Exploiting protein structure data to explore the evolution of protein function and biological complexity

New directions in biology are being driven by the complete sequencing of genomes, which has given us the protein repertoires of diverse organisms from all kingdoms of life. In tandem with this accumulation of sequence data, worldwide structural genomics initiatives, advanced by the development of improved technologies in X-ray crystallography and NMR, are expanding our knowledge of structural families and increasing our fold libraries. Methods for detecting remote sequence similarities have also been made more sensitive and this means that we can map domains from these structural families onto genome sequences to understand how these families are distributed throughout the genomes and reveal how they might influence the functional repertoires and biological complexities of the organisms. We have used robust protocols to assign sequences from completed genomes to domain structures in the CATH database, allowing up to 60% of domain sequences in these genomes, depending on the organism, to be assigned to a domain family of known structure. Analysis of the distribution of these families throughout bacterial genomes identified more than 300 universal families, some of which had expanded significantly in proportion to genome size. These highly expanded families are primarily involved in metabolism and regulation and appear to make major contributions to the functional repertoire and complexity of bacterial organisms. When comparisons are made across all kingdoms of life, we find a smaller set of universal domain families (approx. 140), of which families involved in protein biosynthesis are the largest conserved component. Analysis of the behaviour of other families reveals that some (e.g. those involved in metabolism, regulation) have remained highly innovative during evolution, making it harder to trace their evolutionary ancestry. Structural analyses of metabolic families provide some insights into the mechanisms of functional innovation, which include changes in domain partnerships and significant structural embellishments leading to modulation of active sites and protein interactions.     

Using multilayer network analysis to explore the temporal dynamics of collective behavior

Social organisms often show collective behaviors such as group foraging or movement.Collective behaviors can emerge from interactions between group members and may depend on the behavior of key individuals.When social interactions change over time,collective behaviors may change because these behaviors emerge from interactions among individuals.Despite the importance of,and growing interest in,the temporal dynamics of social interactions,it is not clear how to quantify changes in interactions over time or measure their stability.Furthermore,the temporal scale at which we should observe changes in social networks to detect biologically meaningful changes is not always apparent.Here we use multilayer network analysis to quantify temporal dynamics of social networks of the social spider Stegodyphus dumicola and determine how these dynamics relate to individual and group behaviors.We found that social interactions changed over time at a constant rate.Variation in both network structure and the identity of a keystone individual was not related to the mean or variance of the collective prey attack speed.Individuals that maintained a large and stable number of connections,despite changes in network structure,were the boldest individuals in the group.Therefore,social interactions and boldness are linked across time,but group collective behavior is not influenced by the stability of the social network.Our work demonstrates that dynamic social networks can be modeled in a multilayer framework.This approach may reveal biologically important temporal changes to social structure in other systems.     

Unmanned aircraft systems to unravel spatial and temporal factors affecting dynamics of colony formation and nesting success in birds

Collecting information of ecological and behavioural processes often requires continuous field monitoring, however, reiterative human presence necessary to obtain monitoring data can disturb both the environment and the study species. An example of this phenomenon is the monitoring of the formation and dynamics of seabird colonies; one of the reasons for colony failure is disturbances caused by the presence of researchers or conservation managers during data collection. In this study, an unmanned aircraft system (UAS) was used throughout the breeding period to monitor the temporal and spatial dynamics of a black‐headed gull colony in the interior of a difficult‐to‐access island. This methodology permitted weekly visits to the colony without disturbance, which allowed for the continuous collection of spatial and temporal data on the process of colony formation. We obtained detailed information about nesting success and its relation with the distance to the nearest incubating neighbour, as well as the colony boundary along breeding season. Thus, we successfully monitored the dynamics of a bird colony and identified factors affecting individual decision making in colony formation using a UAS.     

Adaptive wavelet analysis of oscillations in the human peripheral blood flow

The main principles are outlined for spectral timing analysis of the peripheral blood flow oscillations obtained by laser Doppler flowmetry. The oscillations can be studied in a wide frequency range both in stationary and nonstationary conditions during functional tests. The potential of the method has been demonstrated in experiments with the reaction of the microvascular bed to transcutaneous iontophoretic introduction of acetylcholine chloride. The major advantage of the method over conventional wavelet analysis is a significant increase in the “effective” length of the signal analyzed, which allows correct analysis of low-frequency components in much shorter LDF recordings than those commonly used.     

