Stuttgart, Univ., Diss., 2008.

Doctora en Ciencias de la Ingeniería, Mención Ingeniería Química y Biotecnología / Las células animales son uno de los principales sistemas para la producción de biofármacos, sin embargo la mayoría de las estrategias para mejorar su productividad no están respaldadas por conocimiento específico para las líneas celulares usadas en la industria. En este trabajo se reconstruye un modelo a escala genómica para células CHO para ampliar el conocimiento de procesos celulares asociados con productividad en la síntesis de biofármacos. Para lograr este objetivo analizamos el modelo a escala genómica de ratón iMM1415 usando herramientas desarrolladas para explorar el efecto de knockout de genes y determinación de flujos en crecimiento celular. Nuestros resultados muestran que esta red metabólica está dominada por metabolismo de lípidos. Adicionalmente, confirmamos que un enfoque de sampleo, donde se explora el espacio de soluciones en vez de imponer un objetivo de optimización, es más apropiado para el estudio del metabolismo en sistemas complejos como células animales. Posteriormente, se desarrolla en estudio comparativo de las herramientas desarrolladas para la generación automática de modelos preliminares, donde los resultados obtenidos utilizando tres algoritmos (modelSEED, Pantograph y Pathway tools) muestran que Pantograph es la herramienta más apropiada para la generación de un modelo a escala genómica de células CHO. Este algoritmo produce un modelo basándose en un modelo previo y ortología entre ambos organismos, produciendo un modelo preliminar que hereda características como asociaciones de genes distintas para distintos organelos celulares lo que es crucial para potenciales aplicaciones de modelos para eucariontes. El modelo iNJ1301 para células CHO es reconstruido de acuerdo a la metodología propuesta basándose en iMM1415 y el modelo humano Recon 1. iNJ1301 tiene 3,709 reacciones asociadas a 1,301 genes y fue validado con información experimental para esta línea celular prediciendo correctamente el crecimiento celular en un 88% de los casos simulados. Adicionalmente, este modelo es reducido imponiendo cambios en expresión de genes reportados para representar un metabolismo ineficiente del carbono caracterizado por síntesis de lactato y el shift metabólico observado en esta línea celular, mostrando el potencial de este enfoque para ser usado en la integración de datos transcriptómicos. Al utilizar un nuevo enfoque basado en ortología se pudieron encontrar nuevas asociaciones de genes no incluídas en reconstrucciones creadas utilizando metodologías clásicas para la generación de modelos, por lo que los resultados de este trabajo fueron incorporadas en el modelo consenso iCHO1766. La identificación de marcadores asociados a productividad mejorada en células CHO ha sido abordada desde la perspectiva genómica, transcriptómica y proteómica. En este trabajo integramos datos transcriptómicos para dos clones de células CHO que muestran distintos perfiles de productividad en el modelo iNJ1301. Datos de un alto (HP) y bajo (LP) productor de IgG son integrados al modelo usando iMAT (integrative metabolic analysis tool) obteniéndose modelos reducidos que presentan una alta conservación de vías metabólicas de glutatión y azúcares nucleotídicos. Este enfoque es luego acoplado con sampleo de las redes metabólicas encontrándose que ambos modelos presentan comportamientos distintos, donde el clon HP está enfocado en el uso del ciclo del TCA y la vía pentosas fosfato. Finalmente, concluimos que este enfoque que combina distintas herramientas utilizadas en biología de sistemas es una nueva herramienta que permite el estudio exhaustivo de sistemas biológicos complejos tales como líneas celulares animales.

Made available in DSpace on 2014-10-09T12:55:16Z (GMT). No. of bitstreams: 0 / Made available in DSpace on 2014-10-09T14:06:00Z (GMT). No. of bitstreams: 0 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Dissertação (Mestrado) / IPEN/D / Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP / FAPESP:06/52973-9

