Transcriptional dynamics of the developing sweet cherry (Prunus avium L.) fruit: sequencing, annotation and expression profiling of exocarp-associated genes

The exocarp, or skin, of fleshy fruit is a specialized tissue that protects the fruit, attracts seed dispersing fruit eaters, and has large economical relevance for fruit quality. Development of the exocarp involves regulated activities of many genes. This research analyzed global gene expression in the exocarp of developing sweet cherry (Prunus avium L., 'Regina'), a fruit crop species with little public genomic resources. A catalog of transcript models (contigs) representing expressed genes was constructed from de novo assembled short complementary DNA (cDNA) sequences generated from developing fruit between flowering and maturity at 14 time points. Expression levels in each sample were estimated for 34 695 contigs from numbers of reads mapping to each contig. Contigs were annotated functionally based on BLAST, gene ontology and InterProScan analyses. Coregulated genes were detected using partitional clustering of expression patterns. The results are discussed with emphasis on genes putatively involved in cuticle deposition, cell wall metabolism and sugar transport. The high temporal resolution of the expression patterns presented here reveals finely tuned developmental specialization of individual members of gene families. Moreover, the de novo assembled sweet cherry fruit transcriptome with 7760 full-length protein coding sequences and over 20 000 other, annotated cDNA sequences together with their developmental expression patterns is expected to accelerate molecular research on this important tree fruit crop.

Filling in gaps of Drosophila melanogaster urate degradation metabolic pathway using metabolomics approaches: towards the core metabolome of the fruit fly

The primary goal of systems biology is to integrate complex omics data, and data obtained from traditional experimental studies in order to provide a holistic understanding of organismal function. One way of achieving this aim is to generate genome-scale metabolic models (GEMs), which contain information on all metabolites, enzyme-coding genes, and biochemical reactions in a biological system. Drosophila melanogaster GEM has not been reconstructed to date. Constraint-free genome-wide metabolic model of the fruit fly has been reconstructed in our lab, identifying gaps, where no enzyme was identified and metabolites were either only produced or consume. The main focus of the work presented in this thesis was to develop a pipeline for efficient gap filling using metabolomics approaches combined with standard reverse genetics methods, using 5-hydroxyisourate hydrolase (5-HIUH) as an example. 5-HIUH plays a role in urate degradation pathway. Inability to degrade urate can lead to inborn errors of metabolism (IEMs) in humans, including hyperuricemia. Based on sequence analysis Drosophila CG30016 gene was hypothesised to encode 5- HIUH. CG30016 knockout flies were examined to identify Malpighian tubules phenotype, and shortened lifespan might reflect kidney disorders in hyperuricemia in humans. Moreover, LC-MS analysis of mutant tubules revealed that CG30016 is involved in purine metabolism, and specifically urate degradation pathway. However, the exact role of the gene has not been identified, and the complete method for gap filling has not been developed. Nevertheless, thanks to the work presented here, we are a step closer towards the development of a gap-filling pipeline in Drosophila melanogaster GEM. Importantly, the areas that require further optimisation were identified and are the focus of future research. Moreover, LC-MS analysis confirmed that tubules rather than the whole fly were more suitable for metabolomics analysis of purine metabolism. Previously, Dow/Davies lab has generated the most complete tissue-specific transcriptomic atlas for Drosophila – FlyAtlas.org, which provides data on gene expression across multiple tissues of adult fly and larva. FlyAtlas revealed that transcripts of many genes are enriched in specific Drosophila tissues, and that it is possible to deduce the functions of individual tissues within the fly. Based on FlyAtlas data, it has become clear that the fly (like other metazoan species) must be considered as a set of tissues, each 2 with its own distinct transcriptional and functional profile. Moreover, it revealed that for about 30% of the genome, reverse genetic methods (i.e. mutation in an unknown gene followed by observation of phenotype) are only useful if specific tissues are investigated. Based on the FlyAtlas findings, we aimed to build a primary tissue-specific metabolome of the fruit fly, in order to establish whether different Drosophila tissues have different metabolomes and if they correspond to tissue-specific transcriptome of the fruit fly (FlyAtlas.org). Different fly tissues have been dissected and their metabolome elucidated using LC-MS. The results confirmed that tissue metabolomes differ significantly from each other and from the whole fly, and that some of these differences can be correlated to the tissue function. The results illustrate the need to study individual tissues as well as the whole organism. It is clear that some metabolites that play an important role in a given tissue might not be detected in the whole fly sample because their abundance is much lower in comparison to other metabolites present in all tissues, which prevent the detection of the tissue-specific compound.

