Challenges for the prediction of macromolecular interactions

Macromolecular interactions are central to most cellular processes. Experimental methods generate diverse data on these interactions ranging from high throughput protein-protein interactions (PPIs) to the crystallised structures of complexes. Despite this, only a fraction of interactions have been identified and therefore predictive methods are essential to fill in the numerous gaps. Many predictive methods use information from related proteins. Accordingly, we review the conservation of interface and ligand binding sites within protein families and their association with conserved residues and Specificity Determining Positions. We then review recent developments in predictive methods for the identification of PPIs, protein interface sites and small molecule ligand binding sites. The challenges that are still faced by the community in these areas are discussed.     

Pseudomonas aeruginosa and Saccharomyces cerevisiae Biofilm in Flow Cells

Many microbial cells have the ability to form sessile microbial communities defined as biofilms that have altered physiological and pathological properties compared to free living microorganisms. Biofilms in nature are often difficult to investigate and reside under poorly defined conditions¹. Using a transparent substratum it is possible to device a system where simple biofilms can be examined in a non-destructive way in real-time: here we demonstrate the assembly and operation of a flow cell model system, for in vitro 3D studies of microbial biofilms generating high reproducibility under well-defined conditions^2,3.The system consists of a flow cell that serves as growth chamber for the biofilm. The flow cell is supplied with nutrients and oxygen from a medium flask via a peristaltic pump and spent medium is collected in a waste container. This construction of the flow system allows a continuous supply of nutrients and administration of e.g. antibiotics with minimal disturbance of the cells grown in the flow chamber. Moreover, the flow conditions within the flow cell allow studies of biofilm exposed to shear stress. A bubble trapping device confines air bubbles from the tubing which otherwise could disrupt the biofilm structure in the flow cell.The flow cell system is compatible with Confocal Laser Scanning Microscopy (CLSM) and can thereby provide highly detailed 3D information about developing microbial biofilms. Cells in the biofilm can be labeled with fluorescent probes or proteins compatible with CLSM analysis. This enables online visualization and allows investigation of niches in the developing biofilm. Microbial interrelationship, investigation of antimicrobial agents or the expression of specific genes, are of the many experimental setups that can be investigated in the flow cell system.     

Competence Versus Performance Models of People and Tests: A Commentary on Richardson and Norgate

Corrections are sometimes applied to correlations between IQ and job performance (or other criteria) in order to determine the true correlation between these two measures. However, there is no one true correlation between IQ and job performance. The level of correlation depends on many factors and varies across time and place. Moreover, IQ tests and job criteria measure different things for different people, depending on the people's cultural and socioeconomic backgrounds. In this commentary, I laud Richardson and Norgate (this issue) for their recognition of the complexities of issues relating IQ to job performance. I further point out that although the tendency of some investigators is to suggest factors that should increase the correlation between IQ and job performance, one just as easily could suggest factors that should decrease the correlation.     

Interaction of Sirt3 with OGG1 contributes to repair of mitochondrial DNA and protects from apoptotic cell death under oxidative stress

Sirtuin 3 (Sirt3), a major mitochondrial NAD⁺-dependent deacetylase, targets various mitochondrial proteins for lysine deacetylation and regulates important cellular functions such as energy metabolism, aging, and stress response. In this study, we identified the human 8-oxoguanine-DNA glycosylase 1 (OGG1), a DNA repair enzyme that excises 7,8-dihydro-8-oxoguanine (8-oxoG) from damaged genome, as a new target protein for Sirt3. We found that Sirt3 physically associated with OGG1 and deacetylated this DNA glycosylase and that deacetylation by Sirt3 prevented the degradation of the OGG1 protein and controlled its incision activity. We further showed that regulation of the acetylation and turnover of OGG1 by Sirt3 played a critical role in repairing mitochondrial DNA (mtDNA) damage, protecting mitochondrial integrity, and preventing apoptotic cell death under oxidative stress. We observed that following ionizing radiation, human tumor cells with silencing of Sirt3 expression exhibited deteriorated oxidative damage of mtDNA, as measured by the accumulation of 8-oxoG and 4977 common deletion, and showed more severe mitochondrial dysfunction and underwent greater apoptosis in comparison with the cells without silencing of Sirt3 expression. The results reported here not only reveal a new function and mechanism for Sirt3 in defending the mitochondrial genome against oxidative damage and protecting from the genotoxic stress-induced apoptotic cell death but also provide evidence supporting a new mtDNA repair pathway.     

Incongruence between multi‐locus sequence analysis (MLSA) and whole‐genome‐based phylogenies: Pseudomonas syringae pathovar pisi as a cautionary tale

Previous phylogenies, built using a subset of genomic loci, split Pseudomonas syringae pv. pisi into two well‐supported clades and implied convergence in host range for these lineages. The analysis of phenotypic and genotypic data within the context of this phylogenetic relationship implied further convergence at the level of virulence gene loss and acquisition. We generate draft genome assemblies for two additional P. syringae strains, isolated from diseased pea plants, and demonstrate incongruence between phylogenies created from a subset of the data compared with the whole genomes. Our whole‐genome analysis demonstrates that strains classified as pv. pisi actually form a coherent monophyletic clade, so that apparent convergence is actually the product of shared ancestry. We use this example to urge caution when making evolutionary inferences across closely related strains of P. syringae.     

Evaluating the efficacy of biological and conventional insecticides with the new ‘MCD bottle’ bioassay

Background

Urban malaria is considered to be one of the most significant infectious diseases due to varied socioeconomic problems especially in tropical countries like India. Among the south Indian cities, Chennai is endemic for malaria. The present study aimed to identify the hot spots of malaria prevalence and the relationship with other factors in Chennai during 2005-2011.

