Metazoan-protozoan parasite co-infections and host body weight in St Kilda Soay sheep

For hundreds of years, the unmanaged Soay sheep population on St Kilda has survived despite enduring presumably deleterious co-infections of helminth, protozoan and arthropod parasites and intermittent periods of starvation. Important parasite taxa in young Soay sheep are strongyles (Trichostrongylus axei, Trichostrongylus vitrinus and Teladorsagia circumcincta), coccidia (11 Eimeria species) and keds (Melophagus ovinus) and in older animals, Teladorsagia circumcincta. In this research, associations between the intensity of different parasite taxa were investigated. Secondly, the intensities of different parasite taxa were tested for associations with variation in host weight, which is itself a determinant of over-winter survival in the host population. In lambs, the intensity of strongyle eggs was positively correlated with that of Nematodirus spp. eggs, while in yearlings and adults strongyle eggs and coccidia oocysts were positively correlated. In lambs and yearlings, of the parasite taxa tested, only strongyle eggs were significantly and negatively associated with host weight. However, in adult hosts, strongyles and coccidia were independently and negatively associated with host weight. These results are consistent with the idea that strongyles and coccidia are exerting independent selection on Soay sheep.     

Pat1 contains distinct functional domains that promote P-body assembly and activation of decapping

The control of mRNA degradation and translation are important aspects of gene regulation. Recent results suggest that translation repression and mRNA decapping can be intertwined and involve the formation of a quiescent mRNP, which can accumulate in cytoplasmic foci referred to as P bodies. The Pat1 protein is a key component of this complex and an important activator of decapping, yet little is known about its function. In this work, we analyze Pat1 in Saccharomyces cerevisiae function by deletion and functional analyses. Our results identify two primary functional domains in Pat1: one promoting translation repression and P-body assembly and a second domain promoting mRNA decapping after assembly of the mRNA into a P-body mRNP. In addition, we provide evidence that Pat1 binds RNA and has numerous domain-specific interactions with mRNA decapping factors. These results indicate that Pat1 is an RNA binding protein and a multidomain protein that functions at multiple stages in the process of translation repression and mRNA decapping.     

Density-dependent variation in lifetime breeding success and natural and sexual selection in Soay rams

Variation in male lifetime breeding success (LBS) is central to understanding selection, yet it has rarely been measured in natural populations of large mammals. Here, we first describe variation in the opportunity for selection in cohorts of Soay rams (Ovis aries) on the archipelago of St. Kilda, Scotland, that were born during years of varying population density. Variation in LBS is closely coupled with demography, as rams born in years of low density following population crashes enjoy greater LBS than do those born in high-density years. Paradoxically, the opportunity for selection was greatest in the largest cohorts, those born in years of high population density, owing to low juvenile breeding success and overwinter survival. Variation in longevity and the contribution of nonbreeders were the most important components of the total variance in LBS in cohorts born in years of high density, while variation in fecundity was more important in cohorts born in low-density years. The opportunity for sexual selection is thus stronger in cohorts born in low-density years, as many rams in these cohorts survive to compete for mates as adults in subsequent ruts. Variation in population density in the year of birth also influenced the intensity of selection. Individuals born in years of high population density underwent strong natural selection in favor of longer hindlimbs over their first winter. In contrast, in cohorts born in low-density years, there was no natural selection on hindlimb in the first year of life. Longer hindlimbs were associated with increased fecundity over the entire lifetime of individuals born in low-density years. Natural and sexual selection thus act on the same trait in the same direction at different life-history stages in Soay rams, depending on the population density experienced in the year of birth.     

