The functional analysis of nonsense suppressors derived from in vitro engineered \u3ci\u3eSaccharomyces cerevisiae\u3c/i\u3e tRNA\u3csup\u3eTrp\u3c/sup\u3e genes

Nonsense suppressors derived from Saccharomyces cerevisiae tRNATrp genes have not been identified by classical genetic screens, although one can construct efficient amber (am) suppressors from them by making the appropriate anticodon mutation in vitro. Herein, a series of in vitro constructed putative suppressor genes was produced to test if pre-tRNATrp processing difficulties could help to explain the lack of classical tRNATrp-based suppressors. It is clear that inefficient processing of in-trons from precursor tRNATrp, or inaccurate overall processing, may explain why some of these constructs fail to promote nonsense suppression in vivo. However, deficient processing must be only one of the reasons why classical tRNATrp-based suppressors have not been characterized, as suppres-sion may still be extremely weak or absent in instances where the in vitro construct can lead to an accumulation of mature tRNATrp. Furthermore, suppression is also very weak in strains transformed with an intronless derivative of a putative tRNATrp ochre (oc) suppressor gene, wherein intron removal cannot pose a problem

The functional analysis of nonsense suppressors derived from in vitro engineered \u3ci\u3eSaccharomyces cerevisiae\u3c/i\u3e tRNA\u3csup\u3eTrp\u3c/sup\u3e genes

Nonsense suppressors derived from Saccharomyces cerevisiae tRNATrp genes have not been identified by classical genetic screens, although one can construct efficient amber (am) suppressors from them by making the appropriate anticodon mutation in vitro. Herein, a series of in vitro constructed putative suppressor genes was produced to test if pre-tRNATrp processing difficulties could help to explain the lack of classical tRNATrp-based suppressors. It is clear that inefficient processing of in-trons from precursor tRNATrp, or inaccurate overall processing, may explain why some of these constructs fail to promote nonsense suppression in vivo. However, deficient processing must be only one of the reasons why classical tRNATrp-based suppressors have not been characterized, as suppres-sion may still be extremely weak or absent in instances where the in vitro construct can lead to an accumulation of mature tRNATrp. Furthermore, suppression is also very weak in strains transformed with an intronless derivative of a putative tRNATrp ochre (oc) suppressor gene, wherein intron removal cannot pose a problem

Identifying Old Tidal Dwarf Irregulars

We examine the observational consequences of the two possible origins for irregular galaxies: formation from collapse of a primordial cloud of gas early in the age of the Universe, and formation from tidal tails in an interaction that could have occured any time in the history of the Universe. Because the formation from tidal tails could have occurred a long time ago, proximity to larger galaxies is not sufficient to distinguish tidal dwarfs from traditional dwarfs. We consider the effects of little or no dark matter on rotation speeds and the Tully-Fisher relationship, the metallicity-luminosity relationship, structure, and stellar populations. From these selection criteria, we identify a small list of dwarf irregular galaxies that are candidates for having formed as tidal dwarfs.Comment: ApJ, to appear September 20, 200

MGMR: leveraging RNA-Seq population data to optimize expression estimation

<p>Abstract</p> <p>Background</p> <p>RNA-Seq is a technique that uses Next Generation Sequencing to identify transcripts and estimate transcription levels. When applying this technique for quantification, one must contend with reads that align to multiple positions in the genome (multireads). Previous efforts to resolve multireads have shown that RNA-Seq expression estimation can be improved using probabilistic allocation of reads to genes. These methods use a probabilistic generative model for data generation and resolve ambiguity using likelihood-based approaches. In many instances, RNA-seq experiments are performed in the context of a population. The generative models of current methods do not take into account such population information, and it is an open question whether this information can improve quantification of the individual samples</p> <p>Results</p> <p>In order to explore the contribution of population level information in RNA-seq quantification, we apply a hierarchical probabilistic generative model, which assumes that expression levels of different individuals are sampled from a Dirichlet distribution with parameters specific to the population, and reads are sampled from the distribution of expression levels. We introduce an optimization procedure for the estimation of the model parameters, and use HapMap data and simulated data to demonstrate that the model yields a significant improvement in the accuracy of expression levels of paralogous genes.</p> <p>Conclusions</p> <p>We provide a proof of principal of the benefit of drawing on population commonalities to estimate expression. The results of our experiments demonstrate this approach can be beneficial, primarily for estimation at the gene level.</p

