Hybrid semi-parametric mathematical systems: bridging the gap between systems biology and process engineering

Systems biology is an integrative science that aims at the global characterization of biological systems. Huge amounts of data regarding gene expression, proteins activity and metabolite concentrations are collected by designing systematic genetic or environmental perturbations. Then the challenge is to integrate such data in a global model in order to provide a global picture of the cell. The analysis of these data is largely dominated by nonparametric modelling tools. In contrast, classical bioprocess engineering has been primarily founded on first principles models, but it has systematically overlooked the details of the embedded biological system. The full complexity of biological systems is currently assumed by systems biology and this knowledge can now be taken by engineers to decide how to optimally design and operate their processes. This paper discusses possible methodologies for the integration of systems biology and bioprocess engineering with emphasis on applications involving animal cell cultures. At the mathematical systems level, the discussion is focused on hybrid semi-parametric systems as a way to bridge systems biology and bioprocess engineering.     

Extra-pancreatic insulin production in RAt lachrymal gland after streptozotocin-induced islet β-cells destruction

Previous work has revealed that insulin is secreted in the tear film; its mRNA is expressed in the lachrymal gland (LG) and its receptor in tissues of the ocular surface. To test the hypothesis of insulin production in the LG, we compared normal and diabetic rats for: (1) the presence of insulin and C-peptide, (2) glucose- and carbachol-induced insulin secretion ex-vivo, and (3) biochemical and histological characteristics of diabetic LG that would support this possibility. Four weeks after streptozotocin injection, blood and tears were collected from streptozotocin-diabetic male Wistar rats. Insulin levels in the tear film rose after glucose stimulation in diabetic rats, but remained unchanged in the blood. Ex vivo static secretion assays demonstrated that higher glucose and 200 μM carbachol significantly increased mean insulin levels from LG samples of both groups. Insulin and C-peptide were expressed in LG of diabetic rats as determined by RIA. Comparable synaptophysin immune staining and peroxidase activity in the LG of both groups suggest that the structure and function of these tissues were maintained. These findings provide evidence of insulin production by LG. Higher expression of reactive oxygen species scavengers may prevent oxidative damage to LG compared to pancreatic beta-cells.     

Chromosome polymorphism in Astyanax fasciatus (Teleostei, Characidae), Part 3: Analysis of the RAPD and ISSR molecular markers

The Randomly Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Repeats (ISSR) molecular markers were used to complement the study of chromosomal polymorphism in Astyanax fasciatus (Teleostei, Characidae) from the Mogi-Guaçu River (Southeastern Brazil), analyzed in three collection sites along the river (Ouro Fino – MG, Cachoeira de Emas – SP and Barrinha – SP). Two cytotypes (or karyotypic types), denominated standard cytotypes, were previously characterized, one including 2n = 46 chromosomes and the other 2n = 48 chromosomes, where all the chromosomes of the complement form homologous pairs. Additionally, variant karyotypic forms with 2n = 45, 46 and 47 chromosomes were also detected, although with a lower frequency in relation to the standard cytotypes. RAPD turned out little informative in the analysis of the observed situation, indicating a high value of migrants per generation among the cytotypes. On the other hand, ISSR showed a small structure, especially among the standard cytotypes from the Barrinha region where the Nm was 0.4301 with a genetic identity of 0.6862 and genetic distance of 0.3765. However, the general results obtained do not discard the possibility of interbreeding between both standard cytotypes and/or their descendants as a source of chromosome variation. The association between the cytogenetic and molecular markers viabilized putative explanatory scenery for the origin and evolution of the forms seen in A. fasciatus.     

Molecular assessment of complex microbial communities degrading long chain fatty acids in methanogenic bioreactors

Microbial diversity of anaerobic sludge after extended contact with long chain fatty acids (LCFA) was studied using molecular approaches. Samples containing high amounts of accumulated LCFA were obtained after continuous loading of two bioreactors with oleate or with palmitate. These sludge samples were then incubated in batch assays to allow degradation of the biomass-associated LCFA. In addition, sludge used as inoculum for the reactors was also characterized. Predominant phylotypes of the different samples were monitored using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rRNA gene fragments. Fingerprinting analysis showed changes in bacterial and archaeal communities during LCFA accumulation and degradation. Full-length 16S rRNA gene sequences of 22 clones, representing the predominant bacteria and archaea, were determined. Most bacterial clones (80%) clustered within the Clostridiaceae. Two major groups of methanogens were identified: hydrogen- and formate-utilizing organisms, closely related to Methanobacterium, and acetoclastic organisms closely related to Methanosaeta and Methanosarcina. Quantification by FISH and real-time PCR showed that the relative abundance of archaea increased during degradation of biomass-accumulated LCFA. These results provide insight into the importance and dynamics of balanced communities of bacteria and methanogens in LCFA-accumulation/degradation cycles.     

Characterization of a novel ADPase in Bothrops jararaca snake venom involved in nucleotide hydrolysis

Snake venoms hydrolyze several phosphorylated substrates. However, not is clearly understood which enzyme(s) is (are) involved in these process. Here, we propose the existence of an independent ADPase activity. In addition, we studied the reactions mechanism of nucleotide hydrolysis. This system resembles membrane ecto-nucleotidases and acts with a multi enzymatic complex transforming ATP in adenosine without the accumulation of intermediates.     

