Metabolic engineering with multi-objective optimization of kinetic models

Kinetic models have a great potential for metabolic engineering applications. They can be used for testing which genetic and regulatory modifications can increase the production of metabolites of interest, while simultaneously monitoring other key functions of the host organism. This work presents a methodology for increasing productivity in biotechnological processes exploiting dynamic models. It uses multi-objective dynamic optimization to identify the combination of targets (enzymatic modifications) and the degree of up- or down-regulation that must be performed in order to optimize a set of pre-defined performance metrics subject to process constraints. The capabilities of the approach are demonstrated on a realistic and computationally challenging application: a large-scale metabolic model of Chinese Hamster Ovary cells (CHO), which are used for antibody production in a fed-batch process. The proposed methodology manages to provide a sustained and robust growth in CHO cells, increasing productivity while simultaneously increasing biomass production, product titer, and keeping the concentrations of lactate and ammonia at low values. The approach presented here can be used for optimizing metabolic models by finding the best combination of targets and their optimal level of up/down-regulation. Furthermore, it can accommodate additional trade-offs and constraints with great flexibility.

Chondrogenic potential of injectable κ-carrageenan hydrogel with encapsulated adipose stem cells for cartilage tissue-engineering applications

Due to the limited self-repair capacity of cartilage, regenerative medicine therapies for the treatment of cartilage defects must use a significant amount of cells, preferably applied using a hydrogel system that can promise their delivery and functionality at the specific site. This paper discusses the potential use of k-carrageenan hydrogels for the delivery of stem cells obt ained from adipose tissue in the treatment of cartilage tissue defects. The developed hydrogels were produced by an ionotropic gelation met hod and human adipose stem cells (hASCs) were encapsulated in 1.5% w/v k-carrageenan solution at a cell density of 5  10 6 cells/ml. The results from the analysis of the cell-encapsulating hydrogels, cultured for up to 21 days, indicated that k-carrageenan hydrogels support the viability, proliferation and chondrogenic differentiation of hASCs. Additionally, the mec hanical analysis demonstrated an increase in stiffness and viscoelastic properties of k-carrageenan gels with their encapsulated cells with increasing time in culture with chondrogenic medium. These results allowed the conclusion that k-carrageenan exhibits properties t hat enable the in vitro functionality of encapsulated hASCs and thus may provide the basis for new successful approaches for the treatment of cartilage defects.

Bioactive ceramics for tissue engineering and regenerative medicine derived from marine sponges

Publicado em "Journal of tissue engineering and regenerative medicine". Vol. 8, suppl. s1 (2014)

Marine Collagen/Apatite scaffolds envisaging tissue engineering applications

Despite the vast investigation and the large amount of products already available in the market to treat the different bone defects there is still a growing need to develop more advanced and complex therapeutic strategies. In this context, a mixture of Marine Hydroxyapatite-Fluorapatite:Collagen (HA-FP:ASC) seems to be a promising solution to overcome these bone defects, specifically, dental defects. HA-FP particles (20–63 μm) were obtained through pyrolysis (950°C, 12 h) of shark teeth (Isurus oxyrinchus, P. glauca), and Type I collagen was isolated from Prionace glauca skin as previously described (1). After the steps of purification, collagen was solubilized in 0.5 M acetic acid and HA-FP added producing three different formulations: were produced, 30:70, 50:50 and 70:30 of HA-FP:ASC, respectively. EDC/NHS and HMDI binding agents were used to stabilize the produced scaffolds. Mechanical properties were evaluated by compression tests. SEM analysis allowed observing the mineral deposition, after immersion in simulated body fluid and also permitted to evaluate how homogenous was the distribution of HA-FP in the different scaffold formulations, also confirmed by μ-CT assay. It was readily visible by Cytotoxicity and life/dead CLSM assays that cells were able to adhere and proliferate in the produced scaffolds. Scaffolds crosslinked with EDC/NHS showed lower cytotoxicity, being the ones chosen for further cellular evaluation.

Introducing biomimetic approaches to materials development and product design for engineering students

In this paper, we present a new course entitled “Biomimicry: from life to nanotechnological innovations” at the Mines Nancy Engineering School, Nancy, France, and explain how we developed a specific curriculum covering biomimicry. We discuss strategies that can be followed by teachers to explain selected contents in the multi-disciplinary field of biomimicry and/or bioinspiration to undergraduate students and how practical classroom activities can be conducted as individual or team work. We hope that sharing our experience will help teachers and senior researchers disseminate useful concepts and real examples of biomimetic principles and tools for the development of new materials, new/improved design and fabrication strategies, and innovation methodologies.

