Academic literature on the topic '060114 Systems Biology'

Here, we review the role of control theory in modeling neural control systems through a top-down analysis approach. Specifically, we examine the role of the brain and central nervous system as the controller in the organism, connected to but isolated from the rest of the animal through insulated interfaces. Though biological and engineering control systems operate on similar principles, they differ in several critical features, which makes drawing inspiration from biology for engineering controllers challenging but worthwhile. We also outline a procedure that the control theorist can use to draw inspiration from the biological controller: starting from the intact, behaving animal; designing experiments to deconstruct and model hierarchies of feedback; modifying feedback topologies; perturbing inputs and plant dynamics; using the resultant outputs to perform system identification; and tuning and validating the resultant control-theoretic model using specially engineered robophysical models.

ABSTRACTInteraction of microbes with their environment depends on features of the dynamic microbial surface throughout cell growth and division. Surface modifications, whether used to acquire nutrients, defend against other microbes, or resist the pressures of a host immune system, facilitate adaptation to unique surroundings. The release of bioactive membrane vesicles (MVs) from the cell surface is conserved across microbial life, in bacteria, archaea, fungi, and parasites. MV production occurs not onlyin vitrobut alsoin vivoduring infection, underscoring the influence of these surface organelles in microbial physiology and pathogenesis through delivery of enzymes, toxins, communication signals, and antigens recognized by the innate and adaptive immune systems. Derived from a variety of organisms that span kingdoms of life and called by several names (membrane vesicles, outer membrane vesicles [OMVs], exosomes, shedding microvesicles, etc.), the conserved functions and mechanistic strategies of MV release are similar, including the use of ESCRT proteins and ESCRT protein homologues to facilitate these processes in archaea and eukaryotic microbes. Although forms of MV release by different organisms share similar visual, mechanistic, and functional features, there has been little comparison across microbial life. This underappreciated conservation of vesicle release, and the resulting functional impact throughout the tