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Many Organisms (many + organism)
Selected AbstractsUsing neutral landscapes to identify patterns of aggregation across resource pointsECOGRAPHY, Issue 3 2006Jill Lancaster Many organisms are aggregated within resource patches and aggregated spatially across landscapes with multiple resources. Such patchy distributions underpin models of population regulation and species coexistence, so ecologists require methods to analyse spatially-explicit data of resource distribution and use. I describe a method for analysing maps of resources and testing hypotheses about how resource distribution influences the distribution of organisms, where resource patches can be described as points in a landscape and the number of organisms on each resource point is known. Using a mark correlation function and the linearised form of Ripley's K-function, this version of marked point pattern analysis can characterise and test hypotheses about the spatial distribution of organisms (marks) on resource patches (points). The method extends a version of point pattern analysis that has wide ecological applicability, it can describe patterns over a range of scales, and can detect mixed patterns. Statistically, Monte Carlo permutations are used to estimate the difference between the observed and expected values of the mark correlation function. Hypothesis testing employs a flexible neutral landscape approach in which spatial characteristics of point patterns are preserved to some extent, and marks are randomised across points. I describe the steps required to identify the appropriate neutral landscape and apply the analysis. Simulated data sets illustrate how the choice of neutral landscape can influence ecological interpretations, and how this spatially-explicit method and traditional dispersion indices can yield different interpretations. Interpretations may be general or context-sensitive, depending on information available about the underlying point pattern and the neutral landscape. An empirical example of caterpillars exploiting food plants illustrates how this technique might be used to test hypotheses about adult oviposition and larval dispersal. This approach can increase the value of survey data, by making it possible to quantify the distribution of resource points in the landscape and the pattern of resource use by species. [source] Inaccurate or disparate temperature cues?FUNCTIONAL ECOLOGY, Issue 5 2010Seasonal acclimation of terrestrial, aquatic locomotor capacity in newts Summary 1.,Many organisms respond to seasonal temperature fluctuations by the reversible modification of whole-animal performance. Semiaquatic ectotherms, which possess this acclimatory capacity in swimming speed, lack the plastic response in terrestrial locomotor performance and vice versa. Theory predicts that the presence of reversible (seasonal) thermal acclimation or fixed phenotypes depends on the predictability of future thermal conditions (i.e. accuracy of temperature cues) in a given environment. Alternatively, comparative data suggest that thermal acclimation is induced by disparate temperature cues in water and on land. 2.,We tested both predictions by examining the seasonal acclimation response in thermal sensitivity of maximal swimming and running speed in adult alpine newts, Ichthyosaura (formerly Triturus) alpestris. 3.,Following the seasonal variation in environmental temperatures, we exposed newts to 5 °C from November to March and, after a gradual temperature increase, to either a constant (15 °C) or fluctuating (10,20 °C) thermal regime from May to June. At the end of each treatment, we measured newt swimming and running capacity at five temperatures (range 5,25 °C). In the field, hourly temperatures were recorded in various aquatic and terrestrial microhabitats to obtain information about the predictability of thermal conditions in both environments. 4.,Seasonal acclimation shaped the thermal sensitivity of swimming speed under both constant and fluctuating temperature treatments. Thermal sensitivity of running speed was markedly modified by a fluctuating thermal regime so that newts ran at the highest test temperature faster than cold-acclimated individuals. Natural thermal environment contained a similar proportion of predictable variation in water and on land. 5.,Complex seasonal acclimation of locomotor capacity in newts was influenced by the disparate thermal cues, i.e. mean acclimation temperature or diel temperature fluctuations, rather than by the different accuracy of these cues in water and on land. Future confrontations of theory with empirical data will require more attention not only on the assumptions of adaptive thermal acclimation but also on the ecologically relevant thermal conditions during acclimation experiments. [source] Hatching fraction and timing of resting stage production in seasonal environments: effects of density dependence and uncertain season lengthJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 3 2001M. Spencer Many organisms survive unfavourable seasons as resting stages, some of which hatch each favourable season. Hatching fraction and timing of resting stage production are important life history variables. We model life cycles of freshwater invertebrates in temporary pools, with various combinations of uncertain season length and density-dependent fecundity. In deterministic density-independent conditions, resting stage production begins suddenly. With uncertain season length and density independence, resting stage production begins earlier and gradually. A high