Chestnut and lemon balm based ingredients as natural preserving agents of the nutritional profile in matured “Serra da Estrela” cheese

Chestnut flowers, lemon balm plants and their decoctions were incorporated into "Serra da Estrela" cheese, to assess their potential to preserve its nutritional properties and provide new foodstuffs. The analyses were carried out after the normal ripening period of 1month and after 6months of storage. The most abundant nutrients were proteins and fats. The most abundant minerals were Ca and Na, while C16:0 and C18:1 were the main fatty acids. Saturated fatty acids were the most abundant, followed by the monounsaturated. Moisture seemed to be lower in the samples with the plants incorporated. The dried plants, when incorporated, seemed to be more efficient as preservers then the decoctions, although these better preserved the proteins. These plants can be regarded as promising natural preservers in foodstuffs cheese, given the preservation of key parameters and the slight impact on the nutritional value.

Studying the role of the strawberry Fra protein family in the flavonoid metabolism during fruit ripening

Strawberry fruits are highly appreciated worldwide due to their pleasant flavor and aroma and to the health benefits associated to their consumption. An important part of these properties is due to their content in secondary metabolites, especially phenolic compounds, of which flavonoids are the most abundant in the strawberry fruit. Although the flavonoid biosynthesis pathway is uncovered, little is known about its regulation. The strawberry Fra a (Fra) genes constitute a large family of homologs of the major birch pollen allergen Bet v 1 and for which no equivalents exist in Arabidopsis. Our group has shown that Fra proteins are involved in the formation of colored compounds in strawberries (Muñoz et al., 2010), which mainly depends on the production of certain flavonoids; that they are structurally homologs to the PYR/PYL/RCAR Arabidopsis ABA receptor, and that they are able to bind flavonoids (Casañal et al., 2013). With these previous results, our working hypothesis is that the Fra proteins are involved in the regulation of the flavonoids pathway. They would mechanistically act as the ABA receptor, binding a protein interactor and a ligand to regulate a signaling cascade and/or act as molecular carriers. The main objective of this research is to characterize the Fra family in strawberry and gain insight into their role in the flavonoid metabolism. By RNAseq expression analysis in ripening fruits we have identified transcripts for 10 members of the Fra family. Although expressed in all tissues analyzed, each family member presents a unique pattern of expression, which suggests functional specialization for each Fra protein. Then, our next approach was to identify the proteins that interact with Fras and their ligands to gain knowledge on the role that these proteins play in the flavonoids pathway. To identify the interacting partners of Fras we have performed a yeast two hybrid (Y2H) screening against cDNA libraries of strawberry fruits at the green and red stages. A protein that shares a 95% homology to the Heat stress transcription factor A-4-C like of Fragaria vesca (HSA4C) interacts specifically with Fra1 and not with other family members, which suggests functional diversification of Fra proteins in specific signaling pathways. The Y2H screening is not yet saturated, so characterization of other interacting proteins with other members of the Fra family will shed light on the functional diversity within this gene family. This research will contribute to gain knowledge on how the flavonoid pathway, and hence, the fruit ripening, is regulated in strawberry; an economically important crop but for which basic research is still very limited. References: Muñoz, C, et al. (2010). The Strawberry Fruit Fra a Allergen Functions in Flavonoid Biosynthesis. Molecular Plant, 3(1): 113–124. Casañal, A, et al (2013). The Strawberry Pathogenesis-related 10 (PR-10) Fra a Proteins Control Flavonoid Biosynthesis by Binding Metabolic Intermediates. Journal of Biological Chemistry, 288(49): 35322–35332.

Use of acoustic telemetry techniques to understand the individual variability in movement ecology of juvenile lemon sharks, Negaprion brevirostris, in natural conditions, around Bimini Islands, Bahamas: a comparison study with preliminary personality traits observed in mesocosms

Dissertação de Mestrado, Biologia Marinha, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2016

Citrus as a component of the Mediterranean Diet

Citrus are native to southeastern Asia, but are present in the Mediterranean basin for centuries. This group of species has reached great importance in some of the Mediterranean countries and, in the case of orange, mandarin and lemon trees, they found here soil and climatic conditions which allows them to achieve a high level of fruit quality, even better than in the regions where they came from. Citrus fruits are present in the diet of the peoples living on the Mediterranean basin, at least since the time of the Roman Empire. In the 20th century they became the main crop in various agricultural areas of the Mediterranean, playing an important role in the landscape, in the diet of the overall population, and also in international trade. They are present in the gardens of palaces and monasteries, but also in the courtyards and orchards of the poorest families. Their fruits are not only a refreshing dessert, but also a condiment, or even a major component of many dishes. Citrus fruits have well-documented nutritional and health benefits. They can actually help prevent and cure some diseases and, above all, they are essential in a balanced and tasty diet.

