A standardized kinesin nomenclature

In recent years the kinesin superfamily has become so large that several different naming schemes have emerged, leading to confusion and miscommunication. Here, we set forth a standardized kinesin nomenclature based on 14 family designations. The scheme unifies all previous phylogenies and nomenclature proposals, while allowing individual sequence names to remain the same, and for expansion to occur as new sequences are discovered.     

Zebrafish collapsin response mediator protein (CRMP)-2 is expressed in developing neurons

The collapsin response mediator proteins (CRMPs) are highly expressed in the vertebrate nervous system. CRMP2 has been shown to function in Semaphorin and lysophosphatidic acid induced growth cone collapse. Correspondingly, the highest levels of CRMP2 protein are found in the distal portion of growing axons. To understand the role of CRMP2 during embryonic development we have documented its expression pattern in zebrafish embryos at multiple stages. We find that CRMP2 is expressed in the major neural clusters of the embryonic brain during the primary stages of neurogenesis. From 20 somites through 30 hpf CRMP2 is expressed in the dorsal rostral cluster of the telencephalon, the ventral rostral cluster of the diencephalon, the ventral caudal cluster of the mesencephalon, and the hindbrain clusters. CRMP2 is also expressed in the trigeminal sensory ganglia and the Rohon Beard cells of the neural tube from 15 somites. By 48 hpf, we find expression of CRMP2 throughout the developing brain, trigeminal sensory ganglia, and Rohon Beard cells. CRMP2 is also detected in the retinal ganglion cell layer of the eye, and in the otic vesicle. Finally, we have compared the expression of CRMP2 to PlexinA4, a Semaphorin receptor expressed in sensory neurons, and find that their expression partially overlaps.     

Relative and absolute quantitative expression profiling of cytochromes P450 using isotope-coded affinity tags

The development of a novel method for absolute quantification of proteins based on isotope-coded affinity tagging using ICAT reagents is described. The method exploits synthetic peptide standards to determine protein content at the femtomole level in biological samples. The approach is generally applicable to any subset of proteins, but is particularly appropriate for quantitative analysis of multiple, closely related isoforms, and for hydrophobic proteins that are poorly represented in 2-D gels. Relative and absolute quantification techniques are applied to an important group of microsomal metabolic enzymes, the cytochromes P450 (P450), which are critical in determining the disposition, safety and efficacy of drugs in man. Measurement of the P450 induction profile in response to chemicals is a fundamental aspect of drug safety evaluation and is currently achieved by low-throughput methods employing poorly discriminatory antibodies or substrates. Tagging technology is shown to supersede conventional methods for P450 profiling in terms of discriminatory power and throughput, exemplified by the simultaneous detection of distinct induction profiles for cyp2c subfamily members in response to phenobarbitone: cyp2c29 expression, but not cyp2c40 or cyp2c50, was induced threefold by treatment. This technology should abbreviate the drug development pathway, and provide a widely applicable, rapid means of quantifying proteins.     

Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins

Quantitative LC-MS/MS assays were designed for tryptic peptides representing 53 high and medium abundance proteins in human plasma using a multiplexed multiple reaction monitoring (MRM) approach. Of these, 47 produced acceptable quantitative data, demonstrating within-run coefficients of variation (CVs) (n = 10) of 2-22% (78% of assays had CV <10%). A number of peptides gave CVs in the range 2-7% in five experiments (10 replicate runs each) continuously measuring 137 MRMs, demonstrating the precision achievable in complex digests. Depletion of six high abundance proteins by immunosubtraction significantly improved CVs compared with whole plasma, but analytes could be detected in both sample types. Replicate digest and depletion/digest runs yielded correlation coefficients (R(2)) of 0.995 and 0.989, respectively. Absolute analyte specificity for each peptide was demonstrated using MRM-triggered MS/MS scans. Reliable detection of L-selectin (measured at 0.67 microg/ml) indicates that proteins down to the microg/ml level can be quantitated in plasma with minimal sample preparation, yielding a dynamic range of 4.5 orders of magnitude in a single experiment. Peptide MRM measurements in plasma digests thus provide a rapid and specific assay platform for biomarker validation, one that can be extended to lower abundance proteins by enrichment of specific target peptides (stable isotope standards and capture by anti-peptide antibodies (SISCAPA)).     

