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Other Organisms (other + organism)
Selected AbstractsMortality differences among organisms causing septicemia in hemodialysis patientsHEMODIALYSIS INTERNATIONAL, Issue 1 2006Mark D. DANESE Abstract Septicemia is a serious problem in hemodialysis patients because it can lead to life-threatening complications and a persistently elevated risk of death. Most analyses have not examined whether there are differences in mortality risk among the organisms that cause these episodes of septicemia. This study was a retrospective cohort analysis of first septicemia hospitalizations during the first year of hemodialysis. Time to death (both in-hospital and within 12 weeks post-discharge) was compared among the different septicemia-causing organisms based on discharge diagnoses in Medicare billing data from 1996 to 2001. The effect of various complications on mortality risk was also evaluated. There were 22,130 septicemia hospitalizations identified. The most common organism identified was Staphylococcus aureus (27%), with no other organism having an incidence >10%. The overall unadjusted death rate from admission through 12 weeks of follow-up was 34%. During the first hospitalization, the death rate was 14%, and during the 12-week period after the hospitalization it was 20%. In adjusted analyses, S. aureus was associated with a 20% higher risk of death both during the in-hospital period and the 12-week post-discharge period, when compared with all other specified organisms. Hospitalizations complicated by meningitis, stroke, or endocarditis were also associated with increased risk of mortality, independent of the organism causing septicemia. Septicemia hospitalizations are associated with a high mortality rate,both during the initial hospitalization and after discharge. Meningitis, stroke, and endocarditis represent particularly serious complications. Overall, septicemia hospitalizations (especially for S. aureus) are serious events, and patients would benefit from better treatment and prevention. [source] Interaction networks: Lessons from large-scale studies in yeastPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 20 2009Gerard Cagney Abstract Saccharomyces cerevisiae is the simplest eukaryotic model organism and has made countless contributions to cell biology. The ease with which it can be genetically manipulated has made it a favourite organism among technologists for developing methods for large-scale analysis based on reverse genetics. Consequently, more genomewide datasets describing aspects of gene and protein biology are available for yeast than for any other organism. This has led to the pioneering of many computational analysis techniques using yeast data. Here, we make a brief survey of yeast physical and genetic interaction networks, highlighting major experimental and computational achievements first described in this organism. [source] Priority Wetland Invertebrates as Conservation SurrogatesCONSERVATION BIOLOGY, Issue 2 2010S. J. ORMEROD agua dulce; caracoles; conservación; especies paraguas; especies sustitutas; gasterópodos Abstract:,Invertebrates are important functionally in most ecosystems, but seldom appraised as surrogate indicators of biological diversity. Priority species might be good candidates; thus, here we evaluated whether three freshwater invertebrates listed in the U.K. Biodiversity Action Plan indicated the richness, composition, and conservation importance of associated wetland organisms as defined respectively by their alpha diversity, beta diversity, and threat status. Sites occupied by each of the gastropods Segmentina nitida, Anisus vorticulus, and Valvata macrostoma had greater species richness of gastropods and greater conservation importance than other sites. Each also characterized species assemblages associated with significant variations between locations in alpha or beta diversity among other mollusks and aquatic macrophytes. Because of their distinct resource requirements, conserving the three priority species extended the range of wetland types under management for nature conservation by 18% and the associated gastropod niche-space by around 33%. Although nonpriority species indicated variations in richness, composition, and conservation importance among other organisms as effectively as priority species, none characterized such a wide range of high-quality wetland types. We conclude that priority invertebrates are no more effective than nonpriority species as indicators of alpha and beta diversity or conservation importance among associated organisms. Nevertheless, conserving priority species can extend the array of distinct environments that are protected for their specialized biodiversity and environmental quality. We suggest that this is a key role for priority species and conservation surrogates more generally, and, on our evidence, can best be delivered through multiple species with contrasting habitat requirements. Resumen:,Los invertebrados son funcionalmente importantes en la mayoría de los ecosistemas, pero raramente son valorados como indicadores sustitutos de la diversidad biológica. Las especies prioritarias pueden ser buenos candidatos; por lo tanto, aquí evaluamos sí tres especies de invertebrados enlistados en el Plan de Acción para la Biodiversidad del Reino Unido eran indicadores de la riqueza, la composición e importancia para la conservación de organismos de humedal asociados definida por su diversidad alfa, diversidad beta y estatus de amenaza respectivamente. Los sitios ocupados por cada uno de los gasterópodos Segmentina nitida, Anisus vorticulus and Valvata macrostoma tuvieron una mucho mayor riqueza de gasterópodos y mayor importancia para la conservación que otros sitios. Cada uno también caracterizó a los ensambles asociados con variaciones significativas entre localidades en la diversidad alfa o entre otros moluscos y macrofitas acuáticas en la diversidad beta. Debido a sus diferentes requerimientos de recursos, la conservación de las tres especies prioritarias se amplió la extensión de todos los tipos de humedal bajo manejo para la conservación de la naturaleza en 18% y el nicho-espacio de los gasterópodos asociados se amplió alrededor de 33%. Aunque las especies no prioritarias indicaron variaciones en riqueza, composición e importancia de conservación entre otros organismos tan efectivamente como las especies prioritarias, ninguna caracterizó un rango tan amplio de humedales de alta calidad. Concluimos que los invertebrados prioritarios no son más efectivos que las especies no prioritarias como indicadores de la diversidad alfa y beta ni de la importancia para la conservación entre organismos asociados. Sin embargo, la conservación