The imidazopyrrolopyridine analogue AG110 is a novel, highly selective inhibitor of pestiviruses that targets the viral RNA-dependent RNA polymerase at a hot spot for inhibition of viral replication

Ethyl 2-methylimidazo[1,2-a]pyrrolo[2,3-c]pyridin-8-carboxylate (AG110) was identified as a potent inhibitor of pestivirus replication. The 50% effective concentration values for inhibition of bovine viral diarrhea virus (BVDV)-induced cytopathic effect, viral RNA synthesis, and production of infectious virus were 1.2 +/- 0.5 microM, 5 +/- 1 microM, and 2.3 +/- 0.3 microM, respectively. AG110 proved inactive against the hepatitis C virus and a flavivirus. AG110 inhibits BVDV replication at a time point that coincides with the onset of intracellular viral RNA synthesis. Drug-resistant mutants carry the E291G mutation in the viral RNA-dependent RNA polymerase (RdRp). AG110-resistant virus is cross-resistant to the cyclic urea compound 1453 which also selects for the E291G drug resistance mutation. Moreover, BVDV that carries the F224S mutation (because of resistance to the imidazopyridine 5-[(4-bromophenyl)methyl]-2-phenyl-5H-imidazo[4,5-c]pyridine [BPIP]and VP32947) is also resistant to AG110. AG110 did not inhibit the in vitro activity of recombinant BVDV RdRp but inhibited the activity of BVDV replication complexes (RCs). Molecular modeling revealed that E291 is located in a small cavity near the tip of the finger domain of the RdRp about 7 A away from F224. Docking of AG110 in the crystal structure of the BVDV RdRp revealed several potential contacts including with Y257. The E291G mutation might enable the free rotation of Y257, which might in turn destabilize the backbone of the loop formed by residues 223 to 226, rendering more mobility to F224 and, hence, reducing the affinity for BPIP and VP32947. It is concluded that a single drug-binding pocket exists within the finger domain region of the BVDV RdRp that consists of two separate but potentially overlapping binding sites rather than two distinct drug-binding pockets.     

Physical activity-related energy expenditure with the RT3 and TriTrac accelerometers in overweight adults

Objective: The objective was to evaluate two accelerometers, the RT3 and the TriTrac‐R3D for their ability to produce estimates of physical activity‐related energy expenditure (PAEE) in overweight/obese adults. Research Methods and Procedures: PAEE estimates from both accelerometers were obtained in two experiments. In Experiment 1, 13 overweight/obese subjects (BMI 34.2 ± 6.4 kg/m²) were monitored over 2 weeks in everyday life, PAEE being simultaneously measured by the doubly labeled water method (DLW). In Experiment 2, 8 overweight/obese subjects (BMI 34.3 ± 5.0 kg/m²) and 10 normal‐weight subjects (BMI 20.8 ± 2.1 kg/m²) were monitored during a treadmill walking protocol, PAEE being simultaneously measured by indirect calorimetry. Results: In Experiment 1, there was no significant difference between methods in mean PAEE (DLW: 704 ± 223 kcal/d, RT3: 656 ± 140 kcal/d, TriTrac‐R3D 624 ± 419 kcal/d). The relative difference between methods (accelerometer vs. DLW) was ?17.1% ± 16.7% for the RT3 and ?20.0 ± 44.6% for the TriTrac‐R3D. Correlation for PAEE between RT3 and DLW was higher than between TriTrac‐R3D and DLW (r = 0.67, p < 0.05 and r = 0.36, p = 0.25, respectively). The 95% confidence interval (CI) (kcal/d) of the mean difference between methods was large, amounting to ?385 to 145 for the RT3 and ?887 to 590 for the TriTrac‐R3D. In Experiment 2, both accelerometers were sensitive to the changes in treadmill speed, with no significant difference in mean PAEE between methods in overweight/obese subjects. Conclusions: Although both accelerometers did not provide accurate estimates of PAEE at individual levels, the data suggest that RT3 has the potential to assess PAEE at group levels in overweight/obese subjects.     

