Quantitative insertion-site sequencing (QIseq) for high throughput phenotyping of transposon mutants

Genetic screening using random transposon insertions has been a powerful tool for uncovering biology in prokaryotes, where whole-genome saturating screens have been performed in multiple organisms. In eukaryotes, such screens have proven more problematic, in part because of the lack of a sensitive and robust system for identifying transposon insertion sites. We here describe quantitative insertion-site sequencing, or QIseq, which uses custom library preparation and Illumina sequencing technology and is able to identify insertion sites from both the 5' and 3' ends of the transposon, providing an inbuilt level of validation. The approach was developed using piggyBac mutants in the human malaria parasite Plasmodium falciparum but should be applicable to many other eukaryotic genomes. QIseq proved accurate, confirming known sites in >100 mutants, and sensitive, identifying and monitoring sites over a >10,000-fold dynamic range of sequence counts. Applying QIseq to uncloned parasites shortly after transfections revealed multiple insertions in mixed populations and suggests that >4000 independent mutants could be generated from relatively modest scales of transfection, providing a clear pathway to genome-scale screens in P. falciparum QIseq was also used to monitor the growth of pools of previously cloned mutants and reproducibly differentiated between deleterious and neutral mutations in competitive growth. Among the mutants with fitness defects was a mutant with a piggyBac insertion immediately upstream of the kelch protein K13 gene associated with artemisinin resistance, implying mutants in this gene may have competitive fitness costs. QIseq has the potential to enable the scale-up of piggyBac-mediated genetics across multiple eukaryotic systems

Low significance of evidence for black hole echoes in gravitational wave data

Recent detections of merging black holes allow observational tests of the nature of these objects. In some proposed models, non-trivial structure at or near the black hole horizon could lead to echo signals in gravitational wave data. Recently, Abedi et al. claimed tentative evidence for repeating damped echo signals following the gravitational-wave signals of the binary black hole merger events recorded in the first observational period of the Advanced LIGO interferometers. We reanalyse the same data, addressing some of the shortcomings of their method using more background data and a modified procedure. We find a reduced statistical significance for the claims of evidence for echoes, calculating increased p-values for the null hypothesis of echo-free noise. The reduced significance is entirely consistent with noise, and so we conclude that the analysis of Abedi et al. does not provide any observational evidence for the existence of Planck-scale structure at black hole horizons.Comment: As accepted by Physical Review

SO(10) paths to dark matter

The grand-unification gauge group SO(10) contains matter parity as a discrete subgroup. This symmetry could be at the origin of dark matter stability. The properties of the dark matter candidates depend on the path along which SO(10) is broken, in particular through Pati-Salam or left-right symmetric subgroups. We systematically determine the non-supersymmetric dark matter scenarios that can be realized along the various paths. We emphasize that the dark matter candidates may have colored or electrically charged partners at low scale that belong to the same SO(10) multiplet. These states, which in many cases are important for co-annihilation, could be observed more easily than the dark matter particle. We determine the structure of the tree-level and loop-induced mass splittings between the dark matter candidate and their partners and discuss the possible phenomenological implications.Comment: 44 pages; added references, to appear in PR

Evolutionary diversification of an ancient gene family (rhs) through C-terminal displacement

