Flexgrepps--flexible greedy peptide pool search: computation of near-optimal sets of degenerate polypeptides for antigenic screening

Although synthesizing and utilizing individual peptides and DNA primers has become relatively inexpensive, massively parallel probing and next-generation sequencing approaches have dramatically increased the number of molecules that can be subjected to screening; this, in turn, requires vast numbers of peptides and therefore results in significant expenses. To alleviate this issue, pools of related molecules are often used to downselect prior to testing individual sequences. A computational selection process to create pools of related sequences at large scale has not been reported for peptides. In the case of PCR primers, there have been successful attempts to address this problem by designing degenerate primers that can be produced at the same cost as conventional, unique primers and then be used to amplify several different genomic regions. We present an algorithm, "FlexGrePPS" (Flexible Greedy Peptide Pool Search), that can create a near-optimal set of peptide pools. This approach is also applicable to nucleotide sequences and outperforms most DNA primer selection programs. For the proteomic compression with FlexGrePPS, the main body of our work presented here, we demonstrate the feasibility of the computation of an exhaustive cover of pathogenic proteomes with degenerate peptides that lend themselves to antigenic screening. Furthermore, we present preliminary data that demonstrate the experimental utility of highly degenerate peptides for antigenic screening. FlexGrePPS provides a near-optimal solution for proteomic compression and there are no programs available for comparison. We also demonstrate computational performance of our GreedyPrime implementation, which is a modified version of FlexGrePPS applicable to the design of degenerate primers and is comparable to existing programs for the design of degenerate primers. Specifically, we focus on the comparisons with PAMPS and DPS-DIP, software tools that have recently been shown to be superior to other methods. FlexGrePPS forms the foundation of a novel antigenic screening methodology that is based on the representation of an entire proteome by near-optimal degenerate peptide pools. Our preliminary wet lab data indicate that the approach will likely prove successful in comprehensive wet lab studies, and hence will dramatically reduce the expenses for antigenic screening and make whole proteome screening feasible. Although FlexGrePPS was designed for computational performance in order to handle vast data sets, there is the very surprising finding that even for small data sets the primer design version of FlexGrePPS, GreedyPrime, offers similar or even superior results for MP-DPD and most MDPD instances when compared to existing methods; despite the much longer run times, other approaches did not fare significantly better in reducing the original data sets to degenerate primers. The FlexGrePPS and GreedyPrime programs are available at no charge under the GNU LGPL license at http://sourceforge.net/projects/flexgrepps/.     

Experimental inoculation of male rats with Coxiella burnetii: successful infection but no transmission to cage mates

Beginning in 2007, the largest human Q fever outbreak ever described occurred in the Netherlands. Dairy goats from intensive farms were identified as the source, amplifying Coxiella burnetii during gestation and shedding large quantities during abortions. It has been postulated that wild rodents are reservoir hosts from which C. burnetii can be transmitted to domestic animals and humans. However, little is known about the infection dynamics of C. burnetii in wild rodents. The aim of this study was to investigate whether brown rats (Rattus norvegicus) can be experimentally infected with C. burnetii and whether transmission to a cage mates occurs. Fourteen male brown rats (wild type) were intratracheally or intranasally inoculated with a Dutch C. burnetii isolate obtained from a goat. At 3 days postinoculation, a contact rat was placed with each inoculated rat. The pairs were monitored using blood samples and rectal and throat swabs for 8 weeks, and after euthanasia the spleens were collected. Rats became infected by both inoculation routes, and detection of C. burnetii DNA in swabs suggests that excretion occurred. However, based on the negative spleens in PCR and the lack of seroconversion, none of the contact animals was considered infected; thus, no transmission was observed. The reproduction ratio R(0) was estimated to be 0 (95% confidence interval = 0 to 0.6), indicating that it is unlikely that rats act as reservoir host of C. burnetii through sustained transmission between male rats. Future research should focus on other transmission routes, such as vertical transmission or bacterial shedding during parturition.     

Sex-specific SOD levels and DNA damage in painted dragon lizards (Ctenophorus pictus)

When groups of individuals differ in activities that may influence the production of reactive molecules, such as superoxide, we expect selection to result in congruent upregulation of antioxidant production in the group(s) most at risk of suffering concomitant erosion of essential tissue and biomolecules, such as DNA. We investigate this in a (near) annual lizard species, the Australian painted dragon (Ctenophorus pictus), in which males and females have fundamentally different lifestyles, with males being overtly conspicuous and aggressive, whereas females are placid and camouflaged. When kept in identical conditions to females in captivity, males had higher levels of superoxide dismutase (SOD) through the activity season, which is consistent with selection for a higher capacity of superoxide antioxidation and a lower level of DNA damage than females. Males, however, lacked the clear negative, linear relationship between SOD and DNA erosion observed in females, suggesting that female upregulation of SOD results in a more predictable antioxidation and a more immediate target for selection. Lastly, we analysed aspects of female reproduction from a DNA erosion perspective. Females closer to ovulation, hence with less remaining, circulating vitellogenin, had higher superoxide levels. Furthermore, a multiple regression analysis showed that females that produced more clutches over time suffered more DNA erosion, whereas females with higher SOD levels suffered less DNA erosion.     

