Coalescent-based genome analyses resolve the early branches of the euarchontoglires

Despite numerous large-scale phylogenomic studies, certain parts of the mammalian tree are extraordinarily difficult to resolve. We used the coding regions from 19 completely sequenced genomes to study the relationships within the super-clade Euarchontoglires (Primates, Rodentia, Lagomorpha, Dermoptera and Scandentia) because the placement of Scandentia within this clade is controversial. The difficulty in resolving this issue is due to the short time spans between the early divergences of Euarchontoglires, which may cause incongruent gene trees. The conflict in the data can be depicted by network analyses and the contentious relationships are best reconstructed by coalescent-based analyses. This method is expected to be superior to analyses of concatenated data in reconstructing a species tree from numerous gene trees. The total concatenated dataset used to study the relationships in this group comprises 5,875 protein-coding genes (9,799,170 nucleotides) from all orders except Dermoptera (flying lemurs). Reconstruction of the species tree from 1,006 gene trees using coalescent models placed Scandentia as sister group to the primates, which is in agreement with maximum likelihood analyses of concatenated nucleotide sequence data. Additionally, both analytical approaches favoured the Tarsier to be sister taxon to Anthropoidea, thus belonging to the Haplorrhine clade. When divergence times are short such as in radiations over periods of a few million years, even genome scale analyses struggle to resolve phylogenetic relationships. On these short branches processes such as incomplete lineage sorting and possibly hybridization occur and make it preferable to base phylogenomic analyses on coalescent methods

Improved THETA-1 for light olefins oligomerization to diesel: Influence of textural and acidic properties

The increase in diesel demand, especially in Europe, and the need for high fuel quality requirements are forcing refiners to move into additional processes for production of high cetane diesel in order to meet the present market trends. Oligomerization of light olefins into middle distillate range products is a viable option. The fuel produced through this technology is environmentally friendly, free of sulfur and aromatics, and the adequate choice of the heterogeneous catalyst will direct the selectivity towards low branched oligomers, which will result in a high quality product. In this work we show the benefits of combining basic desilication treatments for generation of additional mesoporosity in mono-directional Theta-1 zeolite, with selective acid dealumination steps that restore not only the microporosity to values close to those of the parent samples, but also the total and strong Bronsted acidity. These modified Theta-1 zeolites present an outstanding catalytic behavior for oligomerization of propene, with a largely increased initial activity, a much higher resistance to deactivation with time on stream, and an improved selectivity to products in the diesel fraction, as compared to the original microporous Theta-1.The authors thank BP Products of North America for their financial support and permission to publish this work, and Consolider Ingenio 2010-Multicat, the "Severo Ochoa Program", and MAT2012-31657 for financial support. R. Sanchis is acknowledged for technical support.Martínez, C.; Doskocil, EJ.; Corma Canós, A. (2014). Improved THETA-1 for light olefins oligomerization to diesel: Influence of textural and acidic properties. Topics in Catalysis. 