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Ubiquitous
Terms modified by Ubiquitous Selected AbstractsMaking sense of cilia in disease: The human ciliopathies,AMERICAN JOURNAL OF MEDICAL GENETICS, Issue 4 2009Kate Baker Abstract Ubiquitous in nature, cilia and flagella comprise nearly identical structures with similar functions. The most obvious example of the latter is motility: driving movement of the organism or particle flow across the epithelial surface in fixed structures. In vertebrates, such motile cilia are evident in the respiratory epithelia, ependyma, and oviducts. For over a century, non-motile cilia have been observed on the surface of most vertebrate cells but until recently their function has eluded us. Gathering evidence now points to critical roles for the mono-cilium in sensing the extracellular environment, and perturbation of this function gives rise to a predictable panoply of clinical problems. We review the common clinical phenotypes associated with ciliopathies and interrogate Online Mendelian Inheritance in Man (OMIM) to compile a comprehensive list of putative disorders in which ciliary dysfunction may play a role. © 2009 Wiley-Liss, Inc. [source] Practical CFD Simulations on Programmable Graphics Hardware using SMAC,COMPUTER GRAPHICS FORUM, Issue 4 2005Carlos E. Scheidegger Abstract The explosive growth in integration technology and the parallel nature of rasterization-based graphics APIs (Application Programming Interface) changed the panorama of consumer-level graphics: today, GPUs (Graphics Processing Units) are cheap, fast and ubiquitous. We show how to harness the computational power of GPUs and solve the incompressible Navier-Stokes fluid equations significantly faster (more than one order of magnitude in average) than on CPU solvers of comparable cost. While past approaches typically used Stam's implicit solver, we use a variation of SMAC (Simplified Marker and Cell). SMAC is widely used in engineering applications, where experimental reproducibility is essential. Thus, we show that the GPU is a viable and affordable processor for scientific applications. Our solver works with general rectangular domains (possibly with obstacles), implements a variety of boundary conditions and incorporates energy transport through the traditional Boussinesq approximation. Finally, we discuss the implications of our solver in light of future GPU features, and possible extensions such as three-dimensional domains and free-boundary problems. [source] Usability levels for sparse linear algebra components,CONCURRENCY AND COMPUTATION: PRACTICE & EXPERIENCE, Issue 12 2008M. Sosonkina Abstract Sparse matrix computations are ubiquitous in high-performance computing applications and often are their most computationally intensive part. In particular, efficient solution of large-scale linear systems may drastically improve the overall application performance. Thus, the choice and implementation of the linear system solver are of paramount importance. It is difficult, however, to navigate through a multitude of available solver packages and to tune their performance to the problem at hand, mainly because of the plethora of interfaces, each requiring application adaptations to match the specifics of solver packages. For example, different ways of setting parameters and a variety of sparse matrix formats hinder smooth interactions of sparse matrix computations with user applications. In this paper, interfaces designed for components that encapsulate sparse matrix computations are discussed in the light of their matching with application usability requirements. Consequently, we distinguish three levels of interfaces, high, medium, and low, corresponding to the degree of user involvement in the linear system solution process and in sparse matrix manipulations. We demonstrate when each interface design choice is applicable and how it may be used to further users' scientific goals. Component computational overheads caused by various design choices are also examined, ranging from low level, for matrix manipulation components, to high level, in which a single component contains the entire linear system solver. Published in 2007 by John Wiley & Sons, Ltd. [source] Mock as screen and opticCRITICAL QUARTERLY, Issue 3 2004Simon Jarvis As its unique approach to the question of generational differences, this essay takes the relationship looks at poetry and modernity; that is, what happens when a style [such as the mock heroic, or the poetically inflated] starts to feel its age, yet doesn't die; and how its readers cope with its resurrections. Moving nimbly from Nigel Slater to Alexander Pope and back, the essay abandons the usual and reduced conception of 'mock' - that it describes trivial happenings but in an elevated language - and instead looks for a better conception, suggesting instead that mock is ubiquitous, both in literature and the everyday, as a broad and all-pervasive style of thinking and feeling. [source] Tumoral and tissue-specific expression of the major human ,-tubulin isotypes,CYTOSKELETON, Issue 4 2010Luis J. Leandro-García Abstract The ,-tubulins are microtubule components encoded by a multigene family, which produces slightly different proteins with complex expression patterns. Several widely used anticancer drugs base their activity on ,-tubulin binding, microtubule dynamics alteration, and cell division blockage. The expression of these drug targets in tumoral and normal cells could be of crucial importance for therapy outcome, unfortunately, the complex ,-tubulin expression patterns have been poorly characterized in human. In this study, we developed a quantitative RT-PCR technique that accurately determines the mRNA expression of the eight human ,-tubulin isotypes, encoding class I, IIa, IIb, III, IVa, IVb, V, and VI and applied it to 21 nontumoral tissues and 79 tumor samples belonging to seven cancer types. In the nontumoral tissues, we found that, overall, TUBB (I), TUBB2C (IVb), and TUBB6 (V) were ubiquitous, TUBB1(VI) was hematopoietic cell-specific, and TUBB2A (IIa), TUBB2B (IIb), TUBB3 (III), and TUBB4 (IVa) had high expression in brain; however, the contribution of the different isotypes to the total ,-tubulin content varied for each tissue and had a complex pattern. In tumoral tissues, most isotypes exhibited an altered expression in specific tumor types or related to tumoral characteristics. In general, TUBB3 