A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution

RNA virus genomes are compact, often containing multiple overlapping reading frames and functional secondary structure. Consequently, it is thought that evolutionary interactions between nucleotide sites are commonplace in the genomes of these infectious agents. However, the role of epistasis in natural populations of RNA viruses remains unclear. To investigate the pervasiveness of epistasis in RNA viruses, we used a parsimony-based computational method to identify pairs of co-occurring mutations along phylogenies of 177 RNA virus genes. This analysis revealed widespread evidence for positive epistatic interactions at both synonymous and nonsynonymous nucleotide sites and in both clonal and recombining viruses, with the majority of these interactions spanning very short sequence regions. These findings have important implications for understanding the key aspects of RNA virus evolution, including the dynamics of adaptation. Additionally, many comparative analyses that utilize the phylogenetic relationships among gene sequences assume that mutations represent independent, uncorrelated events. Our results show that this assumption may often be invalid.     

Mortality of fallow deer (Dama dama) experimentally-infected with meningeal worm, Parelaphostrongylus tenuis.

Six fallow deer (Dama dama) fawns died after receiving 25 to 150 infective larvae of Parelaphostrongylus tenuis. Fawns given higher doses usually died sooner (6 to 23 days) than those given lower doses (54 to 67 days). Early deaths were associated with severe acute peritonitis resulting from perforation of the intestinal wall; later deaths were associated with paralysis and inability to rise. Numerous adult P. tenuis were found within neural tissues of the brain and spinal cord in the three fawns with paralysis. One white-tailed deer (Odocoileus virginianus) exposed to infective larvae from the same source survived infection without exhibiting clinical signs and began passing larvae in feces 88 days post-exposure. At the doses used in this study, meningeal worm caused fatal infections in fallow deer. Results are compared to published observations of fallow deer naturally-infected with P. tenuis.     

Biochemical characterization and crystallization of recombinant 3-phosphoglycerate kinase of Plasmodium falciparum

Human malaria parasite Plasmodium falciparum depends largely on glycolytic pathway for energy metabolism during the intraerythrocytic life stage. Therefore, enzymes of the glycolytic pathway could offer potential drug targets provided novel biochemical and/or structural features of the parasitic enzymes, which distinguish them from the host counterpart, could be identified. 3-Phosphoglycerate kinase (EC 2.7.2.3) catalyzes an important phosphorylation step leading to the production of ATP in the glycolytic pathway. We have expressed recombinant 3-phosphoglycerate kinase of P. falciparum in Escherichia coli. The recombinant protein purified from the soluble fraction of E. coli is enzymatically active. The apparent K(m) values determined for adenosine triphosphate (ATP) and 3-phosphoglycerate (3-PGA) are 0.63 and 0.52 mM, respectively. The enzyme activity was temperature-sensitive. Suramin was found to inhibit the recombinant enzyme with an IC(50) value of 7 microM. We have crystallized the enzyme form in hexagonal space group P6(1)22 (or its enantiomorphic space group) with unit cell parameters a=b=130.7, c=263.9 A. Native data have been collected at 3.0-A resolution.     

Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2

Information on global human movement patterns is central to spatial epidemiological models used to predict the behavior of influenza and other infectious diseases. Yet it remains difficult to test which modes of dispersal drive pathogen spread at various geographic scales using standard epidemiological data alone. Evolutionary analyses of pathogen genome sequences increasingly provide insights into the spatial dynamics of influenza viruses, but to date they have largely neglected the wealth of information on human mobility, mainly because no statistical framework exists within which viral gene sequences and empirical data on host movement can be combined. Here, we address this problem by applying a phylogeographic approach to elucidate the global spread of human influenza subtype H3N2 and assess its ability to predict the spatial spread of human influenza A viruses worldwide. Using a framework that estimates the migration history of human influenza while simultaneously testing and quantifying a range of potential predictive variables of spatial spread, we show that the global dynamics of influenza H3N2 are driven by air passenger flows, whereas at more local scales spread is also determined by processes that correlate with geographic distance. Our analyses further confirm a central role for mainland China and Southeast Asia in maintaining a source population for global influenza diversity. By comparing model output with the known pandemic expansion of H1N1 during 2009, we demonstrate that predictions of influenza spatial spread are most accurate when data on human mobility and viral evolution are integrated. In conclusion, the global dynamics of influenza viruses are best explained by combining human mobility data with the spatial information inherent in sampled viral genomes. The integrated approach introduced here offers great potential for epidemiological surveillance through phylogeographic reconstructions and for improving predictive models of disease control.     