Methods

Data on zone-wise and ward-wise monthly malaria positive cases were collected from the Vector Control Office, Chennai Corporation, for the year 2005 to 2011 and verified using field data. This data was used to calculate the prevalence among thousand people. Hotspot analysis for all the years in the study period was done to observe the spatial trend. Association of environmental factors like altitude, population density and climatic variables was assessed using ArcGIS 9.3 version and SPSS 11.5. Pearson’s correlation of climate parameters at 95% and 99% was considered to be the most significant. Social parameters of the highly malaria prone region were evaluated through a structured random questionnaire field survey.

Results

Among the ten zones of Chennai Corporation, Basin Bridge zone showed high malaria prevalence during the study period. The ‘hotspot’ analysis of malaria prevalence showed the emergence of newer hotspots in the Adyar zone. These hotspots of high prevalence are places of moderately populated and moderately elevated areas. The prevalence of malaria in Chennai could be due to rainfall and temperature, as there is a significant correlation with monthly rainfall and one month lag of monthly mean temperature. Further it has been observed that the socioeconomic status of people in the malaria hotspot regions and unhygienic living conditions were likely to aggravate the malaria problem.

Conclusion

Malaria hotspots will be the best method to use for targeting malaria control activities. Proper awareness and periodical monitoring of malaria is one of the quintessential steps to control this infectious disease. It has been argued that identifying the key environmental conditions favourable for the occurrence and spread of malaria must be integrated and documented to aid future predictions of malaria in Chennai.     

Intra-articular injection of micronized dehydrated human amnion/chorion membrane attenuates osteoarthritis development

Introduction

Micronized dehydrated human amnion/chorion membrane (μ-dHACM) is derived from donated human placentae and has anti-inflammatory, low immunogenic and anti-fibrotic properties. The objective of this study was to quantitatively assess the efficacy of μ-dHACM as a disease modifying intervention in a rat model of osteoarthritis (OA). It was hypothesized that intra-articular injection of μ-dHACM would attenuate OA progression.

Methods

Lewis rats underwent medial meniscal transection (MMT) surgery to induce OA. Twenty four hours post-surgery, μ-dHACM or saline was injected intra-articularly into the rat joint. Naïve rats also received μ-dHACM injections. Microstructural changes in the tibial articular cartilage were assessed using equilibrium partitioning of an ionic contrast agent (EPIC-μCT) at 21 days post-surgery. The joint was also evaluated histologically and synovial fluid was analyzed for inflammatory markers at 3 and 21 days post-surgery.

Results

There was no measured baseline effect of μ-dHACM on cartilage in naïve animals. Histological staining of treated joints showed presence of μ-dHACM in the synovium along with local hypercellularity at 3 and 21 days post-surgery. In MMT animals, development of cartilage lesions at 21 days was prevented and number of partial erosions was significantly reduced by treatment with μ-dHACM. EPIC-μCT analysis quantitatively showed that μ-dHACM reduced proteoglycan loss in MMT animals.

Conclusions

μ-dHACM is rapidly sequestered in the synovial membrane following intra-articular injection and attenuates cartilage degradation in a rat OA model. These data suggest that intra-articular delivery of μ-dHACM may have a therapeutic effect on OA development.     

Phylogenetic effects on functional traits and life history strategies of Australian freshwater fish

Understanding the biogeographic and phylogenetic basis to interspecific differences in species’ functional traits is a central goal of evolutionary biology and community ecology. We quantify the extent of phylogenetic influence on functional traits and life‐history strategies of Australian freshwater fish to highlight intercontinental differences as a result of Australia's unique biogeographic and evolutionary history. We assembled data on life history, morphological and ecological traits from published sources for 194 Australian freshwater species. Interspecific variation among species could be described by a specialist–generalist gradient of variation in life‐history strategies associated with spawning frequency, fecundity and spawning migration. In general, Australian fish showed an affinity for life‐history strategies that maximise fitness in hydrologically unpredictable environments. We also observed differences in trait lability between and within life history, morphological and ecological traits where in general morphological and ecological traits were more labile. Our results showed that life‐history strategies are relatively evolutionarily labile and species have potentially evolved or colonised in freshwaters frequently and independently allowing them to maximise population performance in a range of environments. In addition, reproductive guild membership showed strong phylogenetic constraint indicating that evolutionary history is an important component influencing the range and distribution of reproductive strategies in extant species assemblages. For Australian freshwater fish, biogeographic and phylogenetic history contribute to broad taxonomic differences in species functional traits, while finer scale ecological processes contribute to interspecific differences in smaller taxonomic units. These results suggest that the lability or phylogenetic relatedness of different functional traits affects their suitability for testing hypothesis surrounding community level responses to environmental change.     

Influence of lipids on the hydrophobic barrier within the pore of the TWIK-1 K2P channel

Several recent ion channel structures have revealed large side portals, or ‘fenestrations’ at the interface between their transmembrane helices that potentially expose the ion conduction pathway to the lipid core of the bilayer. In a recent study we demonstrated that functional activity of the TWIK-1 K2P channel is influenced by the presence of hydrophobic residues deep within the inner pore. These residues are located near the fenestrations in the TWIK-1 structure and promote dewetting of the pore by forming a hydrophobic barrier to ion conduction. During our previous MD simulations, lipid tails were observed to enter these fenestrations. In this addendum to that study, we investigate lipid contribution to the dewetting process. Our results demonstrate that lipid tails from both the upper and lower leaflets can occupy the fenestrations and partially penetrate into the pore. The lipid tails do not sterically occlude the pore, but there is an inverse correlation between the presence of water within the hydrophobic barrier and the number of lipids tails within the lining of the pore. However, dewetting still occurs in the absence of lipids tails, and pore hydration appears to be determined primarily by those side-chains lining the narrowest part of the pore cavity.