On the limitations of standard statistical modeling in biological systems: A full Bayesian approach for biology

One of the most important scientific challenges today is the quantitative and predictive understanding of biological function. Classical mathematical and computational approaches have been enormously successful in modeling inert matter, but they may be inadequate to address inherent features of biological systems. We address the conceptual and methodological obstacles that lie in the inverse problem in biological systems modeling. We introduce a full Bayesian approach (FBA), a theoretical framework to study biological function, in which probability distributions are conditional on biophysical information that physically resides in the biological system that is studied by the scientist.     

Tropical surface temperature response to vegetation cover changes and the role of drylands

Vegetation cover creates competing effects on land surface temperature: it typically cools through enhancing energy dissipation and warms via decreasing surface albedo. Global vegetation has been previously found to overall net cool land surfaces with cooling contributions from temperate and tropical vegetation and warming contributions from boreal vegetation. Recent studies suggest that dryland vegetation across the tropics strongly contributes to this global net cooling feedback. However, observation-based vegetation-temperature interaction studies have been limited in the tropics, especially in their widespread drylands. Theoretical considerations also call into question the ability of dryland vegetation to strongly cool the surface under low water availability. Here, we use satellite observations to investigate how tropical vegetation cover influences the surface energy balance. We find that while increased vegetation cover would impart net cooling feedbacks across the tropics, net vegetal cooling effects are subdued in drylands. Using observations, we determine that dryland plants have less ability to cool the surface due to their cooling pathways being reduced by aridity, overall less efficient dissipation of turbulent energy, and their tendency to strongly increase solar radiation absorption. As a result, while proportional greening across the tropics would create an overall biophysical cooling feedback, dryland tropical vegetation reduces the overall tropical surface cooling magnitude by at least 14%, instead of enhancing cooling as suggested by previous global studies.     

Eggsac development rates and phenology of agrobiont linyphiid spiders in relation to temperature

Spider densities are often low after winter in annual crops, and crop management decimates spider populations several times per year. Population recovery rates and phenology depend on reproductive and development rates, which in turn are driven largely by temperature. We aimed to quantify the relationships between eggsac development rates and temperature in order to understand the relative value of different linyphiid species for the biological control of agricultural pests. Female adults of nine linyphiid species were collected from winter wheat in the UK over 3 years; Bathyphantes gracilis (Blackwall), Erigone atra (Blackwall), Erigone dentipalpis (Wider), Erigone promiscua O.P.‐Cambridge), Tenuiphantes tenuis (Blackwall) [formerly Lepthyphantes tenuis (Blackwall)], Meioneta rurestris (C.L. Koch), Oedothorax apicatus (Blackwall), Oedothorax fuscus (Blackwall), and Oedothorax retusus (Westring). These are agrobiont species that are dominant in agroecosystems. We tested how well development in the field can be predicted on the basis of laboratory experiments. We also built a simple phenology simulation model to test whether spider phenology in the field can be predicted by a general knowledge of the relationship between temperature and development rate. The relationships between temperature and development rates of eggsacs were not linear as described by a day‐degree model, but exponential as described by a biophysical model. Duration of the eggsac development period in the field was predicted accurately from laboratory experiments. We only found minor differences between development thresholds of eggsacs at constant temperatures compared with fluctuating temperatures. The phenology model predicted the phenology of L. tenuis and E. atra well, but the number of generations predicted for O. fuscus was not realised in the field. This suggests that development of this species may be affected by factors other than temperature. The methods used here could also be applied to other natural enemies, to determine whether their thermal biology is conducive to a role as biocontrol agents in disturbed agricultural systems.     

人脑神经元特异性烯醇化酶的纯化方法

采用改良的Grace层析方法,经一次DEAE-Sephadex A50柱层析即从人脑中纯化了神经元特异性烯醇化酶,比活力为92.1U/mg,纯化倍数为59.4.该酶纯化后,经SDS-聚丙烯酰胺凝胶电泳鉴定为单一蛋白质谱带.此外,还测定了其部分理化性质,其亚单位分子量为45000,等电点pI为4.7,氨基酸组成分析表明其为一种酸性蛋白质;对2-磷酸甘油酸的K_m值为5.6×10^-4mol/L.     