Bigger teeth for longer life? Longevity and molar height in two roe deer populations

The role of tooth wear as a proximate cause of senescence in ruminants has recently been highlighted. There are two competing hypotheses to explain variation in tooth height and wear; the diet-quality hypothesis predicting increased wear in low-quality habitats, and the life-history hypothesis predicting molar height to be related to expected longevity. We compared tooth height and wear from roe deer of known age from two contrasting populations of roe deer (Capreolus capreolus) in France: Trois Fontaines (TF) with good habitat and shorter animal life expectancy and Chizé (CH) with poor habitat and longer animal life expectancy. There was no population difference in tooth wear, leading to rejection of the diet-quality hypothesis. However, despite their smaller body size, initial molar height for animals from CH was larger than for animals from TF. This provides the first evidence that variation in longevity between populations can lead to differences in molar height within a species.     

The proinflammatory cytokines IL-2, IL-15 and IL-21 modulate the repertoire of mature human natural killer cell receptors

Natural killer (NK) cells play a crucial role in the immune response to micro-organisms and tumours. Recent evidence suggests that NK cells also regulate the adaptive T-cell response and that it might be possible to exploit this ability to eliminate autoreactive T cells in autoimmune disease and alloreactive T cells in transplantation. Mature NK cells consist of a highly diverse population of cells that expresses different receptors to facilitate recognition of diseased cells and possibly pathogens themselves. Ex vivo culture of NK cells with cytokines such as IL-2 and IL-15 is an approach that permits significant expansion of the NK cell subpopulations, which are likely to have potent antitumour, antiviral, or immunomodulatory effects in autoimmunity. Our data indicate that the addition of IL-21 has a synergistic effect by increasing the numbers of NK cells on a large scale. IL-2 and IL-15 may induce the expression of killer cell immunoglobulin-like receptors (KIRs) in KIR-negative populations, the c-lectin receptor NKG2D and the natural cytotoxic receptor NKp44. The addition of IL-21 to IL-15 or IL-2 can modify the pattern of the KIR receptors and inhibit NKp44 expression by reducing the expression of the adaptor DAP-12. IL-21 also preserved the production of interferon-γ and enhanced the cytotoxic properties of NK cells. Our findings indicate that the proinflammatory cytokines IL-2, IL-15 and IL-21 can modify the peripheral repertoire of NK cells. These properties may be used to endow subpopulations of NK cells with specific phenotypes, which may be used in ex vivo cellular immunotherapy strategies.     

A comparison of methods for whole-genome QTL mapping using dense markers in four livestock species

Background

With dense genotyping, many choices exist for methods to detect quantitative trait loci (QTL) in livestock populations. However, no across-species study has been conducted on the performance of different methods using real data. We compared three methods that correct for relatedness either implicitly or explicitly: linkage and linkage disequilibrium haplotype-based analysis (LDLA), efficient mixed-model association (EMMA) analysis, and Bayesian whole-genome regression (BayesC). We analyzed one chromosome in each of five datasets (dairy cattle, beef cattle, sheep, horses, and pigs) using real genotypes based on dense single nucleotide polymorphisms and phenotypes. The P values corrected for multiple testing or Bayes factors greater than 150 were considered to be significant. To complete the real data study, we also simulated quantitative trait loci (QTL) for the same datasets based on the real genotypes. Several scenarios were chosen, with different QTL effects and linkage disequilibrium patterns. A pseudo-null statistical distribution was chosen to make the significance thresholds comparable across methods.

Results

For the real data, the three methods generally agreed within 1 or 2 cM for the locations of QTL regions and disagreed when no signals were significant (e.g. in pigs). For certain datasets, LDLA had more significant signals than EMMA or BayesC, but they were concentrated around the same peaks. Therefore, the three methods detected approximately the same number of QTL regions. For the simulated data, LDLA was slightly less powerful and accurate than either EMMA or BayesC but this depended strongly on how thresholds were set in the simulations.

Conclusions

All three methods performed similarly for real and simulated data. No method was clearly superior across all datasets or for any particular dataset. For computational efficiency and ease of interpretation, EMMA is recommended, but using more than one method is suggested.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0087-7) contains supplementary material, which is available to authorized users.     

