Estimating the Number of Essential Genes in a Genome by Random Transposon Mutagenesis

We describe a Bayesian method for estimating the number of essential genes in a genome, on the basis of data on viable mutants for which a single transposon was inserted after a random TA site in a genome,potentially disrupting a gene. The prior distribution for the number of essential genes was taken to be uniform. A Gibbs sampler was used to estimate the posterior distribution. The method is illustrated with simulated data. Further simulations were used to study the performance of the procedure

New insights on polar mesospheric cloud particle size distributions from a two-satellite common volume study

The particle size distribution of Polar Mesospheric Clouds (PMC) is closely related to the fundamental processes of cloud formation and evolution. Still, despite substantial observational efforts, specific details about the particle size distribution have remained obscure. In this study, we aim at deriving more constraints on PMC size distributions by combining optical measurements from two satellite instruments observing a common PMC volume. We use a special set of 2D tomographic limb observations from the Optical Spectrograph and Infrared Imager System (OSIRIS) on the Odin satellite from 2010 to 2011 in the latitude range 78\ub0 N to 80\ub0 N and compare these to simultaneous PMC observations from the nadir-viewing Cloud Imaging and Particle Size (CIPS) instrument on the AIM satellite. A key goal is to find the assumption on the mathematical shape of the particle size distribution that should be applied to a vertically resolving limb-viewing instrument to reach consistent size results compared to the column-integrated ice distribution as seen by a nadir-viewing instrument. Our results demonstrate that viewing geometry and sampling volume of each instrument must be carefully considered and that the same size distribution assumption cannot simultaneously describe a column-integrated and a local height-resolved size distribution. In particular, applying the standard Gaussian assumption, used by many earlier PMC studies, to both limb and nadir observation leads to an overestimate of particle sizes seen by OSIRIS by about 10 nm as compared to CIPS. We show that the agreement can be improved if a Log-normal assumption with a broad distribution width around σ = 1.42 is adopted for OSIRIS. A reason for this broad distribution best describing the OSIRIS observations we suggest the large retrieval volume of the limb measurement. Gravity waves and other small-scale processes can cause horizontal variations and a co-existence of a wide range of particle populations in the sampling volume. Horizontal integration then leads to apparently much broader size distributions than encountered in a small horizontal sampling volume

Characteristics associated with initiation of hormone replacement therapy among Finnish women : A register-linkage study

Objective: To investigate which patient characteristics are associated with the initiation of hormone replacement therapy (HRT) in a cohort of Finnish women. Study design: Responses to postal questionnaires distributed to a nationwide, randomly selected cohort of women in 1998, 2000, 2003, 2005 and 2010 were analyzed. The cohort members were aged 40-44 years at the beginning of the study. Information on hormone replacement therapy was received from the national prescription register. Women who started taking HRT between January 1, 1999 and December 31, 2011 were included and previous users were excluded from the analysis. Main outcome measures: Initiation of HRT was the main outcome measure. The following explanatory factors for predicting the use of HRT were examined: sociodemographic factors, personality, health behavior, physiological and mental symptoms, chronic diseases and use of psychopharmaceuticals. The associations between starting HRT and the explanatory factors were analyzed with single-predictor and multi-predictor logistic regression models. Results: Factors predicting that a woman would start taking HRT were: living with a partner, weak sense of coherence, BMI less than 30 kg/m(2), heavy or moderate alcohol use, symptoms of hyperactivity of the sympathetic nervous system, climacteric symptoms and use of psychopharmaceuticals. Conclusions: Women with a good sense of coherence can cope with climacteric symptoms without resorting to HRT. Clinicians need to bear in mind the burden of menopausal symptoms on a woman's personal and working life when HRT is being considered. (C) 2016 Elsevier Ireland Ltd. All rights reserved.Peer reviewe

Race Differences in Seeking Help from Social Workers

This paper examines race differences in the use of social workers. A major finding is that blacks are more likely to consult social workers than are whites. Socio-demographic variables did not affect this pattern, nor did the type of problem. Implications for the training of social workers are discussed