<p>Abstract</p> <p>Background</p> <p><it>Rhs </it>genes are prominent features of bacterial genomes that have previously been implicated in genomic rearrangements in <it>E. coli</it>. By comparing <it>rhs </it>repertoires across the Enterobacteriaceae, this study provides a robust explanation of <it>rhs </it>diversification and evolution, and a mechanistic model of how <it>rhs </it>diversity is gained and lost.</p> <p>Results</p> <p><it>Rhs </it>genes are ubiquitous and comprise six structurally distinct lineages within the Enterobacteriaceae. There is considerable intergenomic variation in <it>rhs </it>repertoire; for instance, in <it>Salmonella enterica</it>, <it>rhs </it>are restricted to mobile elements, while in <it>Escherichia coli </it>one <it>rhs </it>lineage has diversified through transposition as older lineages have been deleted. Overall, comparative genomics reveals frequent, independent gene gains and losses, as well as occasional lateral gene transfer, in different genera. Furthermore, we demonstrate that Rhs 'core' domains and variable C-termini are evolutionarily decoupled, and propose that <it>rhs </it>diversity is driven by homologous recombination with circular intermediates. Existing C-termini are displaced by laterally acquired alternatives, creating long arrays of dissociated 'tips' that characterize the appearance of <it>rhs </it>loci.</p> <p>Conclusion</p> <p><it>Rhs </it>repertoires are highly dynamic among Enterobacterial genomes, due to repeated gene gains and losses. In contrast, the primary structures of <it>Rhs </it>genes are evolutionarily conserved, indicating that <it>rhs </it>sequence diversity is driven, not by rapid mutation, but by the relatively slow evolution of novel core/tip combinations. Hence, we predict that a large pool of dissociated <it>rhs </it>C-terminal tips exists episomally and these are potentially transmitted across taxonomic boundaries.</p

Sources of Employment Growth by Occupation and Industry in Canada

Dans cet article, nous utilisons des données canadiennes des modèles d'intrants et d'extrants et des recensements de 1961, 1971 et 1981 afin d'identifier les causes des changements dans l'emploi durant chaque décennie. Neuf causes de changement sont retenues. L'objectif de cet article est de déterminer les causes les plus importantes de la croissance de l'emploi agrégé de même que les facteurs expliquant la croissance plus rapide de l'emploi durant les années 1970. De plus, les déterminants des déplacements de l'emploi entre les secteurs de même que des changements dans la composition de la main-d’œuvre sont identifiés. Une attention particulière est prêtée à l'importance des changements dans l'économie de l'information.L'emploi agrégé du secteur privé a crû de 35,3 % durant les années 1970 alors que dans les années 1960, la croissance ne fut que de 24,4 %. Le taux de croissance supérieur des années 1970, qui survint malgré un déclin de celui de la demande finale, fut accompagné d'un déclin du taux de croissance de la productivité du travail. Le déclin du taux de croissance de la demande finale dans cette décennie était dû à un ralentissement de celui des exportations.Les différences sectorielles du taux de croissance de l'emploi durant les années 1960 peuvent être expliquées par des taux de croissance dans la productivité du travail différents entre les secteurs alors que durant les années 1970, celles-ci furent plutôt attribuables à des variations sectorielles du taux de croissance de la demande finale, et en particulier de la consommation. Durant ces deux décennies, ces déterminants des différences sectorielles ont généré une croissance supérieure dans le secteur des services.Par rapport à l'emploi total, la proportion des emplois reliés au domaine de l'information a crû plus rapidement durant les années 1960 que durant les années 1970. La croissance de cette proportion est due en grande partie aux changements dans la composition de la main-d’œuvre. Il y a cependant d'autres explications de ce déplacement vers des emplois reliés au domaine de l'information. Parmi celles-ci, citons les taux de croissance sectoriels de l'emploi différents dus à des différences dans le taux de changement des heures travaillées, de la productivité du travail, de la demande finale et de la matrice d'intrants-extrants.This paper uses Canadian input-output and census data from 1961, 1971 and 1981 to decompose employment changes during each decade into nine sources. The goals are to identify: the main sources of growth in aggregate employment; factors which facilitated the more rapid rate of growth of employment in the 1970s; and some reasons for intersectoral shifts of employment and changes in the occupational composition of employment. We pay particular attention to the changing importance ofthe 'information economy '

