Irreducibility and efficiency of ESIP to sample marker genotypes in large pedigrees with loops

Markov chain Monte Carlo (MCMC) methods have been proposed to overcome computational problems in linkage and segregation analyses. This approach involves sampling genotypes at the marker and trait loci. Among MCMC methods, scalar-Gibbs is the easiest to implement, and it is used in genetics. However, the Markov chain that corresponds to scalar-Gibbs may not be irreducible when the marker locus has more than two alleles, and even when the chain is irreducible, mixing has been observed to be slow. Joint sampling of genotypes has been proposed as a strategy to overcome these problems. An algorithm that combines the Elston-Stewart algorithm and iterative peeling (ESIP sampler) to sample genotypes jointly from the entire pedigree is used in this study. Here, it is shown that the ESIP sampler yields an irreducible Markov chain, regardless of the number of alleles at a locus. Further, results obtained by ESIP sampler are compared with other methods in the literature. Of the methods that are guaranteed to be irreducible, ESIP was the most efficient.     

Do climatically similar regions contain similar alien floras? A comparison between the mediterranean areas of central Chile and California

Aim Taxonomic comparisons of alien floras across climatically similar regions have been proposed as a powerful approach for increasing our understanding of plant invasions across scales. However, detailed comparisons between the alien biotas of climatically similar regions are scarce. This study aims to compare the taxonomic patterns of alien species richness in mediterranean‐type climate areas of central Chile and California, in order to better understand how climatically similar regions converge or diverge in terms of their alien flora. Location Central Chile and California, United States. Methods We compared the alien floras of the state of California in the United States and central Chile, considering within‐region variation and taxonomic composition up to the species level. To test for within‐region variation, administrative units and counties were grouped within seven latitudinal bands for each region. We tested for differences in the relative contributions of the various origins of the naturalized species to each region. We used a family naturalization index to establish which families had relatively higher numbers of naturalized species in each region. We evaluated the similarity, using cluster analyses with Jaccard’s similarity index, of alien taxa between regions and latitudinal bands using presence–absence matrices at the species, genus and family levels. We used principal components analysis to determine the presence of a compositional gradient including all latitudinal bands. Results We recorded 1212 alien plant species in California and 593 in central Chile, of which 491 are shared between the two regions. These figures include 25 species that are native to California and 37 that are native to Chile. A comparison between the alien floras of central Chile and California reveals three major trends: (1) higher naturalized species diversity for California than for Chile, at all taxonomic levels; (2) differences in the proportion of species according to origin, with America, Africa, Asia and Australia providing a larger number of species in California than in Chile; (3) segregation between regions in terms of taxonomic composition of their alien flora, and a rather weak differentiation within regions; and (4) a trend towards higher similarity between the alien floras of latitudinal bands associated with higher levels of human disturbances. Main conclusions The alien floras of central Chile and California are significantly different, but this difference diminishes in highly disturbed areas. Thus, the current high levels of species movement caused by globalization, together with increasing levels of anthropogenic disturbances, should reduce the differentiation of the alien floras in these regions, increasing overall biotic homogenization.     

Genome‐wide association of functional traits linked with Campylobacter jejuni survival from farm to fork

Campylobacter jejuni is a major cause of bacterial gastroenteritis worldwide, primarily associated with the consumption of contaminated poultry. C. jejuni lineages vary in host range and prevalence in human infection, suggesting differences in survival throughout the poultry processing chain. From 7343 MLST‐characterised isolates, we sequenced 600 C. jejuni and C. coli isolates from various stages of poultry processing and clinical cases. A genome‐wide association study (GWAS) in C. jejuni ST‐21 and ST‐45 complexes identified genetic elements over‐represented in clinical isolates that increased in frequency throughout the poultry processing chain. Disease‐associated SNPs were distinct in these complexes, sometimes organised in haplotype blocks. The function of genes containing associated elements was investigated, demonstrating roles for cj1377c in formate metabolism, nuoK in aerobic survival and oxidative respiration, and cj1368‐70 in nucleotide salvage. This work demonstrates the utility of GWAS for investigating transmission in natural zoonotic pathogen populations and provides evidence that major C. jejuni lineages have distinct genotypes associated with survival, within the host specific niche, from farm to fork.     

