Evaluation of rate law approximations in bottom-up kinetic models of metabolism.

BackgroundThe mechanistic description of enzyme kinetics in a dynamic model of metabolism requires specifying the numerical values of a large number of kinetic parameters. The parameterization challenge is often addressed through the use of simplifying approximations to form reaction rate laws with reduced numbers of parameters. Whether such simplified models can reproduce dynamic characteristics of the full system is an important question.ResultsIn this work, we compared the local transient response properties of dynamic models constructed using rate laws with varying levels of approximation. These approximate rate laws were: 1) a Michaelis-Menten rate law with measured enzyme parameters, 2) a Michaelis-Menten rate law with approximated parameters, using the convenience kinetics convention, 3) a thermodynamic rate law resulting from a metabolite saturation assumption, and 4) a pure chemical reaction mass action rate law that removes the role of the enzyme from the reaction kinetics. We utilized in vivo data for the human red blood cell to compare the effect of rate law choices against the backdrop of physiological flux and concentration differences. We found that the Michaelis-Menten rate law with measured enzyme parameters yields an excellent approximation of the full system dynamics, while other assumptions cause greater discrepancies in system dynamic behavior. However, iteratively replacing mechanistic rate laws with approximations resulted in a model that retains a high correlation with the true model behavior. Investigating this consistency, we determined that the order of magnitude differences among fluxes and concentrations in the network were greatly influential on the network dynamics. We further identified reaction features such as thermodynamic reversibility, high substrate concentration, and lack of allosteric regulation, which make certain reactions more suitable for rate law approximations.ConclusionsOverall, our work generally supports the use of approximate rate laws when building large scale kinetic models, due to the key role that physiologically meaningful flux and concentration ranges play in determining network dynamics. However, we also showed that detailed mechanistic models show a clear benefit in prediction accuracy when data is available. The work here should help to provide guidance to future kinetic modeling efforts on the choice of rate law and parameterization approaches

Revisão do Conhecimento sobre os Mamíferos Aquáticos da Costa Norte do Brasil

The Brazilian north coast represents a new frontier in several fields of knowledge. The aquatic mammals of the Brazilian northern coast were poorly studied until recently. Recent efforts promoted by Projeto Piatam Oceano are changing the scenario. New research groups on aquatic mammals were formed and are conducting a large survey of this unique group of mammals. A total of 22 species of aquatic mammals were recorded along the Brazilian northern region. It should be emphasized the rediscovery of the Antillean manatee in several localities along the coasts of Amapá, Pará and Maranhão states. On the other hand, the estuarine dolphin is widely distributed along the Amazonian coast but is frequently by-caught in gill nets fisheries throughout the northern coast. The intense use of love charms has also a negative effect on these populations and should be better evaluated. An awareness program will be implemented as a first step for changing attitude towards the aquatic mammals of the northern coast.A costa norte do Brasil representa uma nova fronteira para o avanço do conhecimento sobre a fauna de mamíferos aquáticos. A ausência de dados pretéritos sobre os mamíferos aquáticos nessa região e a própria dificuldade logística de monitoramento resultou, até muito recentemente, numa lacuna de conhecimento. A fim de reverter este quadro, o Projeto Piatam Oceano vem incentivando a formação de grupos de pesquisa sobre mamíferos aquáticos da costa amazônica. Como resultado dos esforços recentes, foi reunido um conjunto relevante de informações inéditas ou complementares sobre as 22 espécies de mamíferos aquáticos registradas até o momento na região. Destacam-se as áreas de ocorrência do peixe-boi-marinho no litoral dos Estados do Maranhão, Pará e Amapá, as quais poderiam garantir a manutenção destas populações criticamente ameaçadas. Merece destaque ainda a ocorrência do boto-cinza em toda costa amazônica e sua problemática de interação com a pesca artesanal e o comércio de peças anatômicas. Sugere-se uma ampla campanha de conscientização e a promoção de campanhas educativas visando uma nova tomada de atitude em relação aos mamíferos aquáticos e seus hábitats, respeitando os valores tradicionais e o conhecimento etnoecológico das comunidades costeiras

DNA damage induced by cis- and carboplatin as indicator for in vitro sensitivity of ovarian carcinoma cells

<p>Abstract</p> <p>Background</p> <p>The DNA damage by platinum cytostatics is thought to be the main cause of their cytotoxicity. Therefore the measurement of the DNA damage induced by cis- and carboplatin should reflect the sensitivity of cancer cells toward the platinum chemotherapeutics.</p> <p>Methods</p> <p>DNA damage induced by cis- and carboplatin in primary cells of ovarian carcinomas was determined by the alkaline comet assay. In parallel, the reduction of cell viability was measured by the fluorescein diacetate (FDA) hydrolysis assay.</p> <p>Results</p> <p>While in the comet assay the isolated cells showed a high degree of DNA damage after a 24 h treatment, cell viability revealed no cytotoxicity after that incubation time. The individual sensitivities to DNA damage of 12 tumour biopsies differed up to a factor of about 3. DNA damage after a one day treatment with cis- or carboplatin correlated well with the cytotoxic effects after a 7 day treatment (r = 0,942 for cisplatin r = 0.971 for carboplatin). In contrast to the platinum compounds the correlation of DNA damage and cytotoxicity induced by adriamycin was low (r = 0,692), or did not exist for gemcitabine.</p> <p>Conclusion</p> <p>The measurement of DNA damage induced by cis- and carboplatin is an accurate method to determine the in vitro chemosensitivity of ovarian cancer cells towards these cytostatics, because of its quickness, sensitivity, and low cell number needed.</p

Quantification of cancer cell migration with an integrated experimental-computational pipeline

We describe an integrated experimental-computational pipeline for quantifying cell migration in vitro. This pipeline is robust to image noise, open source, and user friendly. The experimental component uses the Oris cell migration assay (Platypus Technologies) to create migration regions. The computational component of the pipeline creates masks in Matlab (MathWorks) to cell-covered regions, uses a genetic algorithm to automatically select the migration region, and outputs a metric to quantify cell migration. In this work we demonstrate the utility of our pipeline by quantifying the effects of a drug (Taxol) and of the extracellular Anterior Gradient 2 (eAGR2) protein on the migration of MDA-MB-231 cells (a breast cancer cell line). In particular, we show that inhibiting eAGR2 reduces migration of MDA-MB-231 cells

Targeting 3CLpro and SARS-CoV-2 RdRp by Amphimedon sp. Metabolites: A Computational Study

Since December 2019, novel coronavirus disease 2019 (COVID-19) pandemic has caused tremendous economic loss and serious health problems worldwide. In this study, we investigated 14 natural compounds isolated from Amphimedon sp. via a molecular docking study, to examine their ability to act as anti-COVID-19 agents. Moreover, the pharmacokinetic properties of the most promising compounds were studied. The docking study showed that virtually screened compounds were effective against the new coronavirus via dual inhibition of SARS-CoV-2 RdRp and the 3CL main protease. In particular, nakinadine B (1), 20-hepacosenoic acid (11) and amphimedoside C (12) were the most promising compounds, as they demonstrated good interactions with the pockets of both enzymes. Based on the analysis of the molecular docking results, compounds 1 and 12 were selected for molecular dynamics simulation studies. Our results showed Amphimedon sp. to be a rich source for anti-COVID-19 metabolites