Ressonância nuclear magnética no diagnóstico de pseudoaneurisma de ventrículo esquerdo. Antigo problema, nova opção

Paciente feminina, 67 anos, internada por infarto agudo do miocárdio de parede lateral, com edema agudo de pulmão e evolução para choque cardiogênico nas primeiras horas. Ecocardiograma transesofágico e ressonância nuclear magnética confirmaram o diagnóstico de pseudoaneurisma de ventrículo esquerdo. A paciente foi submetida a tratamento cirúrgico com sucesso.

Current approaches and future perspectives on strategies for the development of personalized tissue engineering therapies

Personalized tissue engineering and regenerative medicine (TERM) therapies propose patient-oriented effective solutions, considering individual needs. Cell-based therapies, for example, may benefit from cell sources that enable easier autologous set-ups or from recent developments on IPS cells technologies towards effective personalized therapeutics. Furthermore, the customization of scaffold materials to perfectly fit a patientâ s tissue defect through rapid prototyping technologies, also known as 3D printing, is now a reality. Nevertheless, the timing to expand cells or to obtain functional in vitrotissue substitutes prior to implantation prevents advancements towards routine use upon patient´s needs. Thus, personalized therapies also anticipate the importance of creating off-the-shelf solutions to enable immediately available tissue engineered products. This paper reviews the main recent developments and future challenges to enable personalized TERM approaches and to bring these technologies closer to clinical applications.

Engineering a commercial cold-adapted xylanase for improved low pH stability

Dissertação de mestrado em Genética Molecular

An R package for the integrated analysis of metabolomics and spectral data

Recently, there has been a growing interest in the field of metabolomics, materialized by a remarkable growth in experimental techniques, available data and related biological applications. Indeed, techniques as Nuclear Magnetic Resonance, Gas or Liquid Chromatography, Mass Spectrometry, Infrared and UV-visible spectroscopies have provided extensive datasets that can help in tasks as biological and biomedical discovery, biotechnology and drug development. However, as it happens with other omics data, the analysis of metabolomics datasets provides multiple challenges, both in terms of methodologies and in the development of appropriate computational tools. Indeed, from the available software tools, none addresses the multiplicity of existing techniques and data analysis tasks. In this work, we make available a novel R package, named specmine, which provides a set of methods for metabolomics data analysis, including data loading in different formats, pre-processing, metabolite identification, univariate and multivariate data analysis, machine learning, and feature selection. Importantly, the implemented methods provide adequate support for the analysis of data from diverse experimental techniques, integrating a large set of functions from several R packages in a powerful, yet simple to use environment. The package, already available in CRAN, is accompanied by a web site where users can deposit datasets, scripts and analysis reports to be shared with the community, promoting the efficient sharing of metabolomics data analysis pipelines.

Development of composite auxetic structures for civil engineering applications

Tese de Doutoramento em Engenharia Têxtil

Genetic diversity and population structure in Vicia faba L. landraces and wild related species assessed by nuclear SSRs

Research Article

Estudio básico y aplicado de polímeros elastómeros mediante la Técnica de Resonancia Magnética Nuclear (RMN)

Los polímeros son materiales que poseen una variedad muy grande de aplicaciones. Por esta razón, el estudio de sus propiedades físicas y químicas resulta de gran interés. Un polímero es una macromolécula cuyo peso molecular puede llegar a varios millones de umas. Mediante la selección de el o los monómeros y de su secuenciamiento en el proceso de polimerización (microestructura del polímero), se puede lograr que el material tenga propiedades predeterminadas. Es posible, entonces, encontrar o desarrollar polímeros para las más variadas aplicaciones: elásticos, rígidos, resistentes a la temperatura, conductores, aisladores, inertes, etc. (...) La Resonancia Magnética Nuclear (RMN) de alta resolución es una de las técnicas más poderosas para la caracterización de los polímeros, brindando información sobre la microestructura y la dinámica de estas macromoléculas, tanto cuando se encuentran en estado sólido como cuando están disueltas en soluciones líquidas. El entendimiento de la microestructura de un polímero es de interés porque ella está íntimamente relacionada con las propiedades macroscópicas del material. Por otra parte, la microestructura de un polímero depende del proceso de polimerización utilizado y en consecuencia, es posible obtener información sobre los mecanismos de reacción química que ocurren durante su síntesis, dentro de los reactores de polimerización. NMR permite, también, obtener información detallada sobre la dinámica de los polímeros. La gran longitud de los polímeros hace que su dinámica molecular sea sumamente compleja. Sin embargo, mediante el empleo de secuencias de pulsos particulares y mediciones de los tiempos de relajación característicos de los espines nucleares, se obtiene información sobre la dinámica de la macromolécula, de los segmentos que la componen y de los grupos colgantes que pueda poseer. Objetivos Generales y Específicos El trabajo a realizar en el período correspondiente al subsidio solicitado, es la continuación de las investigaciones comenzadas en septiembre de 1995. Se avanzará en el entendimiento de los elastómeros que se están estudiando actualmente. El estudio abarca los elastómeros sin tratamientos térmicos y con tratamientos térmicos (vulcanizados).