Analysis of patterned neuronal impulses and function of neuregulin

Compared to other cells, except neural cells, the biggest property of neural cells is to have a particular electrical activity in each cell itself. The activity that shows a specific pattern will carry different information as a history of each neural cell. At present, we have examined the roles of neural impulses and revealed that a synaptic plasticity can be controlled by different patterned neural activities, such as different frequencies or oscillation patterns. Even though neural cells have similar genetic backgrounds, different environments give cells different neural activities and finally different characters of cells. Current studies have revealed that a particular pattern of neural activity, e.g. frequency, could be effective in some diseases. In response to environmental changes occurring throughout development and adult life, the brain reorganizes itself by adjusting the pattern of activity. In some cases, a particular pattern of neural activity decides the neural fate and should be able to control brain function even in higher functions. In the future, in order to understand the role of activity patterns and mechanisms of fundamental information processing in the brain, it will be necessary that the meaning of patterns is explained from molecular, biological and morphological perspectives, i.e., not only with metaphysical "phenomena", but also at a physical "material" level.     

Social learning in animals: comparative analysis of different forms and levels

Social learning as one of the key concepts of cognitive ecology includes different forms of behavioural displays from relatively simple, such as "social release" and "stimulus enhancement" up to "teaching" and "cultural transmission" in animal communities. Rapid development of this fields resulted in some contradictions in methods and terminology. In this review different forms and levels of social learning are analyzed. Ecological aspects of social learning are connected with diet shaping, fear of predators and mate choice. The first aspect is the most studied but still discussible. Social learning being an intricate component of feeding behaviour matches with innate behaviour, imprinting as well as early associative learning. Investigation of cognitive aspects of social learning going back to Thorndike's crucial question "Do apes ape?" are now developing into series of questions including even: "Do ants ape?". Elaboration of universal methods of comparative studying of social learning such as "artificial fruit" and "two ways/one outcome" has essentially enlightened these questions and made comparative analysis possible. Large continuum of displays of cognitive skills in social learning has been revealed in non-primate species. One of the discussible issues in the role of social learning is distribution of innovations. Many authors have investigated this intriguing aspect of animal behaviour in different ways, such as long field observations as well as laboratory experiments based on "artificial innovators" that is specimens specially taught by experimentalists. Many impressive results were obtained; in particular it turned out in contradiction with some mathematical models that individuals in groups are rather different in their psychophysiological predisposition to innovative behaviour. Role of teaching in such different forms of behaviour as shaping of species-specific behavioural patterns and spread of innovations is considered. Although the majority of animals in wild populations are not good teachers and pupils, some cultural aspects of behaviour were recently revealed, mostly in primates. At the same time some classical results concerning cultural transmission of new patterns (for example, bottle-opening in tits) were experimentally revised. Many problems still remain unsolved, in particular, how spread of innovations may favour prosperity of populations; to what degree behavioural peculiarities of local groups may be determined by processes of social learning; which internal and external factors and under what circumstances invest into social learning in natural environment.     

Deconstructing death in paleodemography

In 1992 in this Journal (Konigsberg and Frankenberg [1992] Am. J. Phys. Anthropol. 89:235-256), we wrote about the use of maximum likelihood methods for the "estimation of age structure in anthropological demography." More specifically, we presented a particular method (the "iterated age-length key") from the fisheries literature and suggested that the method could be used in human and primate demography and paleodemography as well. In our paper (section titled "Some Future Directions"), we spelled out two broad areas that we expected to see develop over the ensuing years. First, we felt that the use of explicit likelihood methods would open up interest in basic estimation issues, such as the calculation of standard errors for demographic estimates and the formulation of tests for whether samples differed in their demographic structure. Second, we felt that the time was ripe for hazards analyses that would incorporate the uncertainty in estimation that follows from using age "indicators" rather than known ages. While some of these developments have occurred during the last decade, few have been reported in the American Journal of Physical Anthropology. In this paper we resolve some issues from our 1992 paper, and attempt to redress this deficit in the literature by reviewing some recent developments in paleodemography over the past decade.     