energetic cost of resting stages favours later resting stage production and a lower hatching fraction. Deterministic environments with density dependence allow sets of coexisting strategies, dominated by pairs, each switching suddenly to resting stage production on a different date, usually earlier than without density dependence. Uncertain season length and density dependence allow a single evolutionarily stable strategy, around which we observe many mixed strategies with negatively associated yield (resting stages per initial active stage) and optimal hatching fraction. [source] The evolution and ecology of masqueradeBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 1 2010JOHN SKELHORN Many organisms appear to mimic inanimate objects such as twigs, leaves, stones, and bird droppings. Such adaptations are considered to have evolved because their bearers are misidentified as either inedible objects by their predators, or as innocuous objects by their prey. In the past, this phenomenon has been classified by some as Batesian mimicry and by others as crypsis, but now is considered to be conceptually different from both, and has been termed ,masquerade'. Despite the debate over how to classify masquerade, this phenomenon has received little attention from evolutionary biologists. Here, we discuss the limited empirical evidence supporting the idea that masquerade functions to cause misidentification of organisms, provide a testable definition of masquerade, and suggest how masquerade evolved and under what ecological conditions. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99, 1,8. [source] Identification of asymmetrically localized transcripts along the animal,vegetal axis of the Xenopus eggDEVELOPMENT GROWTH & DIFFERENTIATION, Issue 8 2005Kensuke Kataoka In many organisms, proper embryo development depends on the asymmetrical distribution of mRNA in the cytoplasm of the egg. Here we report comprehensive screening of RNA localized in the animal or vegetal hemisphere of the Xenopus egg. Macroarrays including over 40 000 independent embryonic cDNA clones, representing at least 17 000 unigenes, were differentially hybridized with labeled probes synthesized from the mRNA of animal or vegetal blastomeres. After two rounds of screening, we identified 33 clones of transcripts that may be preferentially distributed in the vegetal region of the early stage embryo, but transcripts localized in the animal region were not found. To assess the array results, we performed northern blot and quantitative real-time reverse transcription,polymerase chain reaction analysis. As a result, 21 transcripts of the 33 were confirmed to be localized in the vegetal region of the early stage embryo. Whole-mount in situ hybridization analysis revealed that 11 transcripts, including 7 previously reported genes, were localized in the vegetal hemisphere of the egg. These 11 transcripts were categorized into three groups according to their expression patterns in the egg. The first group, which contained four transcripts, showed uniform expression in the vegetal hemisphere, similar to VegT. The second group, which contained three transcripts, showed gradual expression from the vegetal pole to the equator, similar to Vg1. The last group, which contained three transcripts, was expressed at the germ plasm, similar to Xdazl. One transcript, Xwnt11, showed both the second and the third expression patterns. [source] Local activation of protein kinase A inhibits morphogenetic movements during Xenopus gastrulationDEVELOPMENTAL DYNAMICS, Issue 1 2003Byung-Ho Song Abstract cAMP-dependent protein kinase (PKA) has various biological roles in many organisms. However, little is known about its role in the developmental processes of vertebrates. In this study, we describe the functional analysis of PKA during gastrulation movements in Xenopus laevis. Overexpression of constitutively active PKA (cPKA) in the dorsal equatorial region of the embryo affects morphogenetic movement during gastrulation. We also show that intrinsic differences of PKA activities along the dorsoventral axis are set up and the level of PKA activity on the dorsal region is lower than that on the ventral region from late blastula to gastrula stages. In addition, PKA activation in animal explants inhibits activin-induced elongation. In cPKA-injected embryos, there were no changes in the expressions of markers involved in mesoderm specification, although the correct expression domains of these genes were altered. The effects of PKA activation can be restored by coexpression of PKI, a pseudosubstrate of PKA. We further analyzed the effects of PKA activation on the behavior of migratory gastrulating cells in vitro. Expression of cPKA in head mesoderm cells causes less polarized and/or randomized migration as demonstrated by a directional cell migration assay. Finally, we show that RhoA GTPase lies downstream of PKA, affecting activin-induced convergent extension movements. Taken together, these results suggest that overexpressed PKA can modulate a pathway responsible for morphogenetic movements during Xenopus gastrulation. Developmental Dynamics 227:91,103, 2003. © 2003 Wiley-Liss, Inc. [source] Social experience organizes parallel networks in sensory and limbic forebrainDEVELOPMENTAL NEUROBIOLOGY, Issue 3 2007Eun-Jin Yang Abstract Successful social behavior can directly influence an individual's reproductive success. Therefore, many organisms readily modify social behavior based on past experience. The neural changes induced by social experience, however, remain to be fully elucidated. We