QUANTIFYING EVOLUTIONARY POTENTIAL OF MARINE FISH LARVAE: HERITABILITY,SELECTION, AND EVOLUTIONARY CONSTRAINTS

For many marine fish, intense larval mortality may provide considerable opportunity for selection, yet much less is known about the evolutionary potential of larval traits. We combined field demographic studies and manipulative experiments to estimate quantitative genetic parameters for both larval size and swimming performance for a natural population of a common coral‐reef fish, the bicolor damselfish (Stegastes partitus). We also examined selection on larval size by synthesizing information from published estimates of selective mortality. We introduce a method that uses the Lande–Arnold framework for examining selection on quantitative traits to empirically reconstruct adaptive landscapes. This method allows the relationship between phenotypic value and fitness components to be described across a broad range of trait values. Our results suggested that despite strong viability selection for large larvae and moderate heritability (h²= 0.29), evolutionary responses of larvae would likely be balanced by reproductive selection favoring mothers that produce more, smaller offspring. Although long‐term evolutionary responses of larval traits may be constrained by size‐number trade‐offs, our results suggest that phenotypic variation in larval size may be an ecologically important source of variability in population dynamics through effects on larval survival and recruitment to benthic populations.     

Genotype-by-Diet Interactions Drive Metabolic Phenotype Variation in Drosophila melanogaster

The rising prevalence of complex disease suggests that alterations to the human environment are increasing the proportion of individuals who exceed a threshold of liability. This might be due either to a global shift in the population mean of underlying contributing traits, or to increased variance of such underlying endophenotypes (such as body weight). To contrast these quantitative genetic mechanisms with respect to weight gain, we have quantified the effect of dietary perturbation on metabolic traits in 146 inbred lines of Drosophila melanogaster and show that genotype-by-diet interactions are pervasive. For several metabolic traits, genotype-by-diet interactions account for far more variance (between 12 and 17%) than diet alone (1–2%), and in some cases have as large an effect as genetics alone (11–23%). Substantial dew point effects were also observed. Larval foraging behavior was found to be a quantitative trait exhibiting significant genetic variation for path length (P = 0.0004). Metabolic and fitness traits exhibited a complex correlation structure, and there was evidence of selection minimizing weight under laboratory conditions. In addition, a high fat diet significantly increases population variance in metabolic phenotypes, suggesting decreased robustness in the face of dietary perturbation. Changes in metabolic trait mean and variance in response to diet indicates that shifts in both population mean and variance in underlying traits could contribute to increases in complex disease.METABOLIC syndrome (MetS) is a complex disease that is promoted by interactions between genetic and environmental effects (O''Rahilly and Farooqi 2006), and seems to be increasing in prevalence in response to a transition from traditional toward Westernized lifestyles (Lee et al. 2004; Schulz et al. 2006). MetS is a constellation of metabolic symptoms including insulin resistance, abdominal obesity, and dyslipidemia, and is predictive of cardiovascular disease and type-2 diabetes (Alberti et al. 2006). The condition has reached epidemic proportions in many Westernized countries (Isomaa et al. 2001; Ford and Giles 2003; Lorenzo et al. 2003; Alberti et al. 2006). Not all individuals are susceptible to the deleterious effects of a Westernized lifestyle, but some individuals are very sensitive to the effects of their environment (Schulz et al. 2006).We argued previously that environmental perturbation contributes to the recent increases in chronic disease in Westernized societies by exposing cryptic genetic variation, a phenomenon that may be particularly evident in metabolic syndrome (Gibson 2009). Increases in complex disease