On Two Measures of Unbalancedness in a One-Way Model and Their Relation to Efficiency

This paper discusses two measures of unbalancedness in a one-way model and shows that for a given statistical procedure they may serve as measures of efficiency of a design. They also allow to compare for example estimation methods for variance components in designs with a fixed level of unbalancedness.     

Automated Analysis and Reannotation of Subcellular Locations in Confocal Images from the Human Protein Atlas

The Human Protein Atlas contains immunofluorescence images showing subcellular locations for thousands of proteins. These are currently annotated by visual inspection. In this paper, we describe automated approaches to analyze the images and their use to improve annotation. We began by training classifiers to recognize the annotated patterns. By ranking proteins according to the confidence of the classifier, we generated a list of proteins that were strong candidates for reexamination. In parallel, we applied hierarchical clustering to group proteins and identified proteins whose annotations were inconsistent with the remainder of the proteins in their cluster. These proteins were reexamined by the original annotators, and a significant fraction had their annotations changed. The results demonstrate that automated approaches can provide an important complement to visual annotation.     

Subcellular Distribution of Free Amino Acids in Relation to Protein Synthesis in Cells of Chara corallina

The influence of protein-synthesis inhibitors on the subcellular distribution of free amino acids was studied in internodal cells of Chara corallina. Use of an intracellular perfusion technique allowed separate measurements of amino acids in the vacuole, in the flowing sol endoplasm and in the gel layer. The sol endoplasm predominantly represents the cytosol, while the gel layer is occupied, for the most part, by chloroplasts. When cells were treated with 0.5 mM chloramphenicol (CRP) in the dark, both the total concentration of amino acids and the subcellular distribution were almost the same as in cells without treatment. In the light, however, the subcellular distribution changed dramatically, although the total concentration of amino acids was unchanged. The vacuolar concentration of amino acids was 3 times greater in CRP-treated cells than in the control. The concentrations of amino acids in the sol endoplasm and in the gel layer were only half of those in the control. Amino acid permeability of the chloroplast envelope, measured using the perfused internodal cells, slightly increased after the CRP treatment in the light. Time-dependent changes in concentrations of amino acids in the CRP-treated cells were also measured in the light. The total concentration of amino acids in the cytoplasm gradually decreased, while that in the vacuole increased commensurately. The concentration and/or subcellular distribution of alanine, glutamine, glutamate and glycine changed dramatically. The concentration of alanine increased considerably both in the vacuole and in the cytoplasm. The cytoplasmic concentration of glutamine increased transiently within 1 ?2 h after treatment with CRP. The cytoplasmic concentrations of glutamate and glycine decreased. Although the concentrations of some amino acids changed so markedly both in the vacuole and cytoplasm, only small differences in the activities of glutamic-pyruvic transaminase, glutamic-oxaloacetic transaminase and glutamine synthetase were detected between the control and the CRP-treated cells.     

Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins

Protein subcellular localization has been systematically characterized in budding yeast using fluorescently tagged proteins. Based on the fluorescence microscopy images, subcellular localization of many proteins can be classified automatically using supervised machine learning approaches that have been trained to recognize predefined image classes based on statistical features. Here, we present an unsupervised analysis of protein expression patterns in a set of high-resolution, high-throughput microscope images. Our analysis is based on 7 biologically interpretable features which are evaluated on automatically identified cells, and whose cell-stage dependency is captured by a continuous model for cell growth. We show that it is possible to identify most previously identified localization patterns in a cluster analysis based on these features and that similarities between the inferred expression patterns contain more information about protein function than can be explained by a previous manual categorization of subcellular localization. Furthermore, the inferred cell-stage associated to each fluorescence measurement allows us to visualize large groups of proteins entering the bud at specific stages of bud growth. These correspond to proteins localized to organelles, revealing that the organelles must be entering the bud in a stereotypical order. We also identify and organize a smaller group of proteins that show subtle differences in the way they move around the bud during growth. Our results suggest that biologically interpretable features based on explicit models of cell morphology will yield unprecedented power for pattern discovery in high-resolution, high-throughput microscopy images.     