hypothesize that social modulation of neural systems not only occurs at the level of individual nuclei, but also of functional networks, and their relationships with behavior. We used the green anole lizard (Anolis carolinensis), which displays stereotyped, visually triggered social behaviors particularly suitable for comparisons of multiple functional networks in a social context, to test whether repeated aggressive interactions modify behavior and metabolic activity in limbic,hypothalamic and sensory forebrain regions, assessed by quantitative cytochrome oxidase (a slowly accumulating endogenous metabolic marker) histochemistry. We found that aggressive interactions potentiate aggressive behavior, induce changes in activities of individual nuclei, and organize context-specific functional neural networks. Surprisingly, this experiential effect is not only present in a limbic,hypothalamic network, but also extends to a sensory forebrain network directly relevant to the behavioral expression. Our results suggest that social experience modulates organisms' social behavior via modifying sensory and limbic neural systems in parallel both at the levels of individual regions and networks, potentially biasing perceptual as well as limbic processing. © 2007 Wiley Periodicals, Inc. Develop Neurobiol, 2007 [source] Temperature and hen harrier productivity: from local mechanisms to geographical patternsECOGRAPHY, Issue 5 2002S. M. Redpath Climate is an important factor limiting demography and distribution patterns in many organisms. For species with a broad geographical distribution, the mechanism by which climate influences demography is likely to vary dramatically from one end of the range to the other. In this paper we first assess, in a Scottish population of hen harriers Circus cyaneus, how temperature and rainfall influence adult behaviour and chick mortality patterns at the nest. We then test for associations between harrier productivity and weather across Scotland, towards the northern edge of the range, and Spain, towards the southern edge of the range. We show that during the nestling period, female brooding time increased in cold weather. Male provisioning rate was negatively related to temperature and rainfall. Chick mortality increased in cold temperatures and was most likely to occur at nests where male prey delivery rates were low relative to temperature. Annual values of harrier fledged brood size across Scotland were positively related to summer temperature suggesting that the patterns seen in one population held at a national scale. In Spain, however, the opposite patterns were observed with fledged brood size being negatively related to temperature. This shows that whilst the impact of weather on productivity may be equally strong at two ends of a geographical range, the mechanisms vary dramatically. Large-scale predictive models need to take such patterns into account. [source] Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspectiveELECTROPHORESIS, Issue S1 2009Nicolas Guex Abstract SWISS-MODEL pioneered the field of automated modeling as the first protein modeling service on the Internet. In combination with the visualization tool Swiss-PdbViewer, the Internet-based Workspace and the SWISS-MODEL Repository, it provides a fully integrated sequence to structure analysis and modeling platform. This computational environment is made freely available to the scientific community with the aim to hide the computational complexity of structural bioinformatics and encourage bench scientists to make use of the ever-increasing structural information available. Indeed, over the last decade, the availability of structural information has significantly increased for many organisms as a direct consequence of the complementary nature of comparative protein modeling and experimental structure determination. This has a very positive and enabling impact on many different applications in biomedical research as described in this paper. [source] INBREEDING IN THE SEYCHELLES WARBLER: ENVIRONMENT-DEPENDENT MATERNAL EFFECTSEVOLUTION, Issue 9 2004David S. Richardson Abstract The deleterious effects of inbreeding can be substantial in wild populations and mechanisms to avoid such matings have evolved in many organisms. In situations where social mate choice is restricted, extrapair paternity may be a strategy used by females to avoid inbreeding and increase offspring heterozygosity. In the cooperatively breeding Seychelles warbler, Acrocephalus sechellensis, neither social nor extrapair mate choice was used to avoid inbreeding facultatively, and close inbreeding occurred in approximately 5% of matings. However, a higher frequency of extra-group paternity may be selected for in female subordinates because this did reduce the frequency of mating between close relatives. Inbreeding resulted in reduced individual heterozygosity, which, against expectation, had an almost significant (P= 0.052), positive effect on survival. Conversely, low heterozygosity in the genetic mother was linked to reduced offspring survival, and the magnitude of this intergenerational inbreeding depression effect was environment-dependent. Because we controlled for genetic effects and most environmental effects (through the experimental cross-fostering of nestlings), we conclude that the reduced survival was a result of maternal effects. Our results show that inbreeding can have complicated effects even within a genetic bottlenecked population where the "purging" of recessive alleles is expected to reduce the effects of inbreeding depression. [source] Biochemical