Experimental procedures to identify and validate specific mRNA targets of miRNAs

Functionally matured microRNAs (miRNAs) are small single-stranded non-coding RNA molecules which are emerging as important post-transcriptional regulators of gene expression and consequently are central players in many physiological and pathological processes. Since the biological roles of individual miRNAs will be dictated by the mRNAs that they regulate, the identification and validation of miRNA/mRNA target interactions is critical for our understanding of the regulatory networks governing biological processes. We promulgate the combined use of prediction algorithms, the examination of curated databases of experimentally supported miRNA/mRNA interactions, manual sequence inspection of cataloged miRNA binding sites in specific target mRNAs, and review of the published literature as a reliable practice for identifying and prioritizing biologically important miRNA/mRNA target pairs. Once a preferred miRNA/mRNA target pair has been selected, we propose that the authenticity of a functional miRNA/mRNA target pair be validated by fulfilling four well-defined experimental criteria. This review summarizes our current knowledge of miRNA biology, miRNA/mRNA target prediction algorithms, validated miRNA/mRNA target data bases, and outlines several experimental methods by which miRNA/mRNA targets can be authenticated. In addition, a case study of human endoglin is presented as an example of the utilization of these methodologies

Phylogeny, phylogenetic inference, and cranial evolution in pitheciids and Aotus

Pitheciids, one of the major radiations of New World monkeys endemic to South and Central America, are distributed in the Amazon and Orinoco basins, and include Callicebus, Cacajao, Chiropotes, and Pithecia. Molecular phylogenetics strongly support pitheciid monophyly, whereas morphological analyses infer a range of phylogenies including a sister relationship between Aotus and Callicebus. We collected geometric morphometric cranial data from pitheciids and Aotus, and used cranial data for distance-based phylogenetic analysis and tests of phylogenetic signal. Phylogenetic analyses of pitheciids were repeated with Lagothrix, Callimico, and Saimiri outgroups for Procrustes shape with and without Aotus based on the whole cranium and six anatomical regions. All phylogenetic signal tests were significant, and tree lengths were shortest and had the least morphological change over the phylogeny for Procrustes residuals from the cranial base and palate. The majority of phylogenetic analyses of Procrustes shape for pitheciids without Aotus supported the molecular phylogeny, and with Aotus included the majority inferred an Aotus–Callicebus clade, although three analyses with Callimico as outgroup supported the molecular phylogeny. The morphological similarity of Aotus and Callicebus is likely a mix of plesiomorphy, allometry, and homoplasy, and future phylogenetic inference of living and extinct platyrrhine taxa should consider the impact of these factors alongside outgroup selection and cranial region

The potential and pitfalls of using simple dental metrics to infer the diets of African antelopes (Mammalia: Bovidae)

The use of mesowear to infer diets of extinct species is fast becoming widespread in palaeoecological studies. Nevertheless, traditional mesowear analyses suffer from a specimen number limitation, in that a minimum number of specimens identified to the species level is necessary to make accurate dietary predictions. This is problematic in many fossil African antelope (Mammalia: Bovidae) assemblages, where isolated teeth cannot always be assigned to species. Hereweexplore the possibility of using simple dental metrics to predict diets on the basis of individual teeth as well as gnathic rows using linear discriminant function analyses.We find that browsers are accurately classified at both the individual and species levels, across all models and tooth positions. Mixed feeders and grazers are classified accurately only sometimes, and this is probably a reflection of the more limited sample size of larger bodied species in our study. Body size was a highly significant predictor of the inaccurate classifications obtained in our models, with larger bodied species tending to grazing classifications and smaller bodied species browsing classifications. Nevertheless, the models correctly classify the majority of specimens we examined to their correct trophic group, as determined through stable isotope analyses or as defined through the literature. The methods outlined hold some promise for determining the diets of isolated fossil specimens unassigned to species in a simple manner and, when used in conjunction with other palaeodietary and palaeoecological proxies, may help determine palaeoenvironments more accurately

