Banding studies on the polytene chromosomes of Rhynchosciara hollaenderi

C-, Q-, H-, and Ag-banding have been carried out on the polytene chromosomes of Rhynchosciara hollaenderi. The results of these techniques are presented and are correlated with the molecular data which exists for Rhynchosciara polytene chromosomes. By systematic organization of both banding and molecular data, we have attempted to give as complete a picture as possible of the characteristics of the differentially banding regions. This presents an organized method of approaching mechanisms of banding in terms of structural and functional aspects of the intact chromosome. Polytene chromosomes are particularly suited for this type of analysis and with them, both developmental and evolutionary changes can be conveniently utilized for additional insights into the functions of banding regions.     

面向药物发现和精准医疗的基因表达谱分析

作为功能基因组学中重要的组成部分,基因表达谱在生物学、医学和药物研发等多个领域发挥着重要作用.特别是随着精准医疗概念的提出,整合多组学数据用于个性化医疗是未来的发展趋势.本文从基因表达谱的基本概念出发,重点介绍面向药物发现的基因表达谱分析方法,即基于关联图谱的方法、基于基因调控网络的方法和基于多组学数据整合的方法.系统整理了各种方法的研究进展,特别是在抗癌药物研发领域的最新进展,为利用基因表达谱数据进行药物研发提供方法借鉴.     

Domain selection and familywise error rate for functional data: A unified framework

Functional data are smooth, often continuous, random curves, which can be seen as an extreme case of multivariate data with infinite dimensionality. Just as componentwise inference for multivariate data naturally performs feature selection, subsetwise inference for functional data performs domain selection. In this paper, we present a unified testing framework for domain selection on populations of functional data. In detail, p-values of hypothesis tests performed on pointwise evaluations of functional data are suitably adjusted for providing control of the familywise error rate (FWER) over a family of subsets of the domain. We show that several state-of-the-art domain selection methods fit within this framework and differ from each other by the choice of the family over which the control of the FWER is provided. In the existing literature, these families are always defined a priori. In this work, we also propose a novel approach, coined thresholdwise testing, in which the family of subsets is instead built in a data-driven fashion. The method seamlessly generalizes to multidimensional domains in contrast to methods based on a priori defined families. We provide theoretical results with respect to consistency and control of the FWER for the methods within the unified framework. We illustrate the performance of the methods within the unified framework on simulated and real data examples and compare their performance with other existing methods.     

On Distance‐Based Permutation Tests for Between‐Group Comparisons

Summary Permutation tests based on distances among multivariate observations have found many applications in the biological sciences. Two major testing frameworks of this kind are multiresponse permutation procedures and pseudo‐F tests arising from a distance‐based extension of multivariate analysis of variance. In this article, we derive conditions under which these two frameworks are equivalent. The methods and equivalence results are illustrated by reanalyzing an ecological data set and by a novel application to functional magnetic resonance imaging data.     

Bayesian analysis of climate change impacts in phenology

The identification of changes in observational data relating to the climate change hypothesis remains a topic of paramount importance. In particular, scientifically sound and rigorous methods for detecting changes are urgently needed. In this paper, we develop a Bayesian approach to nonparametric function estimation. The method is applied to blossom time series of Prunus avium L., Galanthus nivalis L. and Tilia platyphyllos SCOP. The functional behavior of these series is represented by three different models: the constant model, the linear model and the one change point model. The one change point model turns out to be the preferred one in all three data sets with considerable discrimination of the other alternatives. In addition to the functional behavior, rates of change in terms of days per year were also calculated. We obtain also uncertainty margins for both function estimates and rates of change. Our results provide a quantitative representation of what was previously inferred from the same data by less involved methods.     

Acetate conversion in anaerobic biogas reactors: Traditional and molecular tools for studying this important group of anaerobic microorganisms

Different methods were applied to study the role of aceticlastic methanogens in biogas reactors treating solid waste and wastewater. We used traditional microbiological methods, immunological and 16S rRNA ribosomal probesfor detection of the methanogens. Using this approach we identified themethanogenic spp. and their activity. In biofilm system, such as the UASBreactors the presence of the two aceticlastic methanogens could be correlatedto the difference in the kinetic properties of the two species. In biogas reactor treating solid wastes, such as manure or mixture of manure and organic industrial waste, only Methanosarcina spp. were identified. Methanosarcina spp. isolated from different plants had different kinetics depending on their origin. Relating the reactor performance data to measurement of the activity by conventional microbiological methods gave a good indication of the microbial status of specific trophic groups. 16S rRNA probing confirmed these observation and gave a more detailed picture of the microbial groups present.     

