Development and application of in vivo expression technology (IVET) for analysing microbial gene expression in complex environments

Establishing the mechanisms by which microbes interact with their environment, including eukaryotic hosts, is a major challenge that is essential for the economic utilisation of microbes and their products. Techniques for determining global gene expression profiles of microbes, such as microarray analyses, are often hampered by methodological restraints, particularly the recovery of bacterial transcripts (RNA) from complex mixtures and rapid degradation of RNA. A pioneering technology that avoids this problem is In Vivo Expression Technology (IVET). IVET is a 'promoter-trapping' methodology that can be used to capture nearly all bacterial promoters (genes) upregulated during a microbe-environment interaction. IVET is especially useful because there is virtually no limit to the type of environment used (examples to date include soil, oomycete, a host plant or animal) to select for active microbial promoters. Furthermore, IVET provides a powerful method to identify genes that are often overlooked during genomic annotation, and has proven to be a flexible technology that can provide even more information than identification of gene expression profiles. A derivative of IVET, termed resolvase-IVET (RIVET), can be used to provide spatio-temporal information about environment-specific gene expression. More recently, niche-specific genes captured during an IVET screen have been exploited to identify the regulatory mechanisms controlling their expression. Overall, IVET and its various spin-offs have proven to be a valuable and robust set of tools for analysing microbial gene expression in complex environments and providing new targets for biotechnological development.

QTLs for shelf life in lettuce co-locate with those for leaf biophysical properties but not with those for leaf developmental traits

Developmental and biophysical leaf characteristics that influence post-harvest shelf life in lettuce, an important leafy crop, have been examined. The traits were studied using 60 informative F-9 recombinant inbed lines (RILs) derived from a cross between cultivated lettuce (Lactuca sativa cv. Salinas) and wild lettuce (L. serriola acc. UC96US23). Quantitative trait loci (QTLs) for shelf life co-located most closely with those for leaf biophysical properties such as plasticity, elasticity, and breakstrength, suggesting that these are appropriate targets for molecular breeding for improved shelf life. Significant correlations were found between shelf life and leaf size, leaf weight, leaf chlorophyll content, leaf stomatal index, and epidermal cell number per leaf, indicating that these pre-harvest leaf development traits confer post-harvest properties. By studying the population in two contrasting environments in northern and southern Europe, the genotype by environment interaction effects of the QTLs relevant to leaf development and shelf life were assessed. In total, 107 QTLs, distributed on all nine linkage groups, were detected from the 29 traits. Only five QTLs were common in both environments. Several areas where many QTLs co-located (hotspots) on the genome were identified, with relatively little overlap between developmental hotspots and those relating to shelf life. However, QTLs for leaf biophysical properties (breakstrength, plasticity, and elasticity) and cell area correlated well with shelf life, confirming that the ideal ideotype lettuce should have small cells with strong cell walls. The identification of QTLs for leaf development, strength, and longevity will lead to a better understanding of processability at a genetic and cellular level, and allow the improvement of salad leaf quality through marker-assisted breeding.

The challenges for molecular nutrition research 1: linking genotype to healthy nutrition

Nutrition science finds itself at a major crossroad. On the one hand we can continue the current path, which has resulted in some substantial advances, but also many conflicting messages which impair the trust of the general population, especially those who are motivated to improve their health through diet. The other road is uncharted and is being built over the many exciting new developments in life sciences. This new era of nutrition recognizes the complex relation between the health of the individual, its genome, and the life-long dietary exposure, and has lead to the realisation that nutrition is essentially a gene - environment interaction science. This review on the relation between genotype, diet and health is the first of a series dealing with the major challenges in molecular nutrition, analyzing the foundations of nutrition research. With the unravelling of the human genome and the linking of its variability to a multitude of phenotypes from " healthy'' to an enormously complex range of predispositions, the dietary modulation of these propensities has become an area of active research. Classical genetic approaches applied so far in medical genetics have steered away from incorporating dietary effects in their models and paradoxically, most genetic studies analyzing diet-associated phenotypes and diseases simply ignore diet. Yet, a modest but increasing number of studies are accounting for diet as a modulator of genetic associations. These range from observational cohorts to intervention studies with prospectively selected genotypes. New statistical and bioinformatics approaches are becoming available to aid in design and evaluation of these studies. This review discusses the various approaches used and provides concrete recommendations for future research.