Made available in DSpace on 2014-10-09T12:55:16Z (GMT). No. of bitstreams: 0 / Made available in DSpace on 2014-10-09T14:06:00Z (GMT). No. of bitstreams: 0 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / A Prolactina humana hPRL é um hormônio protéico com 199 aminoácidos (MM ~ 23.000 Da) com um amplo espectro de atividades biológicas, sendo mais conhecido por estimular a lactação e regular o crescimento e diferenciação da glândula mamária. Além de quebra proteolítica, a maioria dos variantes de prolactina podem ser resultantes de outros processos pós-traducionais como polimerização, fosforilação, desamidação, sulfatação e glicosilação. Essa proteína contém apenas um sítio potencial de glicosilação por ligação à asparagina, localizada no aminoácido 31, que é parcialmente ocupado (10%) quando a proteína é sintetizada em células eucariotas. Apesar da atividade biológica in vitro da prolactina glicosilada (G-hPRL) ser muito menor (~4 vezes) quando comparada à não glicosilada, sua função fisiológica ainda não é bem definida e a porção de carboidrato parece ter um importante papel na biossíntese, secreção, atividade biológica, e clearance plasmático do hormônio. Com o objetivo de melhor caracterizar e estudar esta variante hormonal, foi realizada sua purificação em escala laboratorial a partir de células de ovário de hamster chinês (CHO) modificadas geneticamente, utilizando meio de cultura suplementado com cicloheximida, aumentando ~4 vezes sua concentração absoluta e ~10 vezes a razão entre a isoforma glicosilada e a não-glicosilada. A purificação da G-hPRL seguiu um processo simples e efetivo de duas etapas principais baseado em uma coluna de troca catiônica e uma coluna preparativa de exclusão molecular acoplada a um sistema de cromatografia líquida de excusão molecular de alta eficiência (HPSEC). A caracterização foi feita por HPLC de fase reversa (RP-HPLC) e exclusão molecular, SDS-PAGE, Western Blotting, espectometria de massa (MALDI-TOF) e um bioensaio in vitro utilizando células Nb2 e Ba/F3-LLP. Nossos resultados demostram que a cicloheximida pode ser uma importante ferramenta para aumentar a produção de prolactina glicosilada, facilitando a purificação e caracterização dessa isoforma. / Dissertação (Mestrado) / IPEN/D / Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP / FAPESP:06/52973-9

Understanding the molecular mechanisms that govern productivity and growth of recombinant host cells is essential to devise informed approaches to increase commercial viability and availability of biopharmaceuticals. This work has focused on the roles of the mammalian target of rapamycin complex 1 (mTORC1) signalling pathway in CHO cells, the most widely used expression system in the biopharmaceutical industry. mTORC1 is a master regulator of cell growth, protein synthesis and metabolism in response to availability of nutrients, oxygen and growth factors. Therefore, it was hypothesised that increased activity of mTORC1 enhances growth and productivity of recombinant CHO cells. The study of a recombinant GS-CHO cell line in the serum-free suspension batch culture indicated a gradual decrease in the activity of mTORC1, as defined by the decreased extent of site-specific phosphorylation of two widely ascribed downstream target proteins (ribosomal protein S6 kinase 1 (S6K1) and 4E-BP1, an inhibitor of translation initiation). The decline in the activity of mTORC1 paralleled decreased growth rate, recombinant protein specific productivity and global protein translation. To further clarify the role of the mTOR pathway in cell growth and protein production, cells in batch culture were treated with rapamycin, a specific inhibitor of mTORC1. Treatment with rapamycin stalled the growth of the CHO cell line transiently, but recombinant protein specific productivity, longevity of batch culture, and final antibody titre were greater than control. Rapamycin addition produced discriminating effects on downstream signalling targets, implicating distinct roles for these targets in control of growth and protein synthesis. Engineering the mTORC1 pathway by overexpression of specific components of this pathway (S6K1 and Rheb) generated increased growth and extended viability. Greater proliferation was not associated with improved productivity suggesting highly proliferative phenotypes that prioritise cell growth over synthesis and secretion of recombinant antibody in the recombinant GS-CHO cells examined. Therefore, the engineering of mTORC1 pathway may be beneficial to increase robustness or adaptation to stressed conditions (such as serum- free suspension growth, low nutrition availability and hypoxia).

