Metabolic flexibility as a major predictor of spatial distribution in microbial communities

A better understand the ecology of microbes and their role in the global ecosystem could be achieved if traditional ecological theories can be applied to microbes. In ecology organisms are defined as specialists or generalists according to the breadth of their niche. Spatial distribution is often used as a proxy measure of niche breadth; generalists have broad niches and a wide spatial distribution and specialists a narrow niche and spatial distribution. Previous studies suggest that microbial distribution patterns are contrary to this idea; a microbial generalist genus (Desulfobulbus) has a limited spatial distribution while a specialist genus (Methanosaeta) has a cosmopolitan distribution. Therefore, we hypothesise that this counter-intuitive distribution within generalist and specialist microbial genera is a common microbial characteristic. Using molecular fingerprinting the distribution of four microbial genera, two generalists, Desulfobulbus and the methanogenic archaea Methanosarcina, and two specialists, Methanosaeta and the sulfate-reducing bacteria Desulfobacter were analysed in sediment samples from along a UK estuary. Detected genotypes of both generalist genera showed a distinct spatial distribution, significantly correlated with geographic distance between sites. Genotypes of both specialist genera showed no significant differential spatial distribution. These data support the hypothesis that the spatial distribution of specialist and generalist microbes does not match that seen with specialist and generalist large organisms. It may be that generalist microbes, while having a wider potential niche, are constrained, possibly by intrageneric competition, to exploit only a small part of that potential niche while specialists, with far fewer constraints to their niche, are more capable of filling their potential niche more effectively, perhaps by avoiding intrageneric competition. We suggest that these counter-intuitive distribution patterns may be a common feature of microbes in general and represent a distinct microbial principle in ecology, which is a real challenge if we are to develop a truly inclusive ecology

Tunable Cavity Optomechanics with Ultracold Atoms

We present an atom-chip-based realization of quantum cavity optomechanics with cold atoms localized within a Fabry-Perot cavity. Effective sub-wavelength positioning of the atomic ensemble allows for tuning the linear and quadratic optomechanical coupling parameters, varying the sensitivity to the displacement and strain of a compressible gaseous cantilever. We observe effects of such tuning on cavity optical nonlinearity and optomechanical frequency shifts, providing their first characterization in the quadratic-coupling regime.Comment: 4 pages, 5 figure

A blueprint for integrated eye-controlled environments

Eye-based environmental control requires innovative solutions for supporting effective user interaction, for allowing home automation and control, and for making homes more "attentive" to user needs. Several approaches have already been proposed, which can be seen as isolated attempts to address only partial issues and specific sub-sets of the general problem. This paper aims at tackling gaze-based home automation as a whole, exploiting state of the art technologies and trying to integrate interaction modalities than are currently supported and that may supported in a near future. User-home interaction is sought through two, complementary, interaction patterns: direct interaction and mediated interaction. Integration between home appliances/devices and user interfaces is granted by a central point of abstraction/harmonization called House Manager. Innovative points can be identified in the wide flexibility of the approach which allows on one side to integrate virtually all home devices having a communication interface, and, on the other side, mixes-up direct and mediated user interaction exploiting the advantages of both. A complete discussion about interaction and accessibility issues is provided, justifying the presented approach from the point of view of human-environment interaction

Haptic search with finger movements: using more fingers does not necessarily reduce search times