characterization of rice trehalose-6-phosphate phosphatases supports distinctive functions of these plant enzymesFEBS JOURNAL, Issue 5 2007Shuhei Shima Substantial levels of trehalose accumulate in bacteria, fungi, and invertebrates, where it serves as a storage carbohydrate or as a protectant against environmental stresses. In higher plants, trehalose is detected at fairly low levels; therefore, a regulatory or signaling function has been proposed for this molecule. In many organisms, trehalose-6-phosphate phosphatase is the enzyme governing the final step of trehalose biosynthesis. Here we report that OsTPP1 and OsTPP2 are the two major trehalose-6-phosphate phosphatase genes expressed in vegetative tissues of rice. Similar to results obtained from our previous OsTPP1 study, complementation analysis of a yeast trehalose-6-phosphate phosphatase mutant and activity measurement of the recombinant protein demonstrated that OsTPP2 encodes a functional trehalose-6-phosphate phosphatase enzyme. OsTPP2 expression is transiently induced in response to chilling and other abiotic stresses. Enzymatic characterization of recombinant OsTPP1 and OsTPP2 revealed stringent substrate specificity for trehalose 6-phosphate and about 10 times lower Km values for trehalose 6-phosphate as compared with trehalose-6-phosphate phosphatase enzymes from microorganisms. OsTPP1 and OsTPP2 also clearly contrasted with microbial enzymes, in that they are generally unstable, almost completely losing activity when subjected to heat treatment at 50 °C for 4 min. These characteristics of rice trehalose-6-phosphate phosphatase enzymes are consistent with very low cellular substrate concentration and tightly regulated gene expression. These data also support a plant-specific function of trehalose biosynthesis in response to environmental stresses. [source] Cloning and characterization of genes encoding trehalose-6-phosphate synthase (TPS1) and trehalose-6-phosphate phosphatase (TPS2) from Zygosaccharomyces rouxiiFEMS YEAST RESEARCH, Issue 4 2003Hawk-Bin Kwon Abstract In many organisms, trehalose protects against several environmental stresses, such as heat, desiccation, and salt, probably by stabilizing protein structures and lipid membranes. Trehalose synthesis in yeast is mediated by a complex of trehalose-6-phosphate synthase (TPS1) and trehalose-6-phosphate phosphatase (TPS2). In this study, genes encoding TPS1 and TPS2 were isolated from Zygosaccharomyces rouxii (designated ZrTPS1 and ZrTPS2, respectively). They were functionally identified by their complementation of the tps1 and tps2 yeast deletion mutants, which are unable to grow on glucose medium and with heat, respectively. Full-length ZrTPS1 cDNA is composed of 1476 nucleotides encoding a protein of 492 amino acids with a molecular mass of 56 kDa. ZrTPS2 cDNA consists of 2843 nucleotides with an open reading frame of 2700 bp, which encodes a polypeptide of 900 amino acids with a molecular mass of 104 kDa. The amino acid sequence encoded by ZrTPS1 has relatively high homology with TPS1 of Saccharomyces cerevisiae and Schizosaccharomyces pombe, compared with TPS2. Western blot analysis showed that the antibody against S. cerevisiae TPS1 recognizes ZrTPS1. Under normal growth conditions, ZrTPS1 and ZrTPS2 were highly and constitutively expressed, unlike S. cerevisiae TPS1 and TPS2. Salt stress and heat stress reduced the expression of the ZrTPS1 and ZrTPS2 genes, respectively. [source] The Role of DNA Recombination in Herpes Simplex Virus DNA ReplicationIUBMB LIFE, Issue 8 2003Dianna Wilkinson Abstract In many organisms the processes of DNA replication and recombination are closely linked. For instance, in bacterial and eukaryotic systems, replication forks can become stalled or damaged, in many cases leading to the formation of double stranded breaks. Replication restart is an essential mechanism in which the recombination and repair machinery can be used to continue replication after such a catastrophic event. DNA viruses of bacteria such as lambda and T4 also rely heavily on DNA recombination to replicate their genomes and both viruses encode specialized gene products which are required for recombination-dependent replication. In this review, we examine the linkage between replication and recombination in the eukaryotic pathogen, Herpes Simplex Virus Type 1 (HSV-1). The evidence that recombination plays an intrinsic role in HSV-1 DNA replication and the infection process will be reviewed. We have recently demonstrated that HSV-1 encodes two proteins which may be analogous to the lambda phage recombination system, Red ,and ,. The HSV-1 alkaline nuclease, a 5' to 3' exonuclease, and ICP8, a single stranded DNA binding protein, can carry out strand annealing reactions similar to those carried out by the lambda Red system. In addition, evidence suggesting that host recombination proteins may also be important for HSV-1 replication will be reviewed. In summary, it is likely that HSV-1 infection will require both viral and cellular proteins which participate in various pathways of recombination and that recombination-dependent replication is essential for the efficient replication of viral genomes. IUBMB Life, 55: 451-458, 2003 [source] Age-related patterns of reproductive success in house sparrows Passer domesticusJOURNAL OF AVIAN BIOLOGY, Issue 5 2007Margret I. Hatch A common life history pattern in many organisms is that reproductive success increases with age. We report a similar pattern in house sparrows Passer domesticus, older individuals performed better than yearlings for most measures of reproductive