The increasing demand for recombinant therapeutic proteins coupled with advances in technologies allow research to develop approaches to improve the efficiency, yield, and quality of biopharmaceutical products from CHO cells. CHO DG44 cells used in this study were engineered to express erythropoeitin (EPO) as the model recombinant protein in a DHFR-based selection system. From a series of CHO-DG44 cell lines derived from a polyclonal population, one cell line expressed a notable change in growth phenotype during prolonged culture (10 weeks). This cell line (IJ4) exhibited prolonged growth, reached a greater density, and delayed cell death. The change in growth was reflected in an increased total yield of EPO, whilst the specific productivity of cell line IJ4 remained similar. The increased total yield of EPO presents a desirable goal for production and hence detailed ‘omics studies were performed to identify factors associated with better cell growth and survivability. Two different ‘omics analyses were performed (microarray transcriptomic and GC-MS metabolic profiling) to identify potential target genes and key metabolites associated with changes in growth profile. The -omics analyses identified a subset of genes (MMP20, PLA1A, POSTN, SLC46A3, and TOP2A), and a metabolic marker (farnesal) strongly associated with changes in cell growth and nutrient uptake. The use of complementary ‘omics approaches to identify molecular markers has allowed an integrated model to be built, which explains how CHO cell phenotype can adapt to long-term culture, and this defines molecular approaches for cell line screening and engineering.

The number of publications in the biomedical field increases exponentially, which makes the task of keeping up with current research more and more difficult. However, rapid advances in the field of Natural Language Processing (NLP) offer possible solutions to this problem. In this thesis we focus on investigating three main questions of importance for utilizing the field of NLP, or more specifically the two subfields Named Entity Recognition (NER) and Large Language Models (LLM), to help solve this problem. The questions are; comparing LLM performance to NER models on NER-tasks, the importance of normalization, and how the analysis is affected by the availability of data. We find for the first question that the two models offer a reasonably comparable performance for the specific task we are looking at. For the second question, we find that normalization plays a substantial role in improving the results for tasks involving data synthesis and analysis. Lastly, for the third question, we find that it is important to have access to full papers in most cases since important information can be hidden outside of the abstracts.

Electroporation is an efficient, low-toxic physical method which is used to deliver impermeant macromolecules such as genes and drugs into cells. Genetic modification of the cell is critical for many cell and gene therapy techniques. Common electroporation protocols can only handle small volumes of cell samples. Also, most of the conventional electroporation methods require expensive and sophisticated electro-pulsation equipment. In our lab, we have developed new electroporation methods conducted in microfluidic devices. In microfluidic-base electroporation, exogenous macromolecules can be delivered into cells continuously. Flow-through electroporation systems can overcome the issue of low sample volume limitation. In addition, in our method, electro-pulsation can be done by using a simple dc power supply, without the need for any extra equipment. Furthermore, our microfluidic chips are completely disposable and cheap to produce. We show that electroporation and electroporation-based gene delivery can be conducted employing tapered asymmetric curving channels. The size variation in the channel's cross-sectional area makes it possible to produce electric pulses of various parameters by using a dc power supply. We successfully delivered Enhanced Green Fluorescent Protein, EGFP, plasmid DNA into Chinese Hamster Ovary, CHO-K1, cells in our microfluidic chips. We show that the particles/cells undergo Dean flow in our asymmetric curving channels. We demonstrate that there are three main regimes for particle motion in our channels. At low flow rates (from 0 to ~75μl/min) cells do not focus and they randomly follow stream lines. However, as flow rate increases (~75 to 500μl/min), cells begin to focus into one line and they follow a single path throughout the micro-channel. When flow rate exceeds ~500μl/min, cells do not follow a single line and demonstrate more complex pattern. We show that the electric parameters affect the transfection efficiency and cell viability. Higher electric field intensity results in higher transfection efficiency. This is also true in the cases with longer electroporation duration time. In our experimental work, we executed flow-through electroporation for various duration times (t = 2 ms, 5 ms, and 7 ms), and at various electric field intensities (from 300 to 2200 V/cm) while we utilized different flow rates as well, i. e. 150 μl/min (focused flow) and 600 μl/min (complex flow). To explore the impact of individual electric pulse length and electric pulse number on electroporation results, we designed control channels with straight narrow sections. Cells experience different hydrodynamic forces in straight channels compared to curving channels. Flow pattern and cell focusing were also studied in control channels as well. Also, electroporation on CHO-K1 cells was successfully conducted in control channels. The hydrodynamic forces under the conditions we used do not appear to show substantial impact on transfection efficiency. / Master of Science

