Testing nested phylogenetic and phylogeographic hypotheses in the Plethodon vandykei species group

Mesic forests in the North American Pacific Northwest occur in two disjunct areas: along the coastal and Cascade ranges of Oregon, Washington, and British Columbia as well as the Northern Rocky Mountains of Idaho, Montana, and British Columbia. Over 150 species or species complexes have disjunct populations in each area, and a priori hypotheses based on phytogeography and geology potentially explain the disjunction via either dispersal or vicariance. Here, we test these hypotheses in the disjunct salamander complex Plethodon vandykei and P. idahoensisby collecting genetic data (669 bp of Cyt b) from 262 individuals. Maximum likelihood analysis indicated reciprocal monophyly of these species, supporting the ancient vicariance hypothesis, whereas parametric bootstrap and Bayesian hypothesis testing allow rejection of the dispersal hypothesis. The coalescent estimate of the time since population divergence (estimated using MDIV) is 3.75 x 106 years, and the 95%credibility interval of this value overlaps with the geological estimate of vicariance, but not the hypothesized dispersal. These results are congruent with the pattern seen in other mesic forest amphibian lineages and suggest disjunction in amphibians may be a concerted response to a geological/climatological event. WithinP. idahoensis, we tested the corollary hypothesis of an inland Pleistocene refugium in the Clearwater drainage with nested clade analysis and coalescent estimates of population growth rate (g). Both analyses support post-Pleistocene expansion from the Clearwater refugium. We corroborated this result by calculating Tajima's Dand mismatch distribution within each drainage, showing strong evidence for recent population expansion within most drainages. This work demonstrates the utility of statistical phylogeography and contributes two novel analytical tools: tests of stationarity with respect to topology in the Bayesian estimation, and the use of coalescent simulations to test the significance of the population growth-rate parameter.     

Water deficit induces chlorophyll degradation via the ‘PAO/phyllobilin’ pathway in leaves of homoio‐ (Craterostigma pumilum) and poikilochlorophyllous (Xerophyta viscosa) resurrection plants

Angiosperm resurrection plants exhibit poikilo‐ or homoiochlorophylly as a response to water deficit. Both strategies are generally considered as effective mechanisms to reduce oxidative stress associated with photosynthetic activity under water deficiency. The mechanism of water deficit‐induced chlorophyll (Chl) degradation in resurrection plants is unknown but has previously been suggested to occur as a result of non‐enzymatic photooxidation. We investigated Chl degradation during dehydration in both poikilochlorophyllous (Xerophyta viscosa) and homoiochlorophyllous (Craterostigma pumilum) species. We demonstrate an increase in the abundance of PHEOPHORBIDE a OXYGENASE (PAO), a key enzyme of Chl breakdown, together with an accumulation of phyllobilins, that is, products of PAO‐dependent Chl breakdown, in both species. Phyllobilins and PAO levels diminished again in leaves from rehydrated plants. We conclude that water deficit‐induced poikilochlorophylly occurs via the well‐characterized PAO/phyllobilin pathway of Chl breakdown and that this mechanism also appears conserved in a resurrection species displaying homoiochlorophylly. The roles of the PAO/phyllobilin pathway during different plant developmental processes that involve Chl breakdown, such as leaf senescence and desiccation, fruit ripening and seed maturation, are discussed.     

Three members of the human pyruvate dehydrogenase kinase gene family are direct targets of the peroxisome proliferator-activated receptor beta/delta

The nuclear receptors peroxisome proliferator-activated receptors (PPARs) are known for their critical role in the metabolic syndrome. Here, we show that they are direct regulators of the family of pyruvate dehydrogenase kinase (PDK) genes, whose products act as metabolic homeostats in sensing hunger and satiety levels in key metabolic tissues by modulating the activity of the pyruvate dehydrogenase complex. Mis-regulation of this tightly controlled network may lead to hyperglycemia. In human embryonal kidney cells we found the mRNA expression of PDK2, PDK3 and PDK4 to be under direct primary control of PPAR ligands, and in normal mouse kidney tissue Pdk2 and Pdk4 are PPAR targets. Both, treatment of HEK cells with PPARbeta/delta-specific siRNA and the genetic disruption of the Pparbeta/delta gene in mouse fibroblasts resulted in reduced expression of Pdk genes and abolition of induction by PPARbeta/delta ligands. These findings suggest that PPARbeta/delta is a key regulator of PDK genes, in particular the PDK4/Pdk4 gene. In silico analysis of the human PDK genes revealed two candidate PPAR response elements in the PDK2 gene, five in the PDK3 gene and two in the PDK4 gene, but none in the PDK1 gene. For seven of these sites we could demonstrate both PPARbeta/delta ligand responsiveness in context of their chromatin region and simultaneous association of PPARbeta/delta with its functional partner proteins, such as retinoidXreceptor, co-activator and mediator proteins and phosphorylated RNA polymerase II. In conclusion, PDK2, PDK3 and PDK4 are primary PPARbeta/delta target genes in humans underlining the importance of the receptor in the control of metabolism.     