57(6-9):668-682. https://doi.org/10.1007/s11244-013-0224-xS668682576-9Bellussi G, Mizia F, Calemma V, Pollesel P, Millini R (2012) Microporous Mesoporous Mater 164:127–134Bellussi G, Carati A, Millini R (2010) In: Cejka J, Corma A, Zones S (eds) Zeolites and Catalysis. Wiley-VCH Verlag GmbH & Co., Weinheim, pp 449–491Martinez C, Corma A (2011) Coord Chem Rev 255:1558–1580de Klerk A (2005) Ind Eng Chem Res 44:3887–3893de Klerk A (2006) Energy Fuels 20:439–445de Klerk A (2006) Energy Fuels 20:1799–1805Egloff G (1936) Ind Eng Chem Res 28:1461–1467Degnan TF Jr, Smith CM, Venkat CR (2001) Appl Catal A Gen 221:283–294Apelian MR, Boulton JR, Fung AS (1994) US5284989, to Mobil OilQuann RJ, Green LA, Tabak SA, Krambeck FJ (1988) Ind Eng Chem Res 27:565–570Tabak SA, Krambeck FJ, Garwood WE (1986) AIChE J 32:1526–1531Corma A, Martínez C, Doskocil EJ (2013) J Catal 300:183–196Martens JA, Ravishankar R, Mishin IE, Jacobs PE (2000) Angew Chem Int Ed Engl 39:4376–4379Martens JA, Verrelst WH, Mathys GM, Brown SH, Jacobs PA (2005) Angew Chem Int Ed Engl 117(5833–583):6Pater JPG, Jacobs PA, Martens JA (1998) J Catal 179:477–482Tabak SA (1981) US4254295, to Mobil OilOccelli ML, Hsu JT, Galya LG (1985) J Mol Catal A: Chem 32:377–390Tabak SA (1984) US4504693, to Mobil Oil CorpKholer E, Schmidt F, Wernicke HJ, Pontes MD, Roberts HL (1995, Summer) Hydrocarbon Technology InternationalMartens JA, Verduijn JP (1995) WO95/19945, to Exxon Chemical Patents Inc.Verrelst WH (1995) Martens LRM, WO95/22516, to Exxon Chemical Patents Inc.Verrelst WH, Martens LRM (2000) US6143942, to Exxon Chemical Patents Inc.Verrelst WH, Martens LRM, Verduijn JP (2006) US6013851, to Exxon Chemical Patents Inc.Dakka JM, Mathys GMK, Puttemans MPH (2003) WO03/035583 to Exxon-Mobil Chemical LimitedMatias P, Sa CC, Graca I, Lopes JM, Carvalho AP, Ramoa RF, Guisnet M (2011) Appl Catal A 399:100–109Chal R, Gérardin C, Bulut M, van Donk S (2011) ChemCatChem 3:67–81Perez-Ramirez J, Christensen CH, Egeblad K, Groen JC (2008) Chem Soc Rev 37:2530–2542Verboekend D, Perez-Ramirez J (2011) Catal Sci Technol 1:879–890Serrano DP, Escola JM, Pizarro P (2013) Chem Soc Rev 42:4004–4035Verboekend D, Chabaneix AM, Thomas K, Gilson JP, Perez-Ramirez J (2011) Cryst Eng Comm 13:3408–3416Emeis CA (1993) J Catal 141:347–354Perego C, Peratello S (1999) Catal Today 52:133–145Abello S, Bonilla A, Perez-Ramirez J (2009) Appl Catal A Gen 364:191–198Corma A, Martinez C, Doskocil EJ, Yaluris G (2011) WO2011002631A2, to BP Oil International Limited. BP Corporation North America Inc., UKCorma A, Martinez C, Doskocil EJ, Yaluris G (2011) WO2011002630A2, to BP Oil International Limited. BP Corporation North America Inc, UKHan S, Heck RH, DiGuiseppi FT (1993) US5234875, to Mobil Oil CorporationPeratello S, Molinari M, Bellussi G, Perego C (1999) Catal Today 52:271–27