Predicting the expression of recombinant monoclonal antibodies in Chinese hamster ovary cells based on sequence features of the CDR3 domain

Despite the development of high‐titer bioprocesses capable of producing >10 g L^?1 of recombinant monoclonal antibody (MAb), some so called “difficult‐to‐express” (DTE) MAbs only reach much lower process titers. For widely utilized “platform” processes the only discrete variable is the protein coding sequence of the recombinant product. However, there has been little systematic study to identify the sequence parameters that affect expression. This information is vital, as it would allow us to rationally design genetic sequence and engineering strategies for optimal bioprocessing. We have therefore developed a new computational tool that enables prediction of MAb titer in Chinese hamster ovary (CHO) cells based on the recombinant coding sequence of the expressed MAb. Model construction utilized a panel of MAbs, which following a 10‐day fed‐batch transient production process varied in titer 5.6‐fold, allowing analysis of the sequence features that impact expression over a range of high and low MAb productivity. The model identified 18 light chain (LC)‐specific sequence features within complementarity determining region 3 (CDR3) capable of predicting MAb titer with a root mean square error of 0.585 relative expression units. Furthermore, we identify that CDR3 variation influences the rate of LC‐HC dimerization during MAb synthesis, which could be exploited to improve the production of DTE MAb variants via increasing the transfected LC:HC gene ratio. Taken together these data suggest that engineering intervention strategies to improve the expression of DTE recombinant products can be rationally implemented based on an identification of the sequence motifs that render a recombinant product DTE. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 30:188–197, 2014     

Chronic Wasting Disease: Transmission Mechanisms and the Possibility of Harvest Management

We develop a model of CWD management by nonselective deer harvest, currently the most feasible approach available for managing CWD in wild populations. We use the model to explore the effects of 6 common harvest strategies on disease prevalence and to identify potential optimal harvest policies for reducing disease prevalence without population collapse. The model includes 4 deer categories (juveniles, adult females, younger adult males, older adult males) that may be harvested at different rates, a food-based carrying capacity, which influences juvenile survival but not adult reproduction or survival, and seasonal force of infection terms for each deer category under differing frequency-dependent transmission dynamics resulting from environmental and direct contact mechanisms. Numerical experiments show that the interval of transmission coefficients β where the disease can be controlled is generally narrow and efficiency of a harvest policy to reduce disease prevalence depends crucially on the details of the disease transmission mechanism, in particular on the intensity of disease transmission to juveniles and the potential differences in the behavior of older and younger males that influence contact rates. Optimal harvest policy to minimize disease prevalence for each of the assumed transmission mechanisms is shown to depend on harvest intensity. Across mechanisms, a harvest that focuses on antlered deer, without distinguishing between age classes reduces disease prevalence most consistently, whereas distinguishing between young and older antlered deer produces higher uncertainty in the harvest effects on disease prevalence. Our results show that, despite uncertainties, a modelling approach can determine classes of harvest strategy that are most likely to be effective in combatting CWD.     

Termite cohabitation: the relative effect of biotic and abiotic factors on mound biodiversity

1. Termites are important ecosystem engineers that improve primary productivity in trees and animal diversity outside their mounds. However, their ecological relationship with the species nesting inside their mounds is poorly understood. 2. The presence of termite cohabitant colonies inside 145 Cornitermes cumulans mounds of known size and location was recorded. Using network‐theoretical methods in conjunction with a suite of statistical analyses, the relative influence of biotic and abiotic drivers of termite within‐mound diversity on the composition and species richness of the termite community was investigated, specifically builder presence and physical aspects of the mound. 3. We found that richness inside the mound increases with mound size, and the species similarity between mounds decreases with distance. The physical attributes (abiotic drivers) of termite mounds (size and relative distance to other mounds) are the strongest predictors of termite species richness and composition. The biotic driver (presence of a builder colony) has an important, though smaller, negative effect on within‐mound termite species richness. 4. The findings suggest that the termites' physical manipulation of their environment is an important driver of within‐mound community diversity. More generally, the approach taken here, using a combination of statistical and network‐theoretical methods, can be used to determine the relative importance of abiotic and biotic drivers of diversity in a wide range of communities of interacting species.     

Empirical Estimation of R 0 for Unknown Transmission Functions: The Case of Chronic Wasting Disease in Alberta

We consider the problem of estimating the basic reproduction number R ₀ from data on prevalence dynamics at the beginning of a disease outbreak. We derive discrete and continuous time models, some coefficients of which are to be fitted from data. We show that prevalence of the disease is sufficient to determine R ₀. We apply this method to chronic wasting disease spread in Alberta determining a range of possible R ₀ and their sensitivity to the probability of deer annual survival.