Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species

Background Recent studies in budding yeast have shown that antisense transcription occurs at many loci. However, the functional role of antisense transcripts has been demonstrated only in a few cases and it has been suggested that most antisense transcripts may result from promiscuous bi-directional transcription in a dense genome. Results Here, we use strand-specific RNA sequencing to study anti-sense transcription in Saccharomyces cerevisiae. We detect 1,103 putative antisense transcripts expressed in mid-log phase growth, ranging from 39 short transcripts covering only the 3' UTR of sense genes to 145 long transcripts covering the entire sense open reading frame. Many of these antisense transcripts overlap sense genes that are repressed in mid-log phase and are important in stationary phase, stress response, or meiosis. We validate the differential regulation of 67 antisense transcripts and their sense targets in relevant conditions, including nutrient limitation and environmental stresses. Moreover, we show that several antisense transcripts and, in some cases, their differential expression have been conserved across five species of yeast spanning 150 million years of evolution. Divergence in the regulation of antisense transcripts to two respiratory genes coincides with the evolution of respiro-fermentation. Conclusions Our work provides support for a global and conserved role for antisense transcription in yeast gene regulation.Canadian Friends of the Hebrew UniversityHoward Hughes Medical InstituteHuman Frontier Science Program (Strasbourg, France)Burroughs Wellcome Fund (Career Award at the Scientific Interface)National Institutes of Health (U.S.). Pioneer AwardBroad Institute of MIT and HarvardU.S.-Israel Binational Science Foundation (BSF)National Human Genome Research Institute (U.S.)Alfred P. Sloan Foundatio

Evolutionary game dynamics in phenotype space

Evolutionary dynamics can be studied in well-mixed or structured populations. Population structure typically arises from the heterogeneous distribution of individuals in physical space or on social networks. Here we introduce a new type of space to evolutionary game dynamics: phenotype space. The population is well-mixed in the sense that everyone is equally likely to interact with everyone else, but the behavioral strategies depend on distance in phenotype space. Individuals might behave differently towards those who look similar or dissimilar. Individuals mutate to nearby phenotypes. We study the `phenotypic space walk' of populations. We present analytic calculations that bring together ideas from coalescence theory and evolutionary game dynamics. As a particular example, we investigate the evolution of cooperation in phenotype space. We obtain a precise condition for natural selection to favor cooperators over defectors: for a one-dimensional phenotype space and large population size the critical benefit-to-cost ratio is given by b/c=1+2/sqrt{3}. We derive the fundamental condition for any evolutionary game and explore higher dimensional phenotype spaces.Comment: version 2: minor changes; equivalent to final published versio

Peptidomic discovery of short open reading frame-encoded peptides in human cells

The amount of the transcriptome that is translated into polypeptides is of fundamental importance. We developed a peptidomic strategy to detect short ORF (sORF)-encoded polypeptides (SEPs) in human cells. We identified 90 SEPs, 86 of which are novel, the largest number of human SEPs ever reported. SEP abundances range from 10-1000 molecules per cell, identical to known proteins. SEPs arise from sORFs in non-coding RNAs as well as multi-cistronic mRNAs, and many SEPs initiate with non-AUG start codons, indicating that non-canonical translation may be more widespread in mammals than previously thought. In addition, coding sORFs are present in a small fraction (8/1866) of long intergenic non-coding RNAs (lincRNAs). Together, these results provide the strongest evidence to date that the human proteome is more complex than previously appreciated

Disks, Tori, and Cocoons: Emission and Absorption Diagnostics of AGN Environments

