Toward Understanding Protocell Mechanosensation

Mechanosensitive (MS) channels can prevent bacterial bursting during hypo-osmotic shocks by responding to increases in lateral tension at the membrane level through an integrated and coordinated opening mechanism. Mechanical regulation in protocells could have been one of the first mechanisms to evolve in order to preserve their integrity against changing environmental conditions. How has the rich functional diversity found in present cells been created throughout evolution, and what did the primordial MS channels look like? This review has been written with the aim of identifying which factors may have been important for the appearance of the first osmotic valve in a prebiotic context, and what this valve may have been like. It highlights the mechanical properties of lipid bilayers, the association of peptides as aggregates in membranes, and the conservation of sequence motifs as central aspects to understand the evolution of proteins that gate below the tension required for spontaneous pore formation and membrane rupture. The arguments developed here apply to both MscL and MscS homologs, but could be valid to mechano-susceptible proteins in general.     

Impact: Toward a Framework for Understanding the Ecological Effects of Invaders

Although ecologists commonly talk about the impacts of nonindigenous species, little formal attention has been given to defining what we mean by impact, or connecting ecological theory with particular measures of impact. The resulting lack of generalizations regarding invasion impacts is more than an academic problem; we need to be able to distinguish invaders with minor effects from those with large effects in order to prioritize management efforts. This paper focuses on defining, evaluating, and comparing a variety of measures of impact drawn from empirical examples and theoretical reasoning. We begin by arguing that the total impact of an invader includes three fundamental dimensions: range, abundance, and the per-capita or per-biomass effect of the invader. Then we summarize previous approaches to measuring impact at different organizational levels, and suggest some new approaches. Reviewing mathematical models of impact, we argue that theoretical studies using community assembly models could act as a basis for better empirical studies and monitoring programs, as well as provide a clearer understanding of the relationship among different types of impact. We then discuss some of the particular challenges that come from the need to prioritize invasive species in a management or policy context. We end with recommendations about how the field of invasion biology might proceed in order to build a general framework for understanding and predicting impacts. In particular, we advocate studies designed to explore the correlations among different measures: Are the results of complex multivariate methods adequately captured by simple composite metrics such as species richness? How well are impacts on native populations correlated with impacts on ecosystem functions? Are there useful bioindicators for invasion impacts? To what extent does the impact of an invasive species depend on the system in which it is measured? Three approaches would provide new insights in this line of inquiry: (1) studies that measure impacts at multiple scales and multiple levels of organization, (2) studies that synthesize currently available data on different response variables, and (3) models designed to guide empirical work and explore generalities.     

Epitranscriptomics: Toward A Better Understanding of RNA Modifications

<正>Ever since the first RNA nucleoside modification was characterized in 1957~[1],over 100 distinct chemical modifications have been identified in RNA to date~[2].Most of these modifications were characterized in non-coding RNAs(nc RNAs),including t RNA,r RNA,and small nuclear RNA(sn RNA)~[3].Studies in the past few decades have located various modifications in these nc RNAs and revealed their functional roles~[3].For instance,N1-methyladenosine(m~1A),which is typically     

中国虎的概况

虎是世界上最大的猫科动物。曾广泛分布在亚洲13个国家。但由于栖息地的丧失、猎物数量减少以及人类的捕杀,其野生种群已经从一个世纪前的超过10万只锐减到目前的3000～5000只。中国境内分布着4个野生亚种,对于世界范围的老虎保护有着重要作用。建立连接破碎化栖息地的生物走廊带、杜绝由于虎制品贸易消费而造成的疯狂盗猎、有效地保护好老虎残存的自然栖息地及其中的有蹄类猎物种群是维持老虎野外种群持续生存的关键。     

A Computational Systems Biology Study for Understanding Salt Tolerance Mechanism in Rice

