Computational design of self-assembling cyclic protein homo-oligomers

Self-assembling cyclic protein homo-oligomers play important roles in biology, and the ability to generate custom homo-oligomeric structures could enable new approaches to probe biological function. Here we report a general approach to design cyclic homo-oligomers that employs a new residue-pair-transform method to assess the designability of a protein-protein interface. This method is sufficiently rapid to enable the systematic enumeration of cyclically docked arrangements of a monomer followed by sequence design of the newly formed interfaces. We use this method to design interfaces onto idealized repeat proteins that direct their assembly into complexes that possess cyclic symmetry. Of 96 designs that were characterized experimentally, 21 were found to form stable monodisperse homo-oligomers in solution, and 15 (four homodimers, six homotrimers, six homotetramers and one homopentamer) had solution small-angle X-ray scattering data consistent with the design models. X-ray crystal structures were obtained for five of the designs and each is very close to their corresponding computational model

Climate change goes underground: effects of elevated atmospheric CO2 on microbial community structure and activities in the rhizosphere.

General concern about climate change has led to growing interest in the responses of terrestrial ecosystems to elevated concentrations of CO2 in the atmosphere. Experimentation during the last two to three decades using a large variety of approaches has provided sufficient information to conclude that enrichment of atmospheric CO2 may have severe impact on terrestrial ecosystems. This impact is mainly due to the changes in the organic C dynamics as a result of the effects of elevated CO2 on the primary source of organic C in soil, i.e., plant photosynthesis. As the majority of life in soil is heterotrophic and dependent on the input of plant-derived organic C, the activity and functioning of soil organisms will greatly be influenced by changes in the atmospheric CO2 concentration. In this review, we examine the current state of the art with respect to effects of elevated atmospheric CO2 on soil microbial communities, with a focus on microbial community structure. On the basis of the existing information, we conclude that the main effects of elevated atmospheric CO2 on soil microbiota occur via plant metabolism and root secretion, especially in C3 plants, thereby directly affecting the mycorrhizal, bacterial, and fungal communities in the close vicinity of the root. There is little or no direct effect on the microbial community of the bulk soil. In particular, we have explored the impact of these changes on rhizosphere interactions and ecosystem processes, including food web interactions

Plant Growth-Promoting Microbes from Herbal Vermicompost

Overreliance on chemical pesticides and fertilizers has resulted in problems including safety risks, outbreaks of secondary pests normally held in check by natural enemies, insecticide resistance, environmental contamination, and decrease in biodiversity. The increasing costs and negative effects of pesticides and fertilizers necessitate the idea of biological options of crop protection and production. This includes the use of animal manure, crop residues, microbial inoculum, and composts. They provide natural nutrition, reduce the use of inorganic fertilizers, develop biodiversity, increase soil biological activity, maintain soil physical properties, and improve environmental health

Delineating the roles of males and females in sperm competition

Disentangling the relative roles of males, females and their interactive effects on competitive fertilization success remains a challenge in sperm competition. In this study, we apply a novel experimental framework to an ideally suited externally fertilizing model system in order to delineate these roles. We focus on the chinook salmon, Oncorhynchus tshawytscha, a species in which ovarian fluid (OF) has been implicated as a potential arbiter of cryptic female choice for genetically compatible mates. We evaluated this predicted sexually selected function of OF using a series of factorial competitive fertilization trials. Our design involved a series of 10 factorial crosses, each involving two ‘focal’ rival males whose sperm competed against those from a single ‘standardized’ (non-focal) rival for a genetically uniform set of eggs in the presence of OF from two focal females. This design enabled us to attribute variation in competitive fertilization success among focal males, females (OF) and their interacting effects, while controlling for variation attributable to differences in the sperm competitive ability of rival males, and male-by-female genotypic interactions. Using this experimental framework, we found that variation in sperm competitiveness could be attributed exclusively to differences in the sperm competitive ability of focal males, a conclusion supported by subsequent analyses revealing that variation in sperm swimming velocity predicts paternity success. Together, these findings provide evidence that variation in paternity success can be attributed to intrinsic differences in the sperm competitive ability of rival males, and reveal that sperm swimming velocity is a key target of sexual selection