A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes

GC-biased gene conversion (gBGC) is a recombination-associated process that favors the fixation of G/C alleles over A/T alleles. In mammals, gBGC is hypothesized to contribute to variation in GC content, rapidly evolving sequences, and the fixation of deleterious mutations, but its prevalence and general functional consequences remain poorly understood. gBGC is difficult to incorporate into models of molecular evolution and so far has primarily been studied using summary statistics from genomic comparisons. Here, we introduce a new probabilistic model that captures the joint effects of natural selection and gBGC on nucleotide substitution patterns, while allowing for correlations along the genome in these effects. We implemented our model in a computer program, called phastBias, that can accurately detect gBGC tracts about 1 kilobase or longer in simulated sequence alignments. When applied to real primate genome sequences, phastBias predicts gBGC tracts that cover roughly 0.3% of the human and chimpanzee genomes and account for 1.2% of human-chimpanzee nucleotide differences. These tracts fall in clusters, particularly in subtelomeric regions; they are enriched for recombination hotspots and fast-evolving sequences; and they display an ongoing fixation preference for G and C alleles. They are also significantly enriched for disease-associated polymorphisms, suggesting that they contribute to the fixation of deleterious alleles. The gBGC tracts provide a unique window into historical recombination processes along the human and chimpanzee lineages. They supply additional evidence of long-term conservation of megabase-scale recombination rates accompanied by rapid turnover of hotspots. Together, these findings shed new light on the evolutionary, functional, and disease implications of gBGC. The phastBias program and our predicted tracts are freely available. © 2013 Capra et al

Continuity, Deconfinement, and (Super) Yang-Mills Theory

We study the phase diagram of SU(2) Yang-Mills theory with one adjoint Weyl fermion on R^3xS^1 as a function of the fermion mass m and the compactification scale L. This theory reduces to thermal pure gauge theory as m->infinity and to circle-compactified (non-thermal) supersymmetric gluodynamics in the limit m->0. In the m-L plane, there is a line of center symmetry changing phase transitions. In the limit m->infinity, this transition takes place at L_c=1/T_c, where T_c is the critical temperature of the deconfinement transition in pure Yang-Mills theory. We show that near m=0, the critical compactification scale L_c can be computed using semi-classical methods and that the transition is of second order. This suggests that the deconfining phase transition in pure Yang-Mills theory is continuously connected to a transition that can be studied at weak coupling. The center symmetry changing phase transition arises from the competition of perturbative contributions and monopole-instantons that destabilize the center, and topological molecules (neutral bions) that stabilize the center. The contribution of molecules can be computed using supersymmetry in the limit m=0, and via the Bogomolnyi--Zinn-Justin (BZJ) prescription in the non-supersymmetric gauge theory. Finally, we also give a detailed discussion of an issue that has not received proper attention in the context of N=1 theories---the non-cancellation of nonzero-mode determinants around supersymmetric BPS and KK monopole-instanton backgrounds on R^3xS^1. We explain why the non-cancellation is required for consistency with holomorphy and supersymmetry and perform an explicit calculation of the one-loop determinant ratio.Comment: A discussion of the non-cancellation of the nonzero mode determinants around supersymmetric monopole-instantons in N=1 SYM on R^3xS^1 is added, including an explicit calculation. The non-cancellation is, in fact, required by supersymmetry and holomorphy in order for the affine-Toda superpotential to be reproduced. References have also been adde

Markedly Divergent Tree Assemblage Responses to Tropical Forest Loss and Fragmentation across a Strong Seasonality Gradient

We examine the effects of forest fragmentation on the structure and composition of tree assemblages within three seasonal and aseasonal forest types of southern Brazil, including evergreen, Araucaria, and deciduous forests. We sampled three southernmost Atlantic Forest landscapes, including the largest continuous forest protected areas within each forest type. Tree assemblages in each forest type were sampled within 10 plots of 0.1 ha in both continuous forests and 10 adjacent forest fragments. All trees within each plot were assigned to trait categories describing their regeneration strategy, vertical stratification, seed-dispersal mode, seed size, and wood density. We detected differences among both forest types and landscape contexts in terms of overall tree species richness, and the density and species richness of different functional groups in terms of regeneration strategy, seed dispersal mode and woody density. Overall, evergreen forest fragments exhibited the largest deviations from continuous forest plots in assemblage structure. Evergreen, Araucaria and deciduous forests diverge in the functional composition of tree floras, particularly in relation to regeneration strategy and stress tolerance. By supporting a more diversified light-demanding and stress-tolerant flora with reduced richness and abundance of shade-tolerant, old-growth species, both deciduous and Araucaria forest tree assemblages are more intrinsically resilient to contemporary human-disturbances, including fragmentation-induced edge effects, in terms of species erosion and functional shifts. We suggest that these intrinsic differences in the direction and magnitude of responses to changes in landscape structure between forest types should guide a wide range of conservation strategies in restoring fragmented tropical forest landscapes worldwide

