Methods for construction and analysis of computational models in systems biology : applications to the modelling of the heat shock response and the self-assembly of intermediate filaments

Systems biology is a new, emerging and rapidly developing, multidisciplinary research field that aims to study biochemical and biological systems from a holistic perspective, with the goal of providing a comprehensive, system- level understanding of cellular behaviour. In this way, it addresses one of the greatest challenges faced by contemporary biology, which is to compre- hend the function of complex biological systems. Systems biology combines various methods that originate from scientific disciplines such as molecu- lar biology, chemistry, engineering sciences, mathematics, computer science and systems theory. Systems biology, unlike “traditional” biology, focuses on high-level concepts such as: network, component, robustness, efficiency, control, regulation, hierarchical design, synchronization, concurrency, and many others. The very terminology of systems biology is “foreign” to “tra- ditional” biology, marks its drastic shift in the research paradigm and it indicates close linkage of systems biology to computer science. One of the basic tools utilized in systems biology is the mathematical modelling of life processes tightly linked to experimental practice. The stud- ies contained in this thesis revolve around a number of challenges commonly encountered in the computational modelling in systems biology. The re- search comprises of the development and application of a broad range of methods originating in the fields of computer science and mathematics for construction and analysis of computational models in systems biology. In particular, the performed research is setup in the context of two biolog- ical phenomena chosen as modelling case studies: 1) the eukaryotic heat shock response and 2) the in vitro self-assembly of intermediate filaments, one of the main constituents of the cytoskeleton. The range of presented approaches spans from heuristic, through numerical and statistical to ana- lytical methods applied in the effort to formally describe and analyse the two biological processes. We notice however, that although applied to cer- tain case studies, the presented methods are not limited to them and can be utilized in the analysis of other biological mechanisms as well as com- plex systems in general. The full range of developed and applied modelling techniques as well as model analysis methodologies constitutes a rich mod- elling framework. Moreover, the presentation of the developed methods, their application to the two case studies and the discussions concerning their potentials and limitations point to the difficulties and challenges one encounters in computational modelling of biological systems. The problems of model identifiability, model comparison, model refinement, model inte- gration and extension, choice of the proper modelling framework and level of abstraction, or the choice of the proper scope of the model run through this thesis.

Metabolite and light regulation of metabolism in plants: lessons from the study of a single biochemical pathway

We are using molecular, biochemical, and genetic approaches to study the structural and regulatory genes controlling the assimilation of inorganic nitrogen into the amino acids glutamine, glutamate, aspartate and asparagine. These amino acids serve as the principal nitrogen-transport amino acids in most crop and higher plants including Arabidopsis thaliana. We have begun to investigate the regulatory mechanisms controlling nitrogen assimilation into these amino acids in plants using molecular and genetic approaches in Arabidopsis. The synthesis of the amide amino acids glutamine and asparagine is subject to tight regulation in response to environmental factors such as light and to metabolic factors such as sucrose and amino acids. For instance, light induces the expression of glutamine synthetase (GLN2) and represses expression of asparagine synthetase (ASN1) genes. This reciprocal regulation of GLN2 and ASN1 genes by light is reflected at the level of transcription and at the level of glutamine and asparagine biosynthesis. Moreover, we have shown that the regulation of these genes is also reciprocally controlled by both organic nitrogen and carbon metabolites. We have recently used a reverse genetic approach to study putative components of such metabolic sensing mechanisms in plants that may be conserved in evolution. These components include an Arabidopsis homolog for a glutamate receptor gene originally found in animal systems and a plant PII gene, which is a homolog of a component of the bacterial Ntr system. Based on our observations on the biology of both structural and regulatory genes of the nitrogen assimilatory pathway, we have developed a model for metabolic control of the genes involved in the nitrogen assimilatory pathway in plants.

Biochemical changes and color properties of fresh-cut green bean (Phaseolus vulgaris L. cv.gina) treated with calcium chloride during storage

Calcium chloride is widely used in industries as a firming agent, and also to extend shelf-life of vegetables. The aim of this study was to determine, the effect of different doses of calcium chloride on biochemical and color properties of fresh-cut green bean. Fresh-cut green beans were dipped for 90 seconds in 0.5%, 1%, 2% and 3% solution of calcium chloride at 25°C. The fresh-cut green bean samples were packaged in polystyrene foam dishes, wrapped with stretch film and stored in a cold room at 5±1°C temperature and 85-90% RH. Calcium chloride treatments did not retain the green color of samples. Whiteness index, browning index and total color difference (ΔE) values of CaCl2 treated samples were high. Saturation index and hue angle were low compared to the control, especially at higher doses of CaCl2. Polyphenol oxidase (PPO) enzyme activity in samples treated with CaCl2 at 3% doses, was low at the 7th days of storage than with other treatments. Fructose and sucrose content of samples increased in all treatment groups whereas glucose level decreased during the first 4th days of storage.