showed a great increase in expression while TUBB6 expression was largely decreased in most tumors. Thus, normal tissues showed a complex ,-tubulin isotype distribution, which could contribute to the toxicity profile of the microtubule-binding drugs. In addition, the specific isotypes significantly altered in tumors might represent markers for drug response. © 2010 Wiley-Liss, Inc. [source] Myoblast attachment and spreading are regulated by different patterns by ubiquitous calpainsCYTOSKELETON, Issue 4 2006Germain Mazères Abstract The calcium-dependent proteolytic system is a large family of well-conserved ubiquitous and tissue-specific proteases, known as calpains, and an endogenous inhibitor, calpastatin. Ubiquitous calpains are involved in many physiological phenomena, such as the cell cycle, muscle cell differentiation, and cell migration. This study investigates the regulation of crucial steps of cell motility, myoblast adhesion and spreading, by calpains. Inhibition of each ubiquitous calpain isoform by antisense strategy pinpointed the involvement of each of these proteases in myoblast adhesion and spreading. Moreover, the actin cytoskeleton and microtubules were observed in transfected cells, demonstrating that each ubiquitous calpain could be involved in the actin fiber organization. C2C12 cells with reduced ,- or m-calpain levels have a rounded morphology and disorganized stress fibers, but no modification in the microtubule cytoskeleton. Antisense strategy directed against MARCKS, a calpain substrate during C2C12 migration, showed that this protein could play a role in stress fiber polymerization. A complementary proteomic analysis using C2C12 cells over-expressing calpastatin indicated that two proteins were under-expressed, while six, which are involved in the studied phenomena, were overexpressed after calpain inhibition. The possible role of these proteins in adhesion, spreading, and migration was discussed. Cell Motil. Cytoskeleton 63: 2006. © 2006 Wiley-Liss, Inc. [source] Sp1-like transcription factors are regulators of embryonic development in vertebratesDEVELOPMENT GROWTH & DIFFERENTIATION, Issue 4 2005Chengtian Zhao Sp1-like family is an expanding transcription factor family. Members of this family bind to the GC-box or GT-box elements in the promoter/enhancers and regulate the expression of the target genes. Currently, this family consists of at least nine members, which may act as a transactivator or a repressor on target promoters. Sp1-like transcription factors are expressed during development of vertebrate embryos in ubiquitous or tissue-specific manners and play various roles in embryonic development. This review mainly summarises their expression patterns and functions during vertebrate embryogenesis. [source] The evolutionary psychology of left and right: Costs and benefits of lateralizationDEVELOPMENTAL PSYCHOBIOLOGY, Issue 6 2006Giorgio VallortigaraArticle first published online: 2 AUG 200 Abstract Why do the left and right sides of the vertebrate brain play different functions? Having a lateralized brain, in which each hemisphere carries out different functions, is ubiquitous among vertebrates. The different specialization of the left and right side of the brain may increase brain efficiency,and some evidence for that is reported here. However, lateral biases due to brain lateralization (such as preferences in the use of a limb or, in animals with laterally placed eyes, of a visual hemifield) usually occur at the population level, with most individuals showing similar direction of bias. Individual brain efficiency does not require the alignment of lateralization in the population. Why then are not left- and right-type individuals equally common? Not only humans, but most vertebrates show a similar pattern. For instance, in the paper I report evidence that most toads, chickens, and fish react faster when a predator approaches from the left. I argue that invoking individual brain efficiency (lateralization may increase fitness), evolutionary chance or direct genetic mechanisms cannot explain this widespread pattern. Instead, using concepts from mathematical theory of games, I show that alignment of lateralization at the population level may arise as an "evolutionarily stable strategy" when individually asymmetrical organisms must coordinate their behavior with that of other asymmetrical organisms. Thus, the population structure of lateralization may result from genes specifying the direction of asymmetries which have been selected under "social" pressures. © 2006 Wiley Periodicals, Inc. Dev Psychobiol 48: 418,427, 2006. [source] Prescription drug misuse: Is technology friend or foe?DRUG AND ALCOHOL REVIEW, Issue 1 2009SUZANNE NIELSEN Abstract Introduction and Aims. Prescription drug misuse and related harms have been increasing considerably over the past decade. At the same time, there has also been rapid growth in the use of online and Internet technologies. Thus, it is important that we understand the role online and Internet technologies play in prescription drug misuse. Design and Methods. Published work addressing the role of technology in prescription drug misuse is explored. Topics include: Internet supply, online monitoring of prescription drug use trends and electronic prescription monitoring. Results. Little is known about the prevalence of acquiring prescription drugs from online pharmacies. Prescription drugs are easily accessible through vendor websites, and ,rogue' no-prescription websites have proven difficult to control. There has so far been limited application of real-time monitoring to prevent overuse of prescription medications. Online monitoring of drug use trends may also prove to be a useful and timely source of information about new methods of ,off-label' prescription drug use. Discussion and Conclusions. Technology has the potential to play a more prominent role in facilitating drug acquisition, while also enhancing the monitoring and prevention of prescription drug misuse. As technology becomes more ubiquitous in everyday life, the continued investigation of its relationship with prescription drug misuse becomes even more important.