de especies prioritarias puede ampliar el conjunto de ambientes diferentes que son protegidos por su biodiversidad especializada y calidad ambiental. Sugerimos que este es un papel clave para las especies prioritarias y, más generalmente, para los sustitutos de conservación, y, con base en nuestra evidencia, puede ser desarrollado mediante múltiples especies con requerimientos de hábitat contrastantes. [source] Experimental Assessment of Coral Reef Rehabilitation Following Blast FishingCONSERVATION BIOLOGY, Issue 1 2005HELEN E. FOX arrecifes de Indonesia; recuperación de arrecife de coral; restauración de arrecifes Abstract:,Illegal fishing with explosives has damaged coral reefs throughout Southeast Asia. In addition to killing fish and other organisms, the blasts shatter coral skeletons, leaving fields of broken rubble that shift in the current, abrading or burying new coral recruits, and thereby slowing or preventing reef recovery. Successful restoration and rehabilitation efforts can contribute to coral reef conservation. We used field experiments to assess the effectiveness of different low-cost methods for coral reef rehabilitation in Komodo National Park (KNP), Indonesia. Our experiments were conducted at three different spatial scales. At a scale of 1 × 1 m plots, we tested three different rehabilitation methods: rock piles, cement slabs, and netting pinned to the rubble. Significantly more corals per square meter grew on rocks, followed by cement, netting, and untreated rubble, although many plots were scattered by strong water current or buried by rubble after 2.5 years. To test the benefits of the most successful treatment, rocks, at more realistic scales, we established 10 × 10 m plots of rock piles at each of our nine sites in 2000. Three years after installation, coverage by hard corals on the rocks continued to increase, although rehabilitation in high current areas remained the most difficult. In 2002 rehabilitation efforts in KNP were increased over 6000 m2 to test four rock pile designs at each of four rubble field sites. Assuming that there is an adequate larval supply, using rocks for simple, low-budget, large-scale rehabilitation appears to be a viable option for restoring the structural foundation of damaged reefs. Resumen:,La pesca ilegal con explosivos ha dañado a arrecifes de coral en el sureste de Asia. Además de matar a peces y otros organismos, las explosiones destruyen esqueletos de corales, dejando campos de escombros rotos que se mueven con la corriente, erosionando o enterrando a reclutas de coral nuevos y por lo tanto disminuyen o previenen la recuperación del coral. Esfuerzos exitosos de restauración y rehabilitación pueden contribuir a la conservación de arrecifes de coral. Usamos experimentos de campo para evaluar la efectividad de diferentes métodos de bajo costo para la rehabilitación de arrecifes de coral en el Parque Nacional Komodo (PNK), Indonesia. Desarrollamos nuestros experimentos en tres escalas espaciales diferentes. A una escala de parcelas de 1 x 1 m, probamos tres métodos de rehabilitación: pilas de rocas, losas de cemento y redes sobre el escombro. Crecieron significativamente más corales por metro cuadrado sobre rocas, seguido por el cemento, redes y escombro sin tratamiento, aunque muchas parcelas fueron dispersadas por la fuerte corriente de agua o enterradas por escombros después de 2.5 años. Para probar los beneficios del tratamiento más exitoso, rocas, a escalas más realistas, en 2000 establecimos parcelas de 10 x10 m con pilas de rocas en cada unos de nuestros nueve sitios. Tres años después, la cobertura de corales duros sobre las rocas continuó incrementando, aunque la rehabilitación en áreas con corrientes fuertes fue la más difícil. En 2002, los esfuerzos de rehabilitación en PNK se incrementaron a 6000 m2 para probar cuatro diseños de pilas de rocas en cada uno de los cuatro sitios con escombros. Asumiendo que hay una adecuada existencia de larvas, la utilización de rocas para rehabilitación simple, de bajo costo y gran escala parece ser una opción viable para la restauración de la base estructural de arrecifes dañados. [source] Axoneme-dependent tubulin modifications in singlet microtubules of the Drosophila sperm tailCYTOSKELETON, Issue 4 2008Henry D. Hoyle Abstract Drosophila melanogaster sperm tubulins are posttranslationally glutamylated and glycylated. We show here that axonemes are the substrate for these tubulin C-terminal modifications. Axoneme architecture is required, but full length, motile axonemes are not necessary. Tubulin glutamylation occurs during or shortly after assembly into the axoneme; only glutamylated tubulins are glycylated. Tubulins in other testis microtubules are not modified. Only a small subset of total Drosophila sperm axoneme tubulins have these modifications. Biochemical fractionation of Drosophila sperm showed that central pair and accessory microtubules have the majority of poly-modified tubulins, whereas doublet microtubules have only small amounts of mono- and oligo-modified tubulins. Glutamylation patterns for different ,-tubulins experimentally assembled into axonemes were consistent with utilization of modification sites corresponding to those identified in other organisms, but surrounding sequence context was also important. We compared tubulin modifications in the 9 + 9 + 2 insect sperm tail axonemes of Drosophila with the canonical 9 + 2 axonemes of sperm of the sea urchin Lytichinus pictus and the 9 + 0 motile sperm axonemes of the eel Anguilla japonica. In contrast to Drosophila sperm, L. pictus sperm have equivalent levels of modified tubulins in both doublet and central pair microtubule fractions, whereas the doublets of A. japonica sperm exhibit little glutamylation but extensive glycylation. Tubulin C-terminal modifications are a prevalent feature of motile axonemes, but there is no conserved pattern for placement or amount of these modifications. We conclude their functions are likely species-specific. Cell Motil. Cytoskeleton 2008. © 2008 Wiley-Liss, Inc. [source] Single-cell gene profiling of planarian stem cells using fluorescent activated cell sorting and its "index sorting" function for stem cell researchDEVELOPMENT GROWTH & DIFFERENTIATION, Issue 1 2010Tetsutaro Hayashi To achieve an integrated understanding of the stem cell system of planarians at both the cellular and molecular levels, we developed a new method by combining "fluorescent activated cell sorting (FACS) index sorting" analysis and single-cell reverse transcription,polymerase chain reaction (RT,PCR) to detect the gene expression and cell cycle state of stem cells simultaneously. Single cells were collected using FACS, and cDNAs of each cell were used for semi-quantitative