Fruits of Heterocoma (Vernonieae‐Lychnophorinae): taxonomic significance and a new pattern of phytomelanin deposition in Asteraceae

Heterocoma is a Brazilian endemic genus resulting from the dismemberment of Sipolisiinae, in which only representatives with fruit containing phytomelanin were included in the genus. As the fruits of Asteraceae are known to be systematically important at various taxonomic levels and Heterocoma fruit has not been described previously, we studied the morphology and anatomy of the cypselas of all species of the genus, comparing them with other fruits in the family containing phytomelanin and evaluating the systematic potential at the specific and tribal levels. The fruits were analysed by scanning electron microscopy (SEM) and light microscopy. The morphological features of the fruit, including the carpopodium, ribs and pappi, varied in the genus and demonstrated potential for species discrimination. The anatomy showed a pattern for the genus with a uniseriate exocarp, the outer mesocarp composed of fibres arranged in several layers, the inner mesocarp composed of several layers of parenchyma, the endocarp, and phytomelanin deposited between the inner and outer mesocarp. This anatomical pattern of phytomelanin deposition differs from that of other Asteraceae with phytomelanin in their fruit. Heterocoma is also the only genus in Vernonieae that has phytomelanin deposition in the cypselas. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 255–265.     

Glycoengineered cell models for the characterization of cancer O-glycoproteome: an innovative strategy for biomarker discovery

Glycosylation is one of the most abundant forms of protein posttranslational modification. O-glycosylation is a major type of protein glycosylation, comprising different types and structures expressed in several physiologic and pathologic conditions. The understanding of protein attachment site and glycan structure is of the utmost importance for the clarification of the role glycosylation plays in normal cells and in pathological conditions. Neoplastic transformation frequently shows the expression of immature truncated O-glycans. These aberrantly expressed O-glycans have been shown to induce oncogenic properties and can be detected in premalignant lesions, meaning that they are an important source of biomarkers. This article addresses the recent application of genetically engineered cancer cell models to produce simplified homogenous O-glycans allowing the characterization of cancer cells O-glycoproteomes, using advanced mass spectrometry methods and the identification of potential cancer-specific O-glycosylation sites. This article will also discuss possible applications of these biomarkers in the cancer field.     

Identification of a tyrosine phosphatase involved in the response to mechanical injury in leaves of Ricinus communis

Plants defend themselves against biotic or abiotic stress by triggering intracellular signaling pathways that regulate gene expression and responses to the offending agent. Phosphorylation and dephosphorylation represent major mechanisms for the regulation of plant defense pathways. Therefore, MAP kinases and phosphatases have been the focus of many studies in this area. This study identified three phosphatase activities, namely RcPPase I, II and III. Wounding increased the activity levels of RcPPase III, while the activities of RcPPase I and II remained constant compared to the control. N-terminal partial amino acid sequence, biochemical characterization with use of specific substrates and inhibitors indicated that the RcPPase III belong to the family of tyrosine phosphatases (PTPs).     

Functional responses and scaling in predator-prey interactions of marine fishes: contemporary issues and emerging concepts

Predator-prey interactions are a primary structuring force vital to the resilience of marine communities and sustainability of the world's oceans. Human influences on marine ecosystems mediate changes in species interactions. This generality is evinced by the cascading effects of overharvesting top predators on the structure and function of marine ecosystems. It follows that ecological forecasting, ecosystem management, and marine spatial planning require a better understanding of food web relationships. Characterising and scaling predator-prey interactions for use in tactical and strategic tools (i.e. multi-species management and ecosystem models) are paramount in this effort. Here, we explore what issues are involved and must be considered to advance the use of predator-prey theory in the context of marine fisheries science. We address pertinent contemporary ecological issues including (1) the approaches and complexities of evaluating predator responses in marine systems; (2) the 'scaling up' of predator-prey interactions to the population, community, and ecosystem level; (3) the role of predator-prey theory in contemporary fisheries and ecosystem modelling approaches; and (4) directions for the future. Our intent is to point out needed research directions that will improve our understanding of predator-prey interactions in the context of the sustainable marine fisheries and ecosystem management.     

Fish assemblage structure in an estuary of the Atlantic Forest biodiversity hotspot (southern Brazil)