success. Older males and females began breeding earlier in a given season and fledged more young than their yearling counterparts. Individual males also fledged more young in their second breeding season than they did in their first, but individual females did not show consistent improvement in reproductive success from year one to two. A path analysis indicated that age in both sexes acted primarily through the timing of breeding; earlier nesters laid more eggs and hence fledged more young but did not have more nesting attempts. We tested whether the increased reproductive success with age arose from high quality individuals surviving to be older (selection hypothesis). In contrast to the main prediction of this hypothesis that reproductive success and survival should be positively related, we found that survival from one year of age to two years of age was negatively related to reproductive success in the first year for males and females combined. Additionally, individuals that survived to breed as two-year-olds did not differ in total young fledged in their first year from those that did not survive to their second season of breeding. Our results indicate that fledgling production increases with age due to improvements in timing of breeding, particularly in females, and not because of the loss of poor breeders or increased output. Mechanisms producing age-related differences in timing of breeding warrant further study. [source] Susceptibility of zoospores to UV radiation determines upper depth distribution limit of Arctic kelps: evidence through field experimentsJOURNAL OF ECOLOGY, Issue 2 2006CHRISTIAN WIENCKE Summary 1The UV susceptibility of zoospores of the brown seaweeds Saccorhiza dermatodea, Alaria esculenta and Laminaria digitata (Laminariales) was determined in field experiments in June 2004 on Spitsbergen (78°55, N, 11°56, E). 2Freshly released zoospores were exposed for 1 or 2 days at various water depths to ambient solar radiation, ambient solar radiation depleted of UVB radiation (UVBR) and ambient solar radiation depleted of both UVBR and UVAR. Subsequently, germination rates were determined after exposure to favourable light and temperature conditions in the laboratory. 3The radiation regime was monitored at the water surface and in the water column using data loggers attached adjacent to each experimental platform for the duration of the field exposure. 4Under ambient solar radiation, the tolerance of zoospores to UVR was highest in the shallow water species S. dermatodea, intermediate in the upper to mid sublittoral A. esculenta and lowest in the upper to mid sublittoral L. digitata. There was, however, no difference in the susceptibility of the zoospores to ambient solar radiation or to solar radiation depleted of UVBR. 5The water column was relatively UV transparent, especially in the upper water layers. The 1% UVB depth ranged between 5.35 and 6.87 m, although on one stormy day the 1% UVB depth was only 3.57 m, indicating resuspension of sediments. 6Early developmental stages are most susceptible to environmental stress. Tolerance of zoospores to UVR is a major if not one of the most important factors determining the upper distribution limit of different Laminariales on the shore. 7Kelps are very important primary producers in inshore coastal ecosystems, serving as food for herbivores and as habitat for many organisms. Enhanced UVBR due to stratospheric ozone depletion may lead to changes in the depth distribution of kelps and may cause significant ecological domino effects. [source] Morph-specific selection on floral traits in a polymorphic plantJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 6 2010D. VANHOENACKER Abstract Correlations between phenotypic traits are common in many organisms, but the relative importance of nonadaptive mechanisms and selection for the evolution and maintenance of such correlations are poorly understood. In polymorphic species, morphs may evolve quantitative differences in additional characters as a result of morph-specific selection. The perennial rosette herb Primula farinosa is polymorphic for scape length. The short-scaped morph is less damaged by grazers and seed predators but is more strongly pollen limited than the long-scaped morph. We examined whether morph-specific differences in biotic interactions are associated with differences in selection on two other traits affecting floral display (number of flowers and petal size) and on one trait likely to affect pollination efficiency (corolla tube width) in three P. farinosa populations. Differences in selection between morphs were detected in one population. In this population, selection for more flowers and larger petals was stronger in the short-scaped than in the long-scaped morph, and although there was selection for narrower corolla tubes in the short-scaped morph, no statistically significant selection on corolla tube width could be detected in the long-scaped morph. In the study populations, the short-scaped morph produced more and larger flowers and wider corolla tubes. Current morph-specific selection was thus only partly consistent with trait differences between morphs. The results provide evidence of morph-specific selection on traits associated with floral display and pollination efficiency, respectively. [source] Are there interactive effects of mate availability and predation risk on life history and defence in a simultaneous hermaphrodite?JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 5 2008J. R. AULD Abstract Encountering mates and avoiding predators are ubiquitous challenges faced