PLINK: a tool set for whole-genome association and population-based linkage analyses

Whole-genome association studies (WGAS) bring new computational, as well as analytic, challenges to researchers. Many existing genetic-analysis tools are not designed to handle such large data sets in a convenient manner and do not necessarily exploit the new opportunities that whole-genome data bring. To address these issues, we developed PLINK, an open-source C/C++ WGAS tool set. With PLINK, large data sets comprising hundreds of thousands of markers genotyped for thousands of individuals can be rapidly manipulated and analyzed in their entirety. As well as providing tools to make the basic analytic steps computationally efficient, PLINK also supports some novel approaches to whole-genome data that take advantage of whole-genome coverage. We introduce PLINK and describe the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation. In particular, we focus on the estimation and use of identity-by-state and identity-by-descent information in the context of population-based whole-genome studies. This information can be used to detect and correct for population stratification and to identify extended chromosomal segments that are shared identical by descent between very distantly related individuals. Analysis of the patterns of segmental sharing has the potential to map disease loci that contain multiple rare variants in a population-based linkage analysis.     

小鼠着床前胚胎发育中调控因子的时序表达及功能

哺乳动物着床前胚胎发育最基本的问题之一是高度分化的卵母细胞如何过渡到全能性的卵裂球。这一转换过程受到了多种调控因子正或负的调控作用,这些特定调控因子在着床前胚胎发育过程中呈现出较为显著的时空表达特征,它们对早期胚胎的进一步正常发育有重要的作用。研究这些调控因子在着床前胚胎发育中的表达模式和调控机制,将有助于我们对早期胚胎发育机制的进一步了解。作者主要对近些年来有关生长因子与细胞因子（如：PAF、IL－1、IGF、MIF）以及特定转录因子（如：SP1、TBP、mTEF、eIF、myc、c-jun等）在小鼠着床前胚胎发育中的时空表达及其相应功能的研究做一简要介绍。     

Cryptic variation in butterfly eyespot development: the importance of sample size in gene expression studies

Previous studies have shown that development can be robust to variation in parameters such as the timing or level of gene expression. This leads to the prediction that natural populations should be able to host developmental variation that has little phenotypic effect. Cryptic variation is of particular interest because it can result in selectable phenotypes when "released" by environmental or genetic factors. Currently, however, we have little idea of how variation is distributed between genes or over time in pattern formation processes. Here we survey expression of Notch (N), Spalt (Sal), and Engrailed (En) during butterfly eyespot determination to better understand how pattern formation may vary within a population. We observed substantial heterochronic variance in the progress of spatial expression patterns for all three proteins, suggesting some degree of developmental buffering in eyespot development. Peak variance for different proteins was found at both early and late stages of development, contrasting with previous models suggesting that the distribution of variance should be more temporally focused during pattern formation. We speculate that our observations are representative of a standing reservoir of cryptic variation that may contribute to phenotypic evolution under certain circumstances. Our results also provide a strong cautionary message that gene expression studies with limited sample sizes can be positively misleading in terms of inferring expression pattern time series, as well as for making cross-species phylogenetic comparisons.     

Linkage Disequilibrium in Humans: Models and Data

In this review, we describe recent empirical and theoretical work on the extent of linkage disequilibrium (LD) in the human genome, comparing the predictions of simple population-genetic models to available data. Several studies report significant LD over distances longer than those predicted by standard models, whereas some data from short, intergenic regions show less LD than would be expected. The apparent discrepancies between theory and data present a challenge-both to modelers and to human geneticists-to identify which important features are missing from our understanding of the biological processes that give rise to LD. Salient features may include demographic complications such as recent admixture, as well as genetic factors such as local variation in recombination rates, gene conversion, and the potential segregation of inversions. We also outline some implications that the emerging patterns of LD have for association-mapping strategies. In particular, we discuss what marker densities might be necessary for genomewide association scans.     

Using digital photography to study animal coloration

In understanding how visual signals function, quantifying the components of those patterns is vital. With the ever-increasing power and availability of digital photography, many studies are utilizing this technique to study the content of animal colour signals. Digital photography has many advantages over other techniques, such as spectrometry, for measuring chromatic information, particularly in terms of the speed of data acquisition and its relatively cheap cost. Not only do digital photographs provide a method of quantifying the chromatic and achromatic content of spatially complex markings, but also they can be incorporated into powerful models of animal vision. Unfortunately, many studies utilizing digital photography appear to be unaware of several crucial issues involved in the acquisition of images, notably the nonlinearity of many cameras' responses to light intensity, and biases in a camera's processing of the images towards particular wavebands. In the present study, we set out step-by-step guidelines for the use of digital photography to obtain accurate data, either independent of any particular visual system (such as reflection values), or for particular models of nonhuman visual processing (such as that of a passerine bird). These guidelines include how to: (1) linearize the camera's response to changes in light intensity; (2) equalize the different colour channels to obtain reflectance information; and (3) produce a mapping from camera colour space to that of another colour space (such as photon catches for the cone types of a specific animal species).  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 211–237.     