Risk-Seeking versus Risk-Avoiding Investments in Noisy Periodic Environments

We study the performance of various agent strategies in an artificial investment scenario. Agents are equipped with a budget, $x(t)$, and at each time step invest a particular fraction, $q(t)$, of their budget. The return on investment (RoI), $r(t)$, is characterized by a periodic function with different types and levels of noise. Risk-avoiding agents choose their fraction $q(t)$ proportional to the expected positive RoI, while risk-seeking agents always choose a maximum value $q_{max}$ if they predict the RoI to be positive ("everything on red"). In addition to these different strategies, agents have different capabilities to predict the future $r(t)$, dependent on their internal complexity. Here, we compare 'zero-intelligent' agents using technical analysis (such as moving least squares) with agents using reinforcement learning or genetic algorithms to predict $r(t)$. The performance of agents is measured by their average budget growth after a certain number of time steps. We present results of extensive computer simulations, which show that, for our given artificial environment, (i) the risk-seeking strategy outperforms the risk-avoiding one, and (ii) the genetic algorithm was able to find this optimal strategy itself, and thus outperforms other prediction approaches considered.Comment: 27 pp. v2 with minor corrections. See http://www.sg.ethz.ch for more inf

Bottom-Up Control of Parasites

Parasitism is a fundamental ecological interaction. Yet we understand relatively little about the ecological role of parasites compared to the role of free-living organisms. Bottom-up theory predicts that resource enhancement will increase the abundance and biomass of free-living organisms. Similarly, parasite abundance and biomass should increase in an ecosystem with resource enhancement. We tested this hypothesis in a landscape-level experiment in which salt marshes (60,000 m2 each) received elevated nutrient concentrations via flooding tidal waters for 11 yr to mimic eutrophication. Nutrient enrichment elevated the densities of the talitrid amphipod, Orchestia grillus, and the density and biomass of its trematode parasite, Levinseniella byrdi. Strikingly, L. byrdiprevalence increased over time, up to 13 times higher in nutrient-enriched marshes (30%) relative to the mean prevalence in reference marshes (2.4%). The biomass density of infected amphipods was, on average, 11 times higher in nutrient-enriched marshes (1.1 kg/ha) than in reference marshes (0.1 kg/ha), when pooling across all years. Orchestia grillus biomass comprises 67% of the arthropod community biomass; thus, nutrient enrichment elicits a substantial surge in parasitized biomass in the arthropod community. If our results are typical, they suggest that eutrophication can increase parasite abundance and biomass with chronic resource enhancement. Therefore, minimizing aquatic nutrient pollution may prevent outbreaks of parasites with aquatic hosts

The specialty choices of graduates from Brighton and Sussex Medical School: a longitudinal cohort study

BACKGROUND Since 2007 junior doctors in the UK have had to make major career decisions at a point when previously many had not yet chosen a specialty. This study examined when doctors in this new system make specialty choices, which factors influence choices, and whether doctors who choose a specialty they were interested in at medical school are more confident in their choice than those doctors whose interests change post-graduation. METHODS Two cohorts of students in their penultimate year at one medical school (n = 227/239) were asked which specialty interested them as a career. Two years later, 210/227 were sent a questionnaire measuring actual specialty chosen, confidence, influence of perceptions of the specialty and experiences on choice, satisfaction with medicine, personality, self-efficacy, and demographics. Medical school and post-graduation choices in the same category were deemed 'stable'. Predictors of stability, and of not having chosen a specialty, were calculated using bootstrapped logistic regression. Differences between specialties on questionnaire factors were analysed. RESULTS 50% responded (n = 105/277; 44% of the 239 Year 4 students). 65% specialty choices were 'stable'. Factors univariately associated with stability were specialty chosen, having enjoyed the specialty at medical school or since starting work, having first considered the specialty earlier. A regression found doctors who chose psychiatry were more likely to have changed choice than those who chose general practice. Confidence in the choice was not associated with stability. Those who chose general practice valued lifestyle factors. A psychiatry choice was associated with needing a job and using one's intellect to help others. The decision to choose surgical training tended to be made early. Not having applied for specialty training was associated with being lower on agreeableness and conscientiousness. CONCLUSION Medical school experiences are important in specialty choice but experiences post-graduation remain significant, particularly in some specialties (psychiatry in our sample). Career guidance is important at medical school and should be continued post-graduation, with senior clinicians supported in advising juniors. Careers advice in the first year post-graduation may be particularly important, especially for specialties which have difficulty recruiting or are poorly represented at medical school

