On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence.

BACKGROUND: In eukaryotes, most DNA-binding proteins exert their action as members of large effector complexes. The presence of these complexes are revealed in high-throughput genome-wide assays by the co-occurrence of the binding sites of different complex components. Resampling tests are one route by which the statistical significance of apparent co-occurrence can be assessed. RESULTS: We have investigated two resampling approaches for evaluating the statistical significance of binding-site co-occurrence. The permutation test approach was found to yield overly favourable p-values while the independent resampling approach had the opposite effect and is of little use in practical terms. We have developed a new, pragmatically-devised hybrid approach that, when applied to the experimental results of an Polycomb/Trithorax study, yielded p-values consistent with the findings of that study. We extended our investigations to the FL method developed by Haiminen et al, which derives its null distribution from all binding sites within a dataset, and show that the p-value computed for a pair of factors by this method can depend on which other factors are included in that dataset. Both our hybrid method and the FL method appeared to yield plausible estimates of the statistical significance of co-occurrences although our hybrid method was more conservative when applied to the Polycomb/Trithorax dataset.A high-performance parallelized implementation of the hybrid method is available. CONCLUSIONS: We propose a new resampling-based co-occurrence significance test and demonstrate that it performs as well as or better than existing methods on a large experimentally-derived dataset. We believe it can be usefully applied to data from high-throughput genome-wide techniques such as ChIP-chip or DamID. The Cooccur package, which implements our approach, accompanies this paper.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Optimising homing endonuclease gene drive performance in a semi-refractory species: the Drosophila melanogaster experience.

Homing endonuclease gene (HEG) drive is a promising insect population control technique that employs meganucleases to impair the fitness of pest populations. Our previous studies showed that HEG drive was more difficult to achieve in Drosophila melanogaster than Anopheles gambiae and we therefore investigated ways of improving homing performance in Drosophila. We show that homing in Drosophila responds to increased expression of HEGs specifically during the spermatogonia stage and this could be achieved through improved construct design. We found that 3'-UTR choice was important to maximise expression levels, with HEG activity increasing as we employed Hsp70, SV40, vasa and βTub56D derived UTRs. We also searched for spermatogonium-specific promoters and found that the Rcd-1r promoter was able to drive specific expression at this stage. Since Rcd-1 is a regulator of differentiation in other species, it suggests that Rcd-1r may serve a similar role during spermatogonial differentiation in Drosophila. Contrary to expectations, a fragment containing the entire region between the TBPH gene and the bgcn translational start drove strong HEG expression only during late spermatogenesis rather than in the germline stem cells and spermatogonia as expected. We also observed that the fraction of targets undergoing homing was temperature-sensitive, falling nearly four-fold when the temperature was lowered to 18°C. Taken together, this study demonstrates how a few simple measures can lead to substantial improvements in the HEG-based gene drive strategy and reinforce the idea that the HEG approach may be widely applicable to a variety of insect control programs

Gotta catch 'em all or not enough time: Users motivations for playing Pokemon Go (TM) and non-users' reasons for not installing

Urban exergames are played in the real-world environment using built-in mobile phone sensors. The influence of Pokémon Go on physical activity and sitting time has been examined previously, however limited research has explored motivations for using the application. Thus, the aim of this study was to explore Pokémon Go users' motivations for using the application, exusers' reasons for abandoning the game and non-users' reasons for not installing. After institutional ethical approval, the 'Physical Activity and Pokémon Go' questionnaire was developed using QualtricsTM and distributed using social media soon after launch in the United Kingdom (baseline). At baseline a total of 461 participants (n=193 male, n=265 female, n=3 transgender) who were predominantly white (n=420) and did not self-report a disability (n=443) completed the questionnaire. Users' (n=236) were questioned on their motivations for using Pokémon Go and non-users' provided reasons for not installing. At 3 months a total of 127 participants (n=23 users) completed the questionnaire again and all qualitative data was thematically analyzed. The most commonly reported reason for using Pokémon Go was 'to have fun' which was 86% and 83% at baseline and 3 months respectively. The second most frequent reason at baseline was 'friends were using it' (58%) and at 3 months was 'to be outside' (48%). The least common motivation for using Pokémon Go at both baseline and 3 months was 'to meet new people' (8% and 0% respectively). At baseline, social motives and competition were two general themes which encapsulated Pokémon Go users' motivation for using the application. There were two general themes reported by Pokémon Go users' as to why they did not think they would use the application in the future. These were application related factors and factors unrelated to Pokémon Go. Non-users reported a range of reasons for not using Pokémon Go, including lack of interest and a lack of time. Safety concerns and risk of adverse events were reported by both users and non-users. This is the first study to thematically analyze motives for using Pokémon Go in which the findings are: 1) future smartphone applications aiming to increase physical activity must ensure that objectives evolve to maintain initial interest and motivation to engage with applications; 2) game developers must consider the required phone storage and capability which could be a barrier to downloading; and 3) concerns of using the application including the safety of users and those around them

Genomic analysis of heat-shock factor targets in Drosophila.