Systemic restoration of UBA1 ameliorates disease in spinal muscular atrophy

Acknowledgments Blood biochemistry analysis and serum analysis were performed by the Easter Bush Pathology Department, University of Edinburgh. Animal husbandry was performed by Centre for Integrative Physiology bio-research restructure technical staff, University of Edinburgh. Assistance with intravenous injections was provided by Ian Coldicott (University of Sheffield) and Hannah Shorrock (University of Edinburgh). Human blood cDNA was a gift to GH from Kathy Evans, University of Edinburgh. Imaging was performed at the IMPACT imaging facility, University of Edinburgh, with technical assistance from Anisha Kubasik-Thayil. The authors would also like to thank Lyndsay Murray for technical discussions relating to qRT-PCR analysis. This work was supported by funding from the SMA Trust and the Anatomical Society (via grants to THG); the Euan MacDonald Centre for Motor Neurone Disease Research (via grants to THG and SHP); the Wellcome Trust (via grants to EJNG and THG); Muscular Dystrophy UK (via grants to THG and CGB); a Elphinstone Scholarship from the University of Aberdeen (to SHP); and The French Muscular Dystrophy Association (via grants to CM and JC).Peer reviewedPublisher PD

Particle Sensor Using Solidly Mounted Resonators

This paper describes the development of a novel particle sensing system employing zinc oxide based solidly mounted resonator (SMR) devices for the detection of airborne fine particles (i.e., PM2.5 and PM10). The system operates in a dual configuration in which two SMR devices are driven by Colpitts-type oscillators in a differential mode. Particles are detected by the frequency shift caused by the mass of particles present on one resonator with while the other acts as a reference channel. Experimental validation of the system was performed inside an environmental chamber using a dust generator with the particles of known size and concentration. A sensor sensitivity of 4.6 Hz per μg/m3 was demonstrated for the SMRs resonating at a frequency of 970 MHz. Our results demonstrate that the SMR-based system has the potential to be implemented in CMOS technology as a low-cost, miniature smart particle detector for the real-time monitoring of airborne particles

Risk of neuropsychiatric adverse events associated with varenicline:systematic review and meta-analysis

Objective To determine the risk of neuropsychiatric adverse events associated with use of varenicline compared with placebo in randomised controlled trials. Design Systematic review and meta-analysis comparing study effects using two summary estimates in fixed effects models, risk differences, and Peto odds ratios. Data sources Medline, Embase, PsycINFO, the Cochrane Central Register of Controlled Trials (CENTRAL), and clinicaltrials.gov. Eligibility criteria for selecting studies Randomised controlled trials with a placebo comparison group that reported on neuropsychiatric adverse events (depression, suicidal ideation, suicide attempt, suicide, insomnia, sleep disorders, abnormal dreams, somnolence, fatigue, anxiety) and death. Studies that did not involve human participants, did not use the maximum recommended dose of varenicline (1 mg twice daily), and were cross over trials were excluded. Results In the 39 randomised controlled trials (10 761 participants), there was no evidence of an increased risk of suicide or attempted suicide (odds ratio 1.67, 95% confidence interval 0.33 to 8.57), suicidal ideation (0.58, 0.28 to 1.20), depression (0.96, 0.75 to 1.22), irritability (0.98, 0.81 to 1.17), aggression (0.91, 0.52 to 1.59), or death (1.05, 0.47 to 2.38) in the varenicline users compared with placebo users. Varenicline was associated with an increased risk of sleep disorders (1.63, 1.29 to 2.07), insomnia (1.56, 1.36 to 1.78), abnormal dreams (2.38, 2.05 to 2.77), and fatigue (1.28, 1.06 to 1.55) but a reduced risk of anxiety (0.75, 0.61 to 0.93). Similar findings were observed when risk differences were reported. There was no evidence for a variation in depression and suicidal ideation by age group, sex, ethnicity, smoking status, presence or absence of psychiatric illness, and type of study sponsor (that is, pharmaceutical industry or other). Conclusions This meta-analysis found no evidence of an increased risk of suicide or attempted suicide, suicidal ideation, depression, or death with varenicline. These findings provide some reassurance for users and prescribers regarding the neuropsychiatric safety of varenicline. There was evidence that varenicline was associated with a higher risk of sleep problems such as insomnia and abnormal dreams. These side effects, however,are already well recognised. Systematic review registration PROSPERO 2014:CRD42014009224