RT,PCR. The results were plotted on the FACS sorting profile using the "index sorting" function, which enabled us to analyze the gene expression in combination with cell biological data (such as cell cycle phase) for each cell. Here we investigated the adult stem cells of planarians using this method and obtained findings suggesting that the stem cells might undergo commitment during S to G2/M phase. This method could be a powerful and straightforward tool for examining the stem cell biology of not only planarians but also other organisms, including vertebrates. [source] Modeling the model organism Dictyostelium discoideumDEVELOPMENT GROWTH & DIFFERENTIATION, Issue 6 2000Seido Nagano The cellular slime mold Dictyostelium discoideum is a fascinating organism, not only for biologists, but also for physicists. Since the Belousov,Zhabotinskii reaction pattern, a well-known non-linear phenomenon in chemistry, was observed during aggregation of Dictyostelium amoebae, Dictyostelium has been one of the major subjects of non-linear dynamics studies. Macroscopic theory, such as continuous cell density approximation, has been a common approach to studying pattern formation since the pioneering work of Turing. Recently, promising microscopic approaches, such as the cellular dynamics method, have emerged. They have shown that Dictyostelium is useful as a model system in biology. The synchronization mechanism of oscillatory production of cyclic adenosine 3,,5,-monophosphate in Dictyostelium is discussed in detail to show how it is a universal feature that can explain synchronization in other organisms. [source] Xenopus paraxis homologue shows novel domains of expressionDEVELOPMENTAL DYNAMICS, Issue 3 2004Ronald Carpio Abstract The paraxis gene encodes a basic helix-loop-helix transcription factor that is expressed in paraxial mesoderm and whose mutant displays an inability to form epithelial somites. Here, the molecular characterization of Xenopus paraxis is reported. paraxis is expressed in the paraxial mesoderm and somites but is down-regulated during muscle differentiation. In addition to its paraxial mesodermal expression, described in other organisms, two novel expression domains of paraxis were found: the neural tube and the head mesoderm. paraxis expression in the neural tube was compared with the expression of the neural markers Xash and Xiro1, and we concluded that paraxis is expressed in a broad band in the prospective sulcus limitans of the neural tube. Developmental Dynamics 231:609,613, 2004. © 2004 Wiley-Liss, Inc. [source] Inferring historical introduction pathways with mitochondrial DNA: the case of introduced Argentine ants (Linepithema humile) into New ZealandDIVERSITY AND DISTRIBUTIONS, Issue 5 2007Steve E. Corin ABSTRACT The threat imposed by invasive species and difficulties associated with control and management places more impetus on trying to prevent their introduction. The identification of introduction pathways is a vital component towards this goal. In this study, we use a genetic marker-based approach to retrospectively investigate the pathway of origin of the invasive Argentine ant (Linepithema humile) into New Zealand. We intensively sample the mitochondrial gene cytochrome b, from the entire known range of Argentine ants in New Zealand. No genetic variation was found in New Zealand. In order to identify likely introduction pathways, we use two alternative genetic analyses and suggest that a tcs approach that collapses identical haplotypes and calculates the probability of parsimony is superior to standard phylogenetic tree-building algorithms. A minimum spanning network allowed relationships to be examined among sequences collated from previous international studies. The cytochrome b sequence, when compared to a global database, matched that from an Australian population. That Australia is the potential source of Argentine ants is in agreement with the New Zealand interception record, as goods from Australia have the highest number of interception records of Argentine ants. Our approach can easily be duplicated for other organisms and the methodology can be more widely applied to help aid further efforts to identify the routes of transmission for other invasive species and allow us to efficiently direct our biosecurity monitoring effort. [source] Spatial and temporal hotspots of termite-driven decomposition in the SerengetiECOGRAPHY, Issue 3 2010Bernd P. Freymann Ecosystem engineers are organisms that directly or indirectly control the availability of resources to other organisms by causing physical state changes in biotic or abiotic materials. Termites (Insecta, Isoptera) are among the most important ecosystem engineers in tropical ecosystems. We used a field experiment in the tall grasslands of Serengeti National Park, Tanzania, to investigate 1) the consumption by termites of grass litter and dung baits along the landscape gradient of catena position, and 2) seasonal variation in litter and dung removal. Our maps of termitaria and patterns of bait removal revealed clear spatial and temporal hotspots of termite activity. In the dry season termites removed more baits at the top-catena positions than at the bottom positions, but there was no effect of catena position in the wet season. Spatial hotspots of termite activity overlapped with those of both mammalian herbivores and predators. Within the framework of ecosystem engineering, this study suggests that intraspecific aspects of spatial heterogeneity and temporal variability deserve much greater consideration. [source] Postfledging habitat selection of juvenile middle spotted woodpeckers: a multi-scale approachECOGRAPHY, Issue 4 2009Carlos Ciudad Despite its relevance for the persistence of populations, the ecological mechanisms underlying habitat use decisions of juvenile birds are poorly understood. We examined postfledging habitat selection of radio-tracked juvenile middle spotted woodpeckers Dendrocopos medius at multiple hierarchically-nested spatial scales in NW Spain. At the landscape and home range scales, old oak forest was the most used and selected habitat, young oak forests and pine plantations were avoided, and riverside forests were used as available. At a lower scale, birds selected larger diameter trees for foraging. Home ranges had higher densities of large deciduous trees (mainly oaks Quercus spp., but also poplars Populus spp. and willows Salix spp. >22,cm and >33,cm DBH) selected for foraging by juveniles than non-used areas. These results suggest that foraging conditions may drive, at least partly, habitat use decisions by juvenile birds. We also discuss the potential influence of intraspecific competition, the search for a future breeding territory in the early