[Nielsen S, Barratt MJ. Prescription drug misuse: Is technology friend or foe? Drug Alcohol Rev 2009;28:81,86] [source] Mollusk species diversity in the Southeastern Pacific: why are there more species towards the pole?ECOGRAPHY, Issue 2 2003Claudio Valdovinos The most ubiquitous and well recognized diversity pattern at large spatial scales is the latitudinal increase in species richness near the equator and decline towards the poles. Although several exceptions to this pattern have been documented, shallow water mollusks, the most specious group of marine invertebrates, are the epitome of the monotonic decline in species diversity toward higher latitudes along the Pacific and Atlantic coasts of North America. Here we analyze the geographic diversity of 629 mollusk species along the Pacific South American shelf. Our analyses are based on the most complete database of invertebrates assembled for this region of the world, consisting of latitudinal ranges of over 95% of all described mollusks between 10° and 55°S. Along this coast, mollusk diversity did not follow the typical latitudinal trend. The number of species remained constant and relatively low at intermediate latitudes and sharply increased toward higher latitudes, south of 42°S. This trend was explained by changes in shelf area, but not by sea surface temperature, unlike the pattern documented for Northern Hemisphere mollusks. Direct sampling of soft bottom communities along the gradient suggests that regional trends in species richness are produced by increased alpha diversity, and not only by artifacts produced by the increase in sampling area. We hypothesize that increased shelf area south of 42°S, geographic isolation produced by divergence of major oceanic currents, and the existence of refugia during glaciations, enabled species diversification. Radiation could have been limited by narrow continental shelves between 10°,42°. Asymmetries in latitudinal diversity trends between hemispheres show that there is not a single general factor determining large-scale diversity patterns. [source] Community effects of praying mantids: a meta-analysis of the influences of species identity and experimental designECOLOGICAL ENTOMOLOGY, Issue 4 2002William F. Fagan Abstract ,1. Generalist arthropod predators are ubiquitous in terrestrial ecosystems but experimental studies have yielded little agreement as to their effects on prey assemblages. Drawing on results from a suite of experimental field studies, a meta-analysis was conducted of the impact of praying mantids (Mantodea: Mantidae) on arthropod assemblages in order to identify predictable and unpredictable effects of these extremely generalised predators. 2. Results across different experiments were synthesised using the log response ratio framework, with a focus on quantifying net mantid impacts on arthropod density across taxonomic orders and trophic levels of arthropods, paying special attention to the contribution of mantid species identity and experimental design variables, such as the use of cages, length of experiment, and manipulated mantid density. 3. Calculated on a per mantid-day basis, the net impacts of Tenodera sinensis on arthropod density were generally weaker but more predictable than the effects of Mantis religiosa. Mantids in general had weak negative effects on density for most taxa but exhibited strong negative and positive effects on some taxa. Tenodera sinensis tended to have negative effects on Homoptera, Diptera, and Hemiptera and herbivores as a group, however M. religiosa exhibited greater variation in response of different taxa that appeared to be affected more strongly by experimental design. The effects of Stagmomantis carolina tended to be negative or non-significant. 4. Experimental cages had little influence on either the sign or magnitude of net community impacts for T. sinensis, however cage experiments reversed the sign of the mean effect for two of six taxonomic orders when the experimental predator was M. religiosa. Cages also increased the variability of effect size greatly for M. religiosa but not for T. sinensis. 5. It was concluded that it is possible to use log response ratios to determine general, predictable trends in a well-studied system. Similar meta-analyses of generalist predator effects in other systems should produce predictions of how these predators influence food webs, an important step towards defining more clearly the influences of generalist predators on community structure and dynamics. [source] Predator control of ecosystem nutrient dynamicsECOLOGY LETTERS, Issue 10 2010Oswald J. Schmitz Abstract Predators are predominantly valued for their ability to control prey, as indicators of high levels of biodiversity and as tourism attractions. This view, however, is incomplete because it does not acknowledge that predators may play a significant role in the delivery of critical life-support services such as ecosystem nutrient cycling. New research is beginning to show that predator effects on nutrient cycling are ubiquitous. These effects emerge from direct nutrient excretion, egestion or translocation within and across ecosystem boundaries after prey consumption, and from indirect effects mediated by predator interactions with prey. Depending on their behavioural ecology, predators can create heterogeneous or homogeneous nutrient distributions across natural landscapes. Because predator species are disproportionately vulnerable to elimination from ecosystems, we stand to lose much more from their disappearance than their simple charismatic attractiveness. [source] Seasonality and the dynamics of infectious diseasesECOLOGY LETTERS, Issue 4 2006Sonia Altizer Abstract Seasonal variations in temperature, rainfall and resource availability are ubiquitous and can exert strong pressures on population dynamics. Infectious diseases provide some of the best-studied examples of the role of seasonality in shaping population fluctuations. In this paper, we review examples from human and wildlife disease systems to illustrate the challenges inherent in understanding the mechanisms and impacts of seasonal environmental drivers. Empirical evidence points to several biologically distinct mechanisms by which seasonality can impact host,pathogen interactions, including seasonal changes in host social behaviour and contact rates, variation in encounters with infective stages in the environment, annual pulses of host births and deaths and changes in host immune defences. Mathematical models and field observations show that the strength and mechanisms of seasonality can alter the spread and persistence of infectious diseases, and that population-level