Female genitalia,reproductive cycle and sperm storage in Armadillidium vulgare (Crustacea,Isopoda, Oniscidea)

Light and electron microscopic studies that we have published in the past have reported many aspects of the reproductive process in Armadillidium vulgare with particular emphasis on the reconstruction of female genitalia. Together this body of work provides an almost complete, albeit fragmented picture of these processes and include many data on sperm storage and sperm translocation. Females of A. vulgare have a pair of cuticular genitalia in the lumen of the oviduct. For insemination, these genitalia can receive the copulatory organs of males formed by the elongated tips of the first two pleon endopods. During transitions between reproductive (parturial) and non-reproductive (normal, non-parturial) moult cycles the genitalia undergo intriguing structural changes resulting in two types of genitalia. Throughout their reproductive lifetime, either type is reconstructed after each moult depending on the reproductive phase of the female. In this review, we integrate the events that occur during a reproductive cycle with particular emphasis on the genitalia reconstruction and sperm storage, and discuss functional aspects of the genitalia. Thereby, we provide a case model that can be useful for further studies on genitalia diversity and female reproductive strategies in terrestrial isopods.     

Tubulogenesis during blood vessel formation

The ability to form and maintain a functional system of contiguous hollow tubes is a critical feature of vascular endothelial cells (ECs). Lumen formation, or tubulogenesis, occurs in blood vessels during both vasculogenesis and angiogenesis in the embryo. Formation of vascular lumens takes place prior to the establishment of blood flow and to vascular remodeling which results in a characteristic hierarchical vessel organization. While epithelial lumen formation has received intense attention in past decades, more recent work has only just begun to elucidate the mechanisms controlling the initiation and morphogenesis of endothelial lumens. Studies using in vitro and in vivo models, including zebrafish and mammals, are beginning to paint an emerging picture of how blood vessels establish their characteristic morphology and become patent. In this article, we review and discuss the molecular and cellular mechanisms driving the formation of vascular tubes, primarily in vivo, and we compare and contrast proposed models for blood vessel lumen formation.     

Molecular, Biochemical, and Physiological Approaches forUnderstanding the Ecology of Denitrification

One of the major challenges in microbial ecology for the future is to establish links between structural and functional biodiversity. This is particularly difficult when one is interested in a phylogenetically diversified function such as denitrification. The data banks are very rich in functional gene sequences (nirS in this study), but most of them were obtained from not yet cultivated bacteria, and thus must be supplemented by sequences of organisms from the environment for which we could associate a taxonomic position and physiological characteristics. Combined analysis including molecular (16S-rRNA or nirS genes), physiological, and biochemical approaches was carried out on a bacterial set of 89 strains isolated from marine sediment. The denaturing gradient gel electrophoresis (DGGE) technique was successfully applied on unclamped polymerase chain reaction (PCR) products of nirS genes to compare the picture of the biodiversity obtained with 16S rRNA and nirS genes. The diversity of nirS genes and denitrifier characteristics were found within several of the 16S rDNA phylotypes. In contrast, the nirS phylotypes were no diverse both with respect to 16S rDNA and to physiology and biochemistry of denitrification. Sequences of the nirS PCR products were very close to marine environmental clones and were analyzed within the same phylogenetic tree.     

Systems approach to explore components and interactions in the presynapse

The application of proteomic techniques to neuroscientific research provides an opportunity for a greater understanding of nervous system structure and function. As increasing amounts of neuroproteomic data become available, it is necessary to formulate methods to integrate these data in a meaningful way to obtain a more comprehensive picture of neuronal subcompartments. Furthermore, computational methods can be used to make biologically relevant predictions from large proteomic data sets. Here, we applied an integrated proteomics and systems biology approach to characterize the presynaptic (PRE) nerve terminal. For this, we carried out proteomic analyses of presynaptically enriched fractions, and generated a PRE literature‐based protein–protein interaction network. We combined these with other proteomic analyses to generate a core list of 117 PRE proteins, and used graph theory‐inspired algorithms to predict 92 additional components and a PRE complex containing 17 proteins. Some of these predictions were validated experimentally, indicating that the computational analyses can identify novel proteins and complexes in a subcellular compartment. We conclude that the combination of techniques (proteomics, data integration, and computational analyses) used in this study are useful in obtaining a comprehensive understanding of functional components, especially low‐abundance entities and/or interactions in the PRE nerve terminal.     