postfledging period and predation avoidance on habitat use decisions by juvenile birds. Contrary to previous studies on migrant forest birds, postfledging juvenile woodpeckers selected the same habitat as for the breeding adults (i.e. old oak forest), indicating that migrant and resident specialist avian species may require different conservation actions. Conservation strategies of woodpecker populations should consider the protection of old oak forests with high densities of large trees to provide suitable habitat to breeding adults and postfledging juveniles. The habitat improvement for this indicator and umbrella species would also favour other organisms that depend on characteristics of old-growth oak forests. [source] Contemporary richness of holarctic trees and the historical pattern of glacial retreatECOGRAPHY, Issue 2 2007Daniel Montoya The length of time land has been available for colonization by plants and other organisms could provide a partial explanation of the contemporary richness gradients of trees. According to this hypothesis, increasing times of land availability entail higher chances of recolonization, which eventually have positive effects on tree richness. To test this, we generated a dataset of the Holarctic trees and evaluated the influence of cell age, a measure of the time since an area became free of ice, on the observed tree richness gradients. We found that cell age is associated with richness in both Europe and North America, after controlling for contemporary climate patterns, suggesting that the historical pattern of glacial retreat in response to post-Pleistocene global warming has left a signal still detectable after at least 14,000 yr. The results were consistent using a range of modelling approaches or whether Europe and North America were analyzed separately or in concert. We conclude that, although secondary to contemporary climate, the post-glacial recolonization hypothesis is broadly supported at temperate latitudes. [source] Biological warfare in the garden pond: tadpoles suppress the growth of mosquito larvaeECOLOGICAL ENTOMOLOGY, Issue 1 2003Allie Mokany Abstract. 1. Although tadpoles and mosquito larvae may compete for scarce resources in natural freshwater systems, the mechanisms involved in such competition remain largely unstudied. 2. Replicated artificial ponds were set up to examine the role of pathogenic interference (water-borne growth inhibitors) in two tadpole,mosquito systems from south-eastern Australia. One system comprised taxa that are commonly sympatric in freshwater ponds (tadpoles of Limnodynastes peronii and larvae of Culex quinquefasciatus) while the other comprised species that co-occur in brackish water ponds (tadpoles of Crinia signifera and larvae of Ochlerotatus australis). 3. Water that had previously contained tadpoles suppressed the rates of survival and pupation of mosquito larvae in both systems. Fungicide reduced or eliminated this effect, suggesting that the growth inhibitors may be fungal organisms (possibly the yeast Rhodotorula glutinis) from tadpole faeces. Fungicide also enhanced growth rates of tadpoles. 4. These results suggest that interference competition between tadpoles and mosquito larvae is mediated by other organisms in some ecological systems. [source] Fish movement and habitat use depends on water body size and shapeECOLOGY OF FRESHWATER FISH, Issue 1 2009D. A. Woolnough Abstract,,, Home ranges are central to understanding habitat diversity, effects of fragmentation and conservation. The distance that an organism moves yields information on life history, genetics and interactions with other organisms. Present theory suggests that home range is set by body size of individuals. Here, we analyse estimates of home ranges in lakes and rivers to show that body size of fish and water body size and shape influence home range size. Using 71 studies including 66 fish species on five continents, we show that home range estimates increased with increasing water body size across water body shapes. This contrasts with past studies concluding that body size sets home range. We show that water body size was a consistently significant predictor of home range. In conjunction, body size and water body size can provide improved estimates of home range than just body size alone. As habitat patches are decreasing in size worldwide, our findings have implications for ecology, conservation and genetics of populations in fragmented ecosystems. [source] Removal of high-abundance proteins for nuclear subproteome studies in rice (Oryza sativa) endospermELECTROPHORESIS, Issue 3 2008Guosheng Li Abstract Endosperm is a highly specialized storage organ with three sets of genomes. It is one of the most economically important organs in plants. Endosperm development involves parental imprinting and endoreduplication. A thorough study of the endosperm proteome, particularly the nuclear proteome, may provide critical insight into the regulation of seed development. Unfortunately, endosperm is extremely rich in starch grains and protein bodies of different sizes, making proteome studies on nonstorage proteins, particularly the low-abundance proteins, very challenging. Here we have developed a chromatographic method to remove large starch grains and an electrophoresis method to recover low-abundance proteins, respectively. Using these methods, we have identified 468 proteins from the nuclear enriched fraction of rice endosperm, including transcription factors, histone modification proteins, kinetochore proteins, centromere/microtubule binding proteins, and transposon proteins. Among the 468 proteins, 208 (44%) are hypothetical proteins, indicating that the endosperm proteome is poorly explored. In addition, analyses of the MS/MS data using BioWorks 3.1 have identified 59 putative acetylated proteins and 40 putative methylated proteins. Our studies have developed a method to remove starch grains and recover low-abundance proteins, respectively. The methods should be applicable to other organisms. [source] Dispersal and influences on movement for Anoplophora glabripennis calculated from individual mark-recaptureENTOMOLOGIA EXPERIMENTALIS ET APPLICATA, Issue 2 2005J.S. Bancroft Abstract We conducted an individual mark-release-recapture experiment on the beetle, Anoplophora glabripennis Motchulsky (Coleoptera: Cerambycidae). This invasive beetle has been introduced from Asia to Europe and North America and poses a serious threat to several important species of tree. Eradication efforts may benefit from knowledge of dispersal behaviour. Trees were cut and held to determine emergence rate of A. glabripennis. Unique marks were painted onto 912 beetles released into a group of 165 trees in Gansu, China. Data