two or more virulence genes); moreover, 9.8% of the isolates had all five genes. Three pathotypes containing irp2, iucC and tsh genes were found in La Libertad and Lima area

Bacterial communities in the rumen of Holstein heifers differ when fed orchardgrass as pasture vs. hay

The rich and diverse microbiota of the rumen provides ruminant animals the capacity to utilize highly fibrous feedstuffs as their energy source, but there is surprisingly little information on the composition of the microbiome of ruminants fed all-forage diets, despite the importance of such agricultural production systems worldwide. In three 28-d periods, three ruminally-cannulated Holstein heifers sequentially grazed orchardgrass pasture (OP), then were fed orchardgrass hay (OH), then returned to OP. These heifers displayed greater shifts in ruminal bacterial community composition (determined by automated ribosomal intergenic spacer analysis and by pyrotag sequencing of 16S rRNA genes) than did two other heifers maintained 84 d on the same OP. Phyla Firmicutes and Bacteroidetes dominated all ruminal samples, and quantitative PCR indicated that members of the genus Prevotella averaged 23 % of the 16S rRNA gene copies, well below levels previously reported with cows fed total mixed rations. Differences in bacterial community composition and ruminal volatile fatty acid (VFA) profiles were observed between the OP and OH despite similarities in gross chemical composition. Compared to OP, feeding OH increased the molar proportion of ruminal acetate (P = 0.02) and decreased the proportion of ruminal butyrate (P < 0.01), branched-chain VFA (P < 0.01) and the relative population size of the abundant genus Butyrivibrio (P < 0.001), as determined by pyrotag sequencing. Despite the low numbers of animals examined, the observed changes in VFA profile in the rumens of heifers on OP vs. OH are consistent with the shifts in Butyrivibrio abundance and its known physiology as a butyrate producer that ferments both carbohydrates and proteins

The political ecology of human-wildlife conflict: Producing wilderness, insecurity, and displacement in the Limpopo National Park

Like conservation-induced displacement, human-wildlife conflict (HWC) has potentially negative implications for communities in and around protected areas. While the ways in which displacement emerges from the creation of 'wilderness' conservation landscapes are well documented, how the production of 'wilderness' articulates with intensifications in HWC remains under examined both empirically and conceptually. Using a political-ecological approach, I analyse increases of HWC in Mozambique's Limpopo National Park (LNP) and the subsequent losses of fields and livestock, as well as forms of physical displacement suffered by resident communities. While intensifications of encounters between wildlife on the one hand and people and livestock on the other result in part from increases in wildlife populations, I argue that HWC and the ways in which it constitutes and contributes to various forms of displacement results more centrally from changing relations between wildlife and people and the power and authority to manage conflict between them. Both of these contributing factors, moreover, are the consequence of practices that aim to transform the LNP into a wilderness landscape of conservation and tourism. HWC and its negative impacts are thus not natural phenomena, but are the result of political decisions to create a particular type of conservation landscape

Dietary Choline Supplementation Attenuates High-Fat-Diet-Induced Hepatocellular Carcinoma in Mice

Background: Hepatocellular carcinoma (HCC) is the third most common cause of cancer-related death in the world. Choline deficiency has been well studied in the context of liver disease; however, less is known about the effects of choline supplementation in HCC. Objective: The objective of this study was to test whether choline supplementation could influence the progression of HCC in a high-fat-diet (HFD)-driven mouse model. Methods: Four-day-old male C57BL/6J mice were treated with the chemical carcinogen, 7,12-dimethylbenz[a]anthracene, and were randomly assigned at weaning to a cohort fed an HFD (60% kcal fat) or an HFD with supplemental choline (60% kcal fat, 1.2% choline; HFD+C) for 30 wk. Blood was isolated at 15 and 30 wk to measure immune cells by flow cytometry, and glucose-tolerance tests were performed 2 wk prior to killing. Overall tumor burden was quantified, hepatic lipids were measured enzymatically, and phosphatidylcholine species were measured by targeted MS methods. Gene expression and mitochondrial DNA were quantified by quantitative PCR. Results: HFD+C mice exhibited a 50-90% increase in both circulating choline and betaine concentrations in the fed state (P ≤ 0.05). Choline supplementation resulted in a 55% decrease in total tumor numbers, a 67% decrease in tumor surface area, and a 50% decrease in hepatic steatosis after 30 wk of diet (P ≤ 0.05). Choline supplementation increased the abundance of mitochondria and the relative expression of β-oxidation genes by 21% and ∼75-100%, respectively, in the liver. HFD+C attenuated circulating myeloid-derived suppressor cells at 15 wk of feeding (P ≤ 0.05). Conclusions: Choline supplementation attenuated HFD-induced HCC and hepatic steatosis in male C57BL/6J mice. These results suggest a therapeutic benefit of choline supplementation in blunting HCC progression