Salinity is one of the most common abiotic stresses in agriculture production. Salt tolerance of rice (Oryza sativa) is an important trait controlled by various genes. The mechanism of rice salt tolerance, currently with limited understanding, is of great interest to molecular breeding in improving grain yield. In this study, a gene regulatory network of rice salt tolerance is constructed using a systems biology approach with a number of novel computational methods. We developed an improved volcano plot method in conjunction with a new machine-learning method for gene selection based on gene expression data and applied the method to choose genes related to salt tolerance in rice. The results were then assessed by quantitative trait loci (QTL), co-expression and regulatory binding motif analysis. The selected genes were constructed into a number of network modules based on predicted protein interactions including modules of phosphorylation activity, ubiquity activity, and several proteinase activities such as peroxidase, aspartic proteinase, glucosyltransferase, and flavonol synthase. All of these discovered modules are related to the salt tolerance mechanism of signal transduction, ion pump, abscisic acid mediation, reactive oxygen species scavenging and ion sequestration. We also predicted the three-dimensional structures of some crucial proteins related to the salt tolerance QTL for understanding the roles of these proteins in the network. Our computational study sheds some new light on the mechanism of salt tolerance and provides a systems biology pipeline for studying plant traits in general.     

Application of Molecular Simulations Toward Understanding Cellulase Mechanisms

Computational approaches have provided new biological insights into the chemical mechanism of action of cellulases, which are used in the industrial production of bioethanol. Fine-grained methods, such as molecular dynamics and quantum mechanics, as well as coarse-grained methods, such as elastic network models, were used to investigate how the chemistry and structural dynamics of these enzymes contribute to their function. In this review, we highlight recent computational studies to understand this crucial biofuel enzyme class’s chemistry and structural dynamics, as well as their significance in revealing enzymatic mechanism of action. Computational methods can complement and amplify the findings of experimental methods, which can be used in tandem to create more efficient industrial enzymes.     

玉米耐盐分子机制研究进展

玉米是我国总产量最大的农作物,它对盐胁迫耐受性较差.玉米主产区日益加剧的土壤盐渍化已成为导致玉米产量和品质下降的主要环境胁迫之一.因此,研究玉米的耐盐机制,改良玉米的耐盐性对保障我国乃至世界玉米生产的可持续发展有重要意义.土壤中盐浓度过高会导致玉米根系外围土壤溶液的水势降低,引起渗透胁迫,而盐离子(Na+、Cl-等)的...     

Bacterial Filament Systems: Toward Understanding Their Emergent Behavior and Cellular Functions

Bacteria use homologs of eukaryotic cytoskeletal filaments to conduct many different tasks, controlling cell shape, division, and DNA segregation. These filaments, combined with factors that regulate their polymerization, create emergent self-organizing machines. Here, we summarize the current understanding of the assembly of these polymers and their spatial regulation by accessory factors, framing them in the context of being dynamical systems. We highlight how comparing the in vivo dynamics of the filaments with those measured in vitro has provided insight into the regulation, emergent behavior, and cellular functions of these polymeric systems.     

The BLyS Family: Toward a Molecular Understanding of B Cell Homeostasis

The B Lymphocyte Stimulator (BLyS) family of ligands and receptors regulates humoral immunity by controlling B lymphocyte survival and differentiation. Herein, we review the ligands and receptors of this family, their biological functions, and the biochemical processes through which they operate. Pre-immune B lymphocytes rely on BLyS signaling for their survival, whereas antigen experienced B lymphocytes generally interact more avidly with a homologous cytokine, A Proliferation Inducing Ligand (APRIL). The molecular basis for signaling via the three BLyS family receptors reveals complex interplay with other B lymphocyte signaling systems, affording the integration of selective and homeostatic processes. As our understanding of this system advances, molecular targets for manipulating humoral immunity in both health and disease should be revealed.     