Perception of temporally interleaved ambiguous patterns

BACKGROUND: Continuous viewing of ambiguous patterns is characterized by wavering perception that alternates between two or more equally valid visual solutions. However, when such patterns are viewed intermittently, either by repetitive presentation or by periodic closing of the eyes, perception can become locked or "frozen" in one configuration for several minutes at a time. One aspect of this stabilization is the possible existence of a perceptual memory that persists during periods in which the ambiguous stimulus is absent. Here, we use a novel paradigm of temporally interleaved ambiguous stimuli to explore the nature of this memory, with particular regard to its potential impact on perceptual organization. RESULTS: We found that the persistence of a perceptual configuration was robust to interposed visual patterns, and, further, that at least three ambiguous patterns, when interleaved in time, could undergo parallel, stable time courses. Then, using an interleaved presentation paradigm, we established that the occasional reversal in one pattern could be coupled with that of its interleaved counterpart, and that this coupling was a function of the structural similarity between the patterns. CONCLUSIONS: We postulate that the stabilization observed with repetitive presentation of ambiguous patterns can be at least partially accounted for by processes that retain a recent perceptual interpretation, and we speculate that such memory may be important in natural vision. We further propose that the interleaved paradigm introduced here may be of great value to gauge aspects of stimulus similarity that appeal to particular mechanisms of perceptual organization.     

On the meanings of nestedness: back to the basics

The ecological concepts of nestedness and β‐diversity first appeared more than five decades ago, but there is still controversy over their precise meaning and application. Here, we focus on the concept of nestedness, the ordered loss of species along environmental or ecological gradients. Because there is no species replacement if the distribution of species among a number of sites is perfectly nested, some studies have defined nestedness as the inverse of species turnover. We argue that such a redefinition relies on a misinterpretation of the original concept of nestedness as the inverse of species replacement. Such a narrow interpretation might result in misleading conclusions about the mechanisms regulating species distribution patterns. We argue, in particular, that any quantification of nestedness must be as explicit as possible about the gradient to be analyzed.     

Neuroethological approaches to the study of motor development in chicks: achievements and challenges.

Chicks and chick embryos provide a useful model system for the study of issues related to the development of motor behaviors. EMG and kinematic analyses of leg movements have been used to provide new data on the organization of embryonic motility. These data suggest that the circuitry needed to produce a basic, coordinated motor pattern is available early in development. This circuitry then appears to be retained throughout life. Evidence from analysis of EMG patterns and leg deafferentation studies suggest that the output of this basic circuit can be modulated by sensory input to produce the motor patterns of later behaviors, such as hatching and walking. If the same circuitry is present throughout life, then mechanisms for initiation and termination of particular behaviors must be available to ensure that specific behaviors are turned on and off at appropriate times. For example, hatching can be turned on by a specific sensory signal: proprioceptive signals from the bent neck. In addition to reviewing current research on the development of chick motor behaviors, methodological considerations and suggestions for future research are presented.     

Use of LCA as a development tool within early research: challenges and issues across different sectors

Purpose

The aim of this paper is to highlight the challenges that face the use of life cycle assessment (LCA) for the development of emerging technologies. LCA has great potential for driving the development of products and processes with improved environmental credentials when used at the early research stage, not only to compare novel processing with existing commercial alternatives but to help identify environmental hotspots. Its use in this way does however provide methodological and practical difficulties, often exacerbated by the speed of analysis required to enable development decisions to be made. Awareness and understanding of the difficulties in such cases is vital for all involved with the development cycle.

Methods

This paper employs three case studies across the diverse sectors of nanotechnology, lignocellulosic ethanol (biofuel), and novel food processes demonstrating both the synergy of issues across different sectors and highlighting the challenges when applying LCA for early research. Whilst several researchers have previously highlighted some of the issues with use of LCA techniques at an early stage, most have focused on a specific product, process development, or sector. The use of the three case studies here is specifically designed to highlight conclusively that such issues are prevalent to use of LCA in early research irrespective of the technology being assessed.

