Genomic approaches to understanding population divergence and speciation in birds

© 2016 American Ornithologists\u27 Union. The widespread application of high-throughput sequencing in studying evolutionary processes and patterns of diversification has led to many important discoveries. However, the barriers to utilizing these technologies and interpreting the resulting data can be daunting for first-time users. We provide an overview and a brief primer of relevant methods (e.g., whole-genome sequencing, reduced-representation sequencing, sequence-capture methods, and RNA sequencing), as well as important steps in the analysis pipelines (e.g., loci clustering, variant calling, whole-genome and transcriptome assembly). We also review a number of applications in which researchers have used these technologies to address questions related to avian systems. We highlight how genomic tools are advancing research by discussing their contributions to 3 important facets of avian evolutionary history. We focus on (1) general inferences about biogeography and biogeographic history, (2) patterns of gene flow and isolation upon secondary contact and hybridization, and (3) quantifying levels of genomic divergence between closely related taxa. We find that in many cases, high-throughput sequencing data confirms previous work from traditional molecular markers, although there are examples in which genome-wide genetic markers provide a different biological interpretation. We also discuss how these new data allow researchers to address entirely novel questions, and conclude by outlining a number of intellectual and methodological challenges as the genomics era moves forward

Identification of regulatory variants associated with genetic susceptibility to meningococcal disease

Non-coding genetic variants play an important role in driving susceptibility to complex diseases but their characterization remains challenging. Here, we employed a novel approach to interrogate the genetic risk of such polymorphisms in a more systematic way by targeting specific regulatory regions relevant for the phenotype studied. We applied this method to meningococcal disease susceptibility, using the DNA binding pattern of RELA - a NF-kB subunit, master regulator of the response to infection - under bacterial stimuli in nasopharyngeal epithelial cells. We designed a custom panel to cover these RELA binding sites and used it for targeted sequencing in cases and controls. Variant calling and association analysis were performed followed by validation of candidate polymorphisms by genotyping in three independent cohorts. We identified two new polymorphisms, rs4823231 and rs11913168, showing signs of association with meningococcal disease susceptibility. In addition, using our genomic data as well as publicly available resources, we found evidences for these SNPs to have potential regulatory effects on ATXN10 and LIF genes respectively. The variants and related candidate genes are relevant for infectious diseases and may have important contribution for meningococcal disease pathology. Finally, we described a novel genetic association approach that could be applied to other phenotypes

Plasma lipid profiles discriminate bacterial from viral infection in febrile children

Fever is the most common reason that children present to Emergency Departments. Clinical signs and symptoms suggestive of bacterial infection ar

Opsoclonus-myoclonus syndrome associated with group A streptococcal infection

This report describes the unusual syndrome of opsoclonus-myoclonus associated with group A streptococcal infection in a 9-year-old Nepalese boy

Sleeping sickness in brothers in London

Brothers 9 and 14 years of age presented in London with fever and skin lesions after a safari in East Africa. Malaria films were negative, but trypanosomes were seen in blood films and chancre fluid. Sleeping sickness should be considered in children returning from East Africa

SCHISTOSOMA MANSONI EGGS, ANTIGENS AND DNA CLEARANCE CURVES AFTER PRAZIQUANTEL TREATMENT AND REINFECTION RATES OVER SIX MONTHS: DIFFERENTIATING BETWEEN RAPID REINFECTION AND DRUG RESISTANCE

Host-parasite interactio

Restorative benefits of the natural environment : enhancing restoration of directed attention & stress reduction through raising levels of cognitive awareness & physical encounter

Interaction with the natural environment has a vital role in human well-being - physical, social, spiritual and psychological - and yet in the twenty-first century many people lead a way of life totally separated from natural environments. Built environments and the increasing complexity of technological tasks necessitate increased demands for attention and a constant processing of information. Adaptation to such demands can result in depletion of psychological resources leading to stress and mental fatigue. Psychological resources must then be “restored” as they are critical for effective functioning. A review of restorative environments literature suggests there is further scope for enhancing restorative opportunities. A hypothetical model of enhanced restoration is proposed. It posits that an individual assuming a more active role, through raised cognitive awareness and physical encounter in the person-natural environment interaction will experience enhanced restoration in terms of restoration of directed attention and reduction of stress. The research hypotheses are tested using a quantitative field-based pretest-posttest experimental design with a sample of 100 volunteers. Data is collected through computerised objective and subjective measurement scales of attention and affect. Data is analysed through ANOVA. The major finding is that posttest scores improved compared to pretest scores in all 3 attention tests, 2 subjective attention scores and both affect measures, averaged over all 4 intervention groups. This means that the participants’ directed attention improved and they considered themselves to be less stressed regardless of the allocated experimental intervention group. Therefore, the most effective intervention in improving directed attention fatigue and reducing stress was raising an individual’s level of physical encounter with the natural environment. Further research is warranted, into the contribution that an individual can make to enhance the restorative process, and the need for education to raise awareness of the importance of the natural environment as a valuable (health-care) resource

New neutron long-counter for delayed neutron investigations with the LOHENGRIN fission fragment separator

Some neutrons are emitted from fission products seconds to minutes after fission occurs. The knowledge of these delayed neutrons is essential in the field of nuclear energy. But the probabilities to emit such delayed neutrons (Pn) are not always well known. A summary of different databases and compilations of Pn values is presented to show these discrepancies and uncertainties. The usual methods used to determine these nuclear data are then reviewed with an emphasis on biases and systematic errors to be avoided. To measure precise Pn values, a new neutron LOng-counter with ENergy Independant Efficiency (LOENIE) has been built for the LOHENGRIN separator facility installed at Institut Laue Langevin (FRANCE). Its characteristics and first results obtained are presented