Characterization of the chestnut germoplasm of Emilia-Romagna region and ancient fruit tree varieties valorization

Molecular characterization represents a valid support for the recovery of germoplasm, also motivated by the interest for the valorization of local productions in order to make their traceability possible. Molecular characterization is also fundamental for the individuation of misnomers in collection fields in which the different varieties are preserved. In particular, microsatellites have been used in this research to investigate the genetic diversity, inside a population and at an individual level, and the correct varietal correspondence. The research is mainly based on the study of European chestnut (Castanea sativa Mill.) cultivars to evaluate the genetic diversity and relationships in Emilia-Romagna region (Italy). A STRUCTURE analysis was carried out at European level with the allelic frequencies of the samples collected in Emilia-Romagna. Variation found at group and subgroup level may reflect a combination of historical migration/selection processes and adaptive factors to different environments between Italian and Spanish regions. In addition, a case study for the valorization of an old local variety and its re-introduction in the cultivation areas was proposed. This research was carried out by a morphological and molecular characterization of the local apple variety 'Rosa Romana'. The conservation of this variety entails the discrimination of different accessions with very similar phenotype that are present in the original cultivation area. The identification of historical trees and most adequate reference plants are fundamental steps for the correct propagation of this old variety and for the development of nursery activities. This will also promote and re-evaluate the exploitation and protection of such ancient Italian apple cultivars. This model could be in future also carried out for chestnut varieties. In conclusion, analysis with molecular markers is of fundamental importance for the protection and the maintenance of local and ancient varieties which allow to increase the allelic variability available for breeding programs.

Genetic Breeding And Diversity Of The Genus Passiflora: Progress And Perspectives In Molecular And Genetic Studies.

Despite the ecological and economic importance of passion fruit (Passiflora spp.), molecular markers have only recently been utilized in genetic studies of this genus. In addition, both basic genetic researches related to population studies and pre-breeding programs of passion fruit remain scarce for most Passiflora species. Considering the number of Passiflora species and the increasing use of these species as a resource for ornamental, medicinal, and food purposes, the aims of this review are the following: (i) to present the current condition of the passion fruit crop; (ii) to quantify the applications and effects of using molecular markers in studies of Passiflora; (iii) to present the contributions of genetic engineering for passion fruit culture; and (iv) to discuss the progress and perspectives of this research. Thus, the present review aims to summarize and discuss the relationship between historical and current progress on the culture, breeding, and molecular genetics of passion fruit.

Influence Of The Stage Of Ripeness On The Composition Of Iridoids And Phenolic Compounds In Genipap (genipa Americana L.).

Genipap fruits, native to the Amazon region, were classified in relation to their stage of ripeness according to firmness and peel color. The influence of the part of the genipap fruit and ripeness stage on the iridoid and phenolic compound profiles was evaluated by HPLC-DAD-MS(n), and a total of 17 compounds were identified. Geniposide was the major compound in both parts of the unripe genipap fruits, representing >70% of the total iridoids, whereas 5-caffeoylquinic acid was the major phenolic compound. In ripe fruits, genipin gentiobioside was the major compound in the endocarp (38%) and no phenolic compounds were detected. During ripening, the total iridoid content decreased by >90%, which could explain the absence of blue pigment formation in the ripe fruits after their injury. This is the first time that the phenolic compound composition and iridoid contents of genipap fruits have been reported in the literature.

Evaluation Of The Cytotoxicity And Phototoxicity Of Caryocar Brasiliense Supercritical Carbon Dioxide Extract.

Caryocar brasiliense Camb (Pequi) is a typical Brazilian Cerrado fruit tree. Its fruit is used as a vitamin source for culinary purposes and as a source of oil for the manufacture of cosmetics. C. brasiliense supercritical CO2 extracts exhibit antimicrobial activity against the bacteria Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus and also possess antioxidant activity. This study was designed to evaluate the in vitro cytotoxicity and phototoxicity of the supercritical CO2 extract obtained from the leaves of this species. In vitro cytotoxicity and phototoxicity of C. brasiliense supercritical CO2 extracts were assessed using a tetrazolium-based colorimetric assay (XTT) and Neutral Red methods. We found that the C. brasiliense (Pequi) extract obtained by supercritical CO2 extraction did not present cytotoxic and phototoxic hazards. This finding suggests that the extract may be useful for the development of cosmetic and/or pharmaceutical products.