Demography of plains zebras (Equus quagga) under heavy predation

In natural ecosystems, ungulate densities show strong temporal variations. The ecological processes driving these fluctuations are complex: food limitation and predation are both important and can interact. Survival rates are central to this debate, but data are sparse for tropical ecosystems. Here, we estimate age- and sex-specific survival rates for plains zebra in Hwange National Park, a nutrient-poor savanna with a high predator–prey ratio. We estimated survival from a detailed Capture-Mark-Recapture (CMR) monitoring based on 248 individual life histories, for the first time in an African grazer. We controlled for variations in detection probabilities among adult females, which resulted from their social structure. As expected, annual survival was low during the first year (0.441); increased in yearlings (0.560) and peaked at 0.795 and 0.847 in adult males and females respectively. The survival of adult females was lower during the dry season, which probably resulted from higher predation due to predictable movements of zebras to waterholes. Survival at all ages was low compared to ungulates without predators. The demographic model we constructed showed a declining trend (λ = 0.94), which was consistent with the data from road counts ( = 0.92). Life Table Response Experiment (LTRE) analyses using the Serengeti and Kruger populations as references showed that the main cause of this declining trend in the Hwange population was low survival in yearling and adult females; low foal survival also contributed. In this ecosystem, predation is likely to be the main ecological process causing low survival, and therefore a decline in the zebra population.     

Bladder Cancer in HIV-infected Adults: An Emerging Issue? Case-Reports and Systematic Review

Objectives

Non-AIDS-related malignancies now represent a frequent cause of death among HIV-infected patients. Albeit bladder cancer is one of the most common malignancies worldwide, it has been rarely reported among HIV-infected patients. We wished to assess the prevalence and characteristics of bladder cancer in HIV-infected patients.

Methods

We conducted a single center retrospective study from 1998 to 2013 in a university hospital in Paris. Cases of bladder cancer among HIV-infected patients were identified using the electronic records of the hospital database and of the HIV-infected cohort. Patient characteristics and outcomes were retrieved from patients charts. A systematic review of published cases of bladder cancers in patients with HIV-infection was also performed.

Results

During the study period we identified 15 HIV-infected patients (0.2% of the cohort) with a bladder cancer. Patients were mostly men (73%) and smokers (67%), with a median age of 56 years at cancer diagnosis. Bladder cancer was diagnosed a median of 14 years after HIV-infection. Most patients were on ART (86%) with median current and nadir CD4 cell counts of 506 and 195 cells/mm³, respectively. Haematuria (73%) was the most frequent presenting symptom and HPV-associated lesions were seen in 6/10 (60%) patients. Histopathology showed transitional cell carcinoma in 80% and a high proportion of tumors with muscle invasion (47%) and high histologic grade (73%). One-year survival rate was 74.6%. The systematic review identified 13 additional cases of urothelial bladder cancers which shared similar features.

Conclusions

Bladder cancers in HIV-infected patients remain rare but may occur in relatively young patients with a low nadir CD4 cell count, have aggressive pathological features and can be fatal.     

Genetic Variations in the TP53 Pathway in Native Americans Strongly Suggest Adaptation to the High Altitudes of the Andes

The diversity of the five single nucleotide polymorphisms located in genes of the TP53 pathway (TP53, rs1042522; MDM2, rs2279744; MDM4, rs1563828; USP7, rs1529916; and LIF, rs929271) were studied in a total of 282 individuals belonging to Quechua, Aymara, Chivay, Cabanaconde, Yanke, Taquile, Amantani, Anapia, Uros, Guarani Ñandeva, and Guarani Kaiowá populations, characterized as Native American or as having a high level (> 90%) of Native American ancestry. In addition, published data pertaining to 100 persons from five other Native American populations (Surui, Karitiana, Maya, Pima, and Piapoco) were analyzed. The populations were classified as living in high altitude (≥ 2,500 m) or in lowlands (< 2,500 m). Our analyses revealed that alleles USP7-G, LIF-T, and MDM2-T showed significant evidence that they were selected for in relation to harsh environmental variables related to high altitudes. Our results show for the first time that alleles of classical TP53 network genes have been evolutionary co-opted for the successful human colonization of the Andes.