We have used a chromatin immunoprecipitation-microarray (ChIP-array) approach to investigate the in vivo targets of heat-shock factor (Hsf) in Drosophila embryos. We show that this method identifies Hsf target sites with high fidelity and resolution. Using cDNA arrays in a genomic search for Hsf targets, we identified 141 genes with highly significant ChIP enrichment. This study firmly establishes the potential of ChIP-array for whole-genome transcription factor target mapping in vivo using intact whole organisms.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

The design and in vivo evaluation of engineered I-OnuI-based enzymes for HEG gene drive.

The homing endonuclease gene (HEG) drive system, a promising genetic approach for controlling arthropod populations, utilises engineered nucleases to spread deleterious mutations that inactivate individual genes throughout a target population. Previous work with a naturally occurring LAGLIDADG homing endonuclease (I-SceI) demonstrated its feasibility in both Drosophila and Anopheles. Here we report on the next stage of this strategy: the redesign of HEGs with customized specificity in order to drive HEG-induced 'homing' in vivo via break-induced homologous recombination. Variants targeting a sequence within the Anopheles AGAP004734 gene were created from the recently characterized I-OnuI endonuclease, and tested for cleavage activity and frequency of homing using a model Drosophila HEG drive system. We observed cleavage and homing at an integrated reporter for all endonuclease variants tested, demonstrating for the first time that engineered HEGs can cleave their target site in insect germline cells, promoting targeted mutagenesis and homing. However, in comparison to our previously reported work with I-SceI, the engineered I-OnuI variants mediated homing with a reduced frequency, suggesting that site-specific cleavage activity is insufficient by itself to ensure efficient homing. Taken together, our experiments take a further step towards the development of a viable HEG-based population control strategy for insects

Asteroid lightcurves from the Palomar Transient Factory survey: Rotation periods and phase functions from sparse photometry

We fit 54,296 sparsely-sampled asteroid lightcurves in the Palomar Transient Factory to a combined rotation plus phase-function model. Each lightcurve consists of 20+ observations acquired in a single opposition. Using 805 asteroids in our sample that have reference periods in the literature, we find the reliability of our fitted periods is a complicated function of the period, amplitude, apparent magnitude and other attributes. Using the 805-asteroid ground-truth sample, we train an automated classifier to estimate (along with manual inspection) the validity of the remaining 53,000 fitted periods. By this method we find 9,033 of our lightcurves (of 8,300 unique asteroids) have reliable periods. Subsequent consideration of asteroids with multiple lightcurve fits indicate 4% contamination in these reliable periods. For 3,902 lightcurves with sufficient phase-angle coverage and either a reliably-fit period or low amplitude, we examine the distribution of several phase-function parameters, none of which are bimodal though all correlate with the bond albedo and with visible-band colors. Comparing the theoretical maximal spin rate of a fluid body with our amplitude versus spin-rate distribution suggests that, if held together only by self-gravity, most asteroids are in general less dense than 2 g/cm$^3$, while C types have a lower limit of between 1 and 2 g/cm$^3$, in agreement with previous density estimates. For 5-20km diameters, S types rotate faster and have lower amplitudes than C types. If both populations share the same angular momentum, this may indicate the two types' differing ability to deform under rotational stress. Lastly, we compare our absolute magnitudes and apparent-magnitude residuals to those of the Minor Planet Center's nominal $G=0.15$, rotation-neglecting model; our phase-function plus Fourier-series fitting reduces asteroid photometric RMS scatter by a factor of 3.Comment: 35 pages, 29 figures. Accepted 15-Apr-2015 to The Astronomical Journal (AJ). Supplementary material including ASCII data tables will be available through the publishing journal's websit

Development of synthetic selfish elements based on modular nucleases in Drosophila melanogaster.