N-Naphthoyl-substituted indole thio-barbituric acid analogs inhibit the helicase activity of the hepatitis C virus NS3

The hepatitis C virus (HCV) represents a substantial threat to human health worldwide. The virus expresses a dual-function protein, NS3 having both protease and RNA helicase activities that are essential for productive viral replication and sustained infections. While viral protease and polymerase inhibitors have shown great successes in treating chronic HCV infections, drugs that specifically target the helicase activity have not advanced. A robust and quantitative 96-well plate-based fluorescent DNA unwinding assay was used to screen a class of indole thio-barbituric acid (ITBA) analogs using the full-length, recombinant HCV NS3, and identified three naphthoyl-containing analogs that efficiently inhibited NS3 helicase activity in a dose-dependent manner, with observed IC₅₀ values of 21–24?µM. Standard gel electrophoresis helicase assays using radiolabeled duplex DNA and RNA NS3 substrates confirmed the inhibition of NS3 unwinding activity. Subsequent anisotropy measurements demonstrated that the candidate compounds did not disrupt NS3 binding to nucleic acids. Additionally, the rate of ATP hydrolysis and the protease activity were also not affected by the inhibitors. Thus, these results indicate that the three ITBA analogs containing N-naphthoyl moieties are the foundation of a potential series of small molecules capable of inhibiting NS3 activity via a novel interaction with the helicase domain that prevents the productive unwinding of nucleic acid substrates, and may represent the basis for a new class of therapeutic agents with the potential to aid in the treatment and eradication of hepatitis C virus.     

Prevalence of and Risk Factors for Oral Human Papillomavirus Infection among HIV-Positive and HIV-Negative People Who Inject Drugs

Background

Human papillomavirus (HPV) causes most oropharyngeal cancers in the United States. Oral HPV prevalence is associated with immunosuppression, and drug use can be immunosuppressive, but the epidemiology of oral HPV among people who use drugs is not well described.

Methods

We enrolled men and women with a current or prior history of injection drug use in this cross-sectional sub-study within the AIDS Linked to the Intravenous Experience (ALIVE) cohort. We tested oral rinse samples for 37 types of HPV DNA and collected self-reported risk factor information. We compared oral HPV prevalence across categories using chi-squared statistics and multivariable logistic regression.

Results

Among 199 subjects, 32% were HIV-positive (median CD4 count 384 cells/μL), 90% were Black, 56% had less than a high school education, 17% had recently used injection drugs, and the median age was 54 years. Most had performed oral sex (82%) but had fewer than 5 lifetime partners (58%). The prevalence of any oral HPV was 29%, and of any oncogenic oral HPV was 13%. Oral HPV prevalence was high among both heterosexual men (30%) and women (20%). After adjustment, odds of oral HPV were increased among HIV-positive individuals with a low CD4 count (<350 cells/μl, aOR = 2.7, 95%CI = 1.2–6.4, vs. HIV-negative individuals), but not among HIV-positive individuals with a higher CD4 cell count. Odds were also elevated for those who had recently performed oral sex on a woman (aOR = 2.2, 95%CI = 1.01–4.6) and, even after this adjustment, among bisexual/lesbian females (aOR = 5.6, 95%CI = 1.4–23, vs. heterosexual females). Oral HPV prevalence was not associated with vaginal sex, performing oral sex on a man, or recent drug use.

Conclusions

Recent drug use was not associated with oral HPV prevalence in our study. However, despite modest numbers of sexual partners, the prevalence of oral HPV among this largely Black population with lower socioeconomic status was high.     

