Horizontal DNA transfer mechanisms of bacteria as weapons of intragenomic conflict

Horizontal DNA transfer (HDT) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. Much recent research has emphasised the adaptive benefit of acquiring novel DNA, but here we argue instead that intragenomic conflict provides a coherent framework for understanding the evolutionary origins of HDT. To test this hypothesis, we developed a mathematical model of a clonally descended bacterial population undergoing HDT through transmission of mobile genetic elements (MGEs) and genetic transformation. Including the known bias of transformation toward the acquisition of shorter alleles into the model suggested it could be an effective means of counteracting the spread of MGEs. Both constitutive and transient competence for transformation were found to provide an effective defence against parasitic MGEs; transient competence could also be effective at permitting the selective spread of MGEs conferring a benefit on their host bacterium. The coordination of transient competence with cell-cell killing, observed in multiple species, was found to result in synergistic blocking of MGE transmission through releasing genomic DNA for homologous recombination while simultaneously reducing horizontal MGE spread by lowering the local cell density. To evaluate the feasibility of the functions suggested by the modelling analysis, we analysed genomic data from longitudinal sampling of individuals carrying Streptococcus pneumoniae. This revealed the frequent within-host coexistence of clonally descended cells that differed in their MGE infection status, a necessary condition for the proposed mechanism to operate. Additionally, we found multiple examples of MGEs inhibiting transformation through integrative disruption of genes encoding the competence machinery across many species, providing evidence of an ongoing "arms race." Reduced rates of transformation have also been observed in cells infected by MGEs that reduce the concentration of extracellular DNA through secretion of DNases. Simulations predicted that either mechanism of limiting transformation would benefit individual MGEs, but also that this tactic's effectiveness was limited by competition with other MGEs coinfecting the same cell. A further observed behaviour we hypothesised to reduce elimination by transformation was MGE activation when cells become competent. Our model predicted that this response was effective at counteracting transformation independently of competing MGEs. Therefore, this framework is able to explain both common properties of MGEs, and the seemingly paradoxical bacterial behaviours of transformation and cell-cell killing within clonally related populations, as the consequences of intragenomic conflict between self-replicating chromosomes and parasitic MGEs. The antagonistic nature of the different mechanisms of HDT over short timescales means their contribution to bacterial evolution is likely to be substantially greater than previously appreciated

The genomes of two key bumblebee species with primitive eusocial organization

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

A novel evolutionary strategy revealed in the Phaeoviruses

Phaeoviruses infect the brown algae, which are major contributors to primary production of coastal waters and estuaries. They exploit a Persistent evolutionary strategy akin to a K- selected life strategy via genome integration and are the only known representatives to do so within the giant algal viruses that are typified by r- selected Acute lytic viruses. In screening the genomes of five species within the filamentous brown algal lineage, here we show an unprecedented diversity of viral gene sequence variants especially amongst the smaller phaeoviral genomes. Moreover, one variant shares features from both the two major sub-groups within the phaeoviruses. These phaeoviruses have exploited the reduction of their giant dsDNA genomes and accompanying loss of DNA proofreading capability, typical of an Acute life strategist, but uniquely retain a Persistent life strategy

Linkage Mapping of Stem Saccharification Digestibility in Rice

Rice is the staple food of almost half of the world population, and in excess 90% of it is grown and consumed in Asia, but the disposal of rice straw poses a problem for farmers, who often burn it in the fields, causing health and environmental problems. However, with increased focus on the development of sustainable biofuel production, rice straw has been recognized as a potential feedstock for non-food derived biofuel production. Currently, the commercial realization of rice as a biofuel feedstock is constrained by the high cost of industrial saccharification processes needed to release sugar for fermentation. This study is focused on the alteration of lignin content, and cell wall chemotypes and structures, and their effects on the saccharification potential of rice lignocellulosic biomass. A recombinant inbred lines (RILs) population derived from a cross between the lowland rice variety IR1552 and the upland rice variety Azucena with 271 molecular markers for quantitative trait SNP (QTS) analyses was used. After association analysis of 271 markers for saccharification potential, 1 locus and 4 pairs of epistatic loci were found to contribute to the enzymatic digestibility phenotype, and an inverse relationship between reducing sugar and lignin content in these recombinant inbred lines was identified. As a result of QTS analyses, several cell-wall associated candidate genes are proposed that may be useful for marker-assisted breeding and may aid breeders to produce potential high saccharification rice varieties