Two haptic serial search tasks were used to investigate how the separations between items, and the number of fingers used to scan them, influence the search time and search strategy. In both tasks participants had to search for a target (cross) between a fixed number of non-targets (circles). The items were placed in a straight line. The target’s position was varied within blocks, and inter-item separation was varied between blocks. In the first experiment participants used their index finger to scan the display. As expected, search time depended on target position as well as on item separation. For larger separations participants’ movements were jerky, resembling ‘saccades’ and ‘fixations’, while for the shortest separation the movements were smooth. When only considering time in contact with an item, search times were the same for all separation conditions. Furthermore, participants never continued their movement after they encountered the target. These results suggest that participants did not use the time during which they were moving between the items to process information about the items. The search times were a little shorter than those in a static search experiment (Overvliet et al. in Percept Psychophys, 2007a), where multiple items were presented to the fingertips simultaneously. To investigate whether this is because the finger was moving or because only one finger was stimulated, we conducted a second experiment in which we asked participants to put three fingers in line and use them together to scan the items. Doing so increased the time in contact with the items for all separations, so search times were presumably longer in the static search experiment because multiple fingers were involved. This may be caused by the time that it takes to switch from one finger to the other

Evolutionary History and Population Dynamics of Hepatitis E Virus

BACKGROUND: Hepatitis E virus (HEV) is an enterically transmitted hepatropic virus. It segregates as four genotypes. All genotypes infect humans while only genotypes 3 and 4 also infect several animal species. It has been suggested that hepatitis E is zoonotic, but no study has analyzed the evolutionary history of HEV. We present here an analysis of the evolutionary history of HEV. METHODS AND FINDINGS: The times to the most recent common ancestors for all four genotypes of HEV were calculated using BEAST to conduct a Bayesian analysis of HEV. The population dynamics for genotypes 1, 3 and 4 were analyzed using skyline plots. Bayesian analysis showed that the most recent common ancestor for modern HEV existed between 536 and 1344 years ago. The progenitor of HEV appears to have given rise to anthropotropic and enzootic forms of HEV, which evolved into genotypes 1 and 2 and genotypes 3 and 4, respectively. Population dynamics suggest that genotypes 1, 3 and 4 experienced a population expansion during the 20(th) century. Genotype 1 has increased in infected population size ∼30-35 years ago. Genotype 3 and 4 have experienced an increase in population size starting late in the 19(th) century until ca.1940-45, with genotype 3 having undergone additional rapid expansion until ca.1960. The effective population size for both genotype 3 and 4 rapidly declined to pre-expansion levels starting in ca.1990. Genotype 4 was further examined as Chinese and Japanese sequences, which exhibited different population dynamics, suggesting that this genotype experienced different evolutionary history in these two countries. CONCLUSIONS: HEV appears to have evolved through a series of steps, in which the ancestors of HEV may have adapted to a succession of animal hosts leading to humans. Analysis of the population dynamics of HEV suggests a substantial temporal variation in the rate of transmission among HEV genotypes in different geographic regions late in the 20(th) Century

Upper crustal structure and axial topography at intermediate spreading ridges : seismic constraints from the southern Juan de Fuca Ridge

Author Posting. © American Geophysical Union, 2005. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 110 (2005): B12104, doi:10.1029/2005JB003630.We use multichannel seismic reflection data to image the upper crustal structure of 0-620 ka crust along the southern Juan de Fuca Ridge (JdFR). The study area comprises two segments spreading at intermediate rate with an axial high morphology with narrow (Cleft) and wide (Vance) axial summit grabens (ASG). Along most of the axis of both segments we image the top of an axial magma chamber (AMC). The AMC along Cleft deepens from south to north, from 2.0 km beneath the RIDGE Cleft Observatory and hydrothermal vents near the southern end of the segment, to 2.3 km at the northern end near the site of the 1980’s eruptive event. Along the Vance segment, the AMC also deepens from south to north, from 2.4 km to 2.7 km. Seismic layer 2A, interpreted as the basaltic extrusive layer, is 250-300 m thick at the ridge axis along the Cleft segment, and 300-350 m thick along the axis of the Vance segment. However off-axis layer 2A is similar in both segments (500-600 m), indicating ~90% and ~60% off-axis thickening at the Cleft and Vance segments, respectively. Half of the thickening occurs sharply at the walls of the ASG, with the remaining thickening occurring within 3-4 km of the ASG. Along the full length of both segments, layer 2A is thinner within the ASG, compared to the ridge flanks. Previous studies argued that the ASG is a cyclic feature formed by alternating periods of magmatism and tectonic extension. Our observations agree with the evolving nature of the ASG. However, we suggest that its evolution is related to large changes in axial morphology produced by small fluctuations in magma supply. Thus the ASG, rather than being formed by excess volcanism, is a rifted flexural axial high. The changes in axial morphology affect the distribution of lava flows along the ridge flanks, as indicated by the pattern of layer 2A thickness. The fluctuations in magma supply may occur at all spreading rates, but its effects on crustal structure and axial morphology are most pronounced along intermediate spreading rate ridges.This study was supported by the National Science Foundation grants OCE-0002551 to Woods Hole Oceanographic Institution, OCE-0002488 to Lamont-Doherty Earth Observatory, and OCE-0002600 to Scripps Institution of Oceanography