Actinomycete Isolates from Arabian Sea and Bay of Bengal: Biochemical, Molecular and Functional Characterization

The thesis is comprised of seven chapters. Chapter 1 gives a general introduction to marine actinomycetes; Chapter 2 gives an account on the morphological, biochemical and physiological characterization of marine actinomycetes. Comprehensive description of molecular identification and phylogenetic analysis of actinomycetes is dealt with in Chapter 3. The antimicrobial property with special reference to antivibrio activity is described in Chapter 4. Chapter 5 explores the melanin production ability of marine actinomycetes, characterization of melanin and evaluation of its bioactivity. Chapter 6 illustrates the study on chitinolytic Streptomyces as antifungal and insecticidal agents. Summary and Conclusion of the study is presented in Chapter 7, followed by References and Appendices.The present study provides an insight into the various actinomycetes occurring in the sediments of Arabian Sea and Bay of Bengal. Streptomyces was found to be the dominant group followed by Nocardiopsis. Eventhough generic level identification is possible by traditional phenotypic methods, species level identification necessitate a polyphasic approach including both phenotypic and genotypic characterization. Antibiotic production coupled with biogranulation property helped in the effective utilization of the actinomycetes for the control of vibrios. Melanin from Streptomyces bikiniensis was proved to be a promising antioxidant and photoprotectant. Marine actinomycetes were found to be a good source of hydrolytic enzymes and the chitinolytic isolates could be explored as biocontrol agents in terms of antifungal and insecticidal property. The present study explored the potential of marine actinomycetes especially Streptomycetes as a promising source of bioactive molecules for application in aquaculture and pharmaceutical industry.

Understanding safety and production risks in rail engineering planning and protection

Much of the published human factors work on risk is to do with safety and within this is concerned with prediction and analysis of human error and with human reliability assessment. Less has been published on human factors contributions to understanding and managing project, business, engineering and other forms of risk and still less jointly assessing risk to do with broad issues of ‘safety’ and broad issues of ‘production’ or ‘performance’. This paper contains a general commentary on human factors and assessment of risk of various kinds, in the context of the aims of ergonomics and concerns about being too risk averse. The paper then describes a specific project, in rail engineering, where the notion of a human factors case has been employed to analyse engineering functions and related human factors issues. A human factors issues register for potential system disturbances has been developed, prior to a human factors risk assessment, which jointly covers safety and production (engineering delivery) concerns. The paper concludes with a commentary on the potential relevance of a resilience engineering perspective to understanding rail engineering systems risk. Design, planning and management of complex systems will increasingly have to address the issue of making trade-offs between safety and production, and ergonomics should be central to this. The paper addresses the relevant issues and does so in an under-published domain – rail systems engineering work.

Microbial and biochemical soil quality indicators and their potential for differentiating areas under contrasting agricultural management regimes

The aim of this study was to examine interrelationships between functional biochemical and microbial indicators of soil quality, and their suitability to differentiate areas under contrasting agricultural management regimes. The study included five 0.8 ha areas on a sandy-loam soil which had received contrasting fertility and cropping regimes over a 5 year period. These were organically managed vegetable, vegetable -cereal and arable rotations, an organically managed grass clover ley, and a conventional cereal rotation. The organic areas had been converted from conventional cereal production 5 years prior to the start of the study. All of the biochemical analyses, including light fraction organic matter (LFOM) C and N, labile organic N (LON), dissolved organic N and water-soluble carbohydrates showed significant differences between the areas, although the nature of the relationships between the areas varied between the different parameters, and were not related to differences in total soil organic matter content. The clearest differences were seen in LFOM C and N and LON, which were higher in the organic arable area relative to the other areas. In the case of the biological parameters, there were differences between the areas for biomass-N, ATP, chitin content, and the ratios of ATP: biomass and basal respiration: biomass. For these parameters, the precise relationships between the areas varied. However, relative to the conventionally managed area, areas under organic management generally had lower biomass-N and higher ATP contents. Arbuscular mycorrhizal fungus colonization potential was extremely low in the conventional area relative to the organic areas. Further, metabolic diversity and microbial community level physiological profiles, determined by analysis of microbial community metabolism using Biolog GN plates and the activities of eight key nutrient cycling enzymes, grouped the organic areas together, but separated them from the conventional area. We conclude that microbial parameters are more effective and consistent indicators of management induced changes to soil quality than biochemical parameters, and that a variety of biochemical and microbial analyses should be used when considering the impact of management on soil quality. (C) 2004 Elsevier Ltd. All rights reserved.