Carbonate alteration of ophiolitic rocks in the Arabian–Nubian Shield of Egypt: sources and compositions of the carbonating fluid and implications for the formation of Au deposits

Ultramafic portions of ophiolitic fragments in the Arabian–Nubian Shield (ANS) show pervasive carbonate alteration forming various degrees of carbonated serpentinites and listvenitic rocks. Notwithstanding the extent of the alteration, little is known about the processes that caused it, the source of the CO2 or the conditions of alteration. This study investigates the mineralogy, stable (O, C) and radiogenic (Sr) isotope composition, and geochemistry of suites of variably carbonate altered ultramafics from the Meatiq area of the Central Eastern Desert (CED) of Egypt. The samples investigated include least-altered lizardite (Lz) serpentinites, antigorite (Atg) serpentinites and listvenitic rocks with associated carbonate and quartz veins. The C, O and Sr isotopes of the vein samples cluster between −8.1‰ and −6.8‰ for δ13C, +6.4‰ and +10.5‰ for δ18O, and 87Sr/86Sr of 0.7028–0.70344, and plot within the depleted mantle compositional field. The serpentinites isotopic compositions plot on a mixing trend between the depleted-mantle and sedimentary carbonate fields. The carbonate veins contain abundant carbonic (CO2±CH4±N2) and aqueous-carbonic (H2O-NaCl-CO2±CH4±N2) low salinity fluid, with trapping conditions of 270–300°C and 0.7–1.1 kbar. The serpentinites are enriched in Au, As, S and other fluid-mobile elements relative to primitive and depleted mantle. The extensively carbonated Atg-serpentinites contain significantly lower concentrations of these elements than the Lz-serpentinites suggesting that they were depleted during carbonate alteration. Fluid inclusion and stable isotope compositions of Au deposits in the CED are similar to those from the carbonate veins investigated in the study and we suggest that carbonation of ANS ophiolitic rocks due to influx of mantle-derived CO2-bearing fluids caused break down of Au-bearing minerals such as pentlandite, releasing Au and S to the hydrothermal fluids that later formed the Au-deposits. This is the first time that gold has been observed to be remobilized from rocks during the lizardite–antigorite transition

Extended homozygosity is not usually due to cytogenetic abnormality

<p>Abstract</p> <p>Background</p> <p>Previous studies have reported frequent stretches of homozygosity in human subjects but have failed to clarify whether these are due to cytogenetic abnormalities or to autozygosity.</p> <p>Methods</p> <p>Trios which had been typed for closely spaced SNPs spanning the genome were studied. Stretches of extended homozygosity were identified in the child members, as were occasions on which the child had been genotyped as not inheriting one parental allele. The number of times such transmission errors occurred within regions of extended homozygosity was compared with the chance expectation.</p> <p>Results</p> <p>Transmission errors occurred more rarely in regions of extended homozygosity than would be expected by chance.</p> <p>Discussion</p> <p>Regions of extended homozygosity are not generally due to cytogenetic abnormalities such as uniparental isodisomy. They reflect the Mendelian inheritance of haplotypes from a common ancestor. This may have implications for mapping disease genes.</p

Anxiety Sensitivity and Retaliatory Aggressive Behavior In Research Volunteers

An important focus of recent aggression research has been to identify personality variables that influence the expression of aggression. One such variable may be anxiety sensitivity (AS). Individuals high in AS fear unpleasant anxiety-related physiological sensations and perhaps physiological arousal in general. Accordingly, people high in AS are motivated to avoid situations that produce these sensations. With respect to aggressive encounters, an intense attack by an opponent involves significant physiological arousal. High anxiety-sensitive individuals may therefore attempt to decrease the intensity of the interaction by responding in a non-aggressive or conciliatory manner. To test this possibility, 112 community volunteers completed a measure of AS and a well-validated laboratory task designed to assess aggressive behavior. As predicted, an inverse relation between AS and extreme aggressive responding was found. Specifically, as AS increases, retaliatory aggression is less likely after intense attack by an opponent