on subsequent sightings of beetles were used in a truncated diffusion model to calculate flight distances. Characteristics of the trees and climatic information were used in statistical tests for influence on movement. A total of 2245 sightings of beetles were observed and 29% of marked beetles were resighted. The scanning technique using binoculars was 90% effective in finding beetles and provided 81% accuracy for determining the sex of the beetles. Experimental manipulation of density quantified how A. glabripennis congregated on unoccupied trees and were repulsed from crowded hosts. The seasonal emergence rate of adults declined exponentially from July 20 to August 5. The results suggested A. glabripennis fly to nearby host trees at a rate of 34% per day. Median flight distance was estimated at 20 m per day. Statistical analysis with a generalized linear model tested the beetle's propensity to leave a tree and distance of flight. Generally, beetle movement showed a significant response to beetle density, weather conditions, beetle size, and tree size, in that order. The techniques developed here improve on previous recapture techniques to quantify dispersal and can be useful for analysing populations of other organisms. [source] A methane-driven microbial food web in a wetland rice soilENVIRONMENTAL MICROBIOLOGY, Issue 12 2007Jun Murase Summary Methane oxidation is a key process controlling methane emission from anoxic habitats into the atmosphere. Methanotrophs, responsible for aerobic methane oxidation, do not only oxidize but also assimilate methane. Once assimilated, methane carbon may be utilized by other organisms. Here we report on a microbial food web in a rice field soil driven by methane. A thin layer of water-saturated rice field soil was incubated under opposing gradients of oxygen and 13C-labelled methane. Bacterial and eukaryotic communities incorporating methane carbon were analysed by RNA-stable isotope probing (SIP). Terminal restriction fragment length polymorphism (T-RFLP) and cloning showed that methanotrophs were the most prominent group of bacteria incorporating methane carbon. In addition, a few Myxobacteria -related sequences were obtained from the ,heavy' rRNA fraction. Denaturing gradient gel electrophoresis (DGGE) targeting 18S rRNA detected various groups of protists in the ,heavy' rRNA fraction including naked amoeba (Lobosea and Heterolobosea), ciliates (Colpodea) and flagellates (Cercozoa). Incubation of soil under different methane concentrations in air resulted in the development of distinct protozoan communities. These results suggest that methane carbon is incorporated into non-methanotrophic pro- and microeukaryotes probably via grazing, and that methane oxidation is a shaping force of the microeukaryotic community depending on methane availability. [source] Factors affecting biodegradation of 2-chlorophenol by Alcaligenes sp. in aerobic reactorsENVIRONMENTAL TOXICOLOGY, Issue 4 2001A. Gallego Abstract The influence of variations in carbon source concentration, cell inocula, pH, presence of other substrates, and other organisms on the biodegradation of 2-chlorophenol (2-CP) was studied for Alcaligenes sp. isolated from natural sources. Assays of biodegradation were performed in batch and continuous-flow fluidized-bed aerobic reactors. Evaluation of biodegradation was performed by determining total phenols, chemical oxygen demand (COD), and 2-CP by ultraviolet (UV) spectrophotometry. Measurement of microbial growth was carried out by the plate count method. Bioassays of acute toxicity were performed to evaluate detoxification by using Daphnia magna. Results obtained show that under batch conditions with initial inocula of 106 cells/mL the strain grew exponentially with 100, 200, and 300 mg/L of 2-CP within 48 hr. A lag period was observed with low cell density inocula (105 cells/mL). The strain showed marked delay in the biodegradation of 2-CP at pH 5. Removal of target substrate from mixtures containing other carbon sources demonstrated the possibility of concurrent growth. Mineralization of 2-CP was assessed by gas chromatography carried out at the end of the batch assays and at the exit of the continuous-flow reactor. The presence of other organisms (bacteria, rotifers, ciliate, and algae) that developed in the fluidized-bed reactor did not affect the efficacy of the biodegradation of 2-CP. The removal of 2-CP in the two assayed systems was over 97% in all cases. Toxicity was not detected at the exit of the continuous reactor. © 2001 John Wiley & Sons, Inc. Environ Toxicol 16: 306,313, 2001 [source] Biotic ligand model of the acute toxicity of metals.ENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 10 2001Abstract The biotic ligand model (BLM) of acute metal toxicity to aquatic organisms is based on the idea that mortality occurs when the metal,biotic ligand complex reaches a critical concentration. For fish, the biotic ligand is either known or suspected to be the sodium or calcium channel proteins in the gill surface that regulate the ionic composition of the blood. For other organisms, it is hypothesized that a biotic ligand exists and that mortality can be modeled in a similar way. The biotic ligand interacts with the metal cations in solution. The amount of metal that binds is determined by a competition for metal ions between the biotic ligand and the other aqueous ligands, particularly dissolved organic matter (DOM), and the competition for the biotic ligand between the toxic metal ion and the other metal cations in solution, for example, calcium. The model is a generalization of the free ion activity model that relates toxicity to the concentration of the divalent metal cation. The difference is the presence of competitive binding at the biotic ligand, which models the protective effects of other metal cations, and the direct influence of pH. The model is implemented using the Windermere humic aqueous model (WHAM) model of metal,DOM complexation. It is applied to copper and silver using gill complexation constants reported by R. Playle and coworkers. Initial application is made to the fathead minnow data set reported by R. Erickson and a water effects ratio data set by J. Diamond. The use of the BLM for determining total maximum daily loadings (TMDLs) and for regional risk assessments is discussed within a probabilistic framework. At first glance, it appears that a large amount of data are required for a successful application. However, the use of lognormal probability distributions reduces the required data to a manageable amount. [source] LRRN6A/LERN1 (leucine-rich repeat neuronal protein 1), a novel gene with enriched expression in limbic system and neocortexEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 