responses can range from simple annual cycles to more complex multiyear fluctuations. From an applied perspective, understanding the timing and causes of seasonality offers important insights into how parasite,host systems operate, how and when parasite control measures should be applied, and how disease risks will respond to anthropogenic climate change and altered patterns of seasonality. Finally, by focusing on well-studied examples of infectious diseases, we hope to highlight general insights that are relevant to other ecological interactions. [source] Clinical Information Systems: Instant Ubiquitous Clinical Data for Error Reduction and Improved Clinical OutcomesACADEMIC EMERGENCY MEDICINE, Issue 11 2004Craig F. Feied MD Abstract Immediate access to existing clinical information is inadequate in current medical practice; lack of existing information causes or contributes to many classes of medical error, including diagnostic and treatment error. A review of the literature finds ample evidence to support a description of the problems caused by data that are missing or unavailable but little evidence to support one proposed solution over another. A primary recommendation of the Consensus Committee is that hospitals and departments should adopt systems that provide fast, ubiquitous, and unified access to all types of existing data. Additional recommendations cover a variety of related functions and operational concepts, from backups and biosurveillance to speed, training, and usability. [source] Hepatitis C virus infection among drug injectors in St Petersburg, Russia: social and molecular epidemiology of an endemic infectionADDICTION, Issue 11 2009Elijah Paintsil ABSTRACT Aims To understand the epidemiology and transmission patterns of hepatitis C virus (HCV), the predominant blood borne-pathogen infecting injection drug users (IDUs), in a part of the former Soviet Union. Design Cross-sectional respondent-driven sample of IDUs. Setting St Petersburg, Russia. Participants A total of 387 IDUs were recruited in late 2005 and throughout 2006. Measurements Participants were surveyed to collect demographic, medical and both general and dyad-specific drug injection and sexual behaviors. A blood sample was collected to detect antibodies to hepatitis C and to amplify viral RNA for molecular analysis. The molecular data, including genotypes, were analyzed spatially and linkage patterns were compared to the social linkages obtained by respondent-driven sampling (RDS) for chains of respondents and among the injection dyads. Findings HCV infection was all but ubiquitous: 94.6% of IDUs were HCV-seropositive. Among the 209 viral sequences amplified, genotype 3a predominated (n = 119, 56.9%), followed by 1b (n = 61, 29.2%) and 1a (n = 25, 11.9%). There was no significant clustering of genotypes spatially. Neither genotypes nor closely related sequences were clustered within RDS chains. Analysis of HCV sequences from dyads failed to find associations of genotype or sequence homology within pairs. Conclusions Genotyping reveals that there have been at least five unique introductions of HCV genotypes into the IDU community in St Petersburg. Analysis of prevalent infections does not appear to correlate with the social networks of IDUs, suggesting that simple approaches to link these networks to prevalent infections, rather than incident transmission, will not prove meaningful. On a more positive note, the majority of IDUs are infected with 3a genotype that is associated with sustained virological response to antiviral therapy. [source] Ecological niche partitioning in the picoplanktonic green alga Micromonas pusilla: evidence from environmental surveys using phylogenetic probesENVIRONMENTAL MICROBIOLOGY, Issue 9 2008Elodie Foulon Summary Very few studies have analysed the niches of pelagic protist in details. This is because for most protists, both an accurate species definition and methods for routine detection and quantification of cells are lacking. The morphospecies Micromonas pusilla, a marine unicellular green alga, is the most ubiquitous and cosmopolitan picoeukaryote described to date. This species comprises several independent genetic lineages or clades, which are not currently distinguishable based on comparison of their morphology or biogeographical distribution. Molecular probes were used to detect and quantify the genetic clades of M. pusilla in samples from temperate, polar and tropical environments in order to assess potential ecological niche partitioning. The three clades were detected in all biogeographical regions studied and were commonly found in sympatry. Cell abundances recorded for clades A and B were high, especially at coastal stations. Clade C, when detected, was always at low abundances and is suggested to be a low-light clade. Shifts in the contribution of clades to total M. pusilla abundance were observed along environmental gradients, both at local and basin-wide scales. This suggests that the phylogenetic clades occupy specific niches and confirms the existence of cryptic species within the morphospecies M. pusilla. Parameters which can precisely explain the distribution of these cryptic species remain to be elucidated. [source] Limits of life in MgCl2 -containing environments: chaotropicity defines the windowENVIRONMENTAL MICROBIOLOGY, Issue 3 2007John E. Hallsworth Summary The biosphere of planet Earth is delineated by physico-chemical conditions that are too harsh for, or inconsistent with, life processes and maintenance of the structure and function of biomolecules. To define the window of life on Earth (and perhaps gain insights into the limits that life could tolerate elsewhere), and hence understand some of the most unusual biological activities that operate at such extremes, it is necessary to understand the causes and cellular basis of systems failure beyond these windows. Because water plays such a central role in biomolecules and bioprocesses, its availability, properties and behaviour are among the key life-limiting parameters. Saline waters dominate the Earth, with the oceans holding 96.5% of the planet's water. Saline groundwater, inland seas or saltwater lakes hold another 1%, a quantity that exceeds the world's available freshwater. About one quarter of Earth's land mass is underlain by salt, often more than 100 m thick. Evaporite deposits contain hypersaline waters within and between their salt crystals, and