Analysis of physiological data from the International Clonal Trial (CFC)

A range of physiological parameters (canopy light transmission, canopy shape, leaf size, flowering and flushing intensity) were measured from the International Clone Trial, typically over the course of two years. Data were collected from six locations, these being: Brazil, Ecuador, Trinidad, Venezuela, Côte d’Ivoire and Ghana. Canopy shape varied significantly between clones, although it showed little variation between locations. Genotypic variation in leaf size was differentially affected by the growth location; such differences appeared to underlie a genotype by environment interaction in relation to canopy light transmission. Flushing data were recorded at monthly intervals over the course of a year. Within each location, a significant interaction was observed between genotype and time of year, suggesting that some genotypes respond to a greater extent than others to environmental stimuli. A similar interaction was observed for flowering data, where significant correlations were found between flowering intensity and temperature in Brazil and flowering intensity and rainfall in Côte d’Ivoire. The results demonstrate the need for local evaluation of cocoa clones and also suggest that the management practices for particular planting material may need to be fine-tuned to the location in which they are cultivated.

The role of the international cocoa germplasm database and the international cocoa quarantine centre in information management and distribution of cocoa genetic resources

A range of physiological parameters (canopy light transmission, canopy shape, leaf size, flowering and flushing intensity) were measured from the International Clone Trial, typically over the course of two years. Data were collected from six locations, these being: Brazil, Ecuador, Trinidad, Venezuela, Côte d’Ivoire and Ghana. Canopy shape varied significantly between clones, although it showed little variation between locations. Genotypic variation in leaf size was differentially affected by the growth location; such differences appeared to underlie a genotype by environment interaction in relation to canopy light transmission. Flushing data were recorded at monthly intervals over the course of a year. Within each location, a significant interaction was observed between genotype and time of year, suggesting that some genotypes respond to a greater extent than others to environmental stimuli. A similar interaction was observed for flowering data, where significant correlations were found between flowering intensity and temperature in Brazil and flowering intensity and rainfall in Côte d’Ivoire. The results demonstrate the need for local evaluation of cocoa clones and also suggest that the management practices for particular planting material may need to be fine-tuned to the location in which they are cultivated.

A climate of control: flooding, displacement and planned resettlement in the Lower Zambezi River valley, Mozambique

In recent years, the potential role of planned, internal resettlement as a climate change adaptation measure has been highlighted by national governments and the international policy community. However, in many developing countries, resettlement is a deeply political process that often results in an unequal distribution of costs and benefits amongst relocated persons. This paper examines these tensions in Mozambique, drawing on a case study of flood-affected communities in the Lower Zambezi River valley. It takes a political ecology approach – focusing on discourses of human-environment interaction, as well as the power relationships that are supported by such discourses – to show how a dominant narrative of climate change-induced hazards for small-scale farmers is contributing to their involuntary resettlement to higher-altitude, less fertile areas of land. These forced relocations are buttressed by a series of wider economic and political interests in the Lower Zambezi River region, such dam construction for hydroelectric power generation and the extension of control over rural populations, from which resettled people derive little direct benefit. Rather than engaging with these challenging issues, most international donors present in the country accept the ‘inevitability’ of extreme weather impacts and view resettlement as an unfortunate and, in some cases, necessary step to increase people’s ‘resilience’, thus rationalising the top-down imposition of unpopular social policies. The findings add weight to the argument that a depoliticised interpretation of climate change can deflect attention away from underlying drivers of vulnerability and poverty, as well as obscure the interests of governments that are intent on reordering poor and vulnerable populations.