Neuroinflammation, Mast Cells, and Glia: Dangerous Liaisons

The perspective of neuroinflammation as an epiphenomenon following neuron damage is being replaced by the awareness of glia and their importance in neural functions and disorders. Systemic inflammation generates signals that communicate with the brain and leads to changes in metabolism and behavior, with microglia assuming a pro-inflammatory phenotype. Identification of potential peripheral-to-central cellular links is thus a critical step in designing effective therapeutics. Mast cells may fulfill such a role. These resident immune cells are found close to and within peripheral nerves and in brain parenchyma/meninges, where they exercise a key role in orchestrating the inflammatory process from initiation through chronic activation. Mast cells and glia engage in crosstalk that contributes to accelerate disease progression; such interactions become exaggerated with aging and increased cell sensitivity to stress. Emerging evidence for oligodendrocytes, independent of myelin and support of axonal integrity, points to their having strong immune functions, innate immune receptor expression, and production/response to chemokines and cytokines that modulate immune responses in the central nervous system while engaging in crosstalk with microglia and astrocytes. In this review, we summarize the findings related to our understanding of the biology and cellular signaling mechanisms of neuroinflammation, with emphasis on mast cell-glia interactions

Submillimeter Studies of Prestellar Cores and Protostars: Probing the Initial Conditions for Protostellar Collapse

Improving our understanding of the initial conditions and earliest stages of protostellar collapse is crucial to gain insight into the origin of stellar masses, multiple systems, and protoplanetary disks. Observationally, there are two complementary approaches to this problem: (1) studying the structure and kinematics of prestellar cores observed prior to protostar formation, and (2) studying the structure of young (e.g. Class 0) accreting protostars observed soon after point mass formation. We discuss recent advances made in this area thanks to (sub)millimeter mapping observations with large single-dish telescopes and interferometers. In particular, we argue that the beginning of protostellar collapse is much more violent in cluster-forming clouds than in regions of distributed star formation. Major breakthroughs are expected in this field from future large submillimeter instruments such as Herschel and ALMA.Comment: 12 pages, 9 figures, to appear in the proceedings of the conference "Chemistry as a Diagnostic of Star Formation" (C.L. Curry & M. Fich eds.

APOLO-Bari, an internet-based program for longitudinal support of bariatric surgery patients: study protocol for a randomized controlled trial

Background: Despite evidence of successful weight loss for bariatric surgery patients, some patients experience considerable weight regain over the long term. Given the strong association between post-surgery health behaviors and outcomes, aftercare intervention to address key behaviors appears to be a reasonable relapse-prevention strategy. As the burden of obesity rates increases in healthcare centers, an internet-based program appears to be a reasonable strategy for supporting bariatric surgery patients in the long term. The primary purpose of the current project is to develop and test the efficacy and perceived utility of APOLO-Bari.Methods/design: This study is a randomized control trial, which will be conducted in two hospital centers in the North of Portugal; it includes a control group receiving treatment as usual and an intervention group receiving the APOLO-Bari program for one year in addition to treatment as usual. A total of 180 male and female participants who underwent bariatric surgery (gastric sleeve or gastric bypass surgery) for 12 to 20 months will be recruited. Both groups will complete a similar set of questionnaires at baseline, every 4 months until the end of the intervention, and at 6 and 12 months follow-up. Assessment includes anthropometric variables and psychological self-report measures. The primary outcome measure will be weight regain measured at the end of treatment, and at 6 and 12 months follow-up. The secondary aims are to test the cost-effectiveness of the intervention and to investigate psychological predictors and trajectories of weight regain. APOLO-Bari was developed to address the weight regain problem in the bariatric population by offering additional guidance to bariatric patients during the postoperative period. The program includes: (a) a psychoeducational cognitive-behavioral-based self-help manual, (b) a weekly feedback messaging system that sends a feedback statement related to information reported by the participant, and (c) interactive chat sessions scheduled witThis research was partially supported by the Fundacao para a Ciencia e a Tecnologia through a European Union COMPETE program grant to Eva Conceicao (IF/01219/2014 and PTDC/MHC-PCL/4974/2012), a doctoral scholarship to Ana Pinto-Bastos (SFRH/BD/104159/2014), a doctoral scholarship to Sofia Ramalho (SFRH/BD/104182/2014), and a postdoctoral scholarship to Ana Rita Vaz (SFRH/BPD/94490/2013), co-financed by FEDER under the PT2020 Partnership Agreement (UID/PSI/01662/2013).info:eu-repo/semantics/publishedVersio