even contain large subterranean salt lakes, and therefore represent significant microbial habitats. Salts have a major impact on the nature and extent of the biosphere, because solutes radically influence water's availability (water activity) and exert other activities that also affect biological systems (e.g. ionic, kosmotropic, chaotropic and those that affect cell turgor), and as a consequence can be major stressors of cellular systems. Despite the stressor effects of salts, hypersaline environments can be heavily populated with salt-tolerant or -dependent microbes, the halophiles. The most common salt in hypersaline environments is NaCl, but many evaporite deposits and brines are also rich in other salts, including MgCl2 (several hundred million tonnes of bischofite, MgCl2·6H2O, occur in one formation alone). Magnesium (Mg) is the third most abundant element dissolved in seawater and is ubiquitous in the Earth's crust, and throughout the Solar System, where it exists in association with a variety of anions. Magnesium chloride is exceptionally soluble in water, so can achieve high concentrations (> 5 M) in brines. However, while NaCl-dominated hypersaline environments are habitats for a rich variety of salt-adapted microbes, there are contradictory indications of life in MgCl2 -rich environments. In this work, we have sought to obtain new insights into how MgCl2 affects cellular systems, to assess whether MgCl2 can determine the window of life, and, if so, to derive a value for this window. We have dissected two relevant cellular stress-related activities of MgCl2 solutions, namely water activity reduction and chaotropicity, and analysed signatures of life at different concentrations of MgCl2 in a natural environment, namely the 0.05,5.05 M MgCl2 gradient of the seawater : hypersaline brine interface of Discovery Basin , a large, stable brine lake almost saturated with MgCl2, located on the Mediterranean Sea floor. We document here the exceptional chaotropicity of MgCl2, and show that this property, rather than water activity reduction, inhibits life by denaturing biological macromolecules. In vitro, a test enzyme was totally inhibited by MgCl2 at concentrations below 1 M; and culture medium with MgCl2 concentrations above 1.26 M inhibited the growth of microbes in samples taken from all parts of the Discovery interface. Although DNA and rRNA from key microbial groups (sulfate reducers and methanogens) were detected along the entire MgCl2 gradient of the seawater : Discovery brine interface, mRNA, a highly labile indicator of active microbes, was recovered only from the upper part of the chemocline at MgCl2 concentrations of less than 2.3 M. We also show that the extreme chaotropicity of MgCl2 at high concentrations not only denatures macromolecules, but also preserves the more stable ones: such indicator molecules, hitherto regarded as evidence of life, may thus be misleading signatures in chaotropic environments. Thus, the chaotropicity of MgCl2 would appear to be a window-of-life-determining parameter, and the results obtained here suggest that the upper MgCl2 concentration for life, in the absence of compensating (e.g. kosmotropic) solutes, is about 2.3 M. [source] Diversity of the cadmium-containing carbonic anhydrase in marine diatoms and natural watersENVIRONMENTAL MICROBIOLOGY, Issue 2 2007Haewon Park Summary A recent report of a novel carbonic anhydrase (CDCA1) with Cd as its metal centre in the coastal diatom Thalassiosira weissflogii has led us to search for the occurrence of this Cd enzyme (CDCA) in other marine phytoplankton and in the environment. Using degenerate primers designed from the published sequences from T. weissflogii and a putative sequence in the genome of Thalassiosira pseudonana, we show that CDCA is widespread in diatom species and ubiquitous in the environment. All detected genes share more than 64% amino acid identity with the CDCA of T. pseudonana. Analysis of the amino acid sequence of CDCA shows that the putative Cd binding site resembles that of beta-class carbonic anhydrases (CAs). The prevalence of CAs in diatoms that presumably contain Cd at their active site probably reflects the very low concentration of Zn in the marine environment and the difficulty in acquiring inorganic carbon for photosynthesis. The cdca primers developed in this study should be useful for detecting cdca genes in the field, and studying the conditions under which they are expressed. [source] Hypolithic community shifts occur as a result of liquid water availability along environmental gradients in China's hot and cold hyperarid desertsENVIRONMENTAL MICROBIOLOGY, Issue 2 2007Stephen B. Pointing Summary Hypolithic cyanobacterial communities occur in hot and cold hyperarid environments but the physical factors determining their diversity are not well understood. Here we report hypolithic diversity and colonization of a common quartz substrate at several hyperarid locations in the ancient deserts of north-western China, that experience varying mean annual temperature, rainfall and concomitant availability of liquid water in soil. Microscopy and enrichment culture resulted only in Chroococcidiopsis morphotypes which were ubiquitous, but community phylogenetic analysis revealed considerable cyanobacterial and heterotrophic bacterial diversity. Species Richness and Shannon's Diversity Index displayed a significant positive linear correlation with availability of liquid water but not temperature or rainfall alone. Several taxonomic groups occurred only in specific climatically defined locations, while for Chroococcidiopsis, Deinococcus and Phormidium location specific lineages within these genera were also evident. Multivariate analysis was used to illustrate pronounced community shifts due to liquid water availability, although these did not significantly affect the predicted functional relationships within any given assemblage in either hot or cold, wet or dry hyperarid deserts. This study clearly demonstrates that availability of liquid water, rather than temperature or rainfall per se is the key determinant of hypolithic diversity in hyperarid locations, and furthermore that functionally similar yet taxonomically distinct communities occur, characterized by the presence of taxa that are specific to defined levels of aridity. [source] The impact of grassland management on archaeal community structure in upland pasture