12 2003Laura Carim-Todd Abstract Human chromosome 15q24-q26 is a very complex genomic region containing several blocks of segmental duplications to which susceptibility to anxiety disorders has been mapped (Gratacos et al., 2001, Cell, 106, 367,379; Pujana et al., 2001, Genome Res., 11, 98,111). Through an in silico gene content analysis of the 15q24-q26 region we have identifie1d a novel gene, LRRN6A (leucine-rich repeat neuronal 6A), and confirmed its location to the centromeric end of this complex region. LRRN6A encodes a transmembrane leucine-rich repeat protein, LERN1 (leucine-rich repeat neuronal protein 1), with similarity to proteins involved in axonal guidance and migration, nervous system development and regeneration processes. The identification of homologous genes to LRRN6A on chromosomes 9 and 19 and the orthologous genes in the mouse genome and other organisms suggests that LERN proteins constitute a novel subfamily of LRR (leucine-rich repeat)-containing proteins. The LRRN6A expression pattern is specific to the central nervous system, highly and broadly expressed during early stages of development and gradually restricted to forebrain structures as development proceeds. Expression level in adulthood is lower in general but remains stable and significantly enriched in the limbic system and cerebral cortex. Taken together, the confirmation of LRRN6A's expression profile, its predicted protein structure and its similarity to nervous system-expressed LRR proteins with essential roles in nervous system development and maintenance suggest that LRRN6A is a novel gene of relevance in the molecular and cellular neurobiology of vertebrates. [source] Effect of termites on clay minerals in tropical soils: fungus-growing termites as weathering agentsEUROPEAN JOURNAL OF SOIL SCIENCE, Issue 4 2002P. Jouquet Summary Termites of the subfamily Macrotermitinae play an important role in tropical ecosystems: they modify the soil's physical properties and thereby make food available for other organisms. Clay is important in the architecture of Macrotermitinae termite nests, and it has been postulated that termites could modify the mineralogical properties of some clays. We have tested this hypothesis of clay transformation by termites in the laboratory under controlled conditions, using Odontotermes nr. pauperans termite species, one of the main fungus-growing species at Lamto Research Station (Côte d'Ivoire). Soil handled by termites in nest building was saturated with SrCl2, glycol or KCl and afterwards heated at 250°C for X-ray diffraction analyses. Termite handling led to an increase in the expandable layers of the component clay minerals. Heating and saturation by potassium of modified clays did not close the newly formed expandable clay layers. However, differences occurred between parts of the constructions built by termites, and the clays can be ranked according to their degree of alteration in the following order: unhandled soils < galleries < chamber walls. Consequently, termites can be seen as weathering agents of clay minerals, as previously shown for micro-organisms and plants. [source] DOES LARGE BODY SIZE IN MALES EVOLVE TO FACILITATE FORCIBLE INSEMINATION?EVOLUTION, Issue 11 2005A STUDY ON GARTER SNAKES Abstract A trend for larger males to obtain a disproportionately high number of matings, as occurs in many animal populations, typically is attributed either to female choice or success in male-male rivalry; an alternative mechanism, that larger males are better able to coercively inseminate females, has received much less attention. For example, previous studies on garter snakes (Thamnophis sirtalis parietalis) at communal dens in Manitoba have shown that the mating benefit to larger body size in males is due to size-dependent advantages in male-male rivalry. However, this previous work ignored the possibility that larger males may obtain more matings because of male-female interactions. In staged trials within outdoor arenas, larger body size enhanced male mating success regardless of whether a rival male was present. The mechanism involved was coercion rather than female choice, because mating occurred most often (and soonest) in females that were least able to resist courtship-induced hypoxic stress. Males do physically displace rivals from optimal positions in the mating ball, and larger males are better able to resist such displacement. Nonetheless, larger body size enhances male mating success even in the absence of such malemale interactions. Thus, even in mating systems where males compete physically and where larger body size confers a significant advantage in male-male competition, the actual selective force for larger body size in males may relate to forcible insemination of unreceptive females. Experimental studies are needed to determine whether the same situation occurs in other organisms in which body-size advantages have been attributed to male-male rather than male-female interactions. [source] PERSPECTIVE: SIGN EPISTASIS AND GENETIC COSTRAINT ON EVOLUTIONARY TRAJECTORIESEVOLUTION, Issue 6 2005Daniel M. Weinreich Abstract Epistasis for fitness means that the selective effect of a mutation is conditional on the genetic background in which it appears. Although epistasis is widely observed in nature, our understanding of its consequences for evolution by natural selection remains incomplete. In particular, much attention focuses only on its influence on the instantaneous rate of changes in frequency of selected alleles via epistatic contribution to the additive genetic variance for fitness. Thus, in this framework epistasis only has evolutionary importance if the interacting loci are simultaneously segregating in the population. However, the selective accessibility of mutational trajectories to high fitness genotypes may depend on the genetic background in which novel mutations appear, and this effect is independent of population polymorphism at other loci. Here we explore this second influence of epistasis on evolution by natural selection. We show that it is the consequence of a particular form of epistasis, which we designate sign epistasis. Sign epistasis means that the sign of the fitness effect of a mutation is under epistatic control; thus, such a mutation is beneficial on some genetic backgrounds and deleterious on others. Recent experimental innovations in microbial systems now permit assessment of the fitness effects of individual mutations on multiple genetic backgrounds. We review this literature and identify many examples of sign epistasis, and we suggest that the implications of these results may generalize to other organisms. These theoretical and empirical considerations imply that strong genetic