Thermodynamics of Holographic Defects

Using the AdS/CFT correspondence, we study the thermodynamic properties and the phase diagram of matter fields on (2+1)-dimensional defects coupled to a (3+1)-dimensional N=4 SYM "heat bath". Considering a background magnetic field, (net) quark density, defect "magnitude" $\delta N_c$ and the mass of the matter, we study the defect contribution to the thermodynamic potentials and their first and second derivatives to map the phases and study their physical properties. We find some features that are qualitatively similar to other systems e.g. in (3+1) dimensions and a number of features that are particular to the defect nature, such as its magnetic properties, unexpected properties at T->0 and finite density; and the finite $\delta N_c$ effects, e.g. a diverging susceptibility and vanishing density of states at small temperatures, a physically consistent negative heat capacity and new types of consistent phases.Comment: 33 pages, 16 figures (jpg and pdf), typos fixed and references added, final version published in JHE

Metabolomics demonstrates divergent responses of two Eucalyptus species to water stress

Past studies of water stress in Eucalyptus spp. generally highlighted the role of fewer than five “important” metabolites, whereas recent metabolomic studies on other genera have shown tens of compounds are affected. There are currently no metabolite profiling data for responses of stress-tolerant species to water stress. We used GC–MS metabolite profiling to examine the response of leaf metabolites to a long (2 month) and severe (Ψpredawn < −2 MPa) water stress in two species of the perennial tree genus Eucalyptus (the mesic Eucalyptus pauciflora and the semi-arid Eucalyptus dumosa). Polar metabolites in leaves were analysed by GC–MS and inorganic ions by capillary electrophoresis. Pressure–volume curves and metabolite measurements showed that water stress led to more negative osmotic potential and increased total osmotically active solutes in leaves of both species. Water stress affected around 30–40% of measured metabolites in E. dumosa and 10–15% in E. pauciflora. There were many metabolites that were affected in E. dumosa but not E. pauciflora, and some that had opposite responses in the two species. For example, in E. dumosa there were increases in five acyclic sugar alcohols and four low-abundance carbohydrates that were unaffected by water stress in E. pauciflora. Re-watering increased osmotic potential and decreased total osmotically active solutes in E. pauciflora, whereas in E. dumosa re-watering led to further decreases in osmotic potential and increases in total osmotically active solutes. This experiment has added several extra dimensions to previous targeted analyses of water stress responses in Eucalyptus, and highlights that even species that are closely related (e.g. congeners) may respond differently to water stress and re-waterin

A hippocampal Cdk5 pathway regulates extinction of contextual fear

Treatment of emotional disorders involves the promotion of extinction processes, which are defined as the learned reduction of fear. The molecular mechanisms underlying extinction have only begun to be elucidated. By employing genetic and pharmacological approaches in mice, we show here that extinction requires downregulation of Rac-1 and cyclin-dependent kinase 5 (Cdk5), and upregulation of p21 activated kinase-1 (PAK-1) activity. This is physiologically achieved by a Rac-1–dependent relocation of the Cdk5 activator p35 from the membrane to the cytosol and dissociation of p35 from PAK-1. Moreover, our data suggest that Cdk5/p35 activity prevents extinction in part by inhibition of PAK-1 activity in a Rac-1–dependent manner. We propose that extinction of contextual fear is regulated by counteracting components of a molecular pathway involving Rac-1, Cdk5 and PAK-1. Our data suggest that this pathway could provide a suitable target for therapeutic treatment of emotional disorders.National Institutes of Health (U.S.) (Grant NS051874)Alexander von Humboldt-Stiftung (German Research Foundation Fellowship)European Neuroscience Institute Goettinge