Maximum likelihood models and algorithms for gene tree evolution with duplications and losses

<p>Abstract</p> <p>Background</p> <p>The abundance of new genomic data provides the opportunity to map the location of gene duplication and loss events on a species phylogeny. The first methods for mapping gene duplications and losses were based on a parsimony criterion, finding the mapping that minimizes the number of duplication and loss events. Probabilistic modeling of gene duplication and loss is relatively new and has largely focused on birth-death processes.</p> <p>Results</p> <p>We introduce a new maximum likelihood model that estimates the speciation and gene duplication and loss events in a gene tree within a species tree with branch lengths. We also provide an, in practice, efficient algorithm that computes optimal evolutionary scenarios for this model. We implemented the algorithm in the program DrML and verified its performance with empirical and simulated data.</p> <p>Conclusions</p> <p>In test data sets, DrML finds optimal gene duplication and loss scenarios within minutes, even when the gene trees contain sequences from several hundred species. In many cases, these optimal scenarios differ from the lca-mapping that results from a parsimony gene tree reconciliation. Thus, DrML provides a new, practical statistical framework on which to study gene duplication.</p

Evaluation of a social marketing intervention promoting oral rehydration salts in Burundi

<p>Abstract</p> <p>Background</p> <p>Diarrhea is the second leading cause of death for children under five in Burundi; however, use of oral rehydration salts (ORS), the recommended first-line treatment, remains low. In 2004, PSI/Burundi launched a social marketing intervention to promote ORASEL among caregivers of children under five; the product was relaunched in 2006 with a new flavor. This study evaluates the intervention after the ORASEL relaunch, which included mass media and interpersonal communication activities. The study looks at trends in ORASEL use in Burundi and in behavioral determinants that may be related to its use.</p> <p>Methods</p> <p>In 2006 and 2007, PSI conducted household surveys among Burundian females of reproductive age (15-49). Both surveys used a two-stage sampling process to select 30 households in each of 115 rural and urban collines throughout the nation. Survey respondents were asked about diarrhea treatment-related behavior; key behavioral determinants; and exposure to the ORASEL intervention. Data were analyzed to identify trends over time, characteristics of ORASEL users, and associations between exposure to the intervention and changes in ORASEL use and related behavioral determinants.</p> <p>Results</p> <p>ORASEL use among caregivers at their children's last diarrheal episode increased significantly from 20% in 2006 to 30% in 2007, and there were also desirable changes in several behavioral determinants associated with ORASEL use. Evaluation analysis showed that a higher level of exposure to the social marketing campaign was associated with greater use of ORASEL and with significant improvements in perceived availability, knowledge of the signs of diarrhea and dehydration, social support, and self-efficacy.</p> <p>Conclusions</p> <p>ORS use can be improved through social marketing and educational campaigns that make the public aware of the availability of the product, encourage dialogue about its use, and increase skills and confidence relating to correct product preparation and administration. Further interventions in Burundi and elsewhere should promote ORS through a variety of mass media and interpersonal communication channels, and should be rigorously evaluated in the context of the total market for diarrhea treatment products.</p

Evolution in Australasian Mangrove Forests: Multilocus Phylogenetic Analysis of the Gerygone Warblers (Aves: Acanthizidae)

The mangrove forests of Australasia have many endemic bird species but their evolution and radiation in those habitats has been little studied. One genus with several mangrove specialist species is Gerygone (Passeriformes: Acanthizidae). The phylogeny of the Acanthizidae is reasonably well understood but limited taxon sampling for Gerygone has constrained understanding of its evolution and historical biogeography in mangroves. Here we report on a phylogenetic analysis of Gerygone based on comprehensive taxon sampling and a multilocus dataset of thirteen loci spread across the avian genome (eleven nuclear and two mitochondrial loci). Since Gerygone includes three species restricted to Australia's coastal mangrove forests, we particularly sought to understand the biogeography of their evolution in that ecosystem. Analyses of individual loci, as well as of a concatenated dataset drawn from previous molecular studies indicates that the genus as currently defined is not monophyletic, and that the Grey Gerygone (G. cinerea) from New Guinea should be transferred to the genus Acanthiza. The multilocus approach has permitted the nuanced view of the group's evolution into mangrove ecosystems having occurred on multiple occasions, in three non-overlapping time frames, most likely first by the G. magnirostris lineage, and subsequently followed by those of G. tenebrosa and G. levigaster

Improving prescribing of antihypertensive and cholesterol-lowering drugs: a method for identifying and addressing barriers to change

BACKGROUND: We describe a simple approach we used to identify barriers and tailor an intervention to improve pharmacological management of hypertension and hypercholesterolaemia. We also report the results of a post hoc exercise and survey we carried out to evaluate our approach for identifying barriers and tailoring interventions. METHODS: We used structured reflection, searched for other relevant trials, surveyed general practitioners and talked with physicians during pilot testing of the intervention. The post hoc exercise was carried out as focus groups of international researchers in the field of quality improvement in health care. The post hoc survey was done by telephone interviews with physicians allocated to the experimental group of a randomised trial of our multifaceted intervention. RESULTS: A wide range of barriers was identified and several interventions were suggested through structured reflection. The survey led to some adjustments. Studying other trials and pilot testing did not lead to changes in the design of the intervention. Neither the post hoc focus groups nor the post hoc survey revealed important barriers or interventions that we had not considered or included in our tailored intervention. CONCLUSIONS: A simple approach to identifying barriers to change appears to have been adequate and efficient. However, we do not know for certain what we would have gained by using more comprehensive methods and we do not know whether the resulting intervention would have been more effective if we had used other methods. The effectiveness of our multifaceted intervention is under evaluation in a randomised controlled trial

