An evolutionary space-time model with varying among-site dependencies

It is now widely accepted that sites in a protein do not undergo independent evolutionary processes. The underlying assumption is that proteins are composed of conserved and variable linear domains, and thus rates at neighboring sites are correlated. In this paper, we comprehensively examine the performance of an autocorrelation model of evolutionary rates in protein sequences. We further develop a model in which the level of correlation between rates at adjacent sites is not equal at all sites of the protein. High correlation is expected, for example, in linear functional domains. On the other hand, when we consider nonlinear functional regions (e.g., active sites), low correlation is expected because the interaction between distant sites imposes independence of rates in the linear sequence. Our model is based on a hidden Markov model, which accounts for autocorrelation at certain regions of the protein and rate independence at others. We study the differences between the novel model and models which assume either independence or a fixed level of dependence throughout the protein. Using a diverse set of protein data sets we show that the novel model better fits most data sets. We further analyze the potassium-channel protein family and illustrate the relationship between the dependence of rates at adjacent sites and the tertiary structure of the protein.     

Projecting marine species range shifts from only temperature can mask climate vulnerability

Climate change is causing range shifts in many marine species, with implications for biodiversity and fisheries. Previous research has mainly focused on how species' ranges will respond to changing ocean temperatures, without accounting for other environmental covariates that could affect future distribution patterns. Here, we integrate habitat suitability modeling approaches, a high‐resolution global climate model projection, and detailed fishery‐independent and ‐dependent faunal datasets from one of the most extensively monitored marine ecosystems—the U.S. Northeast Shelf. We project the responses of 125 species in this region to climate‐driven changes in multiple oceanographic factors (e.g., ocean temperature, salinity, sea surface height) and seabed characteristics (i.e., rugosity and depth). Comparing model outputs based on ocean temperature and seabed characteristics to those that also incorporated salinity and sea surface height (proxies for primary productivity and ocean circulation features), we explored how an emphasis on ocean temperature in projecting species' range shifts can impact assessments of species' climate vulnerability. We found that multifactor habitat suitability models performed better in explaining and predicting species historical distribution patterns than temperature‐based models. We also found that multifactor models provided more concerning assessments of species' future distribution patterns than temperature‐based models, projecting that species' ranges will largely shift northward and become more contracted and fragmented over time. Our results suggest that using ocean temperature as a primary determinant of range shifts can significantly alter projections, masking species' climate vulnerability, and potentially forestalling proactive management.     

Models in which many cross-bridges attach simultaneously can explain the filament movement per ATP split during muscle contraction

Contractile filaments in skeletal muscle are moved by less than 2 nm for each ATP used. If just one cross-bridge is attached to each thin filament at any instant then this distance represents the fundamental myosin cross-bridge step size (i.e. the distance one cross-bridge moves a thin filament in one ATP-splitting cycle). However, most contraction models assume many cross-bridges are attached at any instant along each thin filament. The purpose of this study was to establish whether the net filament sliding per ATP used could be explained quantitatively in terms of a cross-bridge model in which multiple cross-bridges are attached along each thin filament. It was found that the relationship between net filament sliding per ATP split and the load against which the muscle shortens is compatible with such a model and furthermore predicts that the cross-bridge step size is between 7.5 and 12.5 nm over most of the range of loads. These values were similar for different muscle fibre types.     

Detection of significant demographic differences between subpopulations of prehispanic Maya from Copan, Honduras, by survival analysis

Heterogeneity and small sample size are problems that affect many paleodemographic studies. The former can cause the overall distribution of age at death to be an amalgam that does not accurately reflect the distributions of any of the groups composing the heterogeneous population. The latter can make it difficult to separate significant from nonsignificant demographic differences between groups. Survival analysis, a methodology that involves the survival distribution function and various regression models, can be applied to distributions of age at death in order to reveal statistically significant demographic differences and to control for heterogeneity. Survival analysis was used on demographic data from a heterogeneous sample of skeletons of low status Maya who lived in and around Copan, Honduras, between A.D. 400 and 1200. Results contribute to understanding the collapse of Classic Maya civilization.     