by many organisms and they can affect the expression of many traits including growth, timing of maturity and resource allocation to reproduction. However, these two factors are commonly considered in isolation rather than simultaneously. We examined whether predation risk and mate availability interact to affect morphology and life-history traits (including lifetime fecundity) of a hermaphroditic snail (Physa acuta). We found that mate availability reduced juvenile growth rate and final size. Predator cues from crayfish induced delayed reproduction, but there were no reduced fecundity costs associated with predator induction. Although there were interactive effects on longevity, lifetime fecundity was determined by the number of reproductive days. Therefore, our results indicate a resource-allocation trade-off among growth, longevity and reproduction. Future consideration of this interaction will be important for understanding how resource-allocation plasticity affects the integration of defensive, life-history and mating-system traits. [source] Functional genomic approach to identify novel genes involved in the regulation of oxidative stress resistance and animal lifespanAGING CELL, Issue 4 2007Yongsoon Kim Summary Genetic studies in many organisms suggest that an increased animal lifespan phenotype is often accompanied by enhanced resistance toward reactive oxygen species (ROS). In Caenorhabditis elegans, mutations in daf-2, which encode an insulin/insulin-like growth factor 1 receptor-like molecule, lead to an extended animal lifespan and increased resistance to ROS. We have optimized an assay to monitor ROS resistance in worms using the ROS-generating chemical paraquat. We have employed this assay to screen the RNAi library along chromosomes III and IV for genes that, when silenced, confer paraquat resistance. The positive RNAi clones were subsequently screened for a lifespan extension phenotype. Using this approach, we have identified 84 genes that, when inactivated by RNAi, lead to significant increases in animal lifespan. Among the 84 genes, 29 were found to act in a manner dependent on daf-16. DAF-16, a forkhead transcription factor, is known to integrate signals from multiple pathways, including the daf-2 pathway, to regulate animal lifespan. Most of the 84 genes have not been previously linked to aging, and potentially participate in important cellular processes such as signal transduction, cell,cell interaction, gene expression, protein degradation, and energy metabolism. Our screen has also identified a group of genes that potentially function in a nutrient-sensing pathway to regulate lifespan in C. elegans. Our study provides a novel approach to identify genes involved in the regulation of aging. [source] The demography of slow aging in male and female Drosophila mutant for the insulin-receptor substrate homologue chicoAGING CELL, Issue 1 2002Meng-Ping Tu Summary Hypomorphic mutants affecting the Drosophila insulin/IGF signal pathway are reported to increase longevity in females but not in males. To understand this sex-difference, we conducted a large-scale demographic study with three new isogenic strains of alleles at chico, the insulin-receptor substrate homologue. We verify that female dwarf homozygotes (ch1/ch1) and normal-sized heterozygotes (ch1/+) are long-lived, as originally reported. We find for the first time that male heterozygotes are long-lived relative to wildtype, by about 50%. The life span of male ch1/ch1 is similar to that of wildtype but these dwarf males age at a slow demographic rate. The levels of demographic frailty and of age-independent mortality are elevated in ch1/ch1 males, counteracting the effect of slow aging upon life expectancy. Mortality deceleration occurs amongst the oldest-old wildtype adults, as seen in many organisms. Remarkably, in similarly sized cohorts of male and female ch1/ch1 and of male ch1/+ mortality deceleration is absent. Mortality deceleration is a phenotype of chico. [source] The ,rare allele phenomenon' in a ribosomal spacerMOLECULAR ECOLOGY, Issue 5 2001Menno Schilthuizen Abstract We describe the increased frequency of a particular length variant of the internal transcribed spacer 1 (ITS-1) of the ribosomal DNA in a hybrid zone of the land snail Albinaria hippolyti. The phenomenon that normally rare alleles or other markers can increase in frequency in the centre of hybrid zones is not new. Under the term ,hybrizyme' or ,rare allele' phenomenon it has been recorded in many organisms and different genetic markers. However, this is the first time that it has been found in a multicopy locus. On the one hand, the pattern fits well with the view that purifying selection in hybrid populations works on many loci across the genome and should thus have its effect on many independent molecular markers. On the other hand, the results are puzzling, given that the multiple copies of rDNA are not expected to respond in unison. We suggest two possible explanations for these conflicting observations. [source] Ternary complex formation between AmtB, GlnZ and the nitrogenase regulatory enzyme DraG reveals a novel facet of nitrogen regulation in bacteriaMOLECULAR MICROBIOLOGY, Issue 6 2007Luciano F. Huergo Summary Ammonium movement across biological membranes is facilitated by a class of ubiquitous channel proteins from the Amt/Rh family. Amt proteins have also been implicated in cellular responses to ammonium availability in many organisms. Ammonium sensing by Amt in bacteria is mediated by complex formation with cytosolic proteins of the PII family. In this study we have