Cellular Radiosensitivity: How much better do we understand it?

Purpose: Ionizing radiation exposure gives rise to a variety of lesions in DNA that result in genetic instability and potentially tumorigenesis or cell death. Radiation extends its effects on DNA by direct interaction or by radiolysis of H2O that generates free radicals or aqueous electrons capable of interacting with and causing indirect damage to DNA. While the various lesions arising in DNA after radiation exposure can contribute to the mutagenising effects of this agent, the potentially most damaging lesion is the DNA double strand break (DSB) that contributes to genome instability and/or cell death. Thus in many cases failure to recognise and/or repair this lesion determines the radiosensitivity status of the cell. DNA repair mechanisms including homologous recombination (HR) and non-homologous end-joining (NHEJ) have evolved to protect cells against DNA DSB. Mutations in proteins that constitute these repair pathways are characterised by radiosensitivity and genome instability. Defects in a number of these proteins also give rise to genetic disorders that feature not only genetic instability but also immunodeficiency, cancer predisposition, neurodegeneration and other pathologies. Conclusions: In the past fifty years our understanding of the cellular response to radiation damage has advanced enormously with insight being gained from a wide range of approaches extending from more basic early studies to the sophisticated approaches used today. In this review we discuss our current understanding of the impact of radiation on the cell and the organism gained from the array of past and present studies and attempt to provide an explanation for what it is that determines the response to radiation

The Hepatitis E Virus Polyproline Region Is Involved in Viral Adaptation

Genomes of hepatitis E virus (HEV), rubivirus and cutthroat virus (CTV) contain a region of high proline density and low amino acid (aa) complexity, named the polyproline region (PPR). In HEV genotypes 1, 3 and 4, it is the only region within the non-structural open reading frame (ORF1) with positive selection (4–10 codons with dN/dS>1). This region has the highest density of sites with homoplasy values >0.5. Genotypes 3 and 4 show ∼3-fold increase in homoplastic density (HD) in the PPR compared to any other region in ORF1, genotype 1 does not exhibit significant HD (p<0.0001). PPR sequence divergence was found to be 2-fold greater for HEV genotypes 3 and 4 than for genotype 1. The data suggest the PPR plays an important role in host-range adaptation. Although the PPR appears to be hypervariable and homoplastic, it retains as much phylogenetic signal as any other similar sized region in the ORF1, indicating that convergent evolution operates within the major HEV phylogenetic lineages. Analyses of sequence-based secondary structure and the tertiary structure identify PPR as an intrinsically disordered region (IDR), implicating its role in regulation of replication. The identified propensity for the disorder-to-order state transitions indicates the PPR is involved in protein-protein interactions. Furthermore, the PPR of all four HEV genotypes contains seven putative linear binding motifs for ligands involved in the regulation of a wide number of cellular signaling processes. Structure-based analysis of possible molecular functions of these motifs showed the PPR is prone to bind a wide variety of ligands. Collectively, these data suggest a role for the PPR in HEV adaptation. Particularly as an IDR, the PPR likely contributes to fine tuning of viral replication through protein-protein interactions and should be considered as a target for development of novel anti-viral drugs