Mom—It Helps When You're Right Here! Attenuation of Neural Stress Markers in Anxious Youths Whose Caregivers Are Present during fMRI

Close proximity to an attachment figure, such as a caregiver, has been shown to attenuate threat-related activity in limbic regions such as the hypothalamus in healthy individuals. We hypothesized that such features might be similarly attenuated by proximity during a potentially stressful situation in a clinically anxious population of youths. Confirmation of this hypothesis could support the role of attachment figures in the management of anxiety among children and adolescents. Three groups were analyzed: anxious children and adolescents who requested that their caregiver accompany them in the scanner room, anxious children and adolescents without their caregiver in the scanner room and healthy controls (each of N = 10). The groups were matched for age and, among the two anxious groups, for diagnosis (mean age 9.5). The children and adolescents were exposed to physical threat words during an fMRI assessment. Results indicate that activity in the hypothalamus, ventromedial, and ventrolateral prefrontal cortex were significantly reduced in anxious children and adolescents who requested that their caregiver accompany them in the scanner room compared to those without their caregiver in the scanner room. Mean activity in these regions in anxious children and adolescents with their caregiver in the scanner room was comparable to that of healthy controls. These data suggest links between social contact and neural mechanisms of emotional reactivity; specifically, presence of caregivers moderates the increase in anxiety seen with stressful stimuli. Capitalizing on the ability of anxious youths to manifest low levels of anxiety-like information processing in the presence of a caregiver could help in modeling adaptive function in behavioral treatments.     

Recent HIV-1 infection contributes to the viral diffusion over the French territory with a recent increasing frequency

Objective

To analyse the contribution of primary human immunodeficiency virus type 1 (HIV-1) infection (PHI) to the French viral epidemic.

Methods

HIV-1 pol sequences included 987 PHI from the French ANRS PRIMO cohort between 1999 and 2010 and were analysed using a population-based phylogenetic approach. Clinical features, risk factors, sexual behaviour and drug resistance for clustered and nonclustered transmission events were ascertained.

Results

Viruses from 125 (12.7%) of PHI cosegregated into 56 transmission chains, with increasing frequency during the last years (10.2% before 2006 versus 15.2% of clusters in 2006–2010, p = 0.02). The mean number of patients per cluster was 2.44. Compared to unique PHI, clusters involved more often men, infected through homosexual intercourse, of young age, with a high number of casual sexual partnerships and frequent previous HIV serological tests. Resistant strains were found in 16.0% and 11.1% of clusters and unique PHI, respectively (p = 0.11). Overall, 34% (n = 19) clusters included patients followed in French regions far apart, involving 13 clusters with at least one Parisian patient.

Conclusions

PHIs are a significant source of onward transmission, especially in the MSM population. Recently infected people contribute to the spread of the viral epidemic throughout the French territory. Survey of transmitted drug resistance and behavioural characteristics of patients involved into clustered PHI may help to guide prevention and treatment interventions.     

Biochemical and Functional Analysis of Two Plasmodium falciparum Blood-Stage 6-Cys Proteins: P12 and P41

The genomes of Plasmodium parasites that cause malaria in humans, other primates, birds, and rodents all encode multiple 6-cys proteins. Distinct 6-cys protein family members reside on the surface at each extracellular life cycle stage and those on the surface of liver infective and sexual stages have been shown to play important roles in hepatocyte growth and fertilization respectively. However, 6-cys proteins associated with the blood-stage forms of the parasite have no known function. Here we investigate the biochemical nature and function of two blood-stage 6-cys proteins in Plasmodium falciparum, the most pathogenic species to afflict humans. We show that native P12 and P41 form a stable heterodimer on the infective merozoite surface and are secreted following invasion, but could find no evidence that this complex mediates erythrocyte-receptor binding. That P12 and P41 do not appear to have a major role as adhesins to erythrocyte receptors was supported by the observation that antisera to these proteins did not substantially inhibit erythrocyte invasion. To investigate other functional roles for these proteins their genes were successfully disrupted in P. falciparum, however P12 and P41 knockout parasites grew at normal rates in vitro and displayed no other obvious phenotypic changes. It now appears likely that these blood-stage 6-cys proteins operate as a pair and play redundant roles either in erythrocyte invasion or in host-immune interactions.     