A genome-wide exploration suggests an oligogenic model of inheritance for the TAFI activity and its antigen levels

Thrombin-Activatable Fibrinolysis Inhibitor (TAFI) is a protein that potently attenuates fibrinolysis. A considerable proportion of its variability levels is genetically determined. It has been associated with arterial and venous thrombosis. We conducted a Genome Wide Scan for genes affecting variation in plasma TAFI levels in 398 subjects from 21 extended Spanish families. The data were analyzed by a variance-component linkage method. A strong linkage signal was found on the long arm of Chromosome 13, near the DNA marker D13S156, where the structural gene encoding for TAFI is located. In addition, other new linkage signals were detected on chromosome regions 5p and 7q. More importantly, we performed another multipoint linkage analysis of functional TAFI conditioned on TAFI antigen levels. We detected a strong linkage signal on Chromosome 19 (LOD = 3.0, P = 0.0001) suggesting a novel QTL in this region involved in the specific functional activity of TAFI, regardless of the TAFI antigen levels. One notable aspect of this study is the identification of new QTLs that reveal a clearer picture of the genetic determinants responsible for variation in TAFI levels. Another is the replication of the linkage signal of the CPB2 gene, which confirms an important genetic determinant for TAFI antigen levels. These results strongly suggest an oligogenic mode of inheritance for TAFI, in which CPB2 gene accounts for a proportion of the variation of the phenotype together with other unknown genes that may represent potential risk factors for thrombotic disease.     

Detecting long‐term growth trends using tree rings: a critical evaluation of methods

Tree‐ring analysis is often used to assess long‐term trends in tree growth. A variety of growth‐trend detection methods (GDMs) exist to disentangle age/size trends in growth from long‐term growth changes. However, these detrending methods strongly differ in approach, with possible implications for their output. Here, we critically evaluate the consistency, sensitivity, reliability and accuracy of four most widely used GDMs: conservative detrending (CD) applies mathematical functions to correct for decreasing ring widths with age; basal area correction (BAC) transforms diameter into basal area growth; regional curve standardization (RCS) detrends individual tree‐ring series using average age/size trends; and size class isolation (SCI) calculates growth trends within separate size classes. First, we evaluated whether these GDMs produce consistent results applied to an empirical tree‐ring data set of Melia azedarach, a tropical tree species from Thailand. Three GDMs yielded similar results – a growth decline over time – but the widely used CD method did not detect any change. Second, we assessed the sensitivity (probability of correct growth‐trend detection), reliability (100% minus probability of detecting false trends) and accuracy (whether the strength of imposed trends is correctly detected) of these GDMs, by applying them to simulated growth trajectories with different imposed trends: no trend, strong trends (?6% and +6% change per decade) and weak trends (?2%, +2%). All methods except CD, showed high sensitivity, reliability and accuracy to detect strong imposed trends. However, these were considerably lower in the weak or no‐trend scenarios. BAC showed good sensitivity and accuracy, but low reliability, indicating uncertainty of trend detection using this method. Our study reveals that the choice of GDM influences results of growth‐trend studies. We recommend applying multiple methods when analysing trends and encourage performing sensitivity and reliability analysis. Finally, we recommend SCI and RCS, as these methods showed highest reliability to detect long‐term growth trends.     

Benchmarking the DFT methodology for assessing antioxidant-related properties: quercetin and edaravone as case studies

The overall objective was to identify an accurate computational electronic method to virtually screen phenolic compounds through their antioxidant and free-radical scavenging activity. The impact of a key parameter of the density functional theory (DFT) approach was studied. Performances of the 21 most commonly used exchange-correlation functionals are thus detailed in the evaluation of the main energetic parameters related to the activities of two prototype antioxidants, namely quercetin and edaravone, is reported. These functionals have been chosen among those belonging to three different families of hybrid functionals, namely global, range separated, and double hybrids. Other computational parameters have also been considered, such as basis set and solvent effects. The selected parameters, namely bond dissociation enthalpy (BDE), ionization potential (IP), and proton dissociation enthalpy (PDE) allow a mechanistic evaluation of the antioxidant activities of free radical scavengers. Our results show that all the selected functionals provide a coherent picture of these properties, predicting the same order of BDEs and PDEs. However, with respect to the reference values, the errors found at CBS-Q3 level significantly vary with the functional. Although it is difficult to evidence a global trend from the reported data, it clearly appears that LC-ωPBE, M05-2X, and M06-2X are the most suitable approaches for the considered properties, giving the lowest cumulative mean absolute errors. These methods are therefore suggested for an accurate and fast evaluation of energetic parameters related to an antioxidant activity via free radical scavenging.     