The global pendulum swing towards community health workers in low- and middle-income countries: A scoping review of trends, geographical distribution and programmatic orientations, 2005 to 2014

BACKGROUND: There has been a substantial increase in publications and interest in community health workers (CHWs) in low- and middle-income countries (LMIC) over the last years. This paper examines the growth, geographical distribution and programmatic orientations of the indexed literature on CHWs in LMIC over a 10-year period. METHODS: A scoping review of publications on CHWs from 2005 to 2014 was conducted. Using an inclusive list of terms, we searched seven databases (including MEDLINE, CINAHL, Cochrane) for all English-language publications on CHWs in LMIC. Two authors independently screened titles/abstracts, downloading full-text publications meeting inclusion criteria. These were coded in an Excel spreadsheet by year, type of publication (e.g. review, empirical), country, region, programmatic orientation (e.g. maternal-child health, HIV/AIDS, comprehensive) and CHW roles (e.g. prevention, treatment) and further analysed in Stata14. Drawing principally on the subset of review articles, specific roles within programme areas were identified and grouped. FINDINGS: Six hundred seventy-eight publications from 46 countries on CHWs were inventoried over the 10-year period. There was a sevenfold increase in annual number of publications from 23 in 2005 to 156 in 2014. Half the publications were reporting on initiatives in Africa, a third from Asia and 11 % from the Americas (mostly Brazil). The largest single focus and driver of the growth in publications was on CHW roles in meeting the Millennium Development Goals of maternal, child and neonatal survival (35 % of total), followed by HIV/AIDS (16 %), reproductive health (6 %), non-communicable diseases (4 %) and mental health (4 %). Only 17 % of the publications approached CHW roles in an integrated fashion. There were also distinct regional (and sometimes country) profiles, reflecting different histories and programme traditions. CONCLUSIONS: The growth in literature on CHWs provides empirical evidence of ever-increasing expectations for addressing health burdens through community-based action. This literature has a strong disease- or programme-specific orientation, raising important questions for the design and sustainable delivery of integrated national programmes.Scopu

Global, regional, and national incidence, prevalence, and mortality of HIV, 1980–2017, and forecasts to 2030, for 195 countries and territories: a systematic analysis for the Global Burden of Diseases, Injuries, and Risk Factors Study 2017

Background Understanding the patterns of HIV/AIDS epidemics is crucial to tracking and monitoring the progress of prevention and control efforts in countries. We provide a comprehensive assessment of the levels and trends of HIV/AIDS incidence, prevalence, mortality, and coverage of antiretroviral therapy (ART) for 1980–2017 and forecast these estimates to 2030 for 195 countries and territories. Methods We determined a modelling strategy for each country on the basis of the availability and quality of data. For countries and territories with data from population-based seroprevalence surveys or antenatal care clinics, we estimated prevalence and incidence using an open-source version of the Estimation and Projection Package—a natural history model originally developed by the UNAIDS Reference Group on Estimates, Modelling, and Projections. For countries with cause-specific vital registration data, we corrected data for garbage coding (ie, deaths coded to an intermediate, immediate, or poorly defined cause) and HIV misclassification. We developed a process of cohort incidence bias adjustment to use information on survival and deaths recorded in vital registration to back-calculate HIV incidence. For countries without any representative data on HIV, we produced incidence estimates by pulling information from observed bias in the geographical region. We used a re-coded version of the Spectrum model (a cohort component model that uses rates of disease progression and HIV mortality on and off ART) to produce age-sex-specific incidence, prevalence, and mortality, and treatment coverage results for all countries, and forecast these measures to 2030 using Spectrum with inputs that were extended on the basis of past trends in treatment scale-up and new infections. Findings Global HIV mortality peaked in 2006 with 1·95 million deaths (95% uncertainty interval 1·87–2·04) and has since decreased to 0·95 million deaths (0·91–1·01) in 2017. New cases of HIV globally peaked in 1999 (3·16 million, 2·79–3·67) and since then have gradually decreased to 1·94 million (1·63–2·29) in 2017. These trends, along with ART scale-up, have globally resulted in increased prevalence, with 36·8 million (34·8–39·2) people living with HIV in 2017. Prevalence of HIV was highest in southern sub-Saharan Africa in 2017, and countries in the region had ART coverage ranging from 65·7% in Lesotho to 85·7% in eSwatini. Our forecasts showed that 54 countries will meet the UNAIDS target of 81% ART coverage by 2020 and 12 countries are on track to meet 90% ART coverage by 2030. Forecasted results estimate that few countries will meet the UNAIDS 2020 and 2030 mortality and incidence targets. Interpretation Despite progress in reducing HIV-related mortality over the past decade, slow decreases in incidence, combined with the current context of stagnated funding for related interventions, mean that many countries are not on track to reach the 2020 and 2030 global targets for reduction in incidence and mortality. With a growing population of people living with HIV, it will continue to be a major threat to public health for years to come. The pace of progress needs to be hastened by continuing to expand access to ART and increasing investments in proven HIV prevention initiatives that can be scaled up to have population-level impact

