Predicting protein domain interactions from coevolution of conserved regions

The knowledge of protein and domain interactions provide crucial insights into their function within a cell. Several computational methods have been proposed to detect interactions between proteins and their constitutive domains. In this work, we focus on approaches based on correlated evolution (coevolution) of sequences of interacting proteins. In this type of approach, often referred to as the mirrortree method, a high correlation of evolutionary histories of two proteins is used as an indicator to predict protein interactions. Recently, it has been observed that subtracting the underlying speciation process by separating coevolution due to common speciation divergence from that due to common function of interacting pairs greatly improves the predictive power of the mirrortree approach. In this article, we investigate possible improvements and limitations of this method. In particular, we demonstrate that the performance of the mirrortree method that can be further improved by restricting the coevolution analysis to the relatively conserved regions in the protein domain sequences (disregarding highly divergent regions). We provide a theoretical validation of our results leading to new insights into the interplay between coevolution and speciation of interacting proteins.     

Discriminating analysis of “in vitro” prostaglandin release by myometrial and luminal sides of the ewe endometrium

An original perifusion device which allows a discrimination between the 30 mn releases of prostaglandins F₂α and E₂ by the luminal and the myometrial faces of sheep endometrium is described. Tissue was sampled on day 4, 14, 16 or 17 of the cycle and on day 14 or 17 of pregnancy. Total prostaglandin (PG) release measured with this device was in good agreement with PG's concentrations in media of in vitro endometrium incubations already described.Discrimination analysis of the PGs release by each side of the endometrial tissue during the 30 mn perifusion time releaved that PGF₂α concentrations of the perifusion medium issued from the lumen compartment were higher than those of the myometrial compartment in all physiological status where corpus luteum is active (including early pregnancy). Therefore in the ewe, it seems that luteal structure maintenance during early pregnancy is not due, as in the giltm to a shift in PGF₂α secretion towards the uterine lumen.     

Sexually antagonistic cytonuclear fitness interactions in Drosophila melanogaster

Theoretical and empirical studies have shown that selection cannot maintain a joint nuclear-cytoplasmic polymorphism within a population except under restrictive conditions of frequency-dependent or sex-specific selection. These conclusions are based on fitness interactions between a diploid autosomal locus and a haploid cytoplasmic locus. We develop a model of joint transmission of X chromosomes and cytoplasms and through simulation show that nuclear-cytoplasmic polymorphisms can be maintained by selection on X-cytoplasm interactions. We test aspects of the model with a "diallel" experiment analyzing fitness interactions between pairwise combinations of X chromosomes and cytoplasms from wild strains of Drosophila melanogaster. Contrary to earlier autosomal studies, significant fitness interactions between X chromosomes and cytoplasms are detected among strains from within populations. The experiment further demonstrates significant sex-by-genotype interactions for mtDNA haplotype, cytoplasms, and X chromosomes. These interactions are sexually antagonistic--i.e., the "good" cytoplasms in females are "bad" in males--analogous to crossing reaction norms. The presence or absence of Wolbachia did not alter the significance of the fitness effects involving X chromosomes and cytoplasms but tended to reduce the significance of mtDNA fitness effects. The negative fitness correlations between the sexes demonstrated in our empirical study are consistent with the conditions that maintain cytoplasmic polymorphism in simulations. Our results suggest that fitness interactions with the sex chromosomes may account for some proportion of cytoplasmic variation in natural populations. Sexually antagonistic selection or reciprocally matched fitness effects of nuclear-cytoplasmic genotypes may be important components of cytonuclear fitness variation and have implications for mitochondrial disease phenotypes that differ between the sexes.     

Gut microbiota of the pine weevil degrades conifer diterpenes and increases insect fitness

The pine weevil (Hylobius abietis), a major pest of conifer forests throughout Europe, feeds on the bark and cambium, tissues rich in terpenoid resins that are toxic to many insect herbivores. Here, we report the ability of the pine weevil gut microbiota to degrade the diterpene acids of Norway spruce. The diterpene acid levels present in ingested bark were substantially reduced on passage through the pine weevil gut. This reduction was significantly less upon antibiotic treatment, and supplementing the diet with gut suspensions from untreated insects restored the ability to degrade diterpenes. In addition, cultured bacteria isolated from pine weevil guts were shown to degrade a Norway spruce diterpene acid. In a metagenomic survey of the insect's bacterial community, we were able to annotate several genes of a previously described diterpene degradation (dit) gene cluster. Antibiotic treatment disrupted the core bacterial community of H. abietis guts and eliminated nearly all dit genes concordant with its reduction in diterpene degradation. Pine weevils reared on an artificial diet spiked with diterpenes, but without antibiotics, were found to lay more eggs with a higher hatching rate than weevils raised on diets with antibiotics or without diterpenes. These results suggest that gut symbionts contribute towards host fitness, but not by detoxification of diterpenes, as these compounds do not show toxic effects with or without antibiotics. Rather the ability to thrive in a terpene‐rich environment appears to allow gut microbes to benefit the weevil in other ways, such as increasing the nutritional properties of their diet.     