成年犬股骨微波灭活骨缺损模型的建立

目的　建立成年犬股骨微波灭活骨缺损的实验动物模型 ,为骨缺损修复的研究提供实验依据。方法应用自行研制的骨肿瘤微波治疗仪 ,以 1 5kHz频率、70W功率加热至 5 0～ 5 5℃ ,维持 2 0min ,造成犬股骨中段不同大小的骨缺损。结果　在保持犬股骨连续性的前提下 ,长度 1 5cm的骨缺损 9个月时有 1 2被新生骨填充 ,长度2 5cm和 3 5cm的骨缺损 9个月时无愈合倾向 ,但后者骨折的发生率高。结论　成年犬股骨微波高温造成的骨缺损 ,长 2 5cm、宽 1 0cm 9个月不能自愈 ,适宜于各种骨修复材料的填充 ,是理想的实验模型     

Rare species habitat suitability assessment and reliability evaluation of an expert-based model: A case study of the insectivorous plant Pinguicula crystallina Sibth. et Smith subsp. hirtiflora (Ten.) Strid (Lentibulariaceae)

The development of habitat suitability models requires a large amount of data which are rarely available. In this case, researchers need to get information on the ecological features of the studied species, based on the opinion of experts or on the literature, to construct a qualitative model. However, such models cannot be rigorously evaluated, as in most cases absence points are not available. In this paper, we assess the habitat suitability for a vulnerable insectivorous plant, Pinguicula crystallina Sibth. et Smith subsp. hirtiflora (Ten.) Strid (Lentibulariaceae) in the Campania region. Our aim was to develop an expert-based, presence-only model in support of possible conservation actions. Topographic and geological features of this species suggested by the literature were used in our model. Both the Boyce index and field surveys were chosen to evaluate the model's reliability. During field surveys, 31 absence sites and 1 new presence site were identified, and differences between sites with regard to water chemistry and quality were investigated, water being an element in the species habitat. Factors that affect reliability of the model, such as the lack of a large amount of information on the species and the limited spatial resolution of geographical information system data, are discussed.     

Detection of process-related changes in plant patterns at extended spatial scales during early dryland desertification

Arid and semiarid shrublands occupy extensive land areas over the world, are susceptible to desertification by anthropic use and can contribute to regional climate change. These prompt the interest to monitor and evaluate these lands adequately in order to detect early stages of degradation. Evaluation topics must refer to biology‐relevant characteristics of these systems, while simultaneously satisfying sampling consistency over extended landscape areas. We present an analysis of process‐relevant parameters related to changes in the spatial arrangement of the plant canopy of shrublands inferred from high‐resolution panchromatic aerial photos and Interferometric Synthetic Aperture Radar imagery. We obtained low‐altitude images systematically located along several gradients of land‐use intensity in a Patagonian Monte shrubland in Argentina. Images were digitized to spatial resolutions ranging from 0.09 to 0.72 m (pixel size) and the average values and an‐isotropic characteristics of the plant canopy patterns were quantified by means of a Fourier metric. We used radar‐derived imagery to overlay the panchromatic images on a digital elevation model in order to study the correspondence of potential runoff patterns and the spatial arrangement of plants. We related an‐isotropic features of the plant canopy images to the prevailing wind regime. Observed trends were further interpreted on the basis of a spatial‐explicit simulation model describing the dynamics of the main functional groups in the plant community. We conclude that early stages of anthropic‐driven dryland degradation in the Patagonian Monte can be characterized by the incipient un‐coupling of spatial vegetation patterns from those of runoff at a landscape scale, and a progressive coupling to the spatial pattern of the wind regime. The method and metrics we present can be used to quantify early desertification changes in other similar drylands at extended spatial scales.     

Recent advances in three-dimensional multicellular spheroid culture for biomedical research

Many types of mammalian cells can aggregate and differentiate into 3-D multicellular spheroids when cultured in suspension or a nonadhesive environment. Compared to conventional monolayer cultures, multicellular spheroids resemble real tissues better in terms of structural and functional properties. Multicellular spheroids formed by transformed cells are widely used as avascular tumor models for metastasis and invasion research and for therapeutic screening. Many primary or progenitor cells on the other hand, show significantly enhanced viability and functional performance when grown as spheroids. Multicellular spheroids in this aspect are ideal building units for tissue reconstruction. Here we review the current understanding of multicellular spheroid formation mechanisms, their biomedical applications, and recent advances in spheroid culture, manipulation, and analysis techniques.