Effects of Aerobic Exercise On Anxiety Sensitivity

Anxiety sensitivity is a known precursor to panic attacks and panic disorder, and involves the misinterpretation of anxiety-related sensations. Aerobic exercise has been shown to reduce generalized anxiety, and may also reduce anxiety sensitivity through exposure to feared physiological sensations. Accordingly, 54 participants with elevated anxiety sensitivity scores completed six 20-min treadmill exercise sessions at either a high-intensity aerobic (n = 29) or low-intensity (n = 25) level. Self-ratings of anxiety sensitivity, fear of physiological sensations associated with anxiety, and generalized anxiety were obtained at pretreatment, post-treatment, and one-week follow-up. Results indicated that both high- and low-intensity exercise reduced anxiety sensitivity. However, high-intensity exercise caused more rapid reductions in a global measure of anxiety sensitivity and produced more treatment responders than low-intensity exercise. Only high-intensity exercise reduced fear of anxiety-related bodily sensations. The implications of these findings are discussed. (C) 2003 Elsevier Ltd. All rights reserved

Haplotype inference based on Hidden Markov Models in the QTL-MAS 2010 multi-generational dataset

<p>Abstract</p> <p>Background</p> <p>We have previously demonstrated an approach for efficient computation of genotype probabilities, and more generally probabilities of allele inheritance in inbred as well as outbred populations. That work also included an extension for haplotype inference, or phasing, using Hidden Markov Models. Computational phasing of multi-thousand marker datasets has not become common as of yet. In this communication, we further investigate the method presented earlier for such problems, in a multi-generational dataset simulated for QTL detection.</p> <p>Results</p> <p>When analyzing the dataset simulated for the 14th QTLMAS workshop, the phasing produced showed zero deviations compared to original simulated phase in the founder generation. In total, 99.93% of all markers were correctly phased. 97.68% of the individuals were correct in all markers over all 5 simulated chromosomes. Results were produced over a weekend on a small computational cluster. The specific algorithmic adaptations needed for the Markov model training approach in order to reach convergence are described.</p> <p>Conclusions</p> <p>Our method provides efficient, near-perfect haplotype inference allowing the determination of completely phased genomes in dense pedigrees. These developments are of special value for applications where marker alleles are not corresponding directly to QTL alleles, thus necessitating tracking of allele origin, and in complex multi-generational crosses. The cnF2freq codebase, which is in a current state of active development, is available under a BSD-style license.</p

High throughput shotgun sequencing of eRNA reveals taxonomic and derived functional shifts across a benthic productivity gradient

Benthic macrofauna is regularly used in monitoring programmes, however the vast majority of benthic eukaryotic biodiversity lies mostly in microscopic organisms, such as meiofauna (invertebrates <1 mm) and protists, that rapidly responds to environmental change. These communities have traditionally been hard to sample and handle in the laboratory, but DNA sequencing has made such work less time consuming. While DNA sequencing captures both alive and dead organisms, environmental RNA (eRNA) better targets living organisms or organisms of recent origin in the environment. Here, we assessed the biodiversity of three known bioindicator microeukaryote groups (nematodes, foraminifera, and ciliates) in sediment samples collected at seven coastal sites along an organic carbon (OC) gradient. We aimed to investigate if eRNA shotgun sequencing can be used to simultaneously detect differences in (i) biodiversity of multiple microeukaryotic communities; and (ii) functional feeding traits of nematodes. Results showed that biodiversity was lower for nematodes and foraminifera in high OC (6.2%-6.9%), when compared to low OC sediments (1.2%-2.8%). Dissimilarity in community composition increased for all three groups between Low OC and High OC, as well as the classified feeding type of nematode genera (with more nonselective deposit feeders in high OC sediment). High relative abundant genera included nematodeSabatieriaand foraminiferaElphidiumin high OC, andCryptocaryon-like ciliates in low OC sediments. Considering that future sequencing technologies are likely to decrease in cost, the use of eRNA shotgun sequencing to assess biodiversity of benthic microeukaryotes could be a powerful tool in recurring monitoring programmes.Peer reviewe