Results and discussion

The four focus areas for the paper are system boundaries, scaling issues, data availability, and uncertainty. Whilst some of the issues identified will be familiar to all LCA practitioners as problems shared with standard LCAs, their importance and difficulty is compounded by factors distinct to novel processes as emerging technology is often associated with unknown future applications, unknown industrial scales, and wider data gaps that contribute to the level of LCA uncertainty. These issues, in addition with others that are distinct to novel applications, such as the challenges of comparing laboratory scale data with well-established commercial processing, are exacerbated by the requirement for rapid analysis to enable development decisions to be made.

Conclusions

Based on the challenges and issues highlighted via illustration through the three case studies, it is clear that whilst transparency of information is paramount for standard LCAs, the sensitivities, complexities, and uncertainties surrounding LCAs for early research are critical. Full reporting and understanding of these must be established prior to utilising such data as part of the development cycle.     

High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups

We recently proposed that patterns of evolution of non-LTR retrotransposable elements can be used to study patterns of spontaneous mutation. Transposition of non-LTR retrotransposable elements commonly results in creation of 5' truncated, "dead-on-arrival" copies. These inactive copies are effectively pseudogenes and, according to the neutral theory, their molecular evolution ought to reflect rates and patterns of spontaneous mutation. Maximum parsimony can be used to separate the evolution of active lineages of a non-LTR element from the fate of the "dead-on-arrival" insertions and to directly assess the relative frequencies of different types of spontaneous mutations. We applied this approach using a non-LTR element, Helena, in the Drosophila virilis group and have demonstrated a surprisingly high incidence of large deletions and the virtual absence of insertions. Based on these results, we suggested that Drosophila in general may exhibit a high rate of spontaneous large deletions and have hypothesized that such a high rate of DNA loss may help to explain the puzzling dearth of bona fide pseudogenes in Drosophila. We also speculated that variation in the rate of spontaneous deletion may contribute to the divergence of genome size in different taxa by affecting the amount of superfluous "junk" DNA such as, for example, pseudogenes or long introns. In this paper, we extend our analysis to the D. melanogaster subgroup, which last shared a common ancestor with the D. virilis group approximately 40 MYA. In a different region of the same transposable element, Helena, we demonstrate that inactive copies accumulate deletions in species of the D. melanogaster subgroup at a rate very similar to that of the D. virilis group. These results strongly suggest that the high rate of DNA loss is a general feature of Drosophila and not a peculiar property of a particular stretch of DNA in a particular species group.      

Landscape issues in plant ecology

In the last decade, we have seen the emergence and consolidation of a conceptual framework that recognizes the landscape as an ecological unit of interest. Plant ecologists have long emphasized landscape-scale issues, but there has been no recent attempt to define how landscape concepts are now integrated in vegetation studies. To help define common research paradigms in both landscape and plant ecology, we discuss issues related to three main landscape concepts in vegetation researches, reviewing theoretical influences and emphasizing recent developments. We first focus on environmental relationships, documenting how vegetation patterns emerge from the influence of local abiotic conditions. The landscape is the physical environment. Disturbances are then considered, with a particular attention to human-driven processes that often overrule natural dynamics. The landscape is a dynamic space. As environmental and historical processes generate heterogeneous patterns, we finally move on to stress current evidence relating spatial structure and vegetation dynamics. This relates to the concept of a landscape as a patch-corridor-matrix mosaic. Future challenges involve: 1) the capacity to evaluate the relative importance of multiple controlling processes at broad spatial scale; 2) better assessment of the real importance of the spatial configuration of landscape elements for plant species and finally; 3) the integration of natural and cultural processes and the recognition of their interdependence in relation to vegetation management issues in human landscapes.     

An algorithm for constructing local regions in a phylogenetic network

The groupings of taxa in a phylogenetic tree cannot represent all the conflicting signals that usually occur among site patterns in aligned homologous genetic sequences. Hence a tree-building program must compromise by reporting a subset of the patterns, using some discriminatory criterion. Thus, in the worst case, out of possibly a large number of equally good trees, only an arbitrarily chosen tree might be reported by the tree-building program as "The Tree." This tree might then be used as a basis for phylogenetic conclusions. One strategy to represent conflicting patterns in the data is to construct a network. The Buneman graph is a theoretically very attractive example of such a network. In particular, a characterization for when this network will be a tree is known. Also the Buneman graph contains each of the most parsimonious trees indicated by the data. In this paper we describe a new method for constructing the Buneman graph that can be used for a generalization of Hadamard conjugation to networks. This new method differs from previous methods by allowing us to focus on local regions of the graph without having to first construct the full graph. The construction is illustrated by an example.     