Contribution of windfarms to ancillary services

International audienceIn the last décade, wind energy has expericnced a substantial growth in Europe with an increase in génération capaciiy from 2,5 GW in 1995 to 34 GW at (lie end of 2004 This incTease has raised new probîems and constraints which led System opéra tors, electric utilities, governments or regulatory boards to define lechnical requirements for the grid connection of wind farms and more generaily of distributed génération (DG) units. At flrst, the requirements for wind fanns were rather "soft" (at least softer than for other DG units) and were mainîy intended to limit the "disturbances" caused by wind energy on power quality and grid opération. But with the ever increasing developmenl of wind power, the impacts on the grids become more and more significant leading to the définition of more and more "scvcrc" requiremcnts, In parltcular, wind farms (WF) arc now more and more often askcd to provide some son of anciilary services such as contribution to voltage/réactive power control and rrequency/active power control. This paper focuscs on the possible provision of such anciilary services by wind faims. Regarcling réactive power and voltage contTOl:-Doubly-fed Induction GÊaerarors (DFIG) and Synchronous or Induction GeneratoTS with full power électron ics interfaces (SIG) can liave réactive power control capabilities (both in production and absorption) depending on the rating of their power electronics converters. Thèse capabilities {characterized by a fast dynamie respon.se) can be used to perform voltage control. Moreover, if required, extemal reactive power compensation device.s niay also be installed.-Classical Induction G encrât ors (OG) do not hâve such réactive power control capahilities and therefore require externat devices for reactive power and voltage control.-Simulations carried oui show that WFs with voltage control capabilîties can significantly sustaîn the network voltage in case of grid events and mus may efficiently support the power System stability.Regard ing frequency control: the resuits show that when the Wind Turbine Generator (WTG) is full y loaded (maximum active power génération], appre-priate use or the pitch control may enabic the WTG (DFIG, SIG or CIG) to contribute to frequency control. In case of partial toad. the contribution to frequency conlrol can be achieved either by "disoplimizing'" the wind energy conversion by mcans of aie pitch control. or by setting a non-optimal rotor speed for DFIG or SIG. However, a judicious way to use variable speed ge&eratCffS may also be looperate them as mertial flywheels

Your Unconscious Knows Your Name

One's own name constitutes a unique part of conscious awareness – but does this also hold true for unconscious processing? The present study shows that the own name has the power to bias a person's actions unconsciously even in conditions that render any other name ineffective. Participants judged whether a letter string on the screen was a name or a non-word while this target stimulus was preceded by a masked prime stimulus. Crucially, the participant's own name was among these prime stimuli and facilitated reactions to following name targets whereas the name of another, yoked participant did not. Signal detection results confirmed that participants were not aware of any of the prime stimuli, including their own name. These results extend traditional findings on “breakthrough” phenomena of personally relevant stimuli to the domain of unconscious processing. Thus, the brain seems to possess adroit mechanisms to identify and process such stimuli even in the absence of conscious awareness

Comparison of weather station and climate reanalysis data for modelling temperature-related mortality

Epidemiological analyses of health risks associated with non-optimal temperature are traditionally based on ground observations from weather stations that offer limited spatial and temporal coverage. Climate reanalysis represents an alternative option that provide complete spatio-temporal exposure coverage, and yet are to be systematically explored for their suitability in assessing temperature-related health risks at a global scale. Here we provide the first comprehensive analysis over multiple regions to assess the suitability of the most recent generation of reanalysis datasets for health impact assessments and evaluate their comparative performance against traditional station-based data. Our findings show that reanalysis temperature from the last ERA5 products generally compare well to station observations, with similar non-optimal temperature-related risk estimates. However, the analysis offers some indication of lower performance in tropical regions, with a likely underestimation of heat-related excess mortality. Reanalysis data represent a valid alternative source of exposure variables in epidemiological analyses of temperature-related risk