characterized in vitro complex formation between the AmtB and PII proteins (GlnB and GlnZ) from the diazotrophic plant-associative bacterium Azospirillum brasilense. AmtB,PII complex formation only occurred in the presence of adenine nucleotides and was sensitive to 2-oxoglutarate when Mg2+ and ATP were present, but not when ATP was substituted by ADP. We have also shown in vitro complex formation between GlnZ and the nitrogenase regulatory enzyme DraG, which was stimulated by ADP. The stoichiometry of this complex was 1:1 (DraG monomer : GlnZ trimer). We have previously reported that in vivo high levels of extracellular ammonium cause DraG to be sequestered to the cell membrane in an AmtB and GlnZ-dependent manner. We now report the reconstitution of a ternary complex involving AmtB, GlnZ and DraG in vitro. Sequestration of a regulatory protein by the membrane-bound AmtB,PII complex defines a new regulatory role for Amt proteins in Prokaryotes. [source] The Hsp70 chaperone machines of Escherichia coli: a paradigm for the repartition of chaperone functionsMOLECULAR MICROBIOLOGY, Issue 4 2007Pierre Genevaux Summary Molecular chaperones are highly conserved in all free-living organisms. There are many types of chaperones, and most are conveniently grouped into families. Genome sequencing has revealed that many organisms contain multiple members of both the DnaK (Hsp70) family and their partner J-domain protein (JDP) cochaperone, belonging to the DnaJ (Hsp40) family. Escherichia coli K-12 encodes three Hsp70 genes and six JDP genes. The coexistence of these chaperones in the same cytosol suggests that certain chaperone,cochaperone interactions are permitted, and that chaperone tasks and their regulation have become specialized over the course of evolution. Extensive genetic and biochemical analyses have greatly expanded knowledge of chaperone tasking in this organism. In particular, recent advances in structure determination have led to significant insights of the underlying complexities and functional elegance of the Hsp70 chaperone machine. [source] Control of fatty acid desaturation: a mechanism conserved from bacteria to humansMOLECULAR MICROBIOLOGY, Issue 6 2006Pablo S. Aguilar Summary Unsaturated fatty acids (UFAs) have profound effects on the fluidity and function of biological membranes. Microorganisms, plants and animals regulate the synthesis of UFAs during changing environmental conditions as well as in response to nutrients. UFAs homeostasis in many organisms is achieved by feedback regulation of fatty acid desaturase gene transcription through signalling pathways that are governed by sensors embedded in cellular membranes. Here, we review recently discovered components of the regulatory machinery governing the transcription of fatty acid desaturases in bacteria, yeasts and animals that indicate an ancient role of transmembrane signalling mechanisms and integrate membrane composition with lipid biosynthesis. [source] Competitive ability not kinship affects growth of Arabidopsis thaliana accessionsNEW PHYTOLOGIST, Issue 1 2010Frédéric Masclaux Summary ,In many organisms, individuals behave more altruistically towards relatives than towards unrelated individuals. Here, we conducted a study to determine if the performance of Arabidopsis thaliana is influenced by whether individuals are in competition with kin or non-kin. ,We selected seven pairs of genetically distinct accessions that originated from local populations throughout Europe. We measured the biomass of one focal plant surrounded by six kin or non-kin neighbours in in vitro growth experiments and counted the number of siliques produced per pot by one focal plant surrounded by four kin or non-kin neighbours. ,The biomass and number of siliques of a focal plant were not affected by the relatedness of the neighbour. Depending on the accession, a plant performed better or worse in a pure stand than when surrounded by non-kin plants. In addition, whole-genome microarray analyses revealed that there were no genes differentially expressed between kin and non-kin conditions. ,In conclusion, our study does not provide any evidence for a differential response to kin vs non-kin in A. thaliana. Rather, the outcome of the interaction between kin and non-kin seems to depend on the strength of the competitive abilities of the accessions. [source] Unusual Cu(I)/Ag(I) coordination of Escherichia coli CusF as revealed by atomic resolution crystallography and X-ray absorption spectroscopyPROTEIN SCIENCE, Issue 10 2007Isabell R. Loftin Abstract Elevated levels of copper or silver ions in the environment are an immediate threat to many organisms. Escherichia coli is able to resist the toxic effects of these ions through strictly limiting intracellular levels of Cu(I) and Ag(I). The CusCFBA system is one system in E. coli responsible for copper/silver tolerance. A key component of this system is the periplasmic copper/silver-binding protein, CusF. Here the X-ray structure and XAS data on the CusF,Ag(I) and CusF,Cu(I) complexes, respectively, are reported. In the CusF,Ag(I) structure, Ag(I) is coordinated by two methionines and a histidine, with a nearby tryptophan capping the metal site. EXAFS measurements on the CusF,Cu(I) complex show a similar environment for Cu(I). The arrangement of ligands effectively sequesters the metal from its periplasmic environment and thus may play a role in protecting the cell from the toxic ion. [source] Bivalve fishing and maerl-bed conservation in France and the UK,retrospect and prospectAQUATIC CONSERVATION: MARINE AND FRESHWATER ECOSYSTEMS, Issue S1 2003J.M. Hall-Spencer Abstract 1.Maerl beds are carbonate sediments, built by a surface layer of slow-growing coralline algae, forming structurally fragile habitats. 