Examining the relationships between Holocene climate change, hydrology, and human society in Ireland

This thesis explores human-environment interactions during the Mid-Late Holocene in raised bogs in central Ireland. The raised bogs of central Ireland are widely-recognised for their considerable palaeoenvironmental and archaeological resources: research over the past few decades has established the potential for such sites to preserve sensitive records of Holocene climatic variability expressed as changes in bog surface wetness (BSW); meanwhile archaeological investigations over the past century have uncovered hundreds of peatland archaeological features dating from the Neolithic through to the Post-Medieval period including wooden trackways, platforms, and deposits of high-status metalwork. Previous studies have attempted to explore the relationship between records of past environmental change and the occurrence of peatland archaeological sites reaching varying conclusions. More recently, environmentally-deterministic models of human-environment interaction in Irish raised bogs at the regional scale have been explicitly tested leading to the conclusion that there is no relationship between BSW and past human activity. These relationships are examined in more detail on a site-by-site basis in this thesis. To that end, testate amoebae-derived BSW records from nine milled former raised bogs in central Ireland were produced from sites with known and dated archaeological records. Relationships between BSW records and environmental conditions within the study area were explored through both the development of a new central Ireland testate amoebae transfer function and through comparisons between recent BSW records and instrumental weather data. Compilation of BSW records from the nine fossil study sites show evidence both for climate forcing, particularly during 3200-2400 cal BP, as well as considerable inter-site variability. Considerable inter-site variability was also evident in the archaeological records of the same sites. Whilst comparisons between BSW and archaeological records do not show a consistent linear relationship, examination of records on a site-by-site basis were shown to reveal interpretatively important contingent relationships. It is concluded therefore, that future research on human-environment interactions should focus on individual sites and should utilise theoretical approaches from the humanities in order to avoid the twin pitfalls of masking important local patterns of change, and of environmental determinism.

A segurança viária e o fator humano : verificação da presença de álcool-direção no sistema de transporte rodoviário do RGS

Esta dissertação examina a situação geral dos Acidentes Viários, no contexto do transporte rodoviário, cujas evidências apontam o Fator Humano como o maior responsável por tais eventos. Entende-se que um maior conhecimento sobre ele possibilitará melhorar a segurança do tráfego e da produção transporte. O estudo pretende destacar a importância das análises relacionadas com a atividade transporte rodoviário, as variações da demanda do sistema de circulação e a tarefa do motorista, sob a ótica da ergonomia. Objetiva ele, também, mostrar importância desses estudos para melhor avaliar as interações dos fatores homemmáquina- ambiente viário e para o desenvolvimento de novas tecnologias e produtos de segurança viária. A revisão bibliográfica dos capítulos iniciais revelam o estado da arte e a importância da segurança de trânsito, em nível internacional. Também revelaram que todas nações sofrem do mesmo mal em suas redes viárias, que varia de acordo com a realidade de cada um. Embora o acidente de trânsito seja um fenômeno comum às nações, aqui eles atingiram a dimensão de flagelo social, em razão da sua severidade; e de calamidade econômica, face a elevação dos custos de produção na atividade do transporte rodoviário. São analisadas as características do fator humano, fundamentais na tarefa de condução, e o respectivo nexo causal das falhas com a gênese do acidente, num sistema multifatorial e interativo. O trabalho fundamenta-se em extensa revisão bibliográfica. O estudo de caso, desenvolvido a partir da revisão dos dados de uma pesquisa anterior, comprova a hipótese que o “álcool-direção”, considerado na literatura como o maior causador de acidentes viários, tem sua presença marcada por elevados índices nas rodovias do RS, contrariando a conclusão da pesquisa anterior. Ao final, também oferece recomendações para o desenvolvimento de ações objetivas para melhorar a segurança viária.

Crescimento e esporulação de duas espécies de arthrobotrys corda em diferentes meios de cultura e dois ambientes