Genome-Wide Patterns of Genetic Variation within and among Alternative Selective Regimes

Environmental heterogeneity has been hypothesized to influence levels of genetic variation but the effect of heterogeneity depends on (i) the form of heterogeneity, (ii) whether ecologically relevant or neutral loci are being considered, and (iii) the genetic basis of ecological adaptation. We surveyed genome-wide SNP diversity in replicate experimental Drosophila melanogaster populations with equal census sizes that evolved for 42 generations under one of four selection regimes: (i) salt-enriched environment (Salt), (ii) cadmium-enriched environment (Cad), (iii) temporally (Temp) or (iv) spatially (Spatial) variable environments. There was significant differentiation between all pairs of treatments but the greatest differentiation occurred between the two homogenous treatments (Cad and Salt). For sites likely under differential ecological selection (and those closely linked to them), the pattern of within-population diversity π followed the expectation from classic antagonistic selection theory: Spatial>Temp>Salt≈Cad. However, neutral diversity unlinked to selected sites followed a different pattern: Spatial>Salt≈Cad>Temp. As implicated by the latter result, measures of F_ST among replicate populations within treatments are consistent with differences in effective population sizes among selective regimes despite equal census sizes. Though there are clear changes in the rank order of treatments when contrasting selected and neutral sites with respect to π, the rank ordering of treatments with respect to F_ST appears reasonably consistent between site categories. These results demonstrate that alternative selective regimes affect within- and among-population diversity differently for different site types.     

Birth and Rapid Subcellular Adaptation of a Hominoid-Specific CDC14 Protein

Gene duplication was prevalent during hominoid evolution, yet little is known about the functional fate of new ape gene copies. We characterized the CDC14B cell cycle gene and the functional evolution of its hominoid-specific daughter gene, CDC14Bretro. We found that CDC14B encodes four different splice isoforms that show different subcellular localizations (nucleus or microtubule-associated) and functional properties. A microtubular CDC14B variant spawned CDC14Bretro through retroposition in the hominoid ancestor 18–25 million years ago (Mya). CDC14Bretro evolved brain-/testis-specific expression after the duplication event and experienced a short period of intense positive selection in the African ape ancestor 7–12 Mya. Using resurrected ancestral protein variants, we demonstrate that by virtue of amino acid substitutions in distinct protein regions during this time, the subcellular localization of CDC14Bretro progressively shifted from the association with microtubules (stabilizing them) to an association with the endoplasmic reticulum. CDC14Bretro evolution represents a paradigm example of rapid, selectively driven subcellular relocalization, thus revealing a novel mode for the emergence of new gene function.     

Spatial Variation in Population Structure and Its Relation to Movement and the Potential for Dispersal in a Model Intertidal Invertebrate

Dispersal, the movement of an individual away from its natal or breeding ground, has been studied extensively in birds and mammals to understand the costs and benefits of movement behavior. Whether or not invertebrates disperse in response to such attributes as habitat quality or density of conspecifics remains uncertain, due in part to the difficulties in marking and recapturing invertebrates. In the upper Bay of Fundy, Canada, the intertidal amphipod Corophium volutator swims at night around the new or full moon. Furthermore, this species is regionally widespread across a large spatial scale with site-to-site variation in population structure. Such variation provides a backdrop against which biological determinants of dispersal can be investigated. We conducted a large-scale study at nine mudflats, and used swimmer density, sampled using stationary plankton nets, as a proxy for dispersing individuals. We also sampled mud residents using sediment cores over 3 sampling rounds (20–28 June, 10–17 July, 2–11 August 2010). Density of swimmers was most variable at the largest spatial scales, indicating important population-level variation. The smallest juveniles and large juveniles or small adults (particularly females) were consistently overrepresented as swimmers. Small juveniles swam at most times and locations, whereas swimming of young females decreased with increasing mud presence of young males, and swimming of large juveniles decreased with increasing mud presence of adults. Swimming in most stages increased with density of mud residents; however, proportionally less swimming occurred as total mud resident density increased. We suggest small juveniles move in search of C. volutator aggregations which possibly act as a proxy for better habitat. We also suggest large juveniles and small adults move if potential mates are limiting. Future studies can use sampling designs over large spatial scales with varying population structure to help understand the behavioral ecology of movement, and dispersal in invertebrate taxa.     

Reproducible Peak Clusters on Differential Mouse Mortality Curves and Their Relation to the Gompertz Model

It is shown that differentiation of mouse mortality curves (number of animals that died at a certain age plotted versus their lifespan) results in the appearance of eight clearly distinguished clusters of peaks corresponding to increased mortality rates. Smoothing of the original mortality curves and subsequent transformation of the differential mortality curves according to the Gompertz model makes the peaks and the corresponding clusters less pronounced and drives the logarithm of the force mortality curve toward a straight line. The positions of the clusters on the lifespan axis (expressed in days) were calculated as weighted means by dividing the sum of the products of multiplication of the peak heights and their position on the lifespan axis by the sum of the peak heights within a cluster. To prove that the peaks and their clusters are not random, we have demonstrated that the positions of the clusters on the lifespan axis do not depend on the extent of mortality curve smoothing or the group of mice analyzed.     

Subcellular Location and Expression of Tobacco Necrosis Necrovirus p7a Protein

A putative movement protein (p7a) of tobacco necrosis Necrovirus , strain D (TNV-D), produced in Escherichia coli using an expression vector, was used to raise an antiserum. Immunoblot analysis using this antiserum showed that the p7a protein was detectable only in the combined cell wall and cell membrane fraction prepared from TNV-D infected Phaseolus vulgaris leaves. The p7a protein was detectable 1 day after inoculation and reached a maximum 3 days later, before declining, whereas coat protein was not detectable until 3 days after inoculation and continued to increase in concentration for a further 2 days before declining. Differences in the detectable amounts of both proteins may reflect their differential stability in extracts from necrotic tissue and/or the transient expression of the putative movement protein early in the replication cycle of TNV-D.     

Parallel Patterns of Morphological and Behavioral Variation among Host-Associated Populations of Two Gall Wasp Species

A powerful approach to address the general factors contributing to ecological speciation is to compare distantly related taxa that inhabit the same selective environments. In this design, similarities among taxa can elucidate general mechanisms of the process whereas differences may uncover specific factors important to the process for individual taxa. Herein, we present evidence of parallel patterns of morphological and behavioral variation among host-associated populations of two species of cynipid gall wasps, Belonocnema treatae and Disholcaspis quercusvirens, that each exhibit a life cycle intimately tied to the same two host plant environments, Quercus geminata and Q. virginiana. Across both gall-former species we find consistent differences in body size and gall morphology associated with host plant use, as well as strong differences in host plant preference, a measure of habitat isolation among populations. These consistent differences among taxa highlight the important role of host plant use in promoting reproductive isolation and morphological variation among herbivorous insect populations–a prerequisite for ecological speciation.     

Demographic and Genetic Patterns of Variation among Populations of Arabidopsis thaliana from Contrasting Native Environments

Background

Understanding the relationship between environment and genetics requires the integration of knowledge on the demographic behavior of natural populations. However, the demographic performance and genetic composition of Arabidopsis thaliana populations in the species'' native environments remain largely uncharacterized. This information, in combination with the advances on the study of gene function, will improve our understanding on the genetic mechanisms underlying adaptive evolution in A. thaliana.

Methodology/Principal Findings

We report the extent of environmental, demographic, and genetic variation among 10 A. thaliana populations from Mediterranean (coastal) and Pyrenean (montane) native environments in northeast Spain. Geographic, climatic, landscape, and soil data were compared. Demographic traits, including the dynamics of the soil seed bank and the attributes of aboveground individuals followed over a complete season, were also analyzed. Genetic data based on genome-wide SNP markers were used to describe genetic diversity, differentiation, and structure. Coastal and montane populations significantly differed in terms of environmental, demographic, and genetic characteristics. Montane populations, at higher altitude and farther from the sea, are exposed to colder winters and prolonged spring moisture compared to coastal populations. Montane populations showed stronger secondary seed dormancy, higher seedling/juvenile mortality in winter, and initiated flowering later than coastal populations. Montane and coastal regions were genetically differentiated, montane populations bearing lower genetic diversity than coastal ones. No significant isolation-by-distance pattern and no shared multilocus genotypes among populations were detected.

Conclusions/Significance

Between-region variation in climatic patterns can account for differences in demographic traits, such as secondary seed dormancy, plant mortality, and recruitment, between coastal and montane A. thaliana populations. In addition, differences in plant mortality can partly account for differences in the genetic composition of coastal and montane populations. This study shows how the interplay between variation in environmental, demographic, and genetic parameters may operate in natural A. thaliana populations.     

GFP与微管结合蛋白和肌动蛋白结合区融合蛋白载体构建与表达

以pCAMBIA1 30 0、pBA0 0 5、pActl D和pMECA等 4个质粒载体为基础 ,根据不同需要 ,选择特定的限制性内切酶作完全或部分酶切 ,通过多步骤的酶切、连接、转化等过程 ,构建完成 2个可通过农杆菌介导转化的植物表达载体。分别命名为 :pActl GFPTALIN和pActl GFP2 MAP4BD。在洋葱表皮细胞中的瞬间表达结果显示 ,两个载体均可正常工作。     

Behavioral Effects of Nightmares and Their Correlations to Personality Patterns

Factors affecting or inducing nightmares have been investigated repeatedly. However, little research is carried out on the behavioral consequences of nightmares. The present study thus served to investigate behavioral effects of nightmares in correlation to personality variables. 41 non-clinical participants, who suffer from about 2 nightmares per month recorded their dreams and nightmares over a 4-week period. A nightmare was defined as a dream that frightens the dreamer and could be recalled in detail on awakening. Anxiety and mood were monitored every morning. All nightmares and their behavioral consequences were noted on a questionnaire. Personality traits and life events were assessed at the beginning of the investigation. 100 nightmares were reported by the subjects over the 4-week period (range: 0–8). Following a nightmare, the subjects were significantly more anxious and were of a less stable mental condition compared to nights without nightmares. Additionally, nightmares induced physical complaints. This was considered to be an indicator that something was wrong in their lives and induced them to solve personal problems. The behavioral effects were most pronounced in subjects scoring high on neuroticism and on the number of physical complaints and low on achievement orientation and openness. The results suggest that sufferers of nightmares intend to change their lives, especially those with a neurotic-like personality.     

Patterns of Variation in the Rdna Cistron within and among World Populations of a Mosquito, Aedes Albopictus (Skuse)

A restriction map was constructed of the ribosomal cistron in a mosquito, Aedes albopictus (Skuse). The 18s, 28s and nontranscribed spacer (NTS) regions were subcloned and used to probe for intraspecific variation. Seventeen populations were examined throughout the world range of the species. No variation was detected in the coding regions but extensive and continuous variation existed in the NTS. The NTS consisted of two nonhomologous regions. The first region contained multiple 190-bp AluI repeats nested within larger XhoI repeats of various sizes. There was a large number of length variants in the AluI repeat region of the NTS. No repeats were found in the second region and it gave rise to relatively fewer variants. An analysis of NTS diversity in individual mosquitoes indicated that most of the diversity arose at the population level. Discriminant analysis was performed on spacer types in individual mosquitoes and demonstrated that individuals within a population carried a unique set of spacers. In contrast with studies of the NTS in Drosophila populations, there seems to be little conservation of spacers in a population. The importance of molecular drive relative to drift and selection in the generation of local population differentiation is discussed.     

Microtubules in the epidermal cells of Carausius morosus (Br.). Their pattern and relation to pigment migration

The existence of one or several systems of microtubules, consisting of a central bundle that branches off towards the basal and distal ends of epidermal cells of Carausius morosus has been shown by indirect immuno-fluorescence microscopy using monospecific anti-tubulin. The pattern of microtubules coincides with the position of the ommochrome granules and their migration path during physiological colour change. The ommochrome granules stick to isolated bundles of microtubules. Small bundles of microtubules extend almost perpendicularly towards the apical cell membrane where they are attached. Distally they are covered by pore channels within the cuticle. Parallel to the basal cell membrane and in close contact with it, there are very small bundles of microtubules. These findings strongly support the idea that during physiological colour change the ommochrome granules migrate along a firmly fixed system of microtubules.