A922 Sequential measurement of 1 hour creatinine clearance (1-CRCL) in critically ill patients at risk of acute kidney injury (AKI)

Meeting abstrac

As funções terapêuticas da atividade: um estudo comparativo em terapia ocupacional

O propósito deste estudo foi verificar as alterações ocorridas em relação a assistência em terapia ocupacional na Unidade Psiquiátrica do Hospital São Paulo, vinculada ao Departamento de Psiquiatria e Psicologia Médica da Universidade Federal de São Paulo, através da análise da aplicação de um instrumento terapêutico da terapia ocupacional, a atividade. Este estudo baseou-se em pesquisa retrospectiva nos prontuários de pacientes internadas na Unidade Psiquiátrica. A pesquisa se propôs sistematizar o registro de procedimentos de terapeutas ocupacionais e de outros profissionais em relação a atividade, no sentido de dar uma contribuição universalização de alguns aspectos do discurso da Terapia Ocupacional, sistematizando-os em categorias. Pretendeu-se verificar a aplicabilidade do instrumento terapêutico pesquisado, através da comparação dos procedimentos encontrados em dois períodos. Os procedimentos metodológicos constaram de: a.- definição dos períodos a serem pesquisados: de 1/1/1988 a 31/12/1988 e de 1/1/1994 a 31/12/1994; b- coleta de dados: foram levantados em 257 prontuários de pacientes internadas na Unidade Psiquiátrica nos períodos acima definidos, os dados sócio demográficos e todos os registros encontrados nos prontuários, sobre uso de atividade e sobre terapia Ocupacional: c- categorização dos dados sobre atividade e terapia ocupacional segundo referências empíricas e funções da atividade e posteriormente em categorias empíricas em terapia ocupacional; d- análise dos dados: através do cotejamento do material encontrados nos dois períodos em relação As categorias criadas e A literatura. A análise dos dados demonstrou que não houve alterações no perfil sócio demográfico da clientela, não se alterando também a pouca atenção da equipe frente a dados relativos a origem, ocupação e perfil econômico. Em relação a idade média das pacientes e tempo de internação a distribuição dos mesmos difere, os indices mais altos encontrados relacionam-se ao segundo período. Quanto ao instrumento terapêutico, a atividade, o estudo comparativo, permitiu identificar modificações em relação a compreensão e uso do mesmo. No primeiro período, o recurso terapêutico, atividade, relaciona-se com a proposta de ambientoterapia, isto 6, toda a utilização da atividade insere-se num movimento mais amplo, grupal, com a participação efetiva de toda a equipe, voltado à experiências sociabilizantes, com raras abordagens especificas de terapeutas ocupacionais. No segundo período a utilização da atividade enquanto instrumento terapêutico, aproxima-se dos recursos teóricos e práticos da terapia ocupacional psicodinâmica, o que permitiu enfoques mais individualizados, introduziu a questão do processo terapêutico, a utilização deste recurso como uma aborgagem eletiva, ampliou o contato das terapeutas ocupacionais com a clientela em grupos específicos de terapia ocupacional e no ambulatório de egressos. Perdeu-se neste segundo período alguns procedimentos relativos a proposta da ambientoterapia e a uniformidade da equipe frente a esta questão. Percebeu-se que, a aplicabilidade deste recurso terapêutico, nos dois períodos, baseia-se nas possíveis funções da atividade, tomadas sempre como recursos estratégicos. Nos dois períodos foi possível verificar que a aplicabilidade deste instrumento terapêutico não se relacionou a categorias diagnósticas, podendo num sentido mais amplo, ter indicação a todos as pacientes.The purpose of this study was to verify the changes occurred within the Occupational Therapy assistance in the Psychiatric Unit of Hospital São Paulo, linked to the Psychiatry and Medical Psychology Department of Universidade Federal de Sao Paulo through the analysis of the use a therapeutic means of Occupational Therapy named the activity. The study was based on retrospective research of inpatients'clinical charts. The research purpose was to sistematyze the procedures of occupational