A possible reconceptualization of food engineering discipline

Food industry is critical to any nation’s health and well-being; it is also critical to the economic health of a nation, since it can typically constitute over a fifth of the nation’s manufacturing GDP. Food Engineering is a discipline that ought to be at the heart of the food industry. Unfortunately, this discipline is not playing its rightful role today: engineering has been relegated to play the role of a service provider to the food industry, instead of it being a strategic driver for the very growth of the industry. This paper hypothesises that food engineering discipline, today, seems to be continuing the way it was in the last century, and has not risen to the challenges that it really faces. This paper therefore categorises the challenges as those being posed by: 1. Business dynamics, 2. Market forces, 3. Manufacturing environment and 4. Environmental Considerations, and finds the current scope and subject-knowledge competencies of food engineering to be inadequate in meeting these challenges. The paper identifies: a) health, b) environment and c) security as the three key drivers of the discipline, and proposes a new definition of food engineering. This definition requires food engineering to have a broader science base which includes biophysical, biochemical and health sciences, in addition to engineering sciences. This definition, in turn, leads to the discipline acquiring a new set of subject-knowledge competencies that is fit-for-purpose for this day and age, and hopefully for the foreseeable future. The possibility of this approach leading to the development of a higher education program in food engineering is demonstrated by adopting a theme based curriculum development with five core themes, supplemented by appropriate enabling and knowledge integrating courses. At the heart of this theme based approach is an attempt to combine engineering of process and product in a purposeful way, termed here as Food Product Realisation Engineering. Finally, the paper also recommends future development of two possible niche specialisation programs in Nutrition and Functional Food Engineering and Gastronomic Engineering. It is hoped that this reconceptualization of the discipline will not only make it more purposeful for the food industry, but it will also make the subject more intellectually challenging and attract bright young minds to the discipline.

Seasonal influence on biochemical profile and serum protein electrophoresis for Boa constrictor amarali in captivity

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Diabetes induced immunological and biochemical changes in human colostrum

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Hematological and biochemical profiles and histopathological evaluation of experimental intoxication by sodium fluoroacetate in cats

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

MORPHOMETRIC AND BIOCHEMICAL EVALUATION OF RAT PROSTATE AND SEMINAL-VESICLE FOLLOWING CHEMICAL SYMPATHECTOMY WITH GUANETHIDINE

Selective chemical sympathectomy of the internal genital organs of adult male rats was undertaken by chronic treatment with low doses of guanethidine. Biochemical and morphometric methods revealed that removal of sympathetic innervation prevents fructose secretion in the prostate and seminal vesicle, in addition to promoting reduced efficiency of delivery by the latter.

Perioperative administration of vedaprofen, tramadol or their combination does not interfere with platelet aggregation, bleeding time and biochemical variables in cats

A randomized double blind and placebo controlled design was used to investigate the hemostatic, biochemical, gastrointestinal and behavioral effects of pre- and postoperative administration of vedaprofen 0.5 mg/kg PO (V), tramadol 2 mg/kg SC (T), their association (VT) or placebo (P) in 40 adult female cats (3.0 +/- 0.32 kg; 1.8 +/- 0.7 years) distributed in groups of 10. Platelet aggregation and bleeding time were measured before and 52 11 after ovariohysterectomy. Serum urea, creatinine, alanine aminotransferase, alkaline phosphatase and gamma-glutamyl transferase concentrations were measured before and 7 days postoperatively. The occurrence of vomiting, frequency and consistency of feces, and behavior were observed for 7 days postoperatively. Morphine (0.5 mg/kg, IM) was used as rescue analgesic. Laboratory variables did not change. Vomiting was observed only after morphine administration. Mild euphoria was observed in T and VT. The perioperative use of vedaprofen and/or tramadol did not modify the hemostatic, biochemical and gastrointestinal function in cats. (C) 2009 ESFM and AAFP. published by Elsevier Ltd. All rights reserved.

Evaluations hematological and biochemical by the use of sodium diclofenac, meloxicam and firocoxib in rats

This work has evaluated the hematological and biochemical profile by the use of sodium diclofenac, meloxicam and firocoxib in Wistar rats. The rats were distributed in groups: G1 (control), G2 (diclofenac sodium: 15 mg/kg), G3 (meloxicam: 2.0 mg/ kg), G4 (meloxicam: 10.0 mg/ kg), G5 (firocoxib: 5.0 mg/ kg) e G6 (firocoxib: 25.0 mg/ kg). The drugs were administered intragastrically (gavage) once a day, during five days and evaluated in three moments: M1 (48 hours after the beginning of the treatment), M2 (96 hours after the beginning of the treatment) and M3 (72 hours after the ending of the treatment). In each moment of each group, five to seven animals were evaluated and laboratory exams were performed. There were no significant changes observed in the biochemical and hematological parameters by the use of meloxicam and firocoxib. One of the effects of the sodium diclofenac was eritrogram variation as hematocrit, erythrocytes, hemoglobin decrease during the treatment. In addition, the platelets and total white blood cells counts did not change except for basophil. There was no changes in AST, ALP, GGT, urea, creatinine, sodium, potassium values. However, the values of protein, globulin and albumin decreased. It was concluded that diclofenac sodium does not provide large variations in the hemogram and biochemical profile than the meloxicam and firocoxib do not provide delletery effects in laboratories tests.

Semen parameters and seminal plasma protein and biochemical profiles of dogs with benign prostatic hyperplasia after botulinum toxin type A intraprostatic injection

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)