rhizosphere soilENVIRONMENTAL MICROBIOLOGY, Issue 3 2003Graeme W. Nicol Summary The community structure of rhizosphere soil Archaea from three grassland types, associated with different management practices, was examined at a site in the Borders region of Scotland, by analysis of 16S rRNA gene fragments amplified from 16S rDNA and from rRNA. Denaturing gradient gel electrophoresis (DGGE) and sequence analysis of amplified products indicated high relative abundance within the archaeal community of two distinct lineages of non-thermophilic (group 1) Crenarchaeota. Grassland management practices influenced archaeal community structure, as characterized by both 16S rRNA- and 16S rDNA-derived DGGE profiles. One band dominated DGGE profiles in all three grassland types examined, and reproducible differences in the presence and intensity of bands were observed between profiles from managed and natural grassland sites. Analysis of 16S rRNA-derived amplicons from managed and natural grasslands at sites in the north of England and the north of Wales also indicated high relative abundance of non-thermophilic crenarchaeotes within the archaeal community. The band dominating the Scottish grassland site also dominated DGGE profiles from the English and Welsh sites, and similar differences were seen between profiles derived from soils subjected to different management regimes. The study indicates that grassland archaeal communities are dominated by Crenarchaeota, with closely related members of this lineage ubiquitous in distribution in UK upland pasture, and indicate that management practices influence the nature of the crenarchaeotal community. [source] Interplay of actors, scales, frameworks and regimes in the governance of biodiversityENVIRONMENTAL POLICY AND GOVERNANCE, Issue 3 2009Jouni Paavola Abstract This article examines the key contributions of the political science and systems theory based literatures on environmental governance, and uses them to analyse the governance of biodiversity in Europe. The article suggests that the key insights of the two bodies of literature are a distinction between governance frameworks and regimes on one hand, and the importance of multifaceted and multiple scales on the other. These key insights draw attention to horizontal and vertical forms of interplay. The article suggests that interplay, both between actors and levels and between frameworks and regimes, is ubiquitous and ambivalent: it can either foster or hinder environmental governance. The article illustrates this discussion in the context of governance of biodiversity in Europe, highlighting how vertical and horizontal interplay between the governance framework for biodiversity and the broader institutional setting or regime have characterized the implementation of the Habitats Directive, both complicating and fostering the governance of biodiversity in Europe. Copyright © 2009 John Wiley & Sons, Ltd and ERP Environment. [source] Contaminant-associated alteration of immune function in black-footed albatross (Phoebastria nigripes), a North Pacific predatorENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 9 2007Myra E. Finkelstein Abstract Environmental pollution is ubiquitous and can pose a significant threat to wild populations through declines in fitness and population numbers. To elucidate the impact of marine pollution on a pelagic species, we assessed whether toxic contaminants accumulated in black-footed albatross (Phoebastria nigripes), a wide-ranging North Pacific predator, are correlated with altered physiological function. Blood samples from adult black-footed albatrosses on Midway Atoll, part of the Hawaiian (USA) archipelago, were analyzed for organochlorines (e.g., polychlorinated biphenyls [PCBs] and chlorinated pesticides), trace metals (silver, cadmium, tin, lead, chromium, nickel, copper, zinc, arsenic, selenium, and total mercury), and a sensitive physiological marker, peripheral white blood cell immune function (mitogen-induced lymphocyte proliferation and macrophage phagocytosis). We found a positive significant relationship between organochlorines, which were highly correlated within individual birds (p < 0.001, r > 0.80, Spearman correlation for all comparisons; PCBs, 160 ± 60 ng/ml plasma [mean ± standard deviation]; DDTs, 140 ± 180 ng/ml plasma; chlordanes, 7.0 ± 3.6 ng/ml plasma; hexachlorobenzene, 2.4 ± 1.5 ng/ml plasma; n = 15) and increased lymphocyte proliferation (p = 0.020) as well as percentage lymphocytes (p = 0.033). Mercury was elevated in black-footed albatrosses (4,500 ± 870 ng/ml whole blood, n = 15), and high mercury levels appeared to be associated (p = 0.017) with impaired macrophage phagocytosis. The associations we documented between multiple contaminant concentrations and immune function in endangered black-footed albatrosses provide some of the first evidence that albatrosses in the North Pacific may be affected by environmental contamination. Our results raise concern regarding detrimental health effects in pelagic predators exposed to persistent marine pollutants. [source] Effects of brominated flame retardants and brominated dioxins on steroidogenesis in H295R human adrenocortical carcinoma cell lineENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 4 2007Ling Ding Abstract Brominated flame retardants (BFRs) and brominated dioxins are emerging persistent organic pollutants that are ubiquitous in the environment and can be accumulated by wildlife and humans. These chemicals can disturb endocrine function. Recent studies have demonstrated that one of the mechanisms of endocrine disruption by chemicals is modulation of steroidogenic gene expression or enzyme activities. In this study, an in vitro assay based on the H295R human adrenocortical carcinoma cell line, which possesses most key genes or enzymes involved in steroidogenesis, was used to examine the effects of five bromophenols, two polybrominated biphenyls (PBBs 77 and 169), 2,3,7,8-tetrabromodibenzo- p -dioxin, and 2,3,7,8-tetrabromodibenzofuran on the expression of 10 key steroidogenic genes. The H295R cells were exposed to various BFR concentrations for 48 h, and the expression of specific genes,cytochrome P450 (CYP11A, CYP11B2, CYP17, CYP19, and CYP21), 3,-hydroxysteroid dehydrogenase (3,HSD2), 17,-hydroxysteroid dehydrogenase (17,HSD1 and 17,HSD4), steroidogenic acute regulatory protein (StAR), and 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR),was