Expression profiling and sequence diversity of novel DREB genes from common bean (Phaseolus vulgaris L.) and their association with drought-related traits

Common bean is a major dietary component in several countries, but its productivity is negatively affected by abiotic stresses. Dissecting candidate genes involved in abiotic stress tolerance is a paramount step toward the improvement of common bean performance under such constraints. Thereby, this thesis presents a systematic analysis of the DEHYDRATION RESPONSIVE ELEMENT-BINDING (DREB) gene subfamily, which encompasses genes that regulate several processes during stress responses, but with limited information for common bean. First, a series of in silico analyses with sequences retrieved from the P. vulgaris genome on Phytozome supported the categorization of 54 putative PvDREB genes distributed within six phylogenetic subgroups (A-1 to A-6), along the 11 chromosomes. Second, we cloned four novel PvDREB genes and determined their inducibility-factors, including the dehydration-, salinity- and cold-inducible genes PvDREB1F and PvDREB5A, and the dehydration- and cold-inducible genes PvDREB2A and PvDREB6B. Afterwards, nucleotide polymorphisms were searched through Sanger sequencing along those genes, revealing a high number of single nucleotide polymorphisms within PvDREB6B by the comparison of Mesoamerican and Andean genotypes. The nomenclature of PvDREB6B is discussed in details. Furthermore, we used the BARCBean6K_3 SNP platform to identify and genotype the closest SNP to each one of the 54 PvDREB genes. We selected PvDREB6B for a broader study encompassing a collection of wild common bean accessions of Mesoamerican origin. The population structure of the wild beans was accessed using sequence polymorphisms of PvDREB6B. The genetic clusters were partially associated with variation in latitude, altitude, precipitation and temperature throughout the areas such beans are distributed. With an emphasis on drought stress, an adapted tube-screening method in greenhouse conditions enabled the phenotyping of several drought-related traits in the wild collection. Interestingly, our data revealed a correlation between root depth, plant height and biomass and the environmental data of the location of the accessions. Correlation was also observed between the population structure determined through PvDREB6B and the environmental data. An association study combining data from the SNP array and DREB polymorphisms enabled the detection of SNP associated with drought-related traits through a compressed mixed linear model (CMLM) analysis. This thesis highlighted important features of DREB genes in common bean, revealing candidates for further strategies aimed at improvement of abiotic stress tolerance, with emphasis on drought tolerance

Common mushrooms / by Leon L. Pray, Field Museum of Natural History.

no.18(1936)

Response and function of cutaneous mucosal and serum antibodies in barramundi (Lates calcarifer) acclimated in seawater and freshwater

Mucosal and serum antibody responses were studied in sibling barramundi (Lates calcarifer) acclimated in either seawater or freshwater following vaccination by intraperitoneal injection or direct immersion in an inactivated Streptococcus iniae vaccine. As expected, route of vaccination had a marked effect on immune response, with direct immersion resulting in low serum antibody levels against S. iniae by ELISA detected 21 days post vaccination at 26 degrees C, whilst a significant response was detected in mucus. A strong specific antibody response was detected in both mucus and serum 21 days following intraperitoneal injection. Fish acclimated in seawater prior to vaccination showed a markedly higher specific mucosal antibody response than sibling fish acclimated in freshwater, regardless of the route of vaccination, whilst the serum antibody response was not affected by salinity. Both mucosal and serum antibodies from fish in seawater and freshwater were capable of binding antigen at salinities similar to full strength seawater in a modified ELISA assay. These results indicate that this euryhaline fish species is riot only able to mount significant specific antibody response in cutaneous mucus, but that these antibodies will function in the marine environment. (c) 2005 Elsevier Ltd. All rights reserved.

Proteomic and phosphoproteomic analysis of polyethylene glycol-induced osmotic stress in root tips of common bean (Phaseolus vulgaris L.)

