Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome

Understanding the molecular mechanisms and evolution of the gene regulatory system remains a major challenge in biology. Transcription start sites (TSSs) are especially interesting because they are central to initiating gene expression. Previous studies revealed widespread transcription initiation and fast turnover of TSSs in mammalian genomes. Yet, how new TSSs originate and how they evolve over time remain poorly understood. To address these questions, we analyzed ∼200,000 human TSSs by integrating evolutionary (inter- and intra-species) and functional genomic data, particularly focusing on evolutionarily young TSSs that emerged in the primate lineage. TSSs were grouped according to their evolutionary age using sequence alignment information as a proxy. Comparisons of young and old TSSs revealed that (1) new TSSs emerge through a combination of intrinsic factors, like the sequence properties of transposable elements and tandem repeats, and extrinsic factors such as their proximity to existing regulatory modules; (2) new TSSs undergo rapid evolution that reduces the inherent instability of repeat sequences associated with a high propensity of TSS emergence; and (3) once established, the transcriptional competence of surviving TSSs is gradually enhanced, with evolutionary changes subject to temporal (fewer regulatory changes in younger TSSs) and spatial constraints (fewer regulatory changes in more isolated TSSs). These findings advance our understanding of how regulatory innovations arise in the genome throughout evolution and highlight the genomic robustness and evolvability in these processes

The Strabo Technique

The Strabo technique is a forecasting and planning strategy whose methodology emphasizes the determination of a concensus of opinion from a group of experts. It is a logical extension of the Delphi technique which was developed originally to assist the decision making processes of the American military (Linstone and Turnoff, 1975, p. 10). Many of the early studies employing Delphi were conducted at the RAND Corporation and were primarily concerned with scientific and technological forecasting. The Delphi Technique has since been used in a variety cf studies including the forecasting of many social "indicators\u27\u27 such as human attitudes are values, and the "quality of life". The technique requires individuals within a group to formulate and assess decisions and opinions and, through this process, establish a convergent group consensus

A patient preference study that evaluated fluticasone furoate and mometasone furoate nasal sprays for allergic rhinitis

Background: Corticosteroid nasal sprays are the mainstay of treatment for allergic rhinitis. These sprays have sensory attributes such as scent and/or odor, taste and aftertaste, and run down the throat and/or the nose, which, when unpleasant, can affect patient preference for, and compliance with, treatment. Objective: This study examined patient preference for fluticasone furoate nasal spray (FFNS) or mometasone furoate nasal spray (MFNS) based on their sensory attributes after administration in patients with allergic rhinitis. Methods: This was a multicenter, randomized, double-blind, cross-over study. Patient preferences were determined by using three questionnaires (Overall Preference, Immediate Attributes, and Delayed Attributes). Results: Overall, 56% of patients stated a preference for FFNS versus 32% for MFNS (p _ 0.001); the remaining 12% stated no preference. More patients stated a preference for FFNS versus MFNS for the attributes of “less drip down the throat” (p _ 0.001), “less run out of the nose” (p _ 0.05), “more soothing” (p _ 0.05), and “less irritating” (p _ 0.001). More patients responded in favor of FFNS versus MFNS for the immediate attributes, “run down the throat” (p _ 0.001), and “run out of the nose” (p _ 0.001), and, in the delayed attributes, “run down the throat” (p _ 0.001), “run out of the nose” (p _ 0.01), “presence of aftertaste” (p _ 0.01), and “no nasal irritation” (p _ 0.001). Conclusion: Patients with allergic rhinitis preferred FFNS versus MFNS overall and based on a number of individual attributes, including “less drip down the throat,” “less run out of the nose,” and “less irritating.” Greater preference may improve patient adherence and thereby improve symptom management of the patient’s allergic rhinitis

Long-term weight maintenance and cardiovascular risk factors are not different following weight loss on carbohydrate-restricted diets high in either monounsaturated fat or protein in obese hyperinsulinaemic men and women

The aim of this study was to determine after 52 weeks whether advice to follow a lower carbohydrate diet, either high in monounsaturated fat or low fat, high in protein had differential effects in a free-living community setting. Following weight loss on either a high monounsaturated fat, standard protein (HMF; 50 % fat, 20 % protein (67 g/d), 30 % carbohydrate) or a high protein, moderate fat (HP) (40 % protein (136 g/d), 30 % fat, 30 % carbohydrate) energy-restricted diet (6000 kJ/d) subjects were asked to maintain the same dietary pattern without intensive dietary counselling for the following 36 weeks. Overall weight loss was 6·2 (sd 7·3) kg (P < 0·01 for time with no diet effect, 7·6 (sd 8·1) kg, HMF v. 4·8 (sd 6·6) kg, HP). In a multivariate regression model predictors of weight loss at the end of the study were sex, age and reported percentage energy from protein (R2 0·22, P < 0·05 for the whole model). Fasting plasma insulin decreased (P < 0·01, with no difference between diets), 13·9 (sd 4·6) to 10·2 (sd 5·2) mIU/l, but fasting plasma glucose was not reduced. Neither total cholesterol nor LDL-cholesterol were different but HDL was higher, 1·19 (sd 0·26) v. 1·04 (sd 0·29) (P < 0·001 for time, no diet effect), while TAG was lower, 1·87 (sd 1·23) v. 2·22 (sd 1·15) mmol/l (P < 0·05 for time, no diet effect). C-reactive protein decreased (3·97 (sd 2·84) to 2·43 (sd 2·29) mg/l, P < 0·01). Food records showed that compliance to the prescribed dietary patterns was poor. After 1 year there remained a clinically significant weight loss and improvement in cardiovascular risk factors with no adverse effects of a high monounsaturated fat diet.Jennifer B. Keogh, Natalie D. Luscombe-Marsh, Manny Noakes, Gary A. Wittert and Peter M. Clifto