The researches on the biological control of nematodes with nematophagous fungi has been intensified in recent years. The knowledge of the ecological conditions for the growth and sporulation of these fungi is a prerequisite for attainment of pure cultures needed to attend the demand for formulation of these organisms. With the objective to evaluate the micelial growth and sporulation of Arthrobotrys musiformis and A. oligospora in two environments (B.O.D at 25 +/- 1 degrees C and the environment of the Laboratory), 20 cultures media prepared with common materials found in the communities and industrialized media such as mycological agar, PDA and CMA were evaluated. The media were tested in Petri dishes, being the micelial growth of the fungi evaluated daily, during six days. The measured sporulation at the end of the experiment was done by estimation of the number of conidia/Petri dish. The experiment was carried out in a random design following a factorial arrangement of 20 x 2 x 2, corresponding to 20 media, two fungi and two environments, with five replicates. The variance analysis of the data evidenced significant statistical difference by the F Test, at 1% probability, among media x fungi x environment interaction. Fifty percent of the tested media provided the adequate micelial growth of A. musiformis and there was no statistical difference among them, namely: cassava meal (FM), sweet starch (PD), "corn meal agar" (CMA), oat in fine flakes (AFF), agar-water + dextrose (AA+D), mycological agar (AM), potato dextrose agar (BDA), meal of maize (FMI), flour of wheat (FT) and wheat for kibble (TK). In relation to A. oligospora, 75% of the tested media promoted the maximum growth of the fungus, which are: AFF, AM, FM, PD, CMA, AA+D, BDA, FT, TK, the water from the decoction of rice (AAZ), rice in grains (AZG), triturated rice (AZT), thread flour (FR), oats flour (FA), oats in thick flakes (AFG) and flour of maize (FU). In relation to the sporulation the media that had better role for A. musiformis, in decreasing order, were: FR, TK, AFG, BDA, FA, AFF, AM, FMI, AZT and FM, varying between 1,01 x 10(6) and 1,4 x 10(4) conidia/Petri dish. For the A. oligospora sporulation, the CMA medium provided the maximum level with an estimated average of 5,7 x 10(6) conidia/Petri dish. In the general, the best media for the micelial growth and sporulation of A. musiformis had also been the best for A. oligospora. However, some that had been the best for the A. oligospora did not had been efficient for the micelial growth or the sporulation of A. musiformis, indicating that the isolate of A. musiformis in case is more demanding than that A. oligospora one. The evidences from the study indicate that, in Jaboticabal, São Paulo state, the growth and the sporulation of these fungi do not demand special chambers. Some adaptations of an environment at the laboratory, enough to obliterate the light are sufficient.

Produtividade, adaptabilidade e estabilidade fenotípica de cultivares de tomateiro sob diferentes condições de ambiente

O objetivo deste trabalho foi estudar o desempenho produtivo, adaptabilidade e estabilidade fenotípica de seis genótipos de tomateiro na região de Marília, SP. Os experimentos foram conduzidos em nove ambientes (seis sob condições de cultivo protegido e três sob condições de céu aberto), com seis genótipos (Carmen, Diva, Donador, Graziela, Vita e HE-295), em blocos casualizados, com quatro repetições. Ocorreram diferenças significativas entre ambientes, e a média geral dos cultivos protegidos superou a dos cultivos a céu aberto quanto à produtividade, apesar de a média geral dos cultivos a céu aberto ser superior quanto ao peso médio de frutos. As cultivares, à exceção de HE-295, demonstraram alta estabilidade, merecendo destaque as cultivares Carmen, Donador e Vita, que tiveram rendimento médio superior ao da média geral, adaptabilidade geral e comportamento previsível em todos os ambientes estudados. Quanto ao peso médio dos frutos, as cultivares Diva e Vita foram as únicas que mostraram ampla adaptabilidade a todos os ambientes, comportamento previsível, além de apresentarem peso médio do fruto superior ao da média geral.

Efeito de períodos de semeadura e das condições de armazenamento sobre a qualidade de grãos de feijão para o cozimento

A conservação adequada pode manter as características do grão recém-colhido por mais tempo, assegurando o valor comercial do produto estocado. Assim, o objetivo deste trabalho foi avaliar o efeito de períodos de semeadura na qualidade de cozimento de grãos de feijão da cultivar TPS Nobre, quando armazenados em diferentes condições de temperatura, de umidade e tempo de estocagem. O delineamento experimental utilizado foi o inteiramente casualizado, com três repetições. Os tratamentos consistiram da combinação de três períodos de semeadura, com três ambientes de armazenamento e três tempos de armazenamento dos grãos (0, 3 e 6 meses). A interpretação dos resultados permitiu inferir que as porcentagens de grãos normais e de grãos duros revelaram comportamento diferenciado em função do ambiente e do tempo de armazenamento. Constatou-se maior porcentagem de grãos duros após seis meses de armazenamento, realizado sob temperatura média do ar de 12 °C e umidade relativa de 45%-50% e também quando os grãos foram resultantes de semeadura realizada tardiamente (21/10/03). A absorção de água e o tempo de cozimento dos grãos de feijão foram alterados em função do período de semeadura, das condições e do tempo de armazenamento, caracterizando a existência de efeitos da interação genótipos x ambientes na qualidade para o cozimento dos grãos. Sendo assim, maior ou menor tempo para a absorção de água ou para o cozimento podem ser requeridos em função da qualidade dos grãos no momento da colheita ou das condições de temperatura e de umidade de armazenamento.