after an environmental shift can be caused by both a change in the population mean or increased variance in a predisposing underlying trait, or endophenotype, causing a larger portion of the population to exceed a disease threshold (Gibson and Reed 2008). Endophenotypes can be molecular, such as rate of uptake of glucose into cells, but also include visible disease covariates, such as body mass. The transition from traditional diets and lifestyles may have perturbed our metabolic homeostasis, thereby promoting increased susceptibility to, and in turn prevalence of, obesity, hyperlipidemia, diabetes, and cardiovascular illness.The complexity of genetic and environmental interactions leads to major challenges in successful disease treatment and prevention strategies, in that it is very difficult to accurately model the relative contributions of nature and nurture to disease susceptibility in a human population. Dietary factors have been demonstrated to interact with specific genetic variants to increase the risk of metabolic disease in humans (Corella and Ordovas 2005; Ordovas 2006; Corella et al. 2009; Warodomwichit et al. 2009), but the relative contribution of overall genotype and environmental effects on human variation is difficult to determine. Modeling population level genotype-by-environment interactions using a model organism like Drosophila can compensate for the research challenges of parameter estimation in human populations.Drosophila share great homology to humans in a number of systems including central metabolism, insulin-signaling pathways, and organs responsible for physiological homoeostasis (e.g., heart, liver, and kidney) (Rizki 1978; Bodmer 1995; Nation 2002; Rulifson et al. 2002; Denholm et al. 2003; Wessells et al. 2004). It has been shown that Drosophila with ablated insulin-producing neurons have elevated hemolymph trehalose levels, considered to parallel a diabetic phenotype (Rulifson et al. 2002). Loss of insulin signaling also restores normal rhythmicity of adult heart rate in old flies (Wessells et al. 2004), providing a link between the obesity and cardiac components of MetS. We have used 146 natural genetic isolates of Drosophila melanogaster to model the relative contributions of genetics, diet, and other environmental effects on the MetS-like phenotypes of larval weight gain, blood sugar concentration, lipid storage, and survival. Individuals from each of these genetic lines were raised on four different diets: their normal lab food, a calorie restricted (0.75% glucose) food, a high (4%) glucose food, and a high fat diet containing (3%) coconut oil.Using this approach, we sought evidence pertaining to two major hypotheses. There are six general types of phenotypic reaction scenarios that a genetically variable population can exhibit in response to an environmental transition: (1) no phenotypic variation in response to genetic or environmental factors, (2) genetic variation in mean phenotype but no change across environments, (3) an additive change in phenotypic mean across genotypes between environments, (4) an interaction effect between genetic and environment leading to a crossing of line means, and (5) a decrease or (6) an increase in variance in the new environment (Gibson and Vanhelden 1997). First, we considered whether the predominant source of metabolic variation within a Drosophila population is genetic, environmental, or the interaction between genetic and environmental effects. Our null was that none of these factors significantly influence weight gain or other phenotypes (scenario 1 above), but it was expected that genetic variation would be prevalent. The more fundamental issue is which of two alternate hypotheses apply: that dietary effects are essentially additive across genotypes (3) or that they are largely genotype dependent (4), possibly also with contributions of behavior and the external environment. Second, we considered whether the transition from a standard laboratory diet to a perturbing diet would change the environmental and/or genetic variance observed in the population: a decrease (5) indicating physiological limitation to the variation or an increase (6) indicating decanalization of the metabolic phenotypes due to loss of physiological buffering.     