Distribution of star-forming complexes in dwarf irregular galaxies

We study the distribution of bright star-forming complexes in a homogeneous sample of 72 late-type (``irregular'') dwarf galaxies located within the 10 Mpc volume. Star-forming complexes are identified as bright lumps in B-band galaxy images and isolated by means of the unsharp-masking method. For the sample as a whole the radial number distribution of bright lumps largely traces the underlying exponential-disk light profiles, but peaks at a 10 percent smaller scale length. Moreover, the presence of a tail of star forming regions out to at least six optical scale lengths provides evidence against a systematic star formation truncation within that galaxy extension. Considering these findings, we apply a scale length-independent concentration index, taking into account the implied non-uniform random spread of star formation regions throughout the disk. The number profiles frequently manifest a second, minor peak at about two scale lengths. Relying on a two-dimensional stochastic self-propagating star formation model, we show these secondary peaks to be consistent with triggered star formation; for a few of the brighter galaxies a peculiar peak distribution is observed that is conceivably due to the onset of shear provided by differential rotation. On scales between 100 and 1000 pc, and by taking into account exponential-disk structure, bright lumps reveal cluster dimensions between 1.3 and 2, with a weak trend to higher dimensions for brighter galaxies. Interpreting cluster dimension in terms of porosity of a self-similar intragalactic medium, we derive a relation between current star formation rate, scale length, and porosity.Comment: 16 pages, accepted for publication in Astronomy & Astrophysic

Asymptomatic bacteriuria in sickle cell disease: a cross-sectional study

BACKGROUND: It is known that there is significant morbidity associated with urinary tract infection and with renal dysfunction in sickle cell disease (SCD). However, it is not known if there are potential adverse outcomes associated with asymptomatic bacteriuria (ASB) infections in sickle cell disease if left untreated. This study was undertaken to determine the prevalence of ASB, in a cohort of patients with SCD. METHODS: This is a cross-sectional study of patients in the Jamaican Sickle Cell Cohort. Aseptically collected mid-stream urine (MSU) samples were obtained from 266 patients for urinalysis, culture and sensitivity analysis. Proteinuria was measured by urine dipsticks. Individuals with abnormal urine culture results had repeat urine culture. Serum creatinine was measured and steady state haematology and uric acid concentrations were obtained from clinical records. This was completed at a primary care health clinic dedicated to sickle cell diseases in Kingston, Jamaica. There were 133 males and 133 females in the sample studied. The mean age (mean ± sd) of participants was 26.6 ± 2.5 years. The main outcome measures were the culture of ≥ 10(5 )colony forming units of a urinary tract pathogen per milliliter of urine from a MSU specimen on a single occasion (probable ASB) or on consecutive occasions (confirmed ASB). RESULTS: Of the 266 urines collected, 234 were sterile and 29 had significant bacteriuria yielding a prevalence of probable ASB of 10.9% (29/266). Fourteen patients had confirmed ASB (prevalence 5.3%) of which 13 had pyuria. Controlling for genotype, females were 14.7 times more likely to have confirmed ASB compared to males (95%CI 1.8 to 121.0). The number of recorded visits for symptomatic UTI was increased by a factor of 2.5 (95% CI 1.4 to 4.5, p < 0.005) but serum creatinine, uric acid and haematology values were not different in patients with confirmed ASB compared with those with sterile urine. There was no association with history of gram negative sepsis. CONCLUSION: ASB is a significant problem in individuals with SCD and may be the source of pathogens in UTI. However, further research is needed to determine the clinical significance of ASB in SCD

Effect modification of greenness on the association between heat and mortality: a multi-city multi-country study

Background: Identifying how greenspace impacts the temperature-mortality relationship in urban environments is crucial, especially given climate change and rapid urbanization. To date, studies on this topic have indicated conflicting findings and typically focus on a localized area or single country. We evaluated the effect modification of greenspace on heat-related mortality in a global setting. Methods: We collected daily ambient temperature and mortality data for 452 locations in 24 countries and used Enhanced Vegetation Index (EVI) as the greenspace measurement. We used distributed lag non-linear model to estimate the heat-mortality relationship in each city and evaluated the effect modification of greenspace. Findings: Cities with high greenspace value had the lowest heat-mortality relative risk of 1·19 (95% CI: 1·13, 1·25), while the heat-related relative risk was 1·46 (95% CI: 1·31, 1·62) for cities with low greenspace. A 1% increase of greenspace in all cities was predicted to reduce all-cause heat-related mortality by 0·48 (95% CI: 0·24, 0·63), decreasing approximately 50 excess deaths per year. 20% increase of greenspace would reduce 9·02% (95%CI: 8·88, 9·16) heat-related attributable fraction, and this would result in saving approximately 933 excess deaths per year in 24 countries. Interpretation: Our findings can inform communities on the potential health benefits of greenspaces in the urban environment and mitigation measures regarding the impacts of climate change