Exploring links between physiology and ecology at macro-scales: the role of respiratory metabolism in insects

The relationships between macro-ecological patterns and physiological investigations in insects, especially those dealing with respiratory metabolism, are assessed in an attempt to encourage the development of the interaction between macroecology and physiological ecology. First, we demonstrate that although physiological ecology has been explicitly concerned with a number of issues relating to species boundaries, many questions remain unanswered. We argue that there are essentially two ways in which the relationship between physiological tolerances and species range boundaries have been investigated. The correlational approach involves physiological inference, physiological prediction, isocline analyses and climatic matching, and has often been criticized for a lack of rigour, while the experimental approach seeks to examine experimentally the relationships between physiological variables and range edges. Second, we use the recent debate on processes underlying latitudinal patterns in body size to caution against the conflation of patterns and processes operating at intraspecific and interspecific levels, the dangers inherent in invoking single explanatory variables, and an undue focus on adaptationist (e.g. optimization) rather than nonadaptationist explanations or some combination of the two. We show that both positive and negative relationships between body size and latitude have been found at the intraspecific level and suggest that interactions between temperature-induced heterochrony, and the relationship between habitat durational stability, growing season length, and generation time can be used to explain these differences. Similar variation in documented patterns is demonstrated at the interspecific level, and the mechanisms usually proffered to explain such clines (especially the starvation/desiccation-resistance hypothesis) are discussed. Interactions between various environmental factors, such as host-plant quality, and their effects on size clines are also discussed. Third, we argue that respiratory metabolism, as a measure of ATP cost, and its spatio-temporal variation are critical to many explanations of macroecological patterns. Adaptive changes in metabolism reputedly involve both depression (stress resistance) and elevation of metabolic rate, although recent studies are increasingly calling these ideas into question. In particular, flow-through respirometry is revolutionizing results by allowing careful separation of resting (or standard) and active metabolic rates. These techniques have rarely been applied to studies of metabolic cold adaptation in insects, one of the most polemical adaptations ascribed to high-latitude and high-altitude species. We conclude by arguing that physiological investigations of species tolerances are important in the context of macroecology, especially species distributional patterns and the possible impact of climate change thereon. However, we caution that relationships between abiotic variables, species tolerances, and distributional ranges may be non-linear and subject to considerable modification by the presence of other species, and that many of the pressing questions posed by macroecology have not been addressed by insect physiologists. Nonetheless, we suggest that because an understanding of the dynamics of species distributions is of considerable importance, especially in the context of current conservation problems, insect physiological ecology has much future scope.     

"ALL TREE HISTOGRAMS" AND THE EVALUATION OF CLADISTIC EVIDENCE: SOME AMBIGUITIES

Abstract— Inspection of trees of varying lengths (by the option ALL TREES, which produces a histogram for tree lengths in PAUP 3.0) has been used to evaluate cladistic data and results. For example, a result may be judged more effective if the groups supported in the most parsimonious tree are preserved in trees that require increasingly greater amounts of homoplasy. Evaluation of grouping purely on the basis of this stability criterion ignores other highly relevant aspects of cladistic results. In particular, some data sets may incorporate additional taxa that introduce homoplasy to the shortest tree in a manner that concurrently allows for a revised understanding of character optimization patterns. These taxa may render groups preserved in the shortest tree less stable, but this result is not necessarily deficient if the homoplasy underlying such instability reveals possible character state changes for the given taxa irretrievable from the original matrix. The hypothetical example described here is relevant to so called "stem", "basal" or "plesiomorphic sister" taxa that are commonly considered in studies of both fossil and extant taxa.     

Critical comparison of consensus methods for molecular sequences.

Consensus methods are recognized as valuable tools for data analysis, especially when some sort of data aggregation is desired. Although consensus methods for sequences play a vital role in molecular biology, researchers pay little heed to the features and limitations of such methods, and so there are risks that criteria for constructing consensus sequences will be misused or misunderstood. To understand better the issues involved, we conducted a critical comparison of nine consensus methods for sequences, of which eight were used in papers appearing in this journal. We report the results of that comparison, and we make recommendations which we hope will assist researchers when they must select particular consensus methods for particular applications.