Consistent abundance distributions of marine fishes in an old,climatically buffered,infertile seascape

Aim Macroecological theory predicts that along direct physiological gradients there will be unimodal abundance distributions of species and consistent rates of assemblage turnover. However, the majority of marine studies that have investigated the realized distribution of species along latitudinal or temperature gradients have generally found unimodal distributions to be rare. We assess fish distributions along a temperature gradient in a stable oligotrophic seascape and suggest that unimodal distributions will be more common. Location Nearshore demersal fish habitat extending 1500 km along the coast of south‐western Australia. Methods The relative abundances of demersal fish species were sampled off the coast of south‐western Australia along a temperature gradient. The confounding influence of other environmental variables was tested, and the assemblage was found to be highly correlated with temperature. For the 20 most abundant species, quantile regression spline models were used to construct a model within which 95% of their abundance was expected to fall. We compared the results from this study with the proportion of unimodal species abundance distributions observed in other studies. Results Of the 20 most abundant species, 19 displayed patterns that indicated temperature was an important factor influencing their range and relative abundance; with 15 species exhibiting unimodal abundance distributions, four having ramped distribution to one end of the sampled range and one showing no consistent pattern. Main conclusions The high diversity and percentage of endemic species in terrestrial and marine habitats of south‐western Australia is likely to be due to the stable geological and oceanographic history of the region. In comparison, studies of abundance distribution in other marine systems have been conducted in relatively heterogeneous and productive environments. The old, climatically buffered, oligotrophic seascape of south‐western Australia has provided a simple system in which the consistent influence of physiological gradients on the abundance distribution of fish species can be observed.     

Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations

Phospho- and sphingolipids are crucial cellular and intracellular compounds. These lipids are required for active transport, a number of enzymatic processes, membrane formation, and cell signalling. Disruption of their metabolism leads to several diseases, with diverse neurological, psychiatric, and metabolic consequences. A large number of phospholipid and sphingolipid species can be detected and measured in human plasma. We conducted a meta-analysis of five European family-based genome-wide association studies (N = 4034) on plasma levels of 24 sphingomyelins (SPM), 9 ceramides (CER), 57 phosphatidylcholines (PC), 20 lysophosphatidylcholines (LPC), 27 phosphatidylethanolamines (PE), and 16 PE-based plasmalogens (PLPE), as well as their proportions in each major class. This effort yielded 25 genome-wide significant loci for phospholipids (smallest P-value = 9.88×10⁻²⁰⁴) and 10 loci for sphingolipids (smallest P-value = 3.10×10⁻⁵⁷). After a correction for multiple comparisons (P-value<2.2×10⁻⁹), we observed four novel loci significantly associated with phospholipids (PAQR9, AGPAT1, PKD2L1, PDXDC1) and two with sphingolipids (PLD2 and APOE) explaining up to 3.1% of the variance. Further analysis of the top findings with respect to within class molar proportions uncovered three additional loci for phospholipids (PNLIPRP2, PCDH20, and ABDH3) suggesting their involvement in either fatty acid elongation/saturation processes or fatty acid specific turnover mechanisms. Among those, 14 loci (KCNH7, AGPAT1, PNLIPRP2, SYT9, FADS1-2-3, DLG2, APOA1, ELOVL2, CDK17, LIPC, PDXDC1, PLD2, LASS4, and APOE) mapped into the glycerophospholipid and 12 loci (ILKAP, ITGA9, AGPAT1, FADS1-2-3, APOA1, PCDH20, LIPC, PDXDC1, SGPP1, APOE, LASS4, and PLD2) to the sphingolipid pathways. In large meta-analyses, associations between FADS1-2-3 and carotid intima media thickness, AGPAT1 and type 2 diabetes, and APOA1 and coronary artery disease were observed. In conclusion, our study identified nine novel phospho- and sphingolipid loci, substantially increasing our knowledge of the genetic basis for these traits.     

Multi-parameter automodels and their applications

Motivated by the modelling of non-Gaussian data or positivelycorrelated data on a lattice, extensions of Besag's automodelsto exponential families with multi-dimensional parameters havebeen proposed recently. We provide a multiple-parameter analogueof Besag's one-dimensional result that gives the necessary formof the exponential families for the Markov random field's conditionaldistributions. We propose estimation of parameters by maximumpseudolikelihood and give a proof of the consistency of theestimators for the multi-parameter automodel. The methodologyis illustrated with examples, in particular the building ofa cooperative system with beta conditional distributions. Wealso indicate future applications of these models to the analysisof mixed-state spatial data.