Exploiting the full power of temporal gene expression profiling through a new statistical test: Application to the analysis of muscular dystrophy data

Background  

The identification of biologically interesting genes in a temporal expression profiling dataset is challenging and complicated by high levels of experimental noise. Most statistical methods used in the literature do not fully exploit the temporal ordering in the dataset and are not suited to the case where temporal profiles are measured for a number of different biological conditions. We present a statistical test that makes explicit use of the temporal order in the data by fitting polynomial functions to the temporal profile of each gene and for each biological condition. A Hotelling T ²-statistic is derived to detect the genes for which the parameters of these polynomials are significantly different from each other.     

Multiple stressors: using the honeybee model BEEHAVE to explore how spatial and temporal forage stress affects colony resilience

The causes underlying the increased mortality of honeybee Apis mellifera colonies observed over the past decade remain unclear. Since so far the evidence for monocausal explanations is equivocal, involvement of multiple stressors is generally assumed. We here focus on various aspects of forage availability, which have received less attention than other stressors because it is virtually impossible to explore them empirically. We applied the colony model BEEHAVE, which links within‐hive dynamics and foraging, to stylized landscape settings to explore how foraging distance, forage supply, and “forage gaps”, i.e. periods in which honeybees cannot find any nectar and pollen, affect colony resilience and the mechanisms behind. We found that colony extinction was mainly driven by foraging distance, but the timing of forage gaps had strongest effects on time to extinction. Sensitivity to forage gaps of 15 days was highest in June or July even if otherwise forage availability was sufficient to survive. Forage availability affected colonies via cascading effects on queen's egg‐laying rate, reduction of new‐emerging brood stages developing into adult workers, pollen debt, lack of workforce for nursing, and reduced foraging activity. Forage gaps in July led to reduction in egg‐laying and increased mortality of brood stages at a time when the queen's seasonal egg‐laying rate is at its maximum, leading to colony failure over time. Our results demonstrate that badly timed forage gaps interacting with poor overall forage supply reduce honeybee colony resilience. Existing regulation mechanisms which in principle enable colonies to cope with varying forage supply in a given landscape and year, such as a reduction in egg‐laying, have only a certain capacity. Our results are hypothetical, as they are obtained from simplified landscape settings, but they are consistent with existing empirical knowledge. They offer ample opportunities for testing the predicted effects of forage stress in controlled experiments.     

IKONOS影像景观格局特征尺度的小波与半方差分析

建立不同方向和尺度下景观格局的小波分析方法,并以IKONOS PAN 1m 影像为例,对城市景观和农田景观格局进行了实例研究,并与半方差函数的分析结果进行比较分析。试验结果发现试验区的城市景观图像表现出不同层次和方向的结构特征,主要是阴影－单个楼房－楼房与道路的组合3个尺度的特征,分别出现在2m,16m和128m以及256m分析尺度上,农田景观主要是树木行－农田2个层次和方向尺度特征组合,分别为2m,128m和256m。半方差分析结果对试验区景观结构的多层次和方向不敏感,但可发现景观结构的总体平均特征。城市景观总体结构在空间上的变程为135m,反映的是楼房与道路组合的总体平均特征;农田景观总体结构在空间上的变程为152m。通过改变半方差函数的分析范围和计算间距可以克服半方差对多尺度分析的不足,如该试验通过缩小城市景观和农田分析范围,也发现城市景观有一个在空间结构上15m的变程,与小波分析的特征尺度16m非常接近,而农田景观出现空穴效应的周期一半长度大约为2m,正好是小波分析出种植树木的行距结构特征尺度的大小。这要分析者对研究有一定的先验知识才能够做到选择合适的分析范围,而这恰是景观格局特征尺度分析服务的目的。通过试验区研究证明小波分析是一非常有应用前景的景观格局研究方法,与半方差分析相比,对在解释多尺度结构和不同方向的结构具有明显的优势,且不受分析数据统计平稳假设的约束,但由于对图像分解是基于2进制,导致分析尺度以2的幂函数变化,不像半方差分析可通过理论模型拟合,对特征尺度的估计可以是连续的。     