Facultative Symbiont Infections Affect Aphid Reproduction

Some bacterial symbionts alter their hosts reproduction through various mechanisms that enhance their transmission in the host population. In addition to its obligatory symbiont Buchnera aphidicola, the pea aphid Acyrthosiphon pisum harbors several facultative symbionts influencing several aspects of host ecology. Aphids reproduce by cyclical parthenogenesis whereby clonal and sexual reproduction alternate within the annual life cycle. Many species, including the pea aphid, also show variation in their reproductive mode at the population level, with some lineages reproducing by cyclical parthenogenesis and others by permanent parthenogenesis. While the role of facultative symbionts has been well studied during the parthenogenetic phase of their aphid hosts, very little is known on their possible influence during the sexual phase. Here we investigated whether facultative symbionts modulate the capacity to produce sexual forms in various genetic backgrounds of the pea aphid with controlled symbiont composition and also in different aphid genotypes from natural populations with previously characterized infection status and reproductive mode. We found that most facultative symbionts exhibited detrimental effects on their hosts fitness under sex-inducing conditions in comparison with the reference lines. We also showed that the loss of sexual phase in permanently parthenogenetic lineages of A. pisum was not explained by facultative symbionts. Finally, we demonstrated that Spiroplasma infection annihilated the production of males in the host progeny by inducing a male-killing phenotype, an unexpected result for organisms such as aphids that reproduce primarily through clonal reproduction

Quantification of codon selection for comparative bacterial genomics

<p>Abstract</p> <p>Background</p> <p>Statistics measuring codon selection seek to compare genes by their sensitivity to selection for translational efficiency, but existing statistics lack a model for testing the significance of differences between genes. Here, we introduce a new statistic for measuring codon selection, the Adaptive Codon Enrichment (ACE).</p> <p>Results</p> <p>This statistic represents codon usage bias in terms of a probabilistic distribution, quantifying the extent that preferred codons are over-represented in the gene of interest relative to the mean and variance that would result from stochastic sampling of codons. Expected codon frequencies are derived from the observed codon usage frequencies of a broad set of genes, such that they are likely to reflect nonselective, genome wide influences on codon usage (<it>e.g</it>. mutational biases). The relative adaptiveness of synonymous codons is deduced from the frequency of codon usage in a pre-selected set of genes relative to the expected frequency. The ACE can predict both transcript abundance during rapid growth and the rate of synonymous substitutions, with accuracy comparable to or greater than existing metrics. We further examine how the composition of reference gene sets affects the accuracy of the statistic, and suggest methods for selecting appropriate reference sets for any genome, including bacteriophages. Finally, we demonstrate that the ACE may naturally be extended to quantify the genome-wide influence of codon selection in a manner that is sensitive to a large fraction of codons in the genome. This reveals substantial variation among genomes, correlated with the tRNA gene number, even among groups of bacteria where previously proposed whole-genome measures show little variation.</p> <p>Conclusions</p> <p>The statistical framework of the ACE allows rigorous comparison of the level of codon selection acting on genes, both within a genome and between genomes.</p

Spiroplasma Bacteria Enhance Survival of Drosophila hydei Attacked by the Parasitic Wasp Leptopilina heterotoma

Maternally-transmitted associations between endosymbiotic bacteria and insects are ubiquitous. While many of these associations are obligate and mutually beneficial, many are facultative, and the mechanism(s) by which these microbes persist in their host lineages remain elusive. Inherited microbes with imperfect transmission are expected to be lost from their host lineages if no other mechanisms increase their persistence (i.e., host reproductive manipulation and/or fitness benefits to host). Indeed numerous facultative heritable endosymbionts are reproductive manipulators. Nevertheless, many do not manipulate reproduction, so they are expected to confer fitness benefits to their hosts, as has been shown in several studies that report defense against natural enemies, tolerance to environmental stress, and increased fecundity.We examined whether larval to adult survival of Drosophila hydei against attack by a common parasitoid wasp (Leptopilina heterotoma), differed between uninfected flies and flies that were artificially infected with Spiroplasma, a heritable endosymbiont of Drosophila hydei that does not appear to manipulate host reproduction. Survival was significantly greater for Spiroplasma-infected flies, and the effect of Spiroplasma infection was most evident during the host's pupal stage. We examined whether or not increased survival of Spiroplasma-infected flies was due to reduced oviposition by the wasp (i.e., pre-oviposition mechanism). The number of wasp eggs per fly larva did not differ significantly between Spiroplasma-free and Spiroplasma-infected fly larvae, suggesting that differential fly survival is due to a post-oviposition mechanism.Our results suggest that Spiroplasma confers protection to D. hydei against wasp parasitism. This is to our knowledge the first report of a potential defensive mutualism in the genus Spiroplasma. Whether it explains the persistence and high abundance of this strain in natural populations of D. hydei, as well as the widespread distribution of heritable Spiroplasma in Drosophila and other arthropods, remains to be investigated