Isolation, Mapping, and Functional Expression of the Mouse X Chromosome Glycerol Kinase Gene

Glycerol kinase (Gyk) participates in the metabolism of endogenously derived and dietary glycerol. Deficiency of the human enzyme activity is an X-linked recessive disorder with a clinical picture varying from childhood metabolic crisis to asymptomatic adults incidentally identified by hyperlipidemia screening (pseudohypertriglyceridemia). Gyk is a member of a small group of kinases termed ambiquitous enzymes that are found in the cytosol or as membrane-bound enzymes associated with the voltage-dependent anion channel of the mitochondrial outer membrane. It was recently reported that in humans there are X-linked and autosomal copies of Gyk sequences, both apparently functional genes and processed pseudogenes. To understand the role of Gyk in normal metabolism and the variable clinical features seen with Gyk deficiency, we have characterized the mouse Gyk gene. We present the sequence of a full-length mouse Gyk cDNA that is alternatively spliced in brain. The Gyk gene was mapped to the mouse X chromosome by both fluorescencein situhybridization and an interspecies backcross panel, demonstrating conservation of synteny withdmd.To confirm the functional identity of the cDNA, transient transfection of the cDNA into COS7 cells was shown to cause a marked elevation in glycerol kinase activity.     

Inferring the temperature dependence of population parameters: the effects of experimental design and inference algorithm

Understanding and quantifying the temperature dependence of population parameters, such as intrinsic growth rate and carrying capacity, is critical for predicting the ecological responses to environmental change. Many studies provide empirical estimates of such temperature dependencies, but a thorough investigation of the methods used to infer them has not been performed yet. We created artificial population time series using a stochastic logistic model parameterized with the Arrhenius equation, so that activation energy drives the temperature dependence of population parameters. We simulated different experimental designs and used different inference methods, varying the likelihood functions and other aspects of the parameter estimation methods. Finally, we applied the best performing inference methods to real data for the species Paramecium caudatum. The relative error of the estimates of activation energy varied between 5% and 30%. The fraction of habitat sampled played the most important role in determining the relative error; sampling at least 1% of the habitat kept it below 50%. We found that methods that simultaneously use all time series data (direct methods) and methods that estimate population parameters separately for each temperature (indirect methods) are complementary. Indirect methods provide a clearer insight into the shape of the functional form describing the temperature dependence of population parameters; direct methods enable a more accurate estimation of the parameters of such functional forms. Using both methods, we found that growth rate and carrying capacity of Paramecium caudatum scale with temperature according to different activation energies. Our study shows how careful choice of experimental design and inference methods can increase the accuracy of the inferred relationships between temperature and population parameters. The comparison of estimation methods provided here can increase the accuracy of model predictions, with important implications in understanding and predicting the effects of temperature on the dynamics of populations.     

Functional Inferences from Blind ab Initio Protein Structure Predictions

Ab initio protein structure prediction methods have improved dramatically in the past several years. Because these methods require only the sequence of the protein of interest, they are potentially applicable to the open reading frames in the many organisms whose sequences have been and will be determined. Ab initio methods cannot currently produce models of high enough resolution for use in rational drug design, but there is an exciting potential for using the methods for functional annotation of protein sequences on a genomic scale. Here we illustrate how functional insights can be obtained from low-resolution predicted structures using examples from blind ab initio structure predictions from the third and fourth critical assessment of structure prediction (CASP3, CASP4) experiments.     

Importance of multi-dimensional analyses of resource partitioning in highly mobile species assemblages

Resource partitioning is an essential mechanism enabling species coexistence. The resources that are used by an animal are linked to its morphology and ecology. Therefore, similar species should use similar resources. The ecological niche of an individual summarizes all used resources and is therefore composed of several dimensions. Many methods are established to study different dimensions of an animal's niche. The aim of this study was to demonstrate that a combination of suitable methods is needed to study spatial and dietary resource partitioning of sympatric species in detail. We hypothesized that, while each individual method might identify differences between species, the combined results of several methods will lead to a more complete picture of spatial and dietary resource partitioning. As model organisms we chose the sympatric insectivorous bat species Myotis bechsteinii, M. nattereri, and P. auritus. We examined horizontal habitat use by telemetry, vertical habitat use by measuring δ¹³C, trophic position by measuring δ¹⁵N in wing membrane, and diet composition by molecular fecal analysis. Our results show that each method is able to provide information about spatial/dietary resource partitioning. However, considering further dimensions by combining several methods allows a more comprehensive assessment of dietary and spatial resource partitioning in bats.     

When assumptions on visual system evolution matter: nestling colouration and parental visual performance in birds

Comparative studies in visual ecology of birds often rely on several assumptions on the evolution of avian vision. In this study, we show that when these assumptions are not upheld, conclusions may be strongly affected. To illustrate this purpose, we reanalysed the data of Avilés & Soler (J. Evol. Biol. 22 : 376–386, 2009) who demonstrated that nestling gape colouration in altricial birds is associated with visual system. We show that a slight change in analysis methodology leads to opposite conclusions. Such conflicting result raises the problem of applying powerful methods developed for continuous variables to a small sample and a small number of independent events of qualitative visual system shift in comparative analyses. Further, we show that the current trend to assume strong phylogenetic inertia of avian visual systems is contradicted by data and that the sequencing of the SWS1 opsin gene should be considered as an alternative approach.