Co-existence of three species of amphibious plants in relation to spatial and temporal variation: Field evidence

Changes in vegetation of Bushells Lagoon, a freshwater body fed intermittently by the Hawkesbury River in the Sydney basin, were studied over three scales of time: broad fluctuations in areas occupied by emergent plants over 28 years; fluctuations in their percentage cover over 21 months; and, over 6 months, seasonal variation in biomass of emergent plants of two native species Ludwigia peploides (Kunth) Raven ssp. montevidensis (Spreng.) Raven and Marsilea mutica Mett., and the introduced Myriophyllum aquaticum (Vellozo) Verde. Differences in distribution and abundance of plants observed between the three species were related to environmental variation in time and space. Wind and wave action varied along the shoreline, and emergent shoots of Myriophyllum were most abundant in sheltered conditions, floating leaves of Marsilea most abundant in relatively exposed conditions and emergent shoots of Ludwigia most abundant in somewhat intermediate conditions in the shallows. Chemical characteristics of the water varied in time but, unlike water temperature, had no obvious seasonal pattern. Seasonal change occurred in the biomass of Marsilea, and to a lesser extent in that of Myriophyllum, with smaller proportions of leaf material present in winter than in summer. Though water levels were apparently stable over a period of some years (1965–74), at other times they varied greatly through flooding and drought with related major change in cover of the three species. Co-existence of the three species in the lagoon may be related to differences between their plants in establishment and growth following disturbance (regeneration niche), tolerance of wind and wave action (habitat niche), or seasonal growth (phenological niche).     

High-resolution spatial and temporal analysis of phytoalexin production in oats

The production of oat (Avena sativa L.) phytoalexins, avenanthramides, occurs in response to elicitor treatment with oligo-N-acetylchitooligosaccharides. In this study, avenanthramides production was investigated by techniques that provide high spatial and temporal resolution in order to clarify the process of phytoalexin production at the cellular level. The amount of avenanthramides accumulation in a single mesophyll cell was quantified by a combination of laser micro-sampling and low-diffuse nanoflow liquid chromatography–electrospray ionization tandem mass spectrometry (LC–ESI-MS/MS) techniques. Avenanthramides, NAD(P)H and chlorophyll were also visualized in elicitor-treated mesophyll cells using line-scanning fluorescence microscopy. We found that elicitor-treated mesophyll cells could be categorized into three characteristic cell phases, which occurred serially over time. Phase 0 indicated the normal cell state before metabolic or morphological change in response to elicitor, in which the cells contained abundant NAD(P)H. In phase 1, rapid NAD(P)H oxidation and marked movement of chloroplasts occurred, and this phase was the early stage of avenanthramides biosynthesis. In phase 2, avenanthramides accumulation was maximized, and chloroplasts were degraded. Avenanthramides appear to be synthesized in the chloroplast, because a fluorescence signal originating from avenanthramides was localized to the chloroplasts. Moreover, our results indicated that avenanthramides biosynthesis and the hypersensitive response (HR) occurred in identical cells. Thus, the avenanthramides production may be one of sequential events programmed in HR leading to cell death. Furthermore, the phase of the defense response was different among mesophyll cells simultaneously treated with elicitor. These results suggest that individual cells may have different susceptibility to the elicitor. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Integrating spatial data and shorebird nesting locations to predict the potential future impact of global warming on coastal habitats: A case study on Farasan Islands,Saudi Arabia

One of the expected effects of the global warming is changing coastal habitats by accelerating the rate of sea level rise. Coastal habitats support large number of marine and wetland species including shorebirds (plovers, sandpipers and allies). In this study, we investigate how coastal habitats may be impacted by sea level rise in the Farasan Islands, Kingdom of Saudi Arabia. We use Kentish plover Charadrius alexandrinus – a common coastal breeding shorebird – as an ecological model species to predict the influence of sea level rise. We found that any rise of sea level is likely to inundate 11% of Kentish plover nests. In addition, 5% of the coastal areas of Farasan Islands, which support 26% of Kentish plover nests, will be flooded, if sea level rises by one metre. Our results are constrained by the availability of data on both elevation and bird populations. Therefore, we recommend follow-up studies to model the impacts of sea level rise using different elevation scenarios, and the establishment of a monitoring programme for breeding shorebirds and seabirds in Farasan Islands to assess the impact of climate change on their populations.     