constraint on the selective accessibility of trajectories to high fitness genotypes may exist and suggest specific areas of investigation for future research. [source] Delayed onset of midline netrin expression in Artemia franciscana coincides with commissural axon growth and provides evidence for homology of midline cells in distantly related arthropodsEVOLUTION AND DEVELOPMENT, Issue 2 2007Molly Duman-Scheel SUMMARY Although many similarities in arthropod central nervous systems (CNS) development exist, differences in midline cell formation and ventral nerve cord axonogenesis have been noted in arthropods. It is possible that changes in the expression of axon guidance molecules such as Netrin, which functions during commissural axon guidance in Drosophila and many other organisms, may parallel these differences. In this investigation, we analyze this hypothesis by examining Netrin accumulation during development of the brine shrimp Artemia franciscana, a branchiopod crustacean. An Artemia franciscana netrin (afrnet) orthologue was cloned. An antibody to the afrNet protein was generated and used to examine the pattern of afrNet accumulation during Artemia development. Despite differences between Drosophila and Artemia nerve cord development, examination of afrNet accumulation suggests that this protein functions to regulate commissure formation during Artemia CNS development. However, detection of afrNet at the midline and on commissural axons occurs at a relatively later time point in Artemia as compared with Drosophila. Detection of afrNet in a subset of midline cells that closely resemble Netrin-expressing cells at the Drosophila midline provides evidence for homology of midline cells in arthropods. Expression of Netrins in many other tissues is comparable, suggesting that Netrin proteins may play many conserved roles during arthropod development. [source] In vivo production of catalase containing haem analoguesFEBS JOURNAL, Issue 12 2010Myriam Brugna Haem (protohaem IX) analogues are toxic compounds and have been considered for use as antibacterial agents, but the primary mechanism behind their toxicity has not been demonstrated. Using the haem protein catalase in the Gram-positive bacterium Enterococcus faecalis as an experimental system, we show that a variety of haem analogues can be taken up by bacterial cells and incorporated into haem-dependent enzymes. The resulting cofactor-substituted proteins are dysfunctional, generally resulting in arrested cell growth or death. This largely explains the cell toxicity of haem analogues. In contrast to many other organisms, E. faecalis does not depend on haem for growth, and therefore resists the toxicity of many haem analogues. We have exploited this feature to establish a bacterial in vivo system for the production of cofactor-substituted haem protein variants. As a pilot study, we produced, isolated and analysed novel catalase variants in which the iron atom of the haem prosthetic group is replaced by other metals, i.e. cobalt, gallium, tin, and zinc, and also variants containing meso-protoheme IX, ruthenium meso-protoporphyrin IX and (metal-free) protoporphyrin IX. Engineered haem proteins of this type are of potential use within basic research and the biotechnical industry. Structured digital abstract ,,MINT-7722358, MINT-7722368: katA (uniprotkb:Q834P5) and katA (uniprotkb:Q834P5) physically interact (MI:0915) by copurification (MI:0025) [source] Molecular responses of Campylobacter jejuni to cadmium stressFEBS JOURNAL, Issue 20 2008Nadeem O. Kaakoush Cadmium ions are a potent carcinogen in animals, and cadmium is a toxic metal of significant environmental importance for humans. Response curves were used to investigate the effects of cadmium chloride on the growth of Camplyobacter jejuni. In vitro, the bacterium showed reduced growth in the presence of 0.1 mm cadmium chloride, and the metal ions were lethal at 1 mm concentration. Two-dimensional gel electrophoresis combined with tandem mass spectrometry analysis enabled identification of 67 proteins differentially expressed in cells grown without and with 0.1 mm cadmium chloride. Cellular processes and pathways regulated under cadmium stress included fatty acid biosynthesis, protein biosynthesis, chemotaxis and mobility, the tricarboxylic acid cycle, protein modification, redox processes and the heat-shock response. Disulfide reductases and their substrates play many roles in cellular processes, including protection against reactive oxygen species and detoxification of xenobiotics, such as cadmium. The effects of cadmium on thioredoxin reductase and disulfide reductases using glutathione as a substrate were studied in bacterial lysates by spectrophotometry and nuclear magnetic resonance spectroscopy, respectively. The presence of 0.1 mm cadmium ions modulated the activities of both enzymes. The interactions of cadmium ions with oxidized glutathione and reduced glutathione were investigated using nuclear magnetic resonance spectroscopy. The data suggested that, unlike other organisms, C. jejuni downregulates thioredoxin reductase and upregulates other disulfide reductases involved in metal detoxification in the presence of cadmium. [source] Characterization of acetyl-CoA/propionyl-CoA carboxylase in Metallosphaera sedulaFEBS JOURNAL, Issue 4 2003Carboxylating enzyme in the 3-hydroxypropionate cycle for autotrophic carbon fixation Autotrophic Archaea of the family Sulfolobaceae (Crenarchaeota) use a modified 3-hydroxypropionate cycle for carbon dioxide assimilation. In this cycle the ATP-dependent carboxylations of acetyl-CoA and propionyl-CoA to malonyl-CoA and methylmalonyl-CoA, respectively, represent the key CO2 fixation reactions. These reactions were studied in the thermophilic and acidophilic Metallosphaera sedula and are shown to be catalyzed by one single large enzyme, which acts equally well on acetyl-CoA and propionyl-CoA. The carboxylase was purified and characterized and the genes were cloned and sequenced. In contrast to the carboxylase of most other organisms, acetyl-CoA/propionyl-CoA carboxylase from M. sedula is active at 75 °C and is isolated as a stabile functional protein complex of 560 ± 50 kDa. The enzyme consists of two large subunits of 57 kDa each representing biotin carboxylase (,) and carboxytransferase (,), respectively, and a small 18.6 kDa biotin carrier protein (,). These subunits probably form an (,,,)4 holoenzyme. It has a catalytic number of 28 s,1 at 65 °C and at the optimal pH of 7.5. The apparent Km values were 0.06 mm for acetyl-CoA, 0.07 mm for propionyl-CoA, 0.04 mm for ATP and 0.3 mm for bicarbonate. Acetyl-CoA/propionyl-CoA carboxylase is considered the main CO2 fixation enzyme of autotrophic members of