One of the most important problems in the study of active galaxies is understanding the detailed geometry, physics, and evolution of the central engines and their environments. The leading models involve an accretion disk and torus structure around a central dense object, thought to be a supermassive black hole. Gas found in the environment of AGN is associated with different structures: molecular accretion disks, larger scale atomic tori, ionized and neutral "cocoons" in which the nuclear regions can be embedded. All of them can be studied at radio wavelengths by various means. Here, we summarize the work that has been done to date in the radio band to characterize these structures. Much has been learned about the central few parsecs of AGN in the last few decades with contemporary instruments but the picture remains incomplete. In order to be able to define a more accurate model of this region, significant advances in sensitivity, spectral and angular resolution, and bandpass stability are required. The necessary advances will only be provided by the Square Kilometer Array and we discuss the possibilities that these dramatic improvements will open for the study of the gas in the central region of AGN.Comment: To appear in "Science with the Square Kilometer Array," eds. C. Carilli and S. Rawlings, New Astronomy Reviews (Elsevier: Amsterdam); 17 pages, 7 figures (four of them in separate gif/tif files) The full paper with high resolution images can be downloaded from http://www.astron.nl/~morganti/Papers/AGNenvironment.ps.g

Are there gender differences in the geography of alcohol-related mortality in Scotland? An ecological study

<b>Background</b> There is growing concern about alcohol-related harm, particularly within Scotland which has some of the highest rates of alcohol-related death in western Europe. There are large gender differences in alcohol-related mortality rates in Scotland and in other countries, but the reasons for these differences are not clearly understood. In this paper, we aimed to address calls in the literature for further research on gender differences in the causes, contexts and consequences of alcohol-related harm. Our primary research question was whether the kind of social environment which tends to produce higher or lower rates of alcohol-related mortality is the same for both men and women across Scotland. <b>Methods</b> Cross-sectional, ecological design. A comparison was made between spatial variation in men's and women's age-standardised alcohol-related mortality rates in Scotland using maps, Moran's Index, linear regression and spatial analyses of residuals. Directly standardised mortality rates were derived from individual level records of death registration, 2000–2005 (n = 8685). <b>Results</b> As expected, men's alcohol-related mortality rate substantially exceeded women's and there was substantial spatial variation in these rates for both men and women within Scotland. However, there was little spatial variation in the relationship between men's and women's alcohol-mortality rates (r2 = 0.73); areas with relatively high rates of alcohol-related mortality for men tended also to have relatively high rates for women. In a small number of areas (8 out of 144) the relationship between men's and women's alcohol-related mortality rates was significantly different. <b>Conclusion</b> In as far as geographic location captures exposure to social and economic environment, our results suggest that the relationship between social and economic environment and alcohol-related harm is very similar for men and women. The existence of a small number of areas in which men's and women's alcohol-related mortality had an different relationship suggests that some places may have unusual drinking cultures. These might prove useful for further investigations into the factors which influence drinking behaviour in men and women

Transition probabilities for general birth-death processes with applications in ecology, genetics, and evolution

A birth-death process is a continuous-time Markov chain that counts the number of particles in a system over time. In the general process with $n$ current particles, a new particle is born with instantaneous rate $\lambda_n$ and a particle dies with instantaneous rate $\mu_n$. Currently no robust and efficient method exists to evaluate the finite-time transition probabilities in a general birth-death process with arbitrary birth and death rates. In this paper, we first revisit the theory of continued fractions to obtain expressions for the Laplace transforms of these transition probabilities and make explicit an important derivation connecting transition probabilities and continued fractions. We then develop an efficient algorithm for computing these probabilities that analyzes the error associated with approximations in the method. We demonstrate that this error-controlled method agrees with known solutions and outperforms previous approaches to computing these probabilities. Finally, we apply our novel method to several important problems in ecology, evolution, and genetics

Developmental and acquired brain injury have opposite effects on finger coordination in children