基于小波变换的卧龙国家级自然保护区植被时空变化分析

提出一种基于小波变换从长时间序列、大范围遥感数据中快速、自动化检测植被动态变化的方法。以MODIS 500m空间分辨率,16d合成的NDVI数据为数据源,对受到2008年5月12日汶川地震严重影响的卧龙国家级自然保护区内2003年至2012年的植被动态变化进行时空分析,为保护生态多样性及生态系统的稳定性提供依据。研究表明:1)地震后保护区内植被指数减少的面积大范围增加,且波动较震前更为明显,统计分析结果能够更为直观地反映地震及其次生灾害等极端现象对该地区植被的破坏程度;2)保护区内植被指数极值变化多发生在夏季或秋季,较低海拔地区极值变化多发生在夏季,而在高海拔地区则多发生在秋季;3)在大熊猫最适宜栖息的区域(2600—2800m)植被指数极值减少量大于0.4的范围大于增加量大于0.4的范围,反映出植被在震后的恢复状况并没达到理想的水平。同时发现在该海拔区域范围内植被指数减少的面积在春夏两季较大,表明在该时间段卧龙地区大熊猫最适宜生存区域的植被情况较为不稳定,需更为关注其动态,采取适当的保护措施。     

Interactions of three sequentially expressed genes control temporal and spatial specificity in Aspergillus development

Aspergillus nidulans brlA, abaA, and wetA form a dependent pathway that regulates asexual reproductive development. The order in which these genes are expressed determines the outcome of development. Expression of brlA in vegetative cells leads to activation of abaA and wetA, cessation of vegetative growth, cellular vacuolization, and spore formation. By contrast, expression of abaA in vegetative cells does not result in conidial differentiation but does lead to activation of brlA and wetA, cessation of vegetative growth, and accentuated cellular vacuolization. brlA, abaA, and wetA act individually and together to regulate their own expression and that of numerous other sporulation-specific genes. We propose that the central pathway controlling development is largely autoregulatory. The timing and extent of expression of the regulatory genes and their targets are determined as development proceeds by intrinsically controlled changes in the relative concentrations of regulatory gene products in the various conidiophore cell types.     

Towards simultaneous analysis of morphological and molecular data in Hymenoptera

Principles and methods of simultaneous analysis in cladistics are reviewed, and the first, preliminary, analysis of combined molecular and morphological data on higher level relationships in Hymenoptera is presented to exemplify these principles. The morphological data from Ronquist et al . (1999) matrix, derived from the character diagnoses of the phylogenetic tree of Rasnitsyn (1988) , are combined with new molecular data for representatives of 10 superfamilies of Hymenoptera by means of optimization alignment. The resulting cladogram supports Apocrita and Aculeata as groups, and the superfamly Chrysidoidea, but not Chalcidoidea, Evanioidea, Vespoidea and Apoidea.     

A probability-based analysis of temporal and spatial co-occurrence in grassland birds

Aim To test for non‐random co‐occurrence in 36 species of grassland birds using a new metric and the C‐score. The analysis used presence–absence data of birds distributed among 305 sites (or landscapes) over a period of 35 years. This analysis departs from traditional analyses of species co‐occurrence in its use of temporal data and of individual species’ probabilities of occurrence to derive analytically the expected co‐occurrence between paired species. Location Great Plains region, USA. Methods Presence–absence data for the bird species were obtained from the North American Breeding Bird Survey. The analysis was restricted to species pairs whose geographic ranges overlapped. Each of 541 species pairs was classified as a positive, negative, or non‐significant association depending on the mean difference between the observed and expected frequencies of co‐occurrence over the 35‐year time‐span. Results Of the 541 species pairs that were examined, 202 to 293 (37–54%) were positively associated, depending on which of two null models was used. However, only a few species pairs (<5%) were negatively associated. An additional 89 species pairs did not have overlapping ranges and hence represented de facto negative associations. The results from analyses based on C‐scores generally agreed with the analyses based on the difference between observed and expected co‐occurrence, although the latter analyses were slightly more powerful. Main conclusions Grassland birds within the Great Plains region are primarily distributed among landscapes either independently or in conjunction with one another. Only a few species pairs exhibited repulsed or segregated distributions. This indicates that the shared preference for grassland habitat may be more important in producing coexistence than are negative species interactions in preventing it. The large number of non‐significant associations may represent random associations and thereby indicate that the presence/absence of other grassland bird species may have little effect on whether a given focal species is also found within the landscape. In a broader context, the probability‐based approach used in this study may be useful in future studies of species co‐occurrence.     