Sulfolobaceae and the sequenced genomes of these Archaea contain the respective genes. Due to its stability the archaeal carboxylase may prove an ideal subject for further structural studies. [source] Three-dimensional structure of the histidine-containing phosphocarrier protein (HPr) from Enterococcus faecalis in solutionFEBS JOURNAL, Issue 3 2001Till Maurer The histidine-containing phosphocarrier protein (HPr) transfers a phosphate group between components of the prokaryotic phosphoenolpyruvate-dependent phosphotransferase system (PTS), which is finally used to phosphorylate the carbohydrate transported by the PTS through the cell membrane. Recently it has also been found to act as an intermediate in the signaling cascade that regulates transcription of genes related to the carbohydrate-response system. Both functions involve phosphorylation/dephosphorylation reactions, but at different sites. Using multidimensional 1H-NMR spectroscopy and angular space simulated annealing calculations, we determined the structure of HPr from Enterococcus faecalis in aqueous solution using 1469 distance and 44 angle constraints derived from homonuclear NMR data. It has a similar overall fold to that found in HPrs from other organisms. Four , strands, A, B, C, D, encompassing residues 2,7, 32,37, 40,42 and 60,66, form an antiparallel , sheet lying opposite the two antiparallel , helices, a and c (residues 16,26 and 70,83). A short , helix, b, from residues 47,53 is also observed. The pairwise root mean square displacement for the backbone heavy atoms of the mean of the 16 NMR structures to the crystal structure is 0.164 nm. In contrast with the crystalline state, in which a torsion angle strain in the active-center loop has been described [Jia, Z., Vandonselaar, M., Quail, J.W. & Delbaere, L.T.J. (1993) Nature (London) 361, 94,97], in the solution structure, the active-site His15 rests on top of helix a, and the phosphorylation site N,1 of the histidine ring is oriented towards the surface, making it easily accessible to the solvent. Back calculation of the 2D NOESY NMR spectra from both the NMR and X-ray structures shows that the active-center structure derived by X-ray crystallography is not compatible with experimental data recorded in solution. The observed torsional strain must either be a crystallization artefact or represents a conformational state that exists only to a small extent in solution. [source] Content and biosynthesis of polyamines in salt and osmotically stressed cells of Synechocystis sp.FEMS MICROBIOLOGY LETTERS, Issue 1 2003PCC 680 Abstract The effects of various NaCl and sorbitol concentrations in the growth medium on polyamine content and on two enzymes of the polyamine biosynthesis pathway, arginine decarboxylase (ADC) and S -adenosyl methionine decarboxylase (SAMDC), were investigated in the unicellular cyanobacterium Synechocystis sp. PCC 6803. Synechocystis cells showed no difference in growth rate when the concentration of NaCl was raised up to 550 mM. The growth rate decreased at 300 mM sorbitol, and complete inhibition of growth occurred at concentrations of ,700 mM sorbitol. Salt stress induced a moderate increase in the total cellular polyamine content, spermine in particular. Osmotic stress caused an apparent increase in the total cellular polyamine content with a marked increase of spermidine induced by 700 mM sorbitol. Importantly, a low level of spermine, which so far has never been detected in cyanobacteria, could be found in Synechocystis sp. PCC 6803. ADC, a key enzyme for putrescine synthesis, was unaffected by salt stress but showed a six-fold increase in enzyme activity upon osmotic stress imposed by 700 mM sorbitol. SAMDC, another important enzyme for spermidine and spermine synthesis, responded to salt and osmotic stresses similarly to the pattern observed for ADC. An analysis by reverse transcription-polymerase chain reaction revealed an increase of ADC mRNA level in cells under salt and osmotic stresses. Most importantly, the increase of ADC mRNA was attributed to its slower turnover rate under both stress conditions. Interestingly, the samdc gene(s) of Synechocystis appear to be unique since comparisons with known gene sequences from other organisms resulted in no homologous sequences identified in the Synechocystis genome. [source] A metapopulation perspective for salmon and other anadromous fishFISH AND FISHERIES, Issue 4 2007Nicolas Schtickzelle Abstract Salmonids are an important component of biodiversity, culture and economy in several regions, particularly the North Pacific Rim. Given this importance, they have been intensively studied for about a century, and the pioneering scientists recognized the critical link between population structure and conservation. Spatial structure is indeed of prime importance for salmon conservation and management. At first glance, the essence of the metapopulation concept, i.e. a population of populations, widely used on other organisms like butterflies, seems to be particularly relevant to salmon, and more generally to anadromous fish. Nevertheless, the concept is rarely used, and barely tested. Here, we present a metapopulation perspective for anadromous fish, assessing in terms of processes rather than of patterns the set of necessary conditions for metapopulation dynamics to exist. Salmon, and particularly sockeye salmon in Alaska, are used as an illustrative case study. A review of life history traits indicates that the three basic conditions are likely to be fulfilled by anadromous salmon: (i) the spawning habitat is discrete and populations are spatially separated by unsuitable habitat; (ii) some asynchrony is present in the dynamics of more or less distant populations and (iii) dispersal links populations because some salmon stray from their natal population. The implications of some peculiarities of salmon life history traits, unusual in classical metapopulations, are also discussed. Deeper understanding of the population structure of anadromous fish will be advanced by future studies on specific topics: (i) criteria must be defined for the delineation of suitable habitats that are based on features of the biotope and not on the presence of fish; (ii) the collection of long-term data and the development of improved methods to determine age structure are essential for correctly estimating levels of asynchrony between populations and (iii) several key aspects of dispersal are still poorly understood and need to be examined in detail: the spatial and temporal scales of dispersal movements, the origin and destination populations instead of simple straying rates, and the relative reproductive success of immigrants and residents. [source] | |||||||||||||||||||||||||||||||||||||||||||