Pathway networks generated from human disease phenome

Background

Understanding the effect of human genetic variations on disease can provide insight into phenotype-genotype relationships, and has great potential for improving the effectiveness of personalized medicine. While some genetic markers linked to disease susceptibility have been identified, a large number are still unknown. In this paper, we propose a pathway-based approach to extend disease-variant associations and find new molecular connections between genetic mutations and diseases.

Methods

We used a compilation of over 80,000 human genetic variants with known disease associations from databases including the Online Mendelian Inheritance in Man (OMIM), Clinical Variance database (ClinVar), Universal Protein Resource (UniProt), and Human Gene Mutation Database (HGMD). Furthermore, we used the Unified Medical Language System (UMLS) to normalize variant phenotype terminologies, mapping 87% of unique genetic variants to phenotypic disorder concepts. Lastly, variants were grouped by UMLS Medical Subject Heading (MeSH) identifiers to determine pathway enrichment in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.

Results

By linking KEGG pathways through underlying variant associations, we elucidated connections between the human genetic variant-based disease phenome and metabolic pathways, finding novel disease connections not otherwise detected through gene-level analysis. When looking at broader disease categories, our network analysis showed that large complex diseases, such as cancers, are highly linked by their common pathways. In addition, we found Cardiovascular Diseases and Skin and Connective Tissue Diseases to have the highest number of common pathways, among 35 significant main disease category (MeSH) pairings.

Conclusions

This study constitutes an important contribution to extending disease-variant connections and new molecular links between diseases. Novel disease connections were made by disease-pathway associations not otherwise detected through single-gene analysis. For instance, we found that mutations in different genes associated to Noonan Syndrome and Essential Hypertension share a common pathway. This analysis also provides the foundation to build novel disease-drug networks through their underlying common metabolic pathways, thus enabling new diagnostic and therapeutic interventions.

     

Lipid-mediated introduction of hepatitis B virus capsids into nonsusceptible cells allows highly efficient replication and facilitates the study of early infection events

The hepatitis B virus (HBV) is an enveloped DNA virus which is highly infectious in vivo. In vitro, only primary hepatocytes of humans and Tupaia belangeri or the novel HepaRG cell line are susceptible to HBV, but infection is inefficient and study of early infection events in single cells is unsatisfactory. Since hepatoma cells replicate the virus efficiently after transfection, this limited infection efficiency must be related to the initial entry phase. Here, we describe the lipid-based delivery of HBV capsids into nonsusceptible cells, circumventing the natural entry pathway. Successful infection was monitored by observing the emergence of the nuclear viral covalently closed circular DNA and the production of progeny virus and subviral particles. Lipid-mediated transfer initiated productive infection that was at least 100-fold more effective than infection of permissive cell cultures. High-dose capsid transfer showed that the uptake was not receptor limited and allowed the intracellular transport of capsids and genomes to be examined microscopically. The addition of inhibitors confirmed an entry pathway by fusion of the lipid with the plasma membrane. By indirect immune fluorescence and native fluorescence in situ hybridization, we followed the pathway of capsids and viral genomes in individual cells. We observed an active microtubule-dependent capsid transfer to the nucleus and a subsequent release of the viral genomes exclusively into the karyoplasm. Lipid-mediated transfer of viral capsids thus appears to allow efficient introduction of genetic information into target cells, facilitating studies of early infection events which are otherwise impeded by the small number of viruses entering the cell.     

Paleolimnological evidence of change in a shallow, hypereutrophic lake: Upper Klamath Lake, Oregon, USA

Sediment cores were collected from Upper Klamath Lake in October, 1998 and analyzed for ²¹⁰Pb, ¹⁴C, ¹⁵N, N, P, C, Ti, Al, diatoms, Pediastrum, and cyanobacterial akinetes. These results were used to reconstruct changes in water quality in Upper Klamath Lake over the last 150 years. The results showed that there was substantial mixing of the upper 10 cm of sediment, representing the previous 20 to 30 years. However, below that, ²¹⁰Pb activity declined monotonically, allowing reasonable dating for the period from about 1850 to 1970. The sediment accumulation rates (SAR) showed a substantial increase in the 20th century. The increase in SAR corresponded with increases in erosional input from the watershed as represented by the increases in sediment concentrations of Ti and Al. The upper 20 cm of sediment, representing the last 150 years, also showed increases in C, N, P, and ¹⁵N. The increases in nutrient concentrations may be affected to various degrees by diagenetic reactions within the sediments, although the changes in concentrations also were marked by changes in the N:P ratio and in a qualitative change in the source of N as reflected in increasing δ¹⁵N. The diatoms showed modest changes in the 20th century, with increases in Asterionella formosa, Stephanodiscus hantzschii, and S. parvus. Pediastrum, a green alga, was well-preserved in the sediments and exhibited a sharp decline in relative abundance in the upper sediments. Total cyanobacteria, as represented by preserved akinetes, exhibited only minor changes in the last 1000 years. However, Aphanizomenon flos-aquae, a taxon which was formerly not present in the lake 150 years ago, but that now dominates the summer phytoplankton, has shown major increases over the past 100 years. The changes in sediment composition are consistent with activities including timber harvest, drainage of wetlands, and agricultural activities associated with livestock grazing, irrigated cropland, and hydrologic modifications.