The combination of two‐dimensional and three‐dimensional analysis methods contributes to the understanding of glioblastoma spatial heterogeneity

Heterogeneity is regarded as the major factor leading to the poor outcomes of glioblastoma (GBM) patients. However, conventional two‐dimensional (2D) analysis methods, such as immunohistochemistry and immunofluorescence, have limited capacity to reveal GBM spatial heterogeneity. Thus, we sought to develop an effective analysis strategy to increase the understanding of GBM spatial heterogeneity. Here, 2D and three‐dimensional (3D) analysis methods were compared for the examination of cell morphology, cell distribution and large intact structures, and both types of methods were employed to dissect GBM spatial heterogeneity. The results showed that 2D assays showed only cross‐sections of specimens but provided a full view. To visualize intact GBM specimens in 3D without sectioning, the optical tissue clearing methods CUBIC and iDISCO+ were used to clear opaque specimens so that they would become more transparent, after which the specimens were imaged with a two‐photon microscope. The 3D analysis methods showed specimens at a large spatial scale at cell‐level resolution and had overwhelming advantages in comparison to the 2D methods. Furthermore, in 3D, heterogeneity in terms of cell stemness, the microvasculature, and immune cell infiltration within GBM was comprehensively observed and analysed. Overall, we propose that 2D and 3D analysis methods should be combined to provide much greater detail to increase the understanding of GBM spatial heterogeneity.     

Integrating the statistical analysis of spatial data in ecology

In many areas of ecology there is an increasing emphasis on spatial relationships. Often ecologists are interested in new ways of analyzing data with the objective of quantifying spatial patterns, and in designing surveys and experiments in light of the recognition that there may be underlying spatial pattern in biotic responses. In doing so, ecologists have adopted a number of widely different techniques and approaches derived from different schools of thought, and from other scientific disciplines. While the adaptation of a diverse array of statistical approaches and methodologies for the analysis of spatial data has yielded considerable insight into various ecological problems, this diversity of approaches has sometimes impeded communication and retarded more rapid progress in this emergent area. Many of these different statistical methods provide similar information about spatial characteristics, but the differences among these methods make it difficult to compare the results of studies that employ contrasting approaches. The papers in this mini-series explore possible areas of agreement and synthesis between a diversity of approaches to spatial analysis in ecology.     

Phylogeography of the Microcoleus vaginatus (Cyanobacteria) from three continents--a spatial and temporal characterization

It has long been assumed that cyanobacteria have, as with other free-living microorganisms, a ubiquitous occurrence. Neither the geographical dispersal barriers nor allopatric speciation has been taken into account. We endeavoured to examine the spatial and temporal patterns of global distribution within populations of the cyanobacterium Microcoleus vaginatus, originated from three continents, and to evaluate the role of dispersal barriers in the evolution of free-living cyanobacteria. Complex phylogeographical approach was applied to assess the dispersal and evolutionary patterns in the cyanobacterium Microcoleus vaginatus (Oscillatoriales). We compared the 16S rRNA and 16S-23S ITS sequences of strains which had originated from three continents (North America, Europe, and Asia). The spatial distribution was investigated using a phylogenetic tree, network, as well as principal coordinate analysis (PCoA). A temporal characterization was inferred using molecular clocks, calibrated from fossil DNA. Data analysis revealed broad genetic diversity within M. vaginatus. Based on the phylogenetic tree, network, and PCoA analysis, the strains isolated in Europe were spatially separated from those which originated from Asia and North America. A chronogram showed a temporal limitation of dispersal barriers on the continental scale. Dispersal barriers and allopatric speciation had an important role in the evolution of M. vaginatus. However, these dispersal barriers did not have a permanent character; therefore, the genetic flow among populations on a continental scale was only temporarily present. Furthermore, M. vaginatus is a recently evolved species, which has been going through substantial evolutionary changes.