Toward Understanding the Dynamics of Microbial Communities in an Estuarine System

Community assembly theories such as species sorting theory provide a framework for understanding the structures and dynamics of local communities. The effect of theoretical mechanisms can vary with the scales of observation and effects of specific environmental factors. Based on 16S rRNA gene tag pyrosequencing, different structures and temporal succession patterns were discovered between the surface sediments and bottom water microbial communities in the Pearl River Estuary (PRE). The microbial communities in the surface sediment samples were more diverse than those in the bottom water samples, and several genera were specific for the water or sediment communities. Moreover, water temperature was identified as the main variable driving community dynamics and the microbial communities in the sediment showed a greater temporal change. We speculate that nutrient-based species sorting and bacterial plasticity to the temperature contribute to the variations observed between sediment and water communities in the PRE. This study provides a more comprehensive understanding of the microbial community structures in a highly dynamic estuarine system and sheds light on the applicability of ecological theoretical mechanisms.     

Understanding Saline and Osmotic Tolerance of Populus euphratica Suspended Cells

Tolerance of Populus euphratica suspended cells to ionic and osmotic stresses implemented respectively by NaCl and PEG (6000) was characterized by monitoring cell growth, morphological features, ion compartmentation and polypeptide patterns. The cells grew and proliferated when submitted to stresses of 137 mM NaCl or 250 g l⁻¹ PEG, and survived at 308 mM of NaCl, showing tolerance to saline and particularly osmotic stress. They were resistant to plasmolysis and had dense cytoplasms, large nuclei and nucleoli, and evident cytoplasmic strands under high saline and osmotic stress. The sequestration of Cl⁻ into the vacuoles was observed in the cells stressed with 137 and 223 mM NaCl. The cellular protein profile was modified by high salt and osmotic stress and showed 28 kDa polypeptides up-regulated by both NaCl and PEG, and 66 and 25 kDa polypeptides up-regulated only by high NaCl stress. The salt tolerance of P. euphratica cells might be related to their capacity of adapting to higher osmotic stress by maintaining cell integrity, sequestrating Cl⁻ into vacuoles and modulating polypeptides that reflect cellular metabolic adaptations.     

Industrial Robustness: Understanding the Mechanism of Tolerance for the Populus Hydrolysate-Tolerant Mutant Strain of Clostridium thermocellum

Background

An industrially robust microorganism that can efficiently degrade and convert lignocellulosic biomass into ethanol and next-generation fuels is required to economically produce future sustainable liquid transportation fuels. The anaerobic, thermophilic, cellulolytic bacterium Clostridium thermocellum is a candidate microorganism for such conversions but it, like many bacteria, is sensitive to potential toxic inhibitors developed in the liquid hydrolysate produced during biomass processing. Microbial processes leading to tolerance of these inhibitory compounds found in the pretreated biomass hydrolysate are likely complex and involve multiple genes.

Methodology/Principal Findings

In this study, we developed a 17.5% v/v Populus hydrolysate tolerant mutant strain of C. thermocellum by directed evolution. The genome of the wild type strain, six intermediate population samples and seven single colony isolates were sequenced to elucidate the mechanism of tolerance. Analysis of the 224 putative mutations revealed 73 high confidence mutations. A longitudinal analysis of the intermediate population samples, a pan-genomic analysis of the isolates, and a hotspot analysis revealed 24 core genes common to all seven isolates and 8 hotspots. Genetic mutations were matched with the observed phenotype through comparison of RNA expression levels during fermentation by the wild type strain and mutant isolate 6 in various concentrations of Populus hydrolysate (0%, 10%, and 17.5% v/v).

Conclusion/Significance

The findings suggest that there are multiple mutations responsible for the Populus hydrolysate tolerant phenotype resulting in several simultaneous mechanisms of action, including increases in cellular repair, and altered energy metabolism. To date, this study provides the most comprehensive elucidation of the mechanism of tolerance to a pretreated biomass hydrolysate by C. thermocellum. These findings make important contributions to the development of industrially robust strains of consolidated bioprocessing microorganisms.