On the theories of biomolecular interactions and their applications in intrinsic protein disorder and bacterial spore germination

Living organisms are complex systems, where complexity arises in part from the large number of interacting components. Here I address interactions in two topics: intrinsically disordered proteins (IDP) and bacterial spore germination. In the first part, I study the role of intrinsic protein disorder in protein function with a standard thermodynamic model. IDPs are proteins without stable structure in their native states. Their ubiquitous presence undercuts the traditional view that a protein’s structure determines its function. Here I propose a quantitative theory that makes predictions regarding the role of intrinsic disorder in protein structure and function. By relating disorder with the free energy of folding, I show that both catalytic and low-affinity binding proteins prefer ordered structures, whereas high-affinity binding proteins can tolerate disorder. Relevant to both transcription and signal transduction, the theory also explains how increasing disorder can tune the binding affinity to maximize the specificity of promiscuous interactions. These claims are supported by a genome-wide survey of disorder. Collectively, the study provides insights into how natural selection acts on folding stability to optimize protein function. In the second part, I study the mechanism of the initiation of bacterial spore germination and propose a quantitative model. Spores are formed by some species of gram positive bacteria (e.g., Bacillus and Clostridium) during starvation. They are metabolically dormant and can later germinate into vegetative cells when nutrients (called germinants) reappear. The lag time of germination after encountering germinants is highly heterogeneous for spores in the same population, and the mechanism is still unclear. Here I propose a quantitative model based on the assumption that the heterogeneity is due to the variability in levels of activated germinant receptors (GR) per spore. The model produces predictions that are consistent with experiments on germination with mixtures of nutrients that trigger different types of GRs, which also suggests that signals from different GRs are summed by a common integrator

Anisotropic Quasi-Wilson Element with Conforming Finite Element Approximation for Coupled Continuum Pipe-Flow/Darcy Model in Karst Aquifers

This paper presents a numerical method for solving systems of partial differential equations describing flow in porous media with an embedded and inclined conduit pipe. This work considers a coupled continuum pipe-flow/Darcy model. The numerical schemes presented are based on combinations of the quasi-Wilson element on anisotropic mesh and the conforming finite element on regular mesh. The existence and uniqueness of the approximation solution are obtained. Optimal error estimates in both L2 and H1 norms are obtained independent of the regularity condition on the mesh. Numerical examples show the accuracy and efficiency of the proposed scheme

Changes in nonlinearity and stability of streamflow recession characteristics under climate warming in a large glaciated basin of the Tibetan Plateau

The accelerated climate warming in the Tibetan Plateau after 1997 has profound consequences in hydrology, geography, and social wellbeing. In hydrology, the change in streamflow as a result of changes in dynamic water storage that originated from glacier melt and permafrost thawing in the warming climate directly affects the available water resources for societies of the most populated nations in the world. In this study, annual streamflow recession characteristics are analyzed using daily climate and hydrological data during 1980–2015 in the Yarlung Zangbo River basin (YRB) of the southern Tibetan Plateau. The recession characteristics are examined in terms of dQ=dt DaQb and the response/ sensitivity of streamflow to changes in groundwater storage. Major results show that climate warming has significantly increased the nonlinearity of the response (b) and streamflow stability [log.a/] in most subbasins of the YRB. These changes in the recession characteristics are attributed to the opposite effects of increases in the available water storage and recession timescale on the recession. Climate warming has increased subbasin water storage considerably due to more recharge from accelerated glacier melting and permafrost thawing after 1997. Meanwhile, the enlarged storage lengthens recession timescales and thereby decreases the sensitivity of discharge to storage. In the recession period when recharge diminished, increased evaporation and the decreased buffering effect of frost soils under warmer temperatures accelerate the initial recession of streamflow. By contrast, enlarged storage and lengthened recession timescales slow down the recession. While reservoir regulations in some basins have helped reduce and even reverse some of these climate warming effects, this short-term remedy can only function before the solid water storage is exhausted should the climate warming continue

Factors Influencing the Impact of Depressive Symptoms on Physical Functional Capacity After Cardiac Rehabilitation

Purpose This study aims to determine (1) if depressive symptoms in the year following completion of cardiac rehabilitation impact physical functional capacity and (2) if exercise, perceived benefits and barriers, self-efficacy, and social support moderate this relationship. Design This longitudinal correlational secondary data analysis included 379 cardiovascular rehabilitation patients. Methods Participants completed measures of depression and potential moderating variables at baseline, 2 months, 6 months, and 12 months and 6-minute work test at baseline and 12 months and wore heart rate monitors to measure exercise for 12 months. Findings Poorer physical functional capacity was predicted by depressed mood score. This relationship was moderated by the percentage of time exercising in target heart rate zone and family support of exercise, but not by perceived benefits and barriers or self-efficacy for exercise. Conclusions Depressive symptoms negatively impact physical functional capacity, and this relationship is moderated by family support and the percentage of time exercising in target heart rate zone

Changes in bacterial community of soil induced by long-term straw returning

Straw returning is an effective way to improve soil quality. Whether the bacterial community development has been changed by long-term straw returning in non-calcareous soil is not clear. In this study, the following five treatments were administered: soil without fertilizer (CK); wheat and corn straw returning (WC); wheat straw returning with 276 kg N ha−1 yr−1 (WN); manure, 60,000 kg ha−1 pig manure compost (M) and wheat and corn straw returning with 276 kg N ha−1 yr−1 (WCN). The high-throughput 16S rRNA sequencing technology was used to evaluate the bacterial communities. The results showed that the community was composed mostly of two dominant groups (Proteobacteria and Acidobacteria). Bacterial diversity increased after the application of straw and manure. Principal component analyses revealed that the soil bacterial community differed significantly between treatments. The WCN treatment showed relatively higher total soil N, available P, available K, and organic carbon and invertase, urease, cellulase activities and yield than the WC treatment. Our results suggested that application of N fertilizer to straw returning soil had significantly higher soil fertility and enzyme activity than straw returning alone, which resulted in a different bacterial community composition, Stenotrophomonas, Pseudoxanthomonas, and Acinetobacter which were the dominant genera in the WC treatment while Candidatus, Koribacter and Granulicella were the dominant genera in the WCN treatment. To summarize, wheat and maize straw returning with N fertilizer would be the optimum proposal for improving soil quality and yield in the future in non-calcareous fluro-acquic-wheat and maize cultivated soils in the North China Plain in China

An evaluation and analysis of incorporating term dependency for ad-hoc retrieval

Although many retrieval models incorporating term dependency have been developed, it is still unclear whether term dependency information can consistently enhance retrieval performance for different queries. We present a novel model that captures the main components of a topic and the relationship between those components and the power of term dependency to improve retrieval performance. Experimental results demonstrate that the power of term dependency strongly depends on the relationship between these components. Without relevance information, the model is still useful by predicting the components based on global statistical information. We show the applicability of the model for adaptively incorporating term dependency for individual queries