Experimental and theoretical studies of emodin interacting with a lipid bilayer of DMPC

Emodin is one of the most abundant anthraquinone derivatives found in nature. It is the active principle of some traditional herbal medicines with known biological activities. In this work, we combined experimental and theoretical studies to reveal information about location, orientation, interaction and perturbing effects of Emodin on lipid bilayers, where we have taken into account the neutral form of the Emodin (EMH) and its anionic/deprotonated form (EM^?). Using both UV/Visible spectrophotometric techniques and molecular dynamics (MD) simulations, we showed that both EMH and EM^? are located in a lipid membrane. Additionally, using MD simulations, we revealed that both forms of Emodin are very close to glycerol groups of the lipid molecules, with the EMH inserted more deeply into the bilayer and more disoriented relative to the normal of the membrane when compared with the EM^?, which is more exposed to interfacial water. Analysis of several structural properties of acyl chains of the lipids in a hydrated pure DMPC bilayer and in the presence of Emodin revealed that both EMH and EM^? affect the lipid bilayer, resulting in a remarkable disorder of the bilayer in the vicinity of the Emodin. However, the disorder caused by EMH is weaker than that caused by EM^?. Our results suggest that these disorders caused by Emodin might lead to distinct effects on lipid bilayers including its disruption which are reported in the literature.     

A statistical model for testing the pleiotropic control of phenotypic plasticity for a count trait

The differences of a phenotypic trait produced by a genotype in response to changes in the environment are referred to as phenotypic plasticity. Despite its importance in the maintenance of genetic diversity via genotype-by-environment interactions, little is known about the detailed genetic architecture of this phenomenon, thus limiting our ability to predict the pattern and process of microevolutionary responses to changing environments. In this article, we develop a statistical model for mapping quantitative trait loci (QTL) that control the phenotypic plasticity of a complex trait through differentiated expressions of pleiotropic QTL in different environments. In particular, our model focuses on count traits that represent an important aspect of biological systems, controlled by a network of multiple genes and environmental factors. The model was derived within a multivariate mixture model framework in which QTL genotype-specific mixture components are modeled by a multivariate Poisson distribution for a count trait expressed in multiple clonal replicates. A two-stage hierarchic EM algorithm is implemented to obtain the maximum-likelihood estimates of the Poisson parameters that specify environment-specific genetic effects of a QTL and residual errors. By approximating the number of sylleptic branches on the main stems of poplar hybrids by a Poisson distribution, the new model was applied to map QTL that contribute to the phenotypic plasticity of a count trait. The statistical behavior of the model and its utilization were investigated through simulation studies that mimic the poplar example used. This model will provide insights into how genomes and environments interact to determine the phenotypes of complex count traits.     

First report on the occurrence of Trypanosoma rangeli Tejera, 1920 in the state of Ceará, Brazil, in naturally infected triatomine Rhodnius nasutus Stål, 1859 (Hemiptera, Reduviidae, Triatominae)

The aim of this work was to identify and report the occurrence of Trypanosoma rangeli and Trypanosoma cruzi in naturally infected Rhodnius nasutus (Hemiptera, Reduviidae, Triatominae) in the state of Ceará, Brazil. Triatomines feces, salivary glands, and hemolymph were collected for fresh examination, and specific detection of T. rangeli and T. cruzi DNA by polymerase chain reaction was carried out. The specific characterization of these two parasites showed the simultaneous presence of both parasites in two (7.7%) of the 26 positive insects. Our results provide further knowledge on the geographical distribution of T. rangeli in Brazil.     

Comparative and predictive phylogeography in the South American diagonal of open formations: Unravelling the biological and environmental influences on multitaxon demography

Phylogeography investigates historical drivers of the geographical distribution of intraspecific lineages. Particular attention has been given to ecological, climatic and geological processes in the diversification of the Neotropical biota. Several species sampled across the South American diagonal of open formations (DOF), comprising the Caatinga, Cerrado and Chaco biomes, experienced range shifts coincident with Quaternary climatic changes. However, comparative studies across different spatial, temporal and biological scales on DOF species are still meagre. Here, we combine phylogeographical model selection and machine learning predictive frameworks to investigate the influence of Pleistocene climatic changes on several plant and animal species from the DOF. We assembled mitochondrial/chloroplastic DNA sequences in public repositories and inferred the demographic responses of 44 species, comprising 70 intraspecific lineages of plants, lizards, frogs, spiders and insects. We then built a random forest model using biotic and abiotic information to identify the best predictors of demographic responses in the Pleistocene. Finally, we assessed the temporal synchrony of species demographic responses with hierarchical approximate Bayesian computation. Biotic variables related to population connectivity, gene flow and habitat preferences largely predicted how species responded to Pleistocene climatic changes, and demographic changes were synchronous primarily during the Middle Pleistocene. Although 22 (~31%) lineages underwent demographic expansion, presumably associated with the spread of aridity during the glacial Pleistocene periods, our findings suggest that nine lineages (~13%) exhibited the opposite response due to taxon-specific attributes.     