The Seeds of Exclusion

First paragraph: It is in the context of all the factors relating to the social, physical and mental wellbeing of Britain in 2008 that The Salvation Army presents The Seeds of Exclusion report. The research findings must be read in the light of the additional pressures we have identified which may be brought to bear on individuals already living in a society which is becoming increasingly fragmented, chaotic and stressful. The Salvation Army hopes its contribution to this ongoing debate will begin to inform us all, including Government, on how we can avoid the mistakes of the past and begin to mend society

Glauber dynamics in a single-chain magnet: From theory to real systems

The Glauber dynamics is studied in a single-chain magnet. As predicted, a single relaxation mode of the magnetization is found. Above 2.7 K, the thermally activated relaxation time is mainly governed by the effect of magnetic correlations and the energy barrier experienced by each magnetic unit. This result is in perfect agreement with independent thermodynamical measurements. Below 2.7 K, a crossover towards a relaxation regime is observed that is interpreted as the manifestation of finite-size effects. The temperature dependences of the relaxation time and of the magnetic susceptibility reveal the importance of the boundary conditions.Comment: Submitted to PRL 10 May 2003. Submitted to PRB 12 December 2003; published 15 April 200

Conformational and thermodynamic hallmarks of DNA operator site specificity in the copper sensitive operon repressor from Streptomyces lividans

Metal ion homeostasis in bacteria relies on metalloregulatory proteins to upregulate metal resistance genes and enable the organism to preclude metal toxicity. The copper sensitive operon repressor (CsoR) family is widely distributed in bacteria and controls the expression of copper efflux systems. CsoR operator sites consist of G-tract containing pseudopalindromes of which the mechanism of operator binding is poorly understood. Here, we use a structurally characterized CsoR from Streptomyces lividans (CsoRSl) together with three specific operator targets to reveal the salient features pertaining to the mechanism of DNA binding. We reveal that CsoRSl binds to its operator site through a 2-fold axis of symmetry centred on a conserved 5′-TAC/GTA-3′ inverted repeat. Operator recognition is stringently dependent not only on electropositive residues but also on a conserved polar glutamine residue. Thermodynamic and circular dichroic signatures of the CsoRSl-DNA interaction suggest selectivity towards the A-DNA-like topology of the G-tracts at the operator site. Such properties are enhanced on protein binding thus enabling the symmetrical binding of two CsoRSl tetramers. Finally, differential binding modes may exist in operator sites having more than one 5′-TAC/GTA-3′ inverted repeat with implications in vivo for a mechanism of modular control. © 2013 The Author(s)

Nyquist method for Wigner-Poisson quantum plasmas

By means of the Nyquist method, we investigate the linear stability of electrostatic waves in homogeneous equilibria of quantum plasmas described by the Wigner-Poisson system. We show that, unlike the classical Vlasov-Poisson system, the Wigner-Poisson case does not necessarily possess a Penrose functional determining its linear stability properties. The Nyquist method is then applied to a two-stream distribution, for which we obtain an exact, necessary and sufficient condition for linear stability, as well as to a bump-in-tail equilibrium.Comment: 6 figure

Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast

Most genomes, including yeast Saccharomyces cerevisiae, are pervasively transcribed producing numerous non-coding RNAs, many of which are unstable and eliminated by nuclear or cytoplasmic surveillance pathways. We previously showed that accumulation of PHO84 antisense RNA (asRNA), in cells lacking the nuclear exosome component Rrp6, is paralleled by repression of sense transcription in a process dependent on the Hda1 histone deacetylase (HDAC) and the H3K4 histone methyl transferase Set1. Here we investigate this process genome-wide and measure the whole transcriptome of various histone modification mutants in a Δrrp6 strain using tiling arrays. We confirm widespread occurrence of potentially antisense-dependent gene regulation and identify three functionally distinct classes of genes that accumulate asRNAs in the absence of Rrp6. These classes differ in whether the genes are silenced by the asRNA and whether the silencing is HDACs and histone methyl transferase-dependent. Among the distinguishing features of asRNAs with regulatory potential, we identify weak early termination by Nrd1/Nab3/Sen1, extension of the asRNA into the open reading frame promoter and dependence of the silencing capacity on Set1 and the HDACs Hda1 and Rpd3 particularly at promoters undergoing extensive chromatin remodelling. Finally, depending on the efficiency of Nrd1/Nab3/Sen1 early termination, asRNA levels are modulated and their capability of silencing is change