2.They are of international conservation significance, often supporting a high biodiversity and abundant bivalve molluscs. 3.Experimental fishing for scallops (Pecten maximus) on French and UK grounds has shown that although large epifauna are often killed, many organisms escape harm as they burrow deeply or are small enough to pass through the dredges. 4.Bivalve dredging is currently one of the main threats to European maerl grounds as it reduces their biodiversity and structural complexity and can lead to long-term degradation of the habitat. 5.Protecting maerl grounds is of importance for fisheries since they provide structurally complex feeding areas for juvenile fish (e.g. Atlantic cod - Gadus morhua) and reserves of commercial brood stock (e.g. Ensis spp., P. maximus and Venus verrucosa). 6.We outline improved mechanisms to conserve these ancient and unique biogenic habitats. Copyright © 2003 John Wiley & Sons, Ltd. [source] The expression patterns of a eukaryotic initiation factor 3 subunit H in the silk glands in Bombyx moriARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY (ELECTRONIC), Issue 1 2010Jia-Lin Wang Abstract Eukaryotic initiation factor 3 subunit H has been characterized in many organisms, and it has been found to play many roles including help regulate translation initiation. In this work, we studied the tissue distribution and expression profiles of Bombyx mori (B. mori) eIF3 subunit H (BmeIF3h). BmeIF3h was prominently expressed in silk glands, with anterior silk glands (ASGs), middle silk glands (MSGs), and posterior silk glands (PSGs) all expressing BmeIF3h. The expression levels of BmeIF3h in MSGs and PSGs were higher than that in ASGs during 0 d and 2 d of the 5th instar larvae. The expression levels of BmeIF3h in MSGs and PSGs were up-regulated once the silk glands began to synthesize silk protein during the feeding stage of the 4th instar larvae. Immunohistochemistry showed that BmeIF3h was distributed in the cytoplasm of MSGs cells and in both the nucleus and the cytoplasm of PSGs cells. These data suggest that BmeIF3h had different action behaviors in the MSGs and PSGs related to the production of the silk glue proteins and silk fibre proteins, respectively. © 2010 Wiley Periodicals, Inc. [source] Crystallization and preliminary X-ray analysis of tubulin-folding cofactor A from Arabidopsis thalianaACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2010Lu Lu Tubulin-folding cofactor A (TFC A) is a molecular post-chaperonin that is involved in the ,-tubulin-folding pathway. It has been identified in many organisms including yeasts, humans and plants. In this work, Arabidopsis thaliana TFC A was expressed in Escherichia coli and purified to homogeneity. After thrombin cleavage, a well diffracting crystal was obtained by the sitting-drop vapour-diffusion method at 289,K. The crystal diffracted to 1.6,Å resolution using synchrotron radiation and belonged to space group I41, with unit-cell parameters a = 55.0, b = 55.0, c = 67.4,Å. [source] Sinusoidal ELF magnetic fields affect acetylcholinesterase activity in cerebellum synaptosomal membranesBIOELECTROMAGNETICS, Issue 4 2010Silvia Ravera Abstract The effects of extremely low frequency magnetic fields (ELF-MF) on acetylcholinesterase (AChE) activity of synaptosomal membranes were investigated. Sinusoidal fields with 50,Hz frequency and different amplitudes caused AChE activity to decrease about 27% with a threshold of about 0.74,mT. The decrease in enzymatic activity was independent of the time of permanence in the field and was completely reversible. Identical results were obtained with exposure to static MF of the same amplitudes. Moreover, the inhibitory effects on enzymatic activity are spread over frequency windows with different maximal values at 60, 200, 350, and 475,Hz. When synaptosomal membranes were solubilized with Triton, ELF-MF did not affect AChE activity, suggesting the crucial role of the membrane, as well as the lipid linkage of the enzyme, in determining the conditions for inactivation. The results are discussed in order to give an interpretation at molecular level of the macroscopic effects produced by ELF-MF on biological systems, in particular the alterations of embryo development in many organisms due to acetylcholine accumulation. Bioelectromagnetics 31:270,276, 2010. © 2009 Wiley-Liss, Inc. [source] Crystallization and preliminary X-ray analysis of the LOV domain of the blue-light receptor YtvA from Bacillus amyloliquefaciens FZB42ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2009Hideaki Ogata Light,oxygen,voltage (LOV) proteins play an important role in blue-light-dependent physiological processes in many organisms. The LOV domain of the blue-light receptor YtvA from Bacillus amyloliquefaciens FZB42 has been purified and crystallized at 277,K using the sitting-drop vapour-diffusion method with 2-ethoxyethanol as a precipitant. A data set was collected to 1.60,Å resolution from a single crystal at 100,K using synchrotron radiation. The LOV domain of YtvA crystallized in space group C2221, with unit-cell parameters a = 64.95, b = 83.76, c = 55.81,Å. The crystal structure of the LOV domain of YtvA was determined by the molecular-replacement method. The crystal contained one molecule per asymmetric unit, with a Matthews coefficient (VM) of 3.04,Å3,Da,1; the solvent content was estimated to be 59.5%. [source] | |||||||||||||||||||||||||||||||