Photoperiod modulates growth,morphoanatomy, and linalool content in Lippia alba L. (Verbenaceae) cultured in vitro

Biotechnology provides valuable tools to support conservation of plant species, especially in case of threatened taxa or when dealing with seed unavailability, low viability or sterility. However, plant cell culture methods have often to face problems associated with tissue recalcitrance to in vitro systems. Recalcitrance can be related to a variety of triggering factors, involving many efforts and manipulations within one or more of the micropropagation stages before obtaining successful results. An in vitro propagation protocol was developed for Zelkova sicula, a very rare and endangered relict tree, endemic to Sicily (Southern Italy). The species revealed extremely recalcitrant to in vitro culture approaches, but after many trials throughout a number of years an effective micropropagation protocol was completed. The rooting rate was about 84% of the treated explants, 8% of which were successfully acclimatized outdoor and reintroduced in the wild within a comprehensive conservation project. The technique allowed to overcome the problems of sexual sterility of this species, hence contributing concretely to contrast the problems connected with its conservation. However, additional efforts need to be carried out in order to refine the acclimatization step and further improve the whole process effectiveness.

     

Optimization of alkaline pretreatment of coffee pulp for production of bioethanol

The use of lignocellulosic raw materials in bioethanol production has been intensively investigated in recent years. However, for efficient conversion to ethanol, many pretreatment steps are required prior to hydrolysis and fermentation. Coffee stands out as the most important agricultural product in Brazil and wastes such as pulp and coffee husk are generated during the wet and dry processing to obtain green grains, respectively. This work focused on the optimization of alkaline pretreatment of coffee pulp with the aim of making its use in the alcoholic fermentation. A central composite rotatable design was used with three independent variables: sodium hydroxide and calcium hydroxide concentrations and alkaline pretreatment time, totaling 17 experiments. After alkaline pretreatment the concentration of cellulose, hemicellulose, and lignin remaining in the material, the subsequent hydrolysis of the cellulose component and its fermentation of substrate were evaluated. The results indicated that pretreatment using 4% (w/v) sodium hydroxide solution, with no calcium hydroxide, and 25 min treatment time gave the best results (69.18% cellulose remaining, 44.15% hemicelluloses remaining, 25.19% lignin remaining, 38.13 g/L of reducing sugars, and 27.02 g/L of glucose) and produced 13.66 g/L of ethanol with a yield of 0.4 g ethanol/g glucose. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 30:451–462, 2014     

Isolation of a glucosamine binding leguminous lectin with mitogenic activity towards splenocytes and anti-proliferative activity towards tumor cells

A dimeric 64-kDa glucosamine-specific lectin was purified from seeds of Phaseolus vulgaris cv. "brown kidney bean." The simple 2-step purification protocol involved affinity chromatography on Affi-gel blue gel and gel filtration by FPLC on Superdex 75. The lectin was absorbed on Affi-gel blue gel and desorbed using 1M NaCl in the starting buffer. Gel filtration on Superdex 75 yielded a major absorbance peak that gave a single 32-kDa band in SDS-PAGE. Hemagglutinating activity was completely preserved when the ambient temperature was in the range of 20 °C-60 °C. However, drastic reduction of the activity occurred at temperatures above 65 °C. Full hemagglutinating activity of the lectin was observed at an ambient pH of 3 to 12. About 50% activity remained at pH 0-2, and only residual activity was observed at pH 13-14. Hemagglutinating activity of the lectin was inhibited by glucosamine. The brown kidney bean lectin elicited maximum mitogenic activity toward murine splenocytes at 2.5 μM. The mitogenic activity was nearly completely eliminated in the presence of 250 mM glucosamine. The lectin also increased mRNA expression of the cytokines IL-2, TNF-α and IFN-γ. The lectin exhibited antiproliferative activity toward human breast cancer (MCF7) cells, hepatoma (HepG2) cells and nasopharyngeal carcinoma (CNE1 and CNE2) cells with IC(50) of 5.12 μM, 32.85 μM, 3.12 μM and 40.12 μM respectively after treatment for 24 hours. Flow cytometry with Annexin V and propidum iodide staining indicated apoptosis of MCF7 cells. Hoechst 33342 staining also indicated formation of apoptotic bodies in MCF7 cells after exposure to brown kidney bean lectin. Western blotting revealed that the lectin-induced apoptosis involved ER stress and unfolded protein response.     