Nestas últimas décadas, investigações sobre compostos naturais, efetivos, não tóxicos, com potencial radioprotetor vêm despertando um grande interesse em consonância com a utilização crescente de vários tipos de radiação ionizante nas mais diversas finalidades. Entre eles a própolis uma resina coletada pelas abelhas (Apis mellifera), vem sendo apontada como promissora por apresentar uma série de características biológicas vantajosas, por exemplo, anti-inflamatória, antimicrobiana, antitumoral, imunomoduladora, antioxidante e também scavenger de radicais livres. O presente estudo teve como objetivo principal, averiguar efeito da própolis brasileira procedente de Rio Grande do Sul (AF 08) em células de ovário de hamster Chinês (CHO-K1) e em células tumorais de próstata (PC3), irradiadas com 60Co. Para tanto, foram utilizados três principais parâmetros interligados entre si: indução de micronúcleo, viabilidade celular e morte clonogênica. A escolha destes parâmetros se justifica pelo seu significado biológico, além do fato de serem prontamente observáveis e mensuráveis em células irradiadas. Os dados citogenéticos obtidos, mostraram um efeito radioprotetor da própolis (5 - 100 μg/ml) na indução de dano ao DNA em ambas as linhagens celulares, irradiadas com doses de 1 - 4 Gy. No entanto, o ensaio de citotoxicidade mostrou um efeito antiproliferativo pronunciado da própolis (50 - 400 μg/ml) em células PC3 irradiadas com 5 Gy. As curvas de sobrevida obtidas foram ajustadas satisfatoriamente pelo modelo linear-quadrático, cujo componente foi mais alto em células CHO-K1. Quanto à capacidade clonogênica, as células PC3 mostraram-se mais radiossensíveis que as células CHO-K1 nas doses mais altas da curva de sobrevida. A própolis, nas concentrações de 30 - 100 μg/ml, não influenciou no potencial clonogênico das células PC3, visto que, as curvas de sobrevida associadas ou não com a própolis, mostraram perfis similares, ao passo que o tratamento combinado em células CHO-K1 exibiu um efeito estimulador da proliferação. Os dados obtidos in vitro mostraram um potencial uso da própolis AF-08, como uma substância natural e não tóxica, na prevenção contra os efeitos danosos da radiação ionizante, nas doses e nas concentrações analisadas. / In the last decades, it has been given a great interest to investigations concerning natural, effective, nontoxic compounds with radioprotective potential together with the increasing utilization of different types of ionizing radiation for various applications. Among them propolis, a resinous compound produced by honeybees (Apis mellifera), has been considered quite promising, since it presents several advantageous biological characteristics, i. e., anti-inflammatory, antimicrobial, anticarcinogenic, antioxidant and also free radical scavenging action. The purpose of the present study was to evaluate the effect of Brazilian propolis, collected in the State of Rio Grande do Sul, on Chinese hamster ovary (CHO-K1) and human prostate cancer (PC3) cells, irradiated with 60Co radiation. For this purpose, three interlinked parameters were analyzed: micronucleus induction, cell viability and clonogenic death. The choice of these parameters was justified by their biological significance, in addition to the fact that they are readily observable and measurable in irradiated cells. The cytogenetic data obtained showed a radioprotective effect of propolis (5-100 μg/ml) in the induction of DNA damage for both cell lines, irradiated with doses of 1 - 4 Gy. The cytotoxicity assay, however, showed a prominent antiproliferative effect of propolis (50 - 400 μg/ml) in PC3 cells irradiated with 5 Gy. The survival curves obtained were adequately fitted by a linear-quadratic model, where the coefficient was higher in CHO-K1 cells. Concerning the clonogenic capacity, PC3 cells were more radiosensitive than CHO-K1 cells at the higher doses of the survival curve. Propolis at the concentrations of 30 - 100 μg/ml, did not influence the clonogenic potential of PC3 cells, since the survival curves, associated or not with propolis, were found similar, although the combined treatment in CHO-K1 cells exhibited a stimulating proliferative effect. The data obtained in vitro showed a potential use of propolis AF-08, a natural and nontoxic compound, in the prevention against the adverse effect of ionizing radiation, at the doses and concentrations here analyzed.