Selfish genes are DNA elements that increase their rate of genetic transmission at the expense of other genes in the genome and can therefore quickly spread within a population. It has been suggested that selfish elements could be exploited to modify the genome of entire populations for medical and ecological applications. Here we report that transcription activator-like effector nuclease (TALEN) and zinc finger nuclease (ZFN) can be engineered into site-specific synthetic selfish elements (SSEs) and demonstrate their transmission of up to 70% in the Drosophila germline. We show here that SSEs can spread via DNA break-induced homologous recombination, a process known as 'homing' similar to that observed for homing endonuclease genes (HEGs), despite their fundamentally different modes of DNA binding and cleavage. We observed that TALEN and ZFN have a reduced capability of secondary homing compared to HEG as their repetitive structure had a negative effect on their genetic stability. The modular architecture of ZFNs and TALENs allows for the rapid design of novel SSEs against specific genomic sequences making them potentially suitable for the genetic engineering of wild-type populations of animals and plants, in applications such as gene replacement or population suppression of pest species

Asteroid Spin-Rate Study using the Intermediate Palomar Transient Factory

Two dedicated asteroid rotation-period surveys have been carried out using data taken on January 6-9 and February 20-23 of 2014 by the Intermediate Palomar Transient Factory (iPTF) in the $R$~band with $\sim 20$-min cadence. The total survey area covered 174~deg$^2$ in the ecliptic plane. Reliable rotation periods for 1,438 asteroids are obtained from a larger data set of 6,551 mostly main-belt asteroids, each with $\geq 10$~detections. Analysis of 1751, PTF based, reliable rotation periods clearly shows the "spin barrier" at $\sim 2$~hours for "rubble-pile" asteroids. We also found a new large-sized super-fast rotator, 2005 UW163 (Chang et al., 2014), and other five candidates as well. Our spin-rate distributions of asteroids with $3 < D < 15$~km shows number decrease when frequency greater than 5 rev/day, which is consistent to that of the Asteroid Light Curve Database (LCDB, Warner et al., 2009) and the result of (Masiero et al., 2009). We found the discrepancy in the spin-rate distribution between our result and (Pravec et al., 2008, update 2014-04-20) is mainly from asteroids with $\Delta m < 0.2$ mag that might be primarily due to different survey strategies. For asteroids with $D \leq 3$~km, we found a significant number drop at $f = 6$ rev/day. The YORP effect timescale for small-sized asteroid is shorter that makes more elongate objets spun up to reach their spin-rate limit and results in break-up. The K-S test suggests a possible difference in the spin-rate distributions of C- and S-type asteroids. We also find that C-type asteroids have a smaller spin-rate limit than the S-type, which agrees with the general sense that the C-type has lower bulk density than the S-type.Comment: Submitted to ApJ (Jan, 2015). Accepted by ApJ (June, 2015). The whole set of the folded lightcurves will be available on the published articl

Intermediate filament–membrane attachments function synergistically with actin-dependent contacts to regulate intercellular adhesive strength

By tethering intermediate filaments (IFs) to sites of intercellular adhesion, desmosomes facilitate formation of a supercellular scaffold that imparts mechanical strength to a tissue. However, the role IF–membrane attachments play in strengthening adhesion has not been directly examined. To address this question, we generated Tet-On A431 cells inducibly expressing a desmoplakin (DP) mutant lacking the rod and IF-binding domains (DPNTP). DPNTP localized to the plasma membrane and led to dissociation of IFs from the junctional plaque, without altering total or cell surface distribution of adherens junction or desmosomal proteins. However, a specific decrease in the detergent-insoluble pool of desmoglein suggested a reduced association with the IF cytoskeleton. DPNTP-expressing cell aggregates in suspension or substrate-released cell sheets readily dissociated when subjected to mechanical stress whereas controls remained largely intact. Dissociation occurred without lactate dehydrogenase release, suggesting that loss of tissue integrity was due to reduced adhesion rather than increased cytolysis. JD-1 cells from a patient with a DP COOH-terminal truncation were also more weakly adherent compared with normal keratinocytes. When used in combination with DPNTP, latrunculin A, which disassembles actin filaments and disrupts adherens junctions, led to dissociation up to an order of magnitude greater than either treatment alone. These data provide direct in vitro evidence that IF–membrane attachments regulate adhesive strength and suggest furthermore that actin- and IF-based junctions act synergistically to strengthen adhesion

313 new asteroid rotation periods from Palomar Transient Factory observations

A new asteroid rotation period survey have been carried out by using the Palomar Transient Factory (PTF). Twelve consecutive PTF fields, which covered an area of 87 deg$^2$ in the ecliptic plane, were observed in $R$ band with a cadence of $\sim$20 min during February 15--18, 2013. We detected 2500 known asteroids with a diameter range of 0.5 km $\leq D \leq$ 200 km. Of these, 313 objects had highly reliable rotation periods and exhibited the "spin barrier" at $\sim2$ hours. In contrast to the flat spin rate distribution of the asteroids with 3 km $\leq D \leq$ 15 km shown by Pravec et al. (2008), our results deviated somewhat from a Maxwellian distribution and showed a decrease at the spin rate greater than 5 rev/day. One super-fast-rotator candidate and two possible binary asteroids were also found in this work.Comment: 18 pages, 20 figures and 2 very long table