Quantitative trait loci (QTL) mapping of resistance to strongyles and coccidia in the free-living Soay sheep (Ovis aries)

A genome-wide scan was performed to detect quantitative trait loci (QTL) for resistance to gastrointestinal parasites and ectoparasitic keds segregating in the free-living Soay sheep population on St. Kilda (UK). The mapping panel consisted of a single pedigree of 882 individuals of which 588 were genotyped. The Soay linkage map used for the scans comprised 251 markers covering the whole genome at average spacing of 15cM. The traits here investigated were the strongyle faecal egg count (FEC), the coccidia faecal oocyst count (FOC) and a count of keds (Melophagus ovinus). QTL mapping was performed by means of variance component analysis so that the genetic parameters of the study traits were also estimated and compared with previous studies in Soay and domestic sheep. Strongyle FEC and coccidia FOC showed moderate heritability (h(2)=0.26 and 0.22, respectively) in lambs but low heritability in adults (h(2)<0.10). Ked count appeared to have very low h(2) in both lambs and adults. Genome scans were performed for the traits with moderate heritability and two genomic regions reached the level of suggestive linkage for coccidia FOC in lambs (logarithm of the odds=2.68 and 2.21 on chromosomes 3 and X, respectively). We believe this is the first study to report a QTL search for parasite resistance in a free-living animal population and therefore may represent a useful reference for similar studies aimed at understanding the genetics of host-parasite co-evolution in the wild.     

Nucleation of β-rich oligomers and β-barrels in the early aggregation of human islet amyloid polypeptide

The self-assembly of human islet amyloid polypeptide (hIAPP) into β-sheet rich amyloid aggregates is associated with pancreatic β-cell death in type 2 diabetes (T2D). Prior experimental studies of hIAPP aggregation reported the early accumulation of α-helical intermediates before the rapid conversion into β-sheet rich amyloid fibrils, as also corroborated by our experimental characterizations with transmission electron microscopy and Fourier transform infrared spectroscopy. Although increasing evidence suggests that small oligomers populating early hIAPP aggregation play crucial roles in cytotoxicity, structures of these oligomer intermediates and their conformational conversions remain unknown, hindering our understanding of T2D disease mechanism and therapeutic design targeting these early aggregation species. We further applied large-scale discrete molecule dynamics simulations to investigate the oligomerization of full-length hIAPP, employing multiple molecular systems of increasing number of peptides. We found that the oligomerization process was dynamic, involving frequent inter-oligomeric exchanges. On average, oligomers had more α-helices than β-sheets, consistent with ensemble-based experimental measurements. However, in ~4–6% independent simulations, β-rich oligomers expected as the fibrillization intermediates were observed, especially in the pentamer and hexamer simulations. These β-rich oligomers could adopt β-barrel conformations, recently postulated to be the toxic oligomer species but only observed computationally in the aggregates of short amyloid protein fragments. Free-energy analysis revealed high energies of these β-rich oligomers, supporting the nucleated conformational changes of oligomers in amyloid aggregation. β-barrel oligomers of full-length hIAPP with well-defined three-dimensional structures may play an important pathological role in T2D etiology and may be a therapeutic target for the disease.     

Quantitative genetics of growth and cryptic evolution of body size in an island population

While evolution occurs when selection acts on a heritable trait, empirical studies of natural systems have frequently reported phenotypic stasis under these conditions. We performed quantitative genetic analyses of weight and hindleg length in a free-living population of Soay sheep (Ovis aries) to test whether genetic constraints can explain previously reported stasis in body size despite evidence for strong positive directional selection. Genetic, maternal and environmental covariance structures were estimated across ontogeny using random regression animal models. Heritability increased with age for weight and hindleg length, though both measures of size were highly heritable across ontogeny. Genetic correlations among ages were generally strong and uniformly positive, and the covariance structures were also highly integrated across ontogeny. Consequently, we found no constraint to the evolution of larger size itself. Rather we expect size at all ages to increase in response to positive selection acting at any age. Consistent with expectation, predicted breeding values for age-specific size traits have increased over a twenty-year period, while maternal performance for offspring size has declined. Re-examination of the phenotypic data confirmed that sheep are not getting larger, but also showed that there are significant negative trends in size at all ages. The genetic evolution is therefore cryptic, with the response to selection presumably being masked at the phenotypic level by a plastic response to changing environmental conditions. Density-dependence, coupled with systematically increasing population size, may contribute to declining body size but is insufficient to completely explain it. Our results demonstrate that an increased understanding of the genetic basis of quantitative traits, and of how plasticity and microevolution can occur simultaneously, is necessary for developing predictive models of phenotypic change in nature.     