Qualidade nutricional e tecnológica de genótipos de feijão cultivados em diferentes safras agrícolas

O feijão é um dos alimentos mais produzidos em todo o território nacional, sendo intensa a busca por cultivares produtivas, adaptadas ao local de cultivo e com boas características culinárias. Assim, este trabalho foi desenvolvido com o objetivo de avaliar o comportamento de genótipos de feijoeiro, quanto ao teor de proteína, tempo para cozimento e capacidade de hidratação dos grãos. O experimento foi desenvolvido em três safras, correspondendo às épocas da seca 2005, das águas 2005 e da seca 2006. O delineamento experimental utilizado foi o de blocos casualizados, com 24 tratamentos, representados pelos genótipos de feijoeiro dos grupos comerciais Carioca e Preto, com quatro repetições. Os grãos de feijão produzidos na safra das águas 2005 tiveram maior tempo médio para cozimento, menor teor de proteína bruta e maior tempo para máxima hidratação. Os genótipos LP 98-20 e CNFC 9494 (Grupo comercial Carioca), como também as cultivares Graúna e IAC Una (Grupo comercial Preto) destacaram-se quanto ao menor tempo para cozimento nas três safras estudadas, enquanto Gen 96A10, CNFC 9484 (Ambos do grupo comercial Carioca) e CNFP 10138 (Grupo comercial Preto) destacaram-se em relação aos demais pela baixa porcentagem de grãos de casca dura e menor tempo para a máxima hidratação dos grãos.

Adaptabilidade e estabilidade fenotípica de genótipos de cenoura

Avaliaram-se a adaptabilidade e a estabilidade fenotípica de dez genótipos de cenoura, nove de polinização aberta [Alvorada (FELTRIN); Tropical (ISLA); Brasília (ISLA); Nova Brasília (ISLA); Carandaí (SVS); Brasília (SVS); Brazlândia (HORTEC); HT-2000 (HORTEC), e Brasília-RL (SAKATA)] e o híbrido AF-845 (SAKATA), em semeaduras, de janeiro e março, em São José do Rio Pardo (SP), janeiro e fevereiro, em Ponta Grossa (PR), e na primeira e última semana de fevereiro, em São Gotardo (MG), e Carandaí (MG), totalizando oito experimentos (SJRP-JAN; SJRP-MAR; PG-JAN; PG-FEV; SG-FEV'; SG-FEV''; C-FEV', e C-FEV''), que foram implementados em blocos casualizados com quatro repetições. Os dados foram submetidos à análise de variância individual e conjunta, e à análise de adaptabilidade e de estabilidade. Dos oito ambientes testados, apenas C-FEV'', PG-JAN e SG-FEV'' foram considerados favoráveis ao cultivo de cenoura, com destaque para C-FEV''. Entre genótipos, na maioria dos ambientes, 'Brazlândia' se destacou tanto na produtividade total, quanto na produtividade comercial de raízes. Na análise de adaptabilidade, 'Brazlândia' e 'Brasília-RL' indicaram possuir desempenho mais do que proporcional à melhoria promovida pelo ambiente, sendo indicados para semeaduras em ambientes favoráveis. O híbrido AF-845 mostrou ter pequena capacidade em responder às variações ambientais, não sendo indicado para nenhum dos ambientes estudados. Os genótipos de cenoura, em geral, apresentaram estabilidade de comportamento nos ambientes estudados.

Adaptabilidade e estabilidade fenotípica de cultivares de cenoura

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Efeito da interação genótipo × ambiente sobre o peso ao nascimento, aos 205 e aos 550 dias de idade de bovinos da raça Nelore na Região Sul do Brasil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)