Antiplasmin activity of natural occurring polyphenols

The equilibrium between proteolytic enzymes and their cognate inhibitors is crucial in a number of physiological as well as pathological processes, including cancer, inflammatory processes and thrombosis. Therefore, both synthetic and natural small molecule inhibitors are object of extensive studies as drugs in the treatment of these pathologies. Two natural occurring polyphenolic compounds, representative of glycosylated and unglycosylated flavonoid structures, namely quercetin and rutin, were thereby tested as potential ligands of plasmin(ogen), a serine (pro)protease, whose role in tumor cell invasion and migration has been reported. Quercetin showed a ten folds higher affinity with plasmin with respect to rutin in terms of equilibrium dissociation constant, both compounds acting as in vitro moderate reversible inhibitors; additionally, quercetin and rutin prevented plasmin-incubated BB1 cells from releasing E-cadherin fragment to a different extent, respectively. Furthermore, a feasible mechanism of interaction was analyzed and discussed using a molecular modeling approach.     

The use of fluorescein for labeling genomic probes in the checkerboard DNA-DNA hybridization method

Molecular methods that permit the simultaneous detection and quantification of a large number of microbial species are currently employed in the evaluation of complex ecosystems. The checkerboard DNA-DNA hybridization technique enables the simultaneous identification of distinct bacterial species in a large number of dental samples. The original technique employed digoxigenin-labeled whole genomic DNA probes which were detected by chemiluminescence. In this study, we present an alternative protocol for labeling and detecting whole genomic DNA probes in the Checkerboard DNA-DNA hybridization method. Whole genomic DNA was extracted from five bacterial species and labeled with fluorescein. The fluorescein labeled whole genomic DNA probes were hybridized against whole genomic DNA or subgingival plaque samples in a checkerboard hybridization format, followed by chemiluminescent detection. Our results reveal that fluorescein is a viable and adequate alternative labeling reagent to be employed in the checkerboard DNA-DNA hybridization technique.     

The xeric side of the Brazilian Atlantic Forest: The forces shaping phylogeographic structure of cacti

In order to investigate biogeographic influences on xeric biota in the Brazilian Atlantic Forest (BAF), a biodiversity hotspot, we used a monophyletic group including three cactus taxa as a model to perform a phylogeographic study: Cereus fernambucensis subsp. fernambucensis, C. fernambucensis subsp. sericifer, and C. insularis. These cacti are allopatric and grow in xeric habitats along BAF, including isolated granite and gneiss rock outcrops (Inselbergs), sand dune vegetation (Restinga forest), and the rocky shore of an oceanic archipelago (islands of Fernando de Noronha). The nucleotide information from nuclear gene phytochrome C and plastid intergenic spacer trnS‐trnG was used to perform different approaches and statistical analyses, comprising population structure, demographic changes, phylogenetic relationships, and biogeographic reconstruction in both spatial and temporal scales. We recovered four allopatric population groups with highly supported branches in the phylogenetic tree with divergence initiated in the middle Pleistocene: southern distribution of C. fernambucensis subsp. fernambucensis, northern distribution of C. fernambucensis subsp. fernambucensis together with C. insularis, southern distribution of C. fernambucensis subsp. sericifer, and northern distribution of C. fernambucensis subsp. sericifer. Further, the results suggest that genetic diversity of population groups was strongly shaped by an initial colonization event from south to north followed by fragmentation. The phylogenetic pattern found for C. insularis is plausible with peripatric speciation in the archipelago of Fernando de Noronha. To explain the phylogeographic patterns, the putative effects of both climatic and sea level changes as well as neotectonic activity during the Pleistocene are discussed.