Determination Of The Phenolic Composition From Brazilian Tropical Fruits By Uhplc-ms/ms.

Although Brazil is the third largest fruit producer in the world, several specimens consumed are not well studied from the chemical viewpoint, especially for quantitative analysis. For this reason and the crescent employment of mass spectrometry (MS) techniques in food science we selected twenty-two phenolic compounds with important biological activities and developed an ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method using electrospray (ESI) in negative ion mode aiming their quantification in largely consumed Brazilian fruits (açaí-do-Amazonas, acerola, cashew apple, camu-camu, pineapple and taperebá). Multiple reaction monitoring (MRM) was applied and the selection of proper product ions for each transition assured high selectivity. Linearity (0.995of detection (28.85-333.3pg/mL), limit of quantification (96.15-1111pg/mL), inter- and intraday accuracy (>80%), precision (CV<20%) and extraction recovery rate (>80%) were satisfactory and showed that the method provides an efficient protocol to analyze phenolic compounds in fruit pulp extracts.

Butterflies (Lepidoptera, Papilionoidea and Hesperioidea) of the "Baixada Santista" region, coastal São Paulo, southeastern Brazil

Butterflies (Lepidoptera, Papilionoidea and Hesperioidea) of the "Baixada Santista" region, coastal São Paulo, southeastern Brazil. A list with 538 species of butterflies recorded in the Baixada Santista, São Paulo ( SE Brazil) is presented. Standard sampling protocols (i.e. with entomological nets) were followed. Baited traps were installed for fruit feeding species. Data from the literature and entomological collections were also considered in the total estimated species richness. The species richness recorded in the Baixada Santista region represents about 16% of the Brazilian butterfly fauna, and 34% of the known butterfly fauna for the state of São Paulo. The present list contains an appreciably higher number of species in comparison to other lists from similar biomes farther south, such as Blumenau in Santa Catarina, and Maquiné in Rio Grande do Sul.

Nutritional aspects of the prevention and treatment of osteoporosis

Osteoporosis is a global health problem characterized by low bone mass and microarchitectural deterioration of bone tissue with a consequent increase in bone fragility and susceptibility to fracture. Nutrition plays a critical role in reducing the risk of osteoporosis through its effect on all of these fragility factors, especially on the development and maintenance of bone mass. An adequate calcium, vitamin D and protein intake resulted in reduced bone remodeling, better calcium retention, reduced age-related bone loss, and reduced fracture risk. Recent evidence indicates that a healthy dietary pattern including dairy products (mainly fat free), fruit and vegetables and adequate amounts of meat, fish and poultry is positively related to bone health. Furthermore, mineral and vitamin supplementation should be closely monitored by health professionals since it could have adverse effects and be insufficient to ensure optimal protection of bone health.

Nutrional aspects of the prevention and treatment of osteoporosis

A osteoporose é um problema de saúde global, caracterizada por baixa massa óssea e deterioração da microarquitetura do tecido ósseo, com consequente aumento da fragilidade óssea e suscetibilidade a fraturas. A nutrição desempenha um papel fundamental na redução do risco de osteoporose por seu efeito sobre todos os fatores relacionados à fragilidade óssea, principalmente no desenvolvimento e na manutenção da massa óssea. Uma adequada ingestão de cálcio, vitamina D e proteína leva à redução da remodelação óssea, à maior retenção de cálcio, à redução da perda óssea relacionada à idade e à redução do risco de fraturas. Evidências recentes indicam que uma alimentação saudável, incluindo a ingestão de produtos lácteos (principalmente os desnatados), frutas e verduras, e uma quantidade adequada de carnes, peixes e aves, está relacionada positivamente com a saúde óssea. Além disso, a suplementação de vitaminas e minerais deve ser monitorada de perto, por profissionais de saúde, uma vez que pode ter efeitos adversos e ser insuficiente para assegurar uma eficaz proteção à saúde óssea

Spiranthera atlantica (Rutaceae, Galipeae), a New Species and the First Record of the Genus for the Brazilian Atlantic Forest

A new species of Spiranthera A. St.-Hil. (Rutaceae, Galipeinae) is illustrated and described from Espirito Santo, Brazil. Spiranthera atlantica Pi rani represents the first species record for the genus in the Atlantic Forest of eastern Brazil. The new (axon resembles the Amazonian S. guianensis Sandwith but differs by its smaller, few-flowered inflorescences and by the fruit and leaflet morphology.