Survival costs of reproduction are mediated by parasite infection in wild Soay sheep

A trade‐off between current and future fitness potentially explains variation in life‐history strategies. A proposed mechanism behind this is parasite‐mediated reproductive costs: individuals that allocate more resources to reproduction have fewer to allocate to defence against parasites, reducing future fitness. We examined how reproduction influenced faecal egg counts (FEC) of strongyle nematodes using data collected between 1989 and 2008 from a wild population of Soay sheep in the St. Kilda archipelago, Scotland (741 individuals). Increased reproduction was associated with increased FEC during the lambing season: females that gave birth, and particularly those that weaned a lamb, had higher FEC than females that failed to reproduce. Structural equation modelling revealed future reproductive costs: a positive effect of reproduction on spring FEC and a negative effect on summer body weight were negatively associated with overwinter survival. Overall, we provide evidence that parasite resistance and body weight are important mediators of survival costs of reproduction.     

Phylogeography of the human mitochondrial L1c haplogroup: genetic signatures of the prehistory of Central Africa

Interindividual variation of human mitochondrial DNA has been extensively studied over the last two decades, and its usefulness for reconstructing evolutionary relationships of extant populations has been proved. However, some mitochondrial lineages still need to be studied using a combination of larger and tailored datasets and increased level of resolution in order to shed light on their origin and on the processes underlying their present distribution. In this study, we analyze the phylogeny of the L1c haplogroup of human mitochondrial DNA using sequence data from hypervariable regions 1 and 2 obtained from 455 individuals (extracted from a total sampling of 2542 individuals) belonging to sub-Saharan African and African-American populations. We propose a substantial revision of L1c phylogeny, by introducing one new sub-haplogroup (L1c4), two new L1c1 clades (L1c1b and L1c1c), and by reassigning the previous L1c1a1 sequences to a clade which we termed L1c5. The new phylogeny encompasses distinct lineages with different evolutionary histories. In fact, based on population frequency, internal variation and mismatch distribution, we propose that L1c1b, L1c1c and L1c2 originated in Bantu ancestors, whereas L1c1a, L1c4 and L1c5 evolved among Western Pygmies. The population structure of L1c is not comparable to any known mitochondrial or, even, Y-chromosomal haplogroup, and challenges the current view that most of mtDNA variation in Pygmies might reflect admixture with Bantu or a persistence of plesiomorphic characters. In fact, the unique feature of the L1c is that it retains a signature of a phase common to the ancestors of the Bantu and Western Pygmies, while encompassing some specific sub-clades which can indicate their divergence. This allowed us to attempt a phylogenetically based assessment of the evolutionary relationships between the two groups. Taking into consideration estimates of the time to the most recent common ancestor of L1c and its clades together with archaeological and paleoclimatological evidence, we propose that the ancestors of Bantu and Western Pygmies separated between 60 and 30 kya.     

The capsule polysaccharide structure and biogenesis for non-O1 Vibrio cholerae NRT36S: genes are embedded in the LPS region

Background  

In V. cholerae, the biogenesis of capsule polysaccharide is poorly understood. The elucidation of capsule structure and biogenesis is critical to understanding the evolution of surface polysaccharide and the internal relationship between the capsule and LPS in this species. V. cholerae serogroup O31 NRT36S, a human pathogen that produces a heat-stable enterotoxin (NAG-ST), is encapsulated. Here, we report the covalent structure and studies of the biogenesis of the capsule in V. cholerae NRT36S.     

Genomics and the renaissance of generalism

A meeting report of the sessions on human, eukaryotic and bacterial genome sequencing at the American Society for Microbiology and Institut Pasteur joint conference: Genomes 2000 International Conference on Microbial and Model Genomes, Paris, April 11-15, 2000