Predicting the impact of the 2011 conflict in Libya on population mental health: PTSD and depression prevalence and mental health service requirements

Background

Mental disorders are likely to be elevated in the Libyan population during the post-conflict period. We estimated cases of severe PTSD and depression and related health service requirements using modelling from existing epidemiological data and current recommended mental health service targets in low and middle income countries (LMIC’s).

Methods

Post-conflict prevalence estimates were derived from models based on a previously conducted systematic review and meta-regression analysis of mental health among populations living in conflict. Political terror ratings and intensity of exposure to traumatic events were used in predictive models. Prevalence of severe cases was applied to chosen populations along with uncertainty ranges. Six populations deemed to be affected by the conflict were chosen for modelling: Misrata (population of 444,812), Benghazi (pop. 674,094), Zintan (pop. 40,000), displaced people within Tripoli/Zlitan (pop. 49,000), displaced people within Misrata (pop. 25,000) and Ras Jdir camps (pop. 3,700). Proposed targets for service coverage, resource utilisation and full-time equivalent staffing for management of severe cases of major depression and post-traumatic stress disorder (PTSD) are based on a published model for LMIC’s.

Findings

Severe PTSD prevalence in populations exposed to a high level of political terror and traumatic events was estimated at 12.4% (95%CI 8.5–16.7) and was 19.8% (95%CI 14.0–26.3) for severe depression. Across all six populations (total population 1,236,600), the conflict could be associated with 123,200 (71,600–182,400) cases of severe PTSD and 228,100 (134,000–344,200) cases of severe depression; 50% of PTSD cases were estimated to co-occur with severe depression. Based upon service coverage targets, approximately 154 full-time equivalent staff would be required to respond to these cases sufficiently which is substantially below the current level of resource estimates for these regions.

Discussion

This is the first attempt to predict the mental health burden and consequent service response needs of such a conflict, and is crucially timed for Libya.     

Dynamic evolution of herbivore-induced sesquiterpene biosynthesis in sorghum and related grass crops

Sorghum (Sorghum bicolor) plants damaged by insects emit a blend of volatiles, predominantly sesquiterpenes, that are implicated in attracting natural enemies of the attacking insects. To characterize sesquiterpene biosynthesis in sorghum, seven terpene synthase (TPS) genes, SbTPS1 through SbTPS7, were identified based on their evolutionary relatedness to known sesquiterpene synthase genes from maize and rice. While SbTPS6 and SbTPS7 encode truncated proteins, all other TPS genes were determined to encode functional sesquiterpene synthases. Both SbTPS1 and SbTPS2 produced the major products zingiberene, β-bisabolene and β-sesquiphellandrene, but with opposite ratios of zingiberene to β-sesquiphellandrene. SbTPS3 produced (E)-α-bergamotene and (E)-β-farnesene. SbTPS4 formed (E)-β-caryophyllene as the major product. SbTPS5 produced mostly (E)-α-bergamotene and (Z)-γ-bisabolene. Based on the genome sequences of sorghum, maize and rice and the sesquiterpene synthase genes they contain, collinearity analysis identified the orthologs of sorghum sesquiterpene synthase genes, except for SbTPS4, in maize and rice. Phylogenetic analysis implied that SbTPS1, SbTPS2 and SbTPS3, which exist as tandem repeats, evolved as a consequence of local gene duplication in a lineage-specific manner. Structural modeling and site-directed mutagenesis experiments revealed that three amino acids in the active site play critical roles in defining product specificity of SbTPS1, SbTPS2, SbTPS3 and their orthologs in maize and rice. The naturally occurring functional variations of sesquiterpene synthases within and between species suggest that multiple mechanisms, including lineage-specific gene duplication, subfunctionalization, neofunctionalization and pseudogenization of duplicated genes, have all played a role in the dynamic evolution of insect-induced sesquiterpene biosynthesis in grasses.     