therapists and of other professionals concerning the activity in order to contribute to the generalization of certains aspects of occupational therapy practices by arranging them into categories.Our intention was to verify the applicability of the therapeutic means under analysis through the comparison of procedures found in two distinct periods. The experimental methods consisted of: a. Definition of periods to be researched: from 01/01/1988 to 31/12/1988 and from 01/01/1994 to 31/12/1994. b.Data collection: Data were collected from 257 inpatineclinical charts during the above defined periods, specifically social demographics data and all the information found in charts concerning use of the activity and occupational therapy. c. data categorization about the activity and occupational therapy according to empirical references and functions of the activity and subsequently to empirical categories in occupational therapy d.data analyses: through comparison of the material found in both periods, through created categories and in reference to the existing literature. Data analyses showed that were no changes in patients social demographics profile, as well as in team members'poor charting of data relative to the source, occupation and economical profile of impatient. Concerning the age of the patients and hospitalization period, their distribution differed with higher levels found in the second period. As for the use of the therapeutic instrument, the activity, the comparison allowed the identification of due to its application.changes. In the first period, the activity relates to the millieu therapy proposal, that is, all the activity application inserts itself in a broader movement, with the effective participation of all the members focused on socialization with rare specif interventions of occupational therapists. In the secon period, the use of the activity as a therapeutic instrument follows the theoretical and practical resource of the psychodinamic occupational therapy; that allowed more specific approaches and introduced the subject of the therapeutic process in occupational therapy. The use of this resource as a choice approach enlarged the contact of occupational therapists with patients in Occupational Therapy groups and in the out patient follow-up treatment. During this second period some procedures relating to the millieu therapy project and the unity of the team concerning this subject were lost. We have noticed that the applicability of this therapeutic resource, the activity, during both periods is based on the possible functions of the activity, always taken as strategis resources. It was possible to verify, in both periods, that the applicability of this therapeutic instrument is not related to diagnostic categories, and it that can be beneficial to all the patients.BV UNIFESP: Teses e dissertaçõe

Harnessing the potential of ligninolytic enzymes for lignocellulosic biomass pretreatment

Abundant lignocellulosic biomass from various industries provides a great potential feedstock for the production of value-added products such as biofuel, animal feed, and paper pulping. However, low yield of sugar obtained from lignocellulosic hydrolysate is usually due to the presence of lignin that acts as a protective barrier for cellulose and thus restricts the accessibility of the enzyme to work on the cellulosic component. This review focuses on the significance of biological pretreatment specifically using ligninolytic enzymes as an alternative method apart from the conventional physical and chemical pretreatment. Different modes of biological pretreatment are discussed in this paper which is based on (i) fungal pretreatment where fungi mycelia colonise and directly attack the substrate by releasing ligninolytic enzymes and (ii) enzymatic pretreatment using ligninolytic enzymes to counter the drawbacks of fungal pretreatment. This review also discusses the important factors of biological pretreatment using ligninolytic enzymes such as nature of the lignocellulosic biomass, pH, temperature, presence of mediator, oxygen, and surfactant during the biodelignification process