Interspecific synchrony of seabird population growth rate and breeding success

Environmental variability can destabilize communities by causing correlated interspecific fluctuations that weaken the portfolio effect, yet evidence of such a mechanism is rare in natural systems. Here, we ask whether the population dynamics of similar sympatric species of a seabird breeding community are synchronized, and if these species have similar exceptional responses to environmental variation. We used a 24‐year time series of the breeding success and population growth rate of a marine top predator species group to assess the degree of synchrony between species demography. We then developed a novel method to examine the species group – all species combined – response to environmental variability, in particular, whether multiple species experience similar, pronounced fluctuations in their demography. Multiple species were positively correlated in breeding success and growth rate. Evidence of “exceptional” years was found, where the species group experienced pronounced fluctuations in their demography. The synchronous response of the species group was negatively correlated with winter sea surface temperature of the preceding year for both growth rate and breeding success. We present evidence for synchronous, exceptional responses of a species group that are driven by environmental variation. Such species covariation destabilizes communities by reducing the portfolio effect, and such exceptional responses may increase the risk of a state change in this community. Our understanding of the future responses to environmental change requires an increased focus on the short‐term fluctuations in demography that are driven by extreme environmental variability.     

Expression and characterization of the intact N-terminal domain of streptokinase

Proteolytic studies have enabled two of the three putative domains of the fibrinolytic protein streptokinase to be isolated and characterized (Conejero-Lara F et al., 1996, Protein Sci 5:2583-2591). The N-terminal domain, however, could not be isolated in these experiments because of its susceptibility to proteolytic cleavage. To complete the biophysical characterization of the domain structure of streptokinase we have overexpressed, purified, and characterized the N-terminal region of the protein, residues 1-146. The results show this is cooperatively folded with secondary structure content and overall stability closely similar to those of the equivalent region in the intact protein.     

Plankton metabolism and physical forcing in a productive embayment of a large oligotrophic lake: insights from stable oxygen isotopes

1. The metabolic balance of plankton communities, commonly assessed by the photosynthesis‐to‐respiration ratio (P : R), has received much attention recently in connection with allochthonous organic subsidies to lakes, while the role of physical, climate‐related forces has received less attention. 2. Here we evaluated the effects of wind and upwelling events on plankton metabolism and the potential of stable oxygen isotopes to characterise P, R and P : R on the scales necessary to characterise properly physical forcing effects in large lakes. 3. We measured the ¹⁸O/¹⁶O ratio of dissolved oxygen and water in a large productive embayment of Lake Ontario (Hamilton Harbour, Canada) and estimated P, R and P : R from the steady state solutions of a widely accepted mass balance model, together with estimates of wind‐driven gas exchange, and compared the results with those from experimental incubations of plankton samples. 4. Estimates of P, but not R, from the isotope model were significantly correlated with bottle estimates while average P : R was similar by both methods. Closer examination of physical forcing events led to a model of how wind events induce mixing, upwelling, exchange and consequent changes in P and R. These physical forcing events were captured more by the isotope model than by the bottle estimates, as episodes of immediately increased R and decreased P : R, with a subsequent stimulation of P. 5. The oxygen isotope approach provided valuable measures of plankton metabolism and helped to characterise more effectively the substantial effects on P : R of physical forcing and, in particular, mixing and exchange events.     

Temporal Aspects in Evaluating the Greenhouse Gas Mitigation Benefits of Using Residues from Forest Products Manufacturing Facilities for Energy Production

Methods for carbon footprinting typically combine all emissions into a single result, representing the emissions of greenhouse gases (GHGs) over the life cycle. The timing of GHG impacts, however, has become a matter of significant interest. In this study, two approaches are used to characterize the timing of GHG emission impacts associated with the production of energy from various biomass residues produced by the forest products industry. The first approach accounts for the timing of emissions and characterizes the impact using Intergovernmental Panel on Climate Change (IPCC) 100‐year global warming potentials (GWPs). The second is a dynamic carbon footprint approach that considers the timing of the GHG emissions, their fate in the atmosphere, and the associated radiative forcing as a function of time. The two approaches generally yield estimates of cumulative impacts over 100 years that differ by less than 5%. The timing of impacts, however, can be significantly affected by the approach used to characterize radiative forcing. For instance, the time required to see net benefits from a system using woody mill residues (e.g., bark and sawdust) is estimated to be 1.2 years when using a fully dynamic approach, compared to 7.5 years when using 100‐year GWPs, with the differences being primarily attributable to methane (CH₄). The results obtained for a number of different biomass residue types from forest products manufacturing highlight the importance of using a fully dynamic approach when studying the timing of emissions impacts in cases where emissions are distributed over time or where CH₄ is a significant contributor to the emissions.