A Natural Plasmid Uniquely Encodes Two Biosynthetic Pathways Creating a Potent Anti-MRSA Antibiotic

Background Understanding how complex antibiotics are synthesised by their producer bacteria is essential for creation of new families of bioactive compounds. Thiomarinols, produced by marine bacteria belonging to the genus Pseudoalteromonas, are hybrids of two independently active species: the pseudomonic acid mixture, mupirocin, which is used clinically against MRSA, and the pyrrothine core of holomycin. Methodology/Principal Findings High throughput DNA sequencing of the complete genome of the producer bacterium revealed a novel 97 kb plasmid, pTML1, consisting almost entirely of two distinct gene clusters. Targeted gene knockouts confirmed the role of these clusters in biosynthesis of the two separate components, pseudomonic acid and the pyrrothine, and identified a putative amide synthetase that joins them together. Feeding mupirocin to a mutant unable to make the endogenous pseudomonic acid created a novel hybrid with the pyrrothine via “mutasynthesis” that allows inhibition of mupirocin-resistant isoleucyl-tRNA synthetase, the mupirocin target. A mutant defective in pyrrothine biosynthesis was also able to incorporate alternative amine substrates. Conclusions/Significance Plasmid pTML1 provides a paradigm for combining independent antibiotic biosynthetic pathways or using mutasynthesis to develop a new family of hybrid derivatives that may extend the effective use of mupirocin against MRSA

Exploring morphological generality in the Old World monkey postcranium using an ecomorphological framework

Nearly all primates are ecologically dependent on trees but they are nonetheless found in an enormous range of habitats, from highly xeric environments to dense rainforest. Most primates have a relatively ‘generalised’ skeleton, enabling locomotor flexibility and facilitating other crucial functions, such as manual foraging and grooming. In this paper we explore associations between habitat, locomotion and morphology in the forelimbs of cercopithecids (Old World monkeys), contextualising their skeletal ecomorphological patterns with those of other mammals, and complementing functional morphological analyses with phylogenetic comparative techniques. We investigate the ecomorphological signals present in the generalised primate postcranium, and how an ancestral arboreal ‘bauplan’ might be modified to incorporate terrestriality or exploit distinct arboreal substrates. Analysis of ecomorphological variation in guenons indicates that terrestrial Chlorocebus species retain core elements of a general guenon form, with modifications for terrestriality that vary by species. Adaptation to different modes of arboreality has also occurred in Cercopithecus. The considerable morphological similarity in the guenons sampled emphasises the importance of generality in the primate postcranium – much forelimb variation appears to have emerged stochastically, with a smaller number of traits having a strong functional signal. Analysis of a broader sample of cercopithecids and comparison with felids, suids and bovids indicates that although the cercopithecid humerus has functional morphological signals that enable specimens to be assigned with a reasonable degree of certainty to habitat groups, there is considerable overlap in the specimens assigned to each habitat group. This probably reflects ecological dependence on trees, even in predominantly terrestrial species, as well as the multiple functions of the forelimb and, in some cases, wide geographic distributions that promote intraspecific variation. The use of phylogenetic correction reduced the discriminatory power of the models, indicating that, like allometry, phylogeny contains important ecomorphological information, and should not necessarily be factored out of analyses