The ability to coordinate finger forces to dexterously perform tasks develops in children as they grow older. Following brain injury, either developmental (as in cerebral palsy–CP) or acquired (as in traumatic brain injury—TBI), this developmental trajectory will likely be impaired. In this study, we compared finger coordination in a group of children aged 4–12 with CP and TBI to a group of typically developing children using an isometric pressing task. As expected, deficits were observed in functional tests (Jebsen Taylor test of hand function, Box and Block test) for both groups, and children in both groups performed the pressing task less well than the control group. However, differing results were observed between the CP and TBI groups when using the uncontrolled manifold hypothesis to look at the synergy index. This index measures the relative amount of “good” (does not affect the outcome measure) and “bad” (does affect the outcome measure) variability, where in this case the outcome measure is the total force produced by the fingers. While children with CP were more variable in their performance, their synergy index was not significantly different from typically developing children, suggesting the development of compensatory strategies. In contrast, the children following TBI showed performance that got worse as a function of age (i.e., the older children with TBI performed worse than the younger children with TBI). These differences between the groups may be a result of different areas of brain injury typically observed in CP and TBI, and the different amount of time that has passed since the injury

Maternal Environmental Contribution to Adult Sensitivity and Resistance to Obesity in Long Evans Rats

The OLETF rat is an animal model of early onset hyperphagia induced obesity, presenting multiple pre-obese characteristics during the suckling period. In the present study, we used a cross-fostering strategy to assess whether interactions with obese dams in the postnatal environment contributed to the development of obesity.On postnatal Day (PND)-1 OLETF and control LETO pups were cross-fostered to same or opposite strain dams. An independent ingestion test was performed on PND11 and a nursing test on PND18. Rats were sacrificed at weaning or on PND90, and plasma leptin, insulin, cholesterol, triglycerides and alanine aminotransferase (ALT) were assayed. Fat pads were collected and weighed and adipocyte size and number were estimated. Body weight and intake, as well as the estrous cycle of the female offspring were monitored.During the suckling period, the pups' phenotype was almost completely determined by the strain of the mother. However, pups independently ingested food according to their genotype, regardless of their actual phenotype. At adulthood, cross fostered males of both strains and LETO females were affected in regard of their adiposity levels in the direction of the foster dam. On the other hand, OLETF females showed almost no alterations in adiposity but were affected by the strain of the dams in parameters related to the metabolic syndrome. Thus, OLETF females showed reduced liver adiposity and circulating levels of ALT, while LETO females presented a disrupted estrous cycle and increased cholesterol and triglycerides in the long term.The present study provides further support for the early postnatal environment playing a sex-divergent role in programming later life phenotype. In addition, it plays a more central role in determining the functioning of mechanisms involved in energy balance that may provide protection from or sensitivity to later life obesity and pathologies related to the metabolic syndrome

Development and evaluation of RNA-seq methods

This article is part of the supplement: Beyond the Genome: The true gene count, human evolution and disease genomicsRNA-seq provides insights at multiple levels into the transcription of the genome as it yields sequence, splicing and expression-level information. We have been developing and comparing a wide range of RNA-seq methods for their ability to annotate transcribed genomic regions, identify differences between normal and cancer states, and quantify mRNA expression levels. We will present results in two areas: (i) strand-specific RNA-seq; and (ii) RNA-seq starting from total RNA. Strand-specific RNA-seq is a powerful tool for novel transcript discovery and genome annotation because it enables the identification of the strand of origin for non-coding RNA and anti-sense RNA, as well as defining the ends of adjacent or overlapping transcripts transcribed in different directions. Using the well-annotated Saccharomyces cerevisiae transcriptome as a benchmark, we directly compared seven library construction protocols, including both published and our own novel methods. We found marked differences in strand-specificity, library complexity, evenness and continuity of coverage, agreement with known annotations, and accuracy for expression profiling. Weighing the performance and ease of conducting each method, we identified the dUTP second strand marking [1] and the Illumina RNA ligation methods as the leading protocols, with the former benefitting from the current availability of paired-end sequencing. Our analysis provides a comprehensive benchmark, and our computational pipeline is applicable for assessment of future protocols in other organisms. RNA-seq methods that do not require the purification of mRNA will be valuable for several applications, including samples with low input amounts and/or partial degradation. In these experiments, it is necessary to reduce the fraction of sequencing reads derived from ribosomal RNA. We will present results from multiple approaches, including the use of Not-So-Random (NSR) primers for reverse transcription [2] and the NuGEN Ovation RNA-Seq kit