Nestas últimas décadas, investigações sobre compostos naturais, efetivos, não tóxicos, com potencial radioprotetor vêm despertando um grande interesse em consonância com a utilização crescente de vários tipos de radiação ionizante nas mais diversas finalidades. Entre eles a própolis uma resina coletada pelas abelhas (Apis mellifera), vem sendo apontada como promissora por apresentar uma série de características biológicas vantajosas, por exemplo, anti-inflamatória, antimicrobiana, antitumoral, imunomoduladora, antioxidante e também scavenger de radicais livres. O presente estudo teve como objetivo principal, averiguar efeito da própolis brasileira procedente de Rio Grande do Sul (AF 08) em células de ovário de hamster Chinês (CHO-K1) e em células tumorais de próstata (PC3), irradiadas com 60Co. Para tanto, foram utilizados três principais parâmetros interligados entre si: indução de micronúcleo, viabilidade celular e morte clonogênica. A escolha destes parâmetros se justifica pelo seu significado biológico, além do fato de serem prontamente observáveis e mensuráveis em células irradiadas. Os dados citogenéticos obtidos, mostraram um efeito radioprotetor da própolis (5 - 100 μg/ml) na indução de dano ao DNA em ambas as linhagens celulares, irradiadas com doses de 1 - 4 Gy. No entanto, o ensaio de citotoxicidade mostrou um efeito antiproliferativo pronunciado da própolis (50 - 400 μg/ml) em células PC3 irradiadas com 5 Gy. As curvas de sobrevida obtidas foram ajustadas satisfatoriamente pelo modelo linear-quadrático, cujo componente foi mais alto em células CHO-K1. Quanto à capacidade clonogênica, as células PC3 mostraram-se mais radiossensíveis que as células CHO-K1 nas doses mais altas da curva de sobrevida. A própolis, nas concentrações de 30 - 100 μg/ml, não influenciou no potencial clonogênico das células PC3, visto que, as curvas de sobrevida associadas ou não com a própolis, mostraram perfis similares, ao passo que o tratamento combinado em células CHO-K1 exibiu um efeito estimulador da proliferação. Os dados obtidos in vitro mostraram um potencial uso da própolis AF-08, como uma substância natural e não tóxica, na prevenção contra os efeitos danosos da radiação ionizante, nas doses e nas concentrações analisadas. / In the last decades, it has been given a great interest to investigations concerning natural, effective, nontoxic compounds with radioprotective potential together with the increasing utilization of different types of ionizing radiation for various applications. Among them propolis, a resinous compound produced by honeybees (Apis mellifera), has been considered quite promising, since it presents several advantageous biological characteristics, i. e., anti-inflammatory, antimicrobial, anticarcinogenic, antioxidant and also free radical scavenging action. The purpose of the present study was to evaluate the effect of Brazilian propolis, collected in the State of Rio Grande do Sul, on Chinese hamster ovary (CHO-K1) and human prostate cancer (PC3) cells, irradiated with 60Co radiation. For this purpose, three interlinked parameters were analyzed: micronucleus induction, cell viability and clonogenic death. The choice of these parameters was justified by their biological significance, in addition to the fact that they are readily observable and measurable in irradiated cells. The cytogenetic data obtained showed a radioprotective effect of propolis (5-100 μg/ml) in the induction of DNA damage for both cell lines, irradiated with doses of 1 - 4 Gy. The cytotoxicity assay, however, showed a prominent antiproliferative effect of propolis (50 - 400 μg/ml) in PC3 cells irradiated with 5 Gy. The survival curves obtained were adequately fitted by a linear-quadratic model, where the coefficient was higher in CHO-K1 cells. Concerning the clonogenic capacity, PC3 cells were more radiosensitive than CHO-K1 cells at the higher doses of the survival curve. Propolis at the concentrations of 30 - 100 μg/ml, did not influence the clonogenic potential of PC3 cells, since the survival curves, associated or not with propolis, were found similar, although the combined treatment in CHO-K1 cells exhibited a stimulating proliferative effect. The data obtained in vitro showed a potential use of propolis AF-08, a natural and nontoxic compound, in the prevention against the adverse effect of ionizing radiation, at the doses and concentrations here analyzed.