We described the fish assemblage in the estuary of the Guaraguaçu River (one of the largest tributaries of the Paranaguá Bay Estuary, located within Brazil’s Atlantic Forest Biosphere Reserve) from June 2005 to May 2006, and assessed the seasonal and spatial effects of abiotic environmental attributes on the fish assemblage structure. Despite some oscillations in salinity, the upper and lower estuaries had year-round persistent oligohaline and polyhaline conditions, respectively. Despite high species richness (55 species), the Guaraguaçu River Estuary fish community contains a few dominant taxa; 11% of the richness accounts for >60% of its density and biomass. The most abundant species (in terms of both biomass and density) was Atherinella brasiliensis. Species whose densities were most strongly associated with the upper estuary were Centropomus parallelus, Ctenogobius schufeldti, Eucinostomus melanopterus, Platanichthys platana, Trinectes paulistanus, and Eugerres brasilianus. Those whose densities were most strongly associated with the lower estuary were A. brasiliensis, Sphoeroides greeleyi, Eucinostomus argenteus, Sphoeroides testudineus, Diapterus rhombeus, and Harengula clupeola. Throughout the year, canonical correspondence analysis identified: (1) the pattern of horizontal stratification of salinity along the river as being the most important variable for explaining most of the fish fauna structure; and (2) a strong relationship between the fish fauna and the salinity gradient along the estuary. Analysis of similarity further confirmed that each estuarine zone supports a year-round persistent and relatively homogeneous fish species assemblage. Total mean density and biomass remained constant over time in each estuarine habitat, but density shifted in the most abundant species, which appears related to recruitment patterns. Such species and abundance persistence likely occurs because seasonal rainfall-induced changes in river discharge are not sufficient to significantly shift runoff and salinity and thus fish assemblage structure (species composition, density and biomass) along the estuary. Such a lack of seasonal fish fauna movement as a response to changes in river flow contrasts with other estuarine systems around the world.     

A preliminary fish assemblage index for a transitional river–reservoir system in southeastern Brazil

Large river–reservoir systems are some of the most difficult aquatic ecosystems to assess because: (1) they typically lack minimally disturbed reference sites; (2) the reservoirs are not natural systems to begin with; and (3) reservoirs with high exchange rates are transitional systems between rivers and lakes. These features are further complicated in Brazil where fish species taxonomy is incomplete (let alone fully described ecologically), where waters naturally have high organic and thermal loadings, and where dams and reservoirs provide most of the nation's electricity and water supplies. As a first step towards generating a biological tool for assessing the effects of reservoirs on rivers, we developed a preliminary River–Reservoir Fish Assemblage Index (RRFAI) in a transitional river–reservoir system in southeastern Brazil. To do so, we gill-netted fish monthly between October 2006 and September 2007 (excluding May and July 2007) immediately upriver of the reservoir, in the upper reservoir, in the lower reservoir, and immediately downriver of the reservoir. In developing our RRFAI we sought fish assemblage metrics to represent ecological characteristics including richness, habitat, trophic, tolerance, and resilience guilds. Despite clear differences in fish assemblage composition between river and reservoir sites, we found 9 metrics common to both systems that were nonredundant and had low sampling variability (number of native species, number of characiform species, number of siluriform species, % omnivorous individuals, % invertivorous individuals, % non-native carnivorous individuals, % intolerant individuals, % tolerant individuals, number of tolerant species). Fish assemblage condition was significantly and consistently lower in the lower reservoir. There was no significant difference between the dry and wet season in RRFAI scores, suggesting that a single season sample should usually suffice. Further research is needed along distinct disturbance gradients in multiple river–reservoir systems in Brazil to confirm the sensitivity of our preliminary RRFAI for assessing the physical and chemical habitat disturbances common to such systems.     

Optimization of fibrolytic enzyme production by Aspergillus japonicus C03 with potential application in ruminant feed and their effects on tropical forages hydrolysis

Fibrolytic enzyme production by Aspergillus japonicus C03 was optimized in a medium containing agro-industrial wastes, supplemented with peptone and yeast extract. A 2³ full factorial composite and response surface methodology were used to design the experiments and analysis of results. Tropical forages were hydrolyzed by A. japonicus C03 enzymatic extract in different levels, and they were also tested as enzymatic substrate. Optimal production to xylanase was obtained with soybean bran added to crushed corncob (1:3), 0.01% peptone, and 0.2% yeast extract, initial pH 5.0, at 30 °C under static conditions for 5 days of incubation. Optimal endoglucanase production was obtained with wheat bran added to sugarcane bagasse (3:1), 0.01% peptone, and 0.2% yeast extract, initial pH 4.0, at 30 °C, for 6 days, under static conditions. Addition of nitrogen sources as ammonium salts either inhibited or did not influence xylanase production. This enzymatic extract had a good result on tropical forage hydrolyzes and showed better performance in the Brachiaria genera, due to their low cell wall lignin quantity. These results represent a step forward toward the use of low-cost agricultural residues for the production of valuable enzymes with potential application in animal feed, using fermentation conditions.     

High-sensitivity TFA-free LC-MS for profiling histones

The analysis of proteins by RPLC commonly involves the use of TFA as an ion‐pairing agent, even though it forms adducts and suppresses sensitivity. The presence of adducts can complicate protein molecular weight assignment especially when protein isoforms coelute as in the case of histones. To mitigate the complicating effects of TFA adducts in protein LC‐MS, we have optimized TFA‐free methods for protein separation. Protein standards and histones were used to evaluate TFA‐free separations using capillary (0.3 mm id) and nanoscale (0.1 mm id) C₈ columns with the ion‐pairing agents, formic acid or acetic acid. The optimized method was then used to examine the applicability of the approach for histone characterization in human cancer cell lines and primary tumor cells from chronic lymphocytic leukemia patients.