The Global Burden of Mental,Neurological and Substance Use Disorders: An Analysis from the Global Burden of Disease Study 2010

BackgroundThe Global Burden of Disease Study 2010 (GBD 2010), estimated that a substantial proportion of the world’s disease burden came from mental, neurological and substance use disorders. In this paper, we used GBD 2010 data to investigate time, year, region and age specific trends in burden due to mental, neurological and substance use disorders.MethodFor each disorder, prevalence data were assembled from systematic literature reviews. DisMod-MR, a Bayesian meta-regression tool, was used to model prevalence by country, region, age, sex and year. Prevalence data were combined with disability weights derived from survey data to estimate years lived with disability (YLDs). Years lost to premature mortality (YLLs) were estimated by multiplying deaths occurring as a result of a given disorder by the reference standard life expectancy at the age death occurred. Disability-adjusted life years (DALYs) were computed as the sum of YLDs and YLLs.ResultsIn 2010, mental, neurological and substance use disorders accounted for 10.4% of global DALYs, 2.3% of global YLLs and, 28.5% of global YLDs, making them the leading cause of YLDs. Mental disorders accounted for the largest proportion of DALYs (56.7%), followed by neurological disorders (28.6%) and substance use disorders (14.7%). DALYs peaked in early adulthood for mental and substance use disorders but were more consistent across age for neurological disorders. Females accounted for more DALYs in all mental and neurological disorders, except for mental disorders occurring in childhood, schizophrenia, substance use disorders, Parkinson’s disease and epilepsy where males accounted for more DALYs. Overall DALYs were highest in Eastern Europe/Central Asia and lowest in East Asia/the Pacific.ConclusionMental, neurological and substance use disorders contribute to a significant proportion of disease burden. Health systems can respond by implementing established, cost effective interventions, or by supporting the research necessary to develop better prevention and treatment options.     

Molecular and biochemical evolution of maize terpene synthase 10, an enzyme of indirect defense

Maize plants attacked by lepidopteran larvae emit a volatile mixture that consists mostly of the sesquiterpene olefins, (E)-α-bergamotene and (E)-β-farnesene. These volatiles are produced by the herbivore-induced terpene synthase TPS10 and attract natural enemies to the damaged plants. A survey of volatiles in maize lines and species of teosinte showed that the TPS10 products (E)-α-bergamotene and (E)-β-farnesene are consistently induced by herbivory, indicating that release of TPS10 volatiles is a defense trait conserved among maize and its wild relatives. Sequence comparison of TPS10 from maize and its apparent orthologs from four teosinte species demonstrated stabilizing selection on this defense trait. The teosinte volatiles and the enzymatic activity of the apparent TPS10 orthologs were not completely uniform but varied in the ratio of (E)-α-bergamotene to (E)-β-farnesene products formed. We identified a single amino acid in the active center which determines the ratio of (E)-α-bergamotene to (E)-β-farnesene and has changed during the evolution of maize and teosinte species. Feeding experiments with the substrate (Z,E)-farnesyl diphosphate revealed that this amino acid controls the rate of isomerization of the (E,E)-farnesyl carbocation intermediate to the (Z,E)-configuration.     

Rational conversion of substrate and product specificity in a Salvia monoterpene synthase: structural insights into the evolution of terpene synthase function

Terpene synthases are responsible for the biosynthesis of the complex chemical defense arsenal of plants and microorganisms. How do these enzymes, which all appear to share a common terpene synthase fold, specify the many different products made almost entirely from one of only three substrates? Elucidation of the structure of 1,8-cineole synthase from Salvia fruticosa (Sf-CinS1) combined with analysis of functional and phylogenetic relationships of enzymes within Salvia species identified active-site residues responsible for product specificity. Thus, Sf-CinS1 was successfully converted to a sabinene synthase with a minimum number of rationally predicted substitutions, while identification of the Asn side chain essential for water activation introduced 1,8-cineole and alpha-terpineol activity to Salvia pomifera sabinene synthase. A major contribution to product specificity in Sf-CinS1 appears to come from a local deformation within one of the helices forming the active site. This deformation is observed in all other mono- or sesquiterpene structures available, pointing to a conserved mechanism. Moreover, a single amino acid substitution enlarged the active-site cavity enough to accommodate the larger farnesyl pyrophosphate substrate and led to the efficient synthesis of sesquiterpenes, while alternate single substitutions of this critical amino acid yielded five additional terpene synthases.