Proline Dehydrogenase Regulates Redox State and Respiratory Metabolism in Trypanosoma cruzi

Over the past three decades, L-proline has become recognized as an important metabolite for trypanosomatids. It is involved in a number of key processes, including energy metabolism, resistance to oxidative and nutritional stress and osmoregulation. In addition, this amino acid supports critical parasite life cycle processes by acting as an energy source, thus enabling host-cell invasion by the parasite and subsequent parasite differentiation. In this paper, we demonstrate that L-proline is oxidized to Δ¹-pyrroline-5-carboxylate (P5C) by the enzyme proline dehydrogenase (TcPRODH, E.C. 1.5.99.8) localized in Trypanosoma cruzi mitochondria. When expressed in its active form in Escherichia coli, TcPRODH exhibits a K_m of 16.58±1.69 µM and a V_max of 66±2 nmol/min mg. Furthermore, we demonstrate that TcPRODH is a FAD-dependent dimeric state protein. TcPRODH mRNA and protein expression are strongly upregulated in the intracellular epimastigote, a stage which requires an external supply of proline. In addition, when Saccharomyces cerevisiae null mutants for this gene (PUT1) were complemented with the TcPRODH gene, diminished free intracellular proline levels and an enhanced sensitivity to oxidative stress in comparison to the null mutant were observed, supporting the hypothesis that free proline accumulation constitutes a defense against oxidative imbalance. Finally, we show that proline oxidation increases cytochrome c oxidase activity in mitochondrial vesicles. Overall, these results demonstrate that TcPRODH is involved in proline-dependant cytoprotection during periods of oxidative imbalance and also shed light on the participation of proline in energy metabolism, which drives critical processes of the T. cruzi life cycle.     

Chemosensory enrichment as a simple and effective way to improve the welfare of captive lizards

Environmental enrichment has proven to be a useful and effective welfare tool in order to evaluate and enhance the well‐being of captive animals, but only when it is based on detailed knowledge of each species' natural behaviour. Chemoreception is fundamental to many aspects of reptilian biology; however, sensory enrichment with chemical stimuli has rarely been applied to reptiles. In this study, we evaluate the use of chemosensory enrichment as a method to enhance the welfare of Podarcis liolepis. For seven weeks, we exposed field‐caught males to scents from donor conspecific males collected on pieces of filter paper (i.e., “enriched” group, n = 18), and compared their behaviour to that of control males provided with unscented pieces of filter paper (n = 18). We measured the occurrence of normal (e.g., locomotion) and abnormal (escape attempts) behaviours each day for three weeks. In addition, we conducted two exploration tests and a visual barrier test. Compared to controls, enriched lizards showed a consistent long‐term decrease (29%–38%) in the occurrence of escape attempts. During exploration tests, enriched lizards spent less time performing escape attempts and devoted more time to perching than controls. As expected, both control and enriched lizards showed a reduction of time in locomotion and an increase in the time spent perching between the first and second exploration test, but these changes were significantly more pronounced for enriched animals. Taken together, our results suggest improved welfare of enriched animals, as they spent less time engaging in abnormal behaviours, more time in normal behaviours, and showed signs of faster habituation to a novel environment. Chemosensory enrichment is a relatively simple enrichment strategy that could potentially be applied to improve the welfare of a wide range of captive lizards, and reptiles at large.     

Proteomic analysis of lysine acetylation sites in rat tissues reveals organ specificity and subcellular patterns

Lysine acetylation is a major posttranslational modification involved in a broad array of physiological functions. Here, we provide an organ-wide map of lysine acetylation sites from 16 rat tissues analyzed by high-resolution tandem mass spectrometry. We quantify 15,474 modification sites on 4,541 proteins and provide the data set as a web-based database. We demonstrate that lysine acetylation displays site-specific sequence motifs that diverge between cellular compartments, with a significant fraction of nuclear sites conforming to the consensus motifs G-AcK and AcK-P. Our data set reveals that the subcellular acetylation distribution is tissue-type dependent and that acetylation targets tissue-specific pathways involved in fundamental physiological processes. We compare lysine acetylation patterns for rat as well as human skeletal muscle biopsies and demonstrate its general involvement in muscle contraction. Furthermore, we illustrate that acetylation of fructose-bisphosphate aldolase and glycerol-3-phosphate dehydrogenase serves as a cellular mechanism to switch off enzymatic activity.