quantitatively measured using real-time polymerase chain reaction. Cell viability was not affected at the doses tested. Most of the genes were either up- or down-regulated, to some extent, by BFR exposure. Among the genes tested, 3,HSD2 was the most markedly up-regulated, with a range of magnitude from 1.6- to 20-fold. The results demonstrate that bromophenol, bromobiphenyls, and bromodibenzo- p -dioxin/furan are able to modulate steroidogenic gene expression, which may lead to endocrine disruption. [source] Human herpes virus 6B: A possible role in epilepsy?EPILEPSIA, Issue 11 2008William H. Theodore Summary Human herpes virus 6 (HHV6) infection is nearly ubiquitous in childhood and may include central nervous system invasion. There are two variants, HHV6A and HHV6B. Usually asymptomatic, it is associated with the common, self-limited childhood illness roseola infantum and rarely with more severe syndromes. In patients with immune compromise, subsequent reactivation of viral activity may lead to severe limbic encephalitis. HHV6 has been identified as a possible etiologic agent in multiple sclerosis, myocarditis, and encephalitis. A preponderance of evidence supports an association between HHV6 and febrile seizures. An ongoing multicenter study is investigating possible links between HHV6 infection, febrile status epilepticus, and development of mesial temporal sclerosis (MTS). Investigation of temporal lobectomy specimens showed evidence of active HHV6B but not HHV6A replication in hippocampal astrocytes in about two-thirds of patients with MTS but not other causes of epilepsy. It has been suggested that HHV6B may cause "excitotoxicity" by interfering with astrocyte excitatory amino acid transport. Although conventional inflammatory changes are not found in most MTS specimens, inflammatory modulators may play a role in neuronal injury leading to MTS as well. If the link between early viral infection, complex or prolonged febrile seizures, and later development of intractable temporal lobe epilepsy is confirmed, new therapeutic approaches to a common intractable epilepsy syndrome may be possible. [source] Hippocampal granule neuron production and population size are regulated by levels of bFGFEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 1 2002Yinghong Cheng Abstract Numerous studies of the proliferative effects of basic fibroblast growth factor (bFGF) in culture, including neonatal and adult hippocampal precursors, suggest that the factor plays a ubiquitous and life-long role in neurogenesis. In contrast, in vivo, bFGF is devoid of effects on neurons in mature hippocampus, raising the possibility that bFGF exhibits developmental stage-specific activity in the complex animal environment. To define neurogenetic effects in the newborn, a single subcutaneous injection of bFGF (20 ng/gm) was administered to postnatal day 1 (P1) rats, and hippocampal DNA content was quantified: bFGF elicited an increase in total DNA throughout adulthood, by 48% at P4, 25% at P22, and 17% at P180, suggesting that bFGF increases hippocampal cell number. To define mechanisms, bromodeoxyuridine (BrdU) was injected at P1 and mitotically labelled cells were assessed at P22: there was a twofold increase in BrdU-positive cells in the dentate granule cell layer (GCL), indicating that bFGF enhanced the generation of neurons, or neuronogenesis, from a cohort of precursors. Moreover, enhanced mitosis and survival led to a 33% increase in absolute GCL neuron number, suggesting that neuron production depends on environmental levels of bFGF. To evaluate this possibility, bFGF-knockout mice were analyzed: hippocampal DNA content was decreased at all ages examined (P3, ,42%; P21, ,28%; P360, ,18%), and total GCL neuron and glial fibrillary acidic protein (GFAP)-positive cell number were decreased by 30%, indicating that bFGF is necessary for normal hippocampal neurogenesis. We conclude that environmental levels of bFGF regulate neonatal hippocampal neurogenesis. As adult hippocampal neuronogenesis was unresponsive to bFGF manipulation in our previous study [Wagner, J.P., Black, I.B. & DiCicco-Bloom, E. (1999) J. Neurosci., 19, 6006], these observations suggest distinct, stage-specific roles of bFGF in the dentate gyrus granule cell lineage. [source] The evolutionary genetics of personality,EUROPEAN JOURNAL OF PERSONALITY, Issue 5 2007Lars Penke Abstract Genetic influences on personality differences are ubiquitous, but their nature is not well understood. A theoretical framework might help, and can be provided by evolutionary genetics. We assess three evolutionary genetic mechanisms that could explain genetic variance in personality differences: selective neutrality, mutation-selection balance, and balancing selection. Based on evolutionary genetic theory and empirical results from behaviour genetics and personality psychology, we conclude that selective neutrality is largely irrelevant, that mutation-selection balance seems best at explaining genetic variance in intelligence, and that balancing selection by environmental heterogeneity seems best at explaining genetic variance in personality traits. We propose a general model of heritable personality differences that conceptualises intelligence as fitness components and personality traits as individual reaction norms of genotypes across environments, with different fitness consequences in different environmental niches. We also discuss the place of mental health in the model. This evolutionary genetic framework highlights the role of gene-environment interactions in the study of personality, yields new insight into the person-situation-debate and the structure of personality, and has practical implications for both quantitative and molecular genetic studies of personality. Copyright © 2007 John Wiley & Sons, Ltd. [source] Free radicals, antioxidants, and soil organic matter recalcitranceEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 2 2006D. L. Rimmer Summary Highly reactive, and potentially damaging, free radicals are readily generated in our oxygen-rich environment, and are ubiquitous in biological systems. However, plants and animals have evolved protection against them with a range of antioxidant molecules, such as vitamins C and E, many of which are phenolic compounds. These stop the destructive chain reaction of free radical formation by being transformed into unreactive, stable free