Commercialization and Use of Snakes in North and Northeastern Brazil: Implications for Conservation and Management

Snakes are sold in many markets and religious article stores in Brazil. Besides their use as food, snakes are exploited in a variety of ways, such as pets, or for use in traditional medicine and magic/religious rituals (especially in Afro-Brazilian religions). Despite widespread commercialization, there is a general lack of information about this snake trade, which makes it difficult to evaluate its magnitude and its impact on reptile populations. This work documents the commercialization and use of snakes in five cities in Northeastern (São Luís, Teresina, João Pessoa and Campina Grande) and Northern (Belém) Brazil, through interviews with 119 merchants of biological products in outdoor markets and religious articles stores. The data was gathered through the use of semi-structured questionnaires, complemented by semi-directed interviews. The products derived from 11 snake species were being commercialized for medicinal or magical/religious purposes. Boa constrictor, Crotalus durissus and Eunectes murinus were the species most commonly sold. The economic importance of snakes as sources of medicines and religious products demonstrates the need for the development of sustainable use programs for these species.     

Reduced in-hospital mortality after improved management of children under 5 years admitted to hospital with malaria: randomised trial

Objective To test whether strict implementation of a standardised protocol for the management of malaria and provision of a financial incentive for health workers reduced mortality.Design Randomised controlled intervention trial.Setting Paediatric ward at the national hospital in Guinea-Bissau. All children admitted to hospital with severe malaria received free drug kits.Participants 951 children aged 3 months to 5 years admitted to hospital with a diagnosis of malaria randomised to normal or intervention wards.Interventions Before the start of the study, all personnel were trained in the use of the standardised guidelines for the management of malaria, including strict follow-up procedures. Nurses and doctors were randomised to work on intervention or control wards. Personnel in the intervention ward received a small financial incentive ($50 (£25; €35)/month for nurses and $160 for doctors) and their compliance with standard case management was closely monitored.Main outcome measures In-hospital mortality and cumulative mortality within 4 weeks of hospital admission.Results In-hospital mortality was 5% for the intervention group and 10% in the control group (risk ratio 0.48, 95% confidence interval 0.29 to 0.79). The effect may have been stronger in patients with positive malaria slides (0.36, 0.16 to 0.80). Cumulative mortality 4 weeks after discharge was also lower in the intervention group (0.61, 0.40 to 0.95).Conclusions Supervising healthcare workers to adhere to a standardised treatment protocol was associated with greatly reduced in-hospital mortality. Financial incentives may be important for the dedication and compliance of staff members.Trial registration Clinical Trials {"type":"clinical-trial","attrs":{"text":"NCT00465777","term_id":"NCT00465777"}}NCT00465777.     

Calculation of binding energy using BLYP/MM for the HIV-1 integrase complexed with the S-1360 and two analogues

Integrase (IN) is one of the three human immunodeficiency virus type 1 (HIV-1) enzymes essential for effective viral replication. S-1360 is a potent and selective inhibitor of HIV-1 IN. In this work, we have carried out molecular dynamics (MD) simulations using a hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) approach, to determine the protein-ligand interaction energy for S-1360 and two analogues. Analysis of the MD trajectories reveals that the strongest protein-inhibitor interactions, observed in the three studied complexes, are established with Lys-159 residue and Mg(2+) cation. Calculations of binding energy using BLYP/MM level of theory reveal that there is a direct relationship between this theoretical computed property and the experimental determined anti-HIV activity.     

Exploring marine resources against neurological disorders– the neuroprotective and anti-inflammatory potential of the brown seaweed Bifurcaria bifurcata

Oxidative stress is strongly involved in the pathogenesis of neurodegenerative diseases, like Parkinson´s disease (PD). Particularly, an excess of reactive oxygen species (ROS) released by the cells promotes an oxidative stress condition, which is a main cause of tissue injury leading to nervous system dysfunction. In this work, the antioxidant, neuroprotective and anti-inflammatory activities of different fractions from the brown seaweed Bifurcaria bifurcata are presented and related with their chemical profile. The antioxidant capacity was evaluated by the Folin-Ciocalteu method, 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, ferric reducing antioxidant power (FRAP) and oxygen radical absorbance capacity (ORAC) assays. Neuroprotective capacity was evaluated to prevent neurological cell death mediated by the neurotoxin 6-hydroxydopamine (6-OHDA) on SH-SY5Y cells, and their anti-inflammatory effects on RAW 264.7 macrophages. The ethyl acetate fractions (100 µg mL^?1) exhibited significant antioxidant and neuroprotective activities in the in vitro models assayed. Furthermore, two of the most polar fractions obtained with methanol and water also evidenced a significant neuroprotective potential. Bifurcaria bifurcata fractions treatment decreased ROS production, mitochondrial dysfunction, and Caspase-3 activity. Regarding the anti-inflammatory potential, five fractions (100 µg mL^?1) inhibited nitric oxide (NO) production and reduced the interleukin – 6 (IL-6) and tumor necrosis factor (TNF-α) levels. Mannitol, identified as the major component of the most bioactive fraction, protected SH-SY5Y cells against the 6-OHDA neurotoxicity mediating ROS generation mitigation, mitochondrial dysfunction, and DNA damage, together with the Caspase-3 activity inhibition. Results suggest that B. bifurcata is a relevant source of neuroprotective agents, with particular interest for preventive therapeutics.