Twenty years of research on community composition and species distribution of arbuscular mycorrhizal fungi in China: a review

The biodiversity and distribution of arbuscular mycorrhizal fungi (AMF) in different ecosystems and plant communities in China has received increasing interest over the past decades. This has led to a steady increase in the number of scientific papers published on this topic. Studies have surveyed AMF-colonizing rhizospheres of most families of angiosperms, bryophytes, pteridophytes, and gymnosperms. China has about 30,000 plant species (one eighth of the plant species worldwide). A total of 104 AMF species within nine genera, including 12 new species, have been reported in environments such as croplands, grasslands, forests, and numerous disturbed environments. In this paper, we review data published over the past 20 years on AMF community composition and species distribution, the mycorrhizal status of plants, AMF spore communities in different habitats, and germplasm collections in China. Possible future trends in the study of the biodiversity of AMF are also briefly discussed. In particular, the aim of our review is to make some of the recent work published in the Chinese literature accessible to a wider international audience.     

Arbuscular mycorrhizal fungi associated with the Meliaceae on Hainan island, China

Species richness, spore density, frequency of occurrence, and relative abundance of AM fungi were determined in rhizosphere soil samples from nine tropical rainforest sites on Hainan island, south China, and the arbuscular mycorrhizal (AM) status of members of the Meliaceae was examined. All 28 plant taxa investigated (25 species including two varieties of 1 species and three varieties of another) were colonized by AM fungi. The mean proportion of root length colonized was 56% (range 10–95%). Vesicles were observed in 27 and hyphal coils in 26 of the 28 plant taxa. Mycorrhizas were of the Paris-type or intermediate-type, with no Arum-type mycorrhizas observed. Species richness of AM fungi varied from 3 to 15 and spore density from 46 to 1,499 per 100 g rhizosphere soil. Of 33 AM fungal taxa in five genera isolated and identified, 18 belonged to Glomus, 9 to Acaulospora, 1 to Entrophospora, 2 to Gigaspora, and 3 to Scutellospora. Acaulospora and Glomus were the dominant genera identified. Glomus claroideum was the taxon most commonly isolated, with a frequency of occurrence of 56.5% and relative abundance of 10.4%. A positive correlation was found between percentage of root length colonization and species richness. However, there was no correlation between spore density and percentage of root length colonized by AM fungi.     

Involvement of ERK1/2 and p38 in Mg2+ accumulation in liver cells

Activation of PKC signaling induces Mg²⁺ accumulation in liver cells. To test the hypothesis that PKC induces Mg²⁺ accumulation via MAPKs activation, hepatocytes were incubated in the presence of PD98059 and SB202190 as specific inhibitors of ERK1/2 and p38, respectively, and stimulated for Mg²⁺ accumulation by addition of PMA or OAG. Accumulation of Mg²⁺ within the cells was measured by atomic absorbance spectrophotometry in the acid extract of cell pellet. The presence of either inhibitor completely abolished Mg²⁺ accumulation irrespective of the dose of agonist utilized while having no discernible effect on β -adrenoceptor mediated Mg²⁺ extrusion. A partial inhibition on α ₁-adrenoceptor mediated Mg²⁺ extrusion was observed only in cells treated with PD98059. To confirm the inhibitory effect of PD98509 and SB202190, total and basolateral liver plasma membrane vesicles were purified in the presence of either MAPK inhibitor during the isolation procedure. Consistent with the data obtained in intact cells, liver plasma membrane vesicles purified in the presence of PD98509 or SB202190 lost the ability to accumulate Mg²⁺in exchange for intra-vesicular entrapped Na⁺ while retaining the ability to extrude entrapped Mg²⁺ in exchange for extra-vesicular Na⁺. These data indicate that ERK1/2 and p38 are involved in mediating Mg²⁺ accumulation in liver cells following activation of PKC signaling. The absence of a detectable effect of either inhibitor on β -adrenoceptor induced, Na⁺-dependent Mg²⁺ extrusion in intact cells and in purified plasma membrane vesicles further support the hypothesis that Mg²⁺ extrusion and accumulation occur through distinct and differently regulated transport mechanisms.     

Eutrophication-induced changes in benthic algae affect the behaviour and fitness of the marine amphipod Gammarus locusta

This study, conducted in mesocosms, natural field sites, and in laboratory aquaria, showed that eutrophication altered the nutrient status and dominance patterns among marine macroalgae, which in turn, stimulated gammaridean density. Gammaridean abundance correlated positively with both nutrient addition and the amount of green algae (also stimulated by nutrient enrichment). Path analysis indicated that the direct effect of nutrients on gammaridean density was of less importance than the indirect effect through increased production of green algae. In cage colonisation experiments, either in the field or in a control mesocosm kept under ambient nutrient conditions, more gammarids colonised nutrient enriched algae (E-algae) than algae with ambient nutrient levels (A-algae). Gammarus locusta generally grew faster on nutrient enriched algal specimens and when reared on green rather than on brown algae (fucoids). The nutrient status of periphytic algae did not affect gammaridean growth significantly, but the number of egg-carrying females (and thus egg production) was significantly higher among gammarids reared on E-periphyton. The gammaridean habitat preference order (red > green > brown > periphyton) was almost the reverse of their growth rate in feeding assays (periphyton > green > brown). This implies that macroalgae may be more important as a habitat than as a food source for these animals, which then have to become mobile in search of optimal food items. In this process, algal nutrient content was important as the gammarids in our study actively chose high quality nutrient-rich food, which, in addition, increased their fitness. Stimulated growth rates and egg production may ultimately lead to population increase, which, combined with the preference for high nutrient food items may dampen the initial effect of nutrient enrichment (i.e. blooms of green macroalgae) in shallow coastal waters.