radicals. The biodegradation of food involves oxidation by free radicals, and is retarded by antioxidants. Similarly, the biodegradation of plant residues in soils involves free radicals; so the questions arise: (i) do soils have antioxidants, and (ii) what function might they have? The evidence suggests that they probably do have antioxidants. First, plant and animal remains added to soils will contain antioxidants. These are likely to persist for a time, particularly tannins, which are polyphenolic compounds with known antioxidant properties and which are relatively resistant to degradation. Second, studies using electron spin resonance spectroscopy have shown that humic materials contain stable semiquinone free radicals, and that their concentration increases as humification progresses. These semiquinone species are most likely to be derived from the reaction of phenolic compounds with reactive radicals. If this is the case, the phenolics are acting as antioxidants, because they are scavenging the reactive free radicals and terminating the oxidative chain reaction responsible for soil organic matter (SOM) degradation. Thus the soil's antioxidant capacity could control the rate of breakdown of organic matter in the more labile pools and could provide a chemical mechanism for the recalcitrance of SOM. Current available evidence for the nature of the recalcitrant pool in SOM is discussed in the light of this hypothesis, and the experimental approaches necessary for testing it are outlined. [source] POLYANDRY PROMOTES ENHANCED OFFSPRING SURVIVAL IN DECORATED CRICKETSEVOLUTION, Issue 1 2005Tracie M. Ivy Abstract Although female multiple mating is ubiquitous in insects, its adaptive significance remains poorly understood. Benefits to multiple mating can accrue via direct material benefits, indirect genetic benefits, or both. We investigated the effects of multiple mating in the decorated cricket, Gryllodes sigillatus, by simultaneously varying the number of times that females mated and the number of different males with which they mated, measuring aspects of female fecundity and elements of offspring performance and viability. Multiple matings resulted in enhanced female fitness relative to single matings when females mated with differnt partners, but not when females mated repeatedly with the same male. Specifically, polyandrous females produced significantly more offspring surviving to reproductive maturity than did monogamous females mating once or mating repeatedly with the same male. These results suggest that the benefit females gain from multiple mating is influenced primarily by genetic and not material benefits. [source] SONG LEARNING ACCELERATES ALLOPATRIC SPECIATIONEVOLUTION, Issue 9 2004R. F. Lachlan Abstract The songs of many birds are unusual in that they serve a role in identifying conspecific mates, yet they are also culturally transmitted. Noting the apparently high rate of diversity in one avian taxon, the songbirds, in which song learning appears ubiquitous, it has often been speculated that cultural transmission may increase the rate of speciation. Here we examine the possibility that song learning affects the rate of allopatric speciation. We construct a population-genetic model of allopatric divergence that explores the evolution of genes that underlie learning preferences (predispositions to learn some songs over others). We compare this with a model in which mating signals are inherited only genetically. Models are constructed for the cases where songs and preferences are affected by the same or different loci, and we analyze them using analytical local stability analysis combined with simulations of drift and directional sexual selection. Under nearly all conditions examined, song divergence occurs more readily in the learning model than in the nonlearning model. This is a result of reduced frequency-dependent selection in the learning models. Cultural evolution causes males with unusual genotypes to tend to learn from the majority of males around them, and thus develop songs compatible with the majority of the females in the population. Unusual genotypes can therefore be masked by learning. Over a wide range of conditions, learning therefore reduces the waiting time for speciation to occur and can be predicted to accelerate the rate of speciation. [source] THE EVOLUTION OF THE VERTEBRATE ,-GLOBIN GENE PROMOTEREVOLUTION, Issue 2 2002Nadia A. Chuzhanova Abstract Complexity analysis is capable of highlighting those gross evolutionary changes in gene promoter regions (loosely termed "promoter shuffling") that are undetectable by conventional DNA sequence alignment. Complexity analysis was therefore used here to identify the modular components (blocks) of the orthologous ,-globin gene promoter sequences of 22 vertebrate species, from zebrafish to humans. Considerable variation between the ,-globin gene promoters was apparent in terms of block presence/absence, copy number, and relative location. Some sequence blocks appear to be ubiquitous, whereas others are restricted to a specific taxon. Block similarities were also evident between the promoters of the paralogous human ,-like globin genes. It may be inferred that a wide variety of different mutational mechanisms have operated upon the ,-globin gene promoter over evolutionary time. Because these include gross changes such as deletion, duplication, amplification, elongation, contraction, and fusion, as well as the steady accumulation of single base-pair substitutions, it is clear that some redefinition of the term "promoter shuffling" is required. This notwithstanding, and as previously described for the vertebrate growth hormone gene promoter, the modular structure of the ,-globin promoter region and those of its paralogous counterparts have continually been rearranged into new combinations through the alteration, or shuffling, of preexisting blocks. Some of these changes may have had no influence on promoter function, but others could have altered either the level of gene expression or the responsiveness of the promoter to external stimuli. The comparative study of vertebrate ,-globin gene promoter regions described here confirms the generality of the phenomenon of sequence block shuffling and thus supports the view that it could have played an important role in the evolution of differential gene expression. [source] | ||||||||||||||||||||||||||||||||||||||||||||||||||||