Previous studies have shown that polyethylene glycol (PEG)-induced osmotic stress (OS) reduces cell-wall (CW) porosity and limits aluminium (Al) uptake by root tips of common bean (Phaseolus vulgaris L.). A subsequent transcriptomic study suggested that genes related to CW processes are involved in adjustment to OS. In this study, a proteomic and phosphoproteomic approach was applied to identify OS-induced protein regulation to further improve our understanding of how OS affects Al accumulation. Analysis of total soluble proteins in root tips indicated that, in total, 22 proteins were differentially regulated by OS; these proteins were functionally categorized. Seventy-seven per- cent of the total expressed proteins were involved in metabolic pathways, particularly of carbohydrate and amino acid metabolism. An analysis of the apoplastic proteome revealed that OS reduced the level of five proteins and increased that of seven proteins. Investigation of the total soluble phosphoproteome suggested that dehydrin responded to OS with an enhanced phosphorylation state without a change in abundance. A cellular immunolocalization analysis indicated that dehydrin was localized mainly in the CW. This suggests that dehydrin may play a major protective role in the OS-induced physical breakdown of the CW structure and thus maintenance of the reversibility of CW extensibility during recovery from OS. The proteomic and phosphoproteomic analyses provided novel insights into the complex mechanisms of OS-induced reduction of Al accumulation in the root tips of common bean and highlight a key role for modification of CW structure.

Alteration of cell-wall porosity is involved in osmotic stress-induced enhancement of aluminium resistance in common bean (Phaseolus vulgaris L.)

Aluminium (Al) toxicity and drought are the two major abiotic stress factors limiting common bean production in the tropics. Using hydroponics, the short-term effects of combined Al toxicity and drought stress on root growth and Al uptake into the root apex were investigated. In the presence of Al stress, PEG 6000 (polyethylene glycol)-induced osmotic (drought) stress led to the amelioration of Al-induced inhibition of root elongation in the Al-sensitive genotype VAX 1. PEG 6000 (>> PEG 1000) treatment greatly decreased Al accumulation in the 1 cm root apices even when the roots were physically separated from the PEG solution using dialysis membrane tubes. Upon removal of PEG from the treatment solution, the root tips recovered from osmotic stress and the Al accumulation capacity was quickly restored. The PEG-induced reduction of Al accumulation was not due to a lower phytotoxic Al concentration in the treatment solution, reduced negativity of the root apoplast, or to enhanced citrate exudation. Also cell-wall (CW) material isolated from PEG-treated roots showed a low Al-binding capacity which, however, was restored after destroying the physical structure of the CW. The comparison of the Al(3+), La(3+), Sr(2+), and Rb(+) binding capacity of the intact root tips and the isolated CW revealed the specificity of the PEG 6000 effect for Al. This could be due to the higher hydrated ionic radius of Al(3+) compared with other cations (Al(3+) >> La(3+) > Sr(2+) > Rb(+)). In conclusion, the results provide circumstantial evidence that the osmotic stress-inhibited Al accumulation in root apices and thus reduced Al-induced inhibition of root elongation in the Al-sensitive genotype VAX 1 is related to the alteration of CW porosity resulting from PEG 6000-induced dehydration of the root apoplast.

Modulação da capacidade antioxidante e de detoxificação no peixe Cyprinus carpio (Cyprinidae) após tratamento com nanocápsulas de ácido lipóico

O metabolismo aeróbico é muito eficiente no processo de geração de energia, no entanto, é uma fonte de produção de espécies reativas de oxigênio (ERO). Para a prevenção dos efeitos potencialmente danosos dessas ERO, os organismos desenvolveram um sistema de defesa antioxidante (SDA), que inclui compostos enzimáticos e não enzimáticos. O ácido lipóico (AL) é uma molécula lipo e hidro solúvel, com capacidade de atravessar membranas celulares. Ele possui propriedades antioxidantes, auxiliando na eliminação de ERO, induzindo a expressão de genes importantes nas defesas antioxidantes, quelando metais e interagindo com outros antioxidantes. Trabalhos prévios demonstraram que nanocápsulas poliméricas de ácido lipóico favoreceram a proteção deste antioxidante, aumentando sua estabilidade físico- química em comparação com formulações contendo ácido lipóico livre. O objetivo deste estudo foi avaliar e comparar o efeito do AL livre e do AL em nanocápsulas sobre a atividade de enzimas antioxidantes (glutamato-cisteína ligase, GCL e glutationa-S- transferase, GST), a concentração de glutationa reduzida (GSH) e sub-produtos da peroxidação lipídica (malondealdeído, método TBARS) e da expressão de genes que codificam para as diferentes formas da enzima GST (alfa e pi). Para isso o peixe Cyprinus carpio (Cyprinidae) foi exposto a uma dose de 40 mg/kg a diferentes formas de AL (livre e em nanocápsulas) por injeção intraperitoneal (duas injeções, sendo a primeira no tempo 0 e a segunda após 24 h), sendo logo sacrificados a diferentes tempos da primeira injeção (48 h, 96 h e uma semana), sendo dissecados o cérebro, fígado e músculo dos peixes de cada tratamento. Os resultados obtidos indicam que os órgãos respondem de forma diferente. A curto prazo, o fígado foi o principal órgão a apresentar respostas antioxidantes após tratamento com AL, enquanto que a longo prazo o cérebro e o músculo se mostraram mais responsivos em termos antioxidantes quando 6 comparado ao fígado. Foi também importante a forma em que o AL é administrado, livre ou em nanocápsulas, sendo observado que um mesmo órgão em um mesmo tempo de exposição pode responder de forma diferente de acordo com o tipo de AL que está sendo utilizado. Além disso, o efeito antioxidante do AL nanoencapsulado parece ser mais efetivo quando utilizado a longo prazo, sugerindo que a forma nanoencapsulada libera o antioxidante em forma mais lenta. Os resultados também indicam que a composição da nanocápsulas deve ser levada em consideração, uma vez que foi observado um efeito antioxidante significativo nos tratamentos que continham apenas a nanocápsulas, sem o AL. Sugere-se que este efeito ocorra devido à produção endógena do próprio antioxidante em questão, favorecida pela composição da própria nanocápsula, que possui ácido octanóico, substrato para a síntese de AL. Também se observou um efeito pró-oxidante em alguns tratamentos onde foi utilizada esta formulação, sugerindo que alguns componentes da nanocápsula, como por exemplo, o surfactante que é utilizado para estabilizar a suspensão, possam aumentar a suscetibilidade dos órgãos ao estresse oxidativo.

Physical and chemical properties of starch and flour from different common bean (Phaseolus vulgaris L.) cultivar.

The physical, chemical and pasting properties of the flour and isolated starches from six different bean cultivars (Phaseolus vulgaris L.) were investigated in order to obtain information for application in new products. The protein and total starch contents of the bean flours ranged from 17.72 to 20.27% and from 39.68 to 43.78%, respectively. The bean starches had low amounts of proteins, lipids and ash and showed an amylose content ranging between 45.32 and 51.11% and absolute density values between 1.55 and 1.78 g.cm?3. The bean starch granules were round to oval with a smooth surface. Results viscoamylographic profiles of the starches and flours showed the possibility of selecting cultivars for specific applications according to these characteristics.

The common bean (Phaseolus vulgaris L.) demonstration unity system - sudf - applicability potential for family farming.

2016

Evaluation and management of demersal stocks in the Adriatic: the case of common sole (Solea solea, L.) in the northern and central Adriatic Sea

This PhD thesis aimed to assess the status of common sole, one of the main commercial stocks in the Adriatic Sea, using a mix of conventional and innovative techniques to provide more reliable estimates of stock status compared to past advice. First, a meta-analysis was carried out using data-poor assessment model to analyze the whole catch assemblage of rapido fishery. The outcomes were used to estimate rebuilding time and forecast catches under different harvest control rule scenarios, with a reduction of 20% of fishing effort being suggested as a way to allow most of the species to recover to sustainable levels. Secondly, an ensemble of data-rich assessment models was developed to better incorporate uncertainty by using alternative hypotheses of main parameters. This was the first time an ensemble of models has been used in the Mediterranean to provide management advice. Consistent with data-poor analysis results, the ensemble outcomes indicated that the common sole stock was showing a recovering trend probably due to the effective management actions underway in the area rather than the moderate effort reduction according to the actual management plan. Moreover, back-calculation measurements were used to fit and compare monophasic and biphasic growth curves through the use of non-linear mixed effects models. The analyses revealed that the fitting of the biphasic curve was superior, confirming the theory that growth in size would decrease as a consequence of reproductive effort. A stock assessment simulation showed how the use of the monophasic pattern would result in a critical overestimation of biomass that could lead to a greater risk of overfishing. As a final step, a simulation-testing procedure was applied to determine the best performing reference points using stock-specific characteristic. The procedure could be routinely adopted to increase transparency in reference points calculation enhancing the credibility of scientific advice.

Functional and structural characterization of isolated perfused stingray liver including effects of ischaemia/reperfusion

The morphological and functional characteristics of stingray liver were studied, including the effect of ischaemia/reperfusion. With an isolated perfused model, it was shown that the stingray liver was more resistant than the rat liver to ischaemia/reperfusion injury; this was consistent with the differing partial oxygen tensions usually present in the two species. This study confirmed that whereas stingray hepatocytes form tubules with central bile canaliculi as in other fish, the stingray liver has portal triads and a lobular architecture as in mammals. Apoptosis of hepatocytes, demonstrated in the normal liver, was only marginally enhanced by ischaemia/reperfusion. Resulting apoptotic bodies were phagocytized by macrophage-like cells in hepatocyte tubules. In contrast to rat liver, the stingray liver showed no necrosis after ischaemia-reperfusion. (C) 1998 W.B. Saunders Company Limited.

Artisanal fisheries in urban reservoirs: a case study from Brazil (Billings Reservoir, São Paulo Metropolitan Region)

Billings Reservoir is an urban reservoir located in the São Paulo Metropolitan Region. Tt supports 101 active artisanal fishermen. To describe this fishery, landings were recorded daily between February 1996 and January 1997 at Colonia (23 degrees 50' 57 S; 46 degrees 40' 02 W). In every landing, a data collector recorded catch, effort, fishing gears and fishing grounds. A total of 147 593 kg of fish were recorded in 3515 fishing trips. The exotic Nile tilapia, Oreochromis niloticus (L.), was the main species exploited (81.4% of the annual catches). Five other species were also targeted: the characid Astyanax eigenmaniorum (Cope) (13.0% of the annual catches); the erythrinid Hoplias aff malabaricus (Block) (2.1%); the exotic cyprinid Cyprinus carpio L. (Campos & Fernandez-Yepez) (2.4%); the curimatid Cyphocharax modestus L. (1.1%); and the pimelodid Rhamdia sp. (0.1%). Two main groups of fishermen were discriminated using Principal Components Analysis; these were associated with the type of fishing gear and fishing strategies, i.e. those who exploited Nile tilapia with cast nets and beating gill nets, and those who exploited other species with set gill nets. Management and maintenance of this fishery should consider the positive top-down effects that Nile tilapia could have in controlling eutrophication and also the social benefits.

Lipidic and proteic absorption in digestive tract of tropical fat snook (Centropomus parallelus, POEY 1860)

The tropical fat snook Centropomus parallelus is a species of recognized ecological importance and with a high economical potential for fisheries and aquaculture. The investigations of digestive tube morphology in association with their feeding abilities are fundamental to improve techniques for aquaculture feeding procedures. Sudan black staining and Perl`s method were used to evaluate their absorption capacity of fat and protein respectively. The Sudan black stain was performed 12 h after the ingestion of lipids. The lipids are intensely absorbed in the ceca epithelium and less intensely in the intestine and rectum. The Perl`s method was performed 12 h after the ingestion of ferritin. The proteins are absorbed only in the rectum. This is the first description of fat and protein absorption ability by the digestive tube of fat snook. These data enhance the possibility of the addition of macromolecules in rations that can show a diversity of physiological effects. The histological implications of each segment of the digestive tube in association with fish biology are further discussed. (C) 2010 Elsevier B.V. All rights reserved.

Frequência de arraçoamento para alevinos de carpa comum

The best frequency of feeding for development of common carp fingerlings Cyprinus carpio was determined. Four hundred fish (4.88 ± 1.41 g and 6.72 ± 0.70 cm) were used, distributed in 20 tanks of 250 L each in completely randomized design with four treatments and five replicates. The four feeding strategies adopted were: providing feed once (T1), twice (T2), three (T3) and four times daily (T4) at the same amount being fractionated as described. At the end of 45 days of experiment were carried out measurements of the final weight (FW), final length (FL), weight gain (WG), feed conversion (FC), specific growth rate (SGR) and survivor (SR). It was evaluated the chemical composition of fish carcass: moisture (MT), crude protein (CP), lipids (LP) and ash (AS) and hematological analyzes performed such as erythrocyte (ER), hemoglobin (HG) and hematocrit (HT). There were significant statistical differences (P<0.01) for FW, FL, WG and SGR. For FC and SR there were no statistical differences (P>0.01). For the chemical composition the moisture, lipids and ash showed significant statistical differences (P>0.01), except only for protein (P>0.01) The hematological composition was not influenced by the feed frequency, it was not observed significant statistical difference (P>0.01) of erythrocytes, hemoglobin and hematocrit among dietary treatments. For common carp fingerlings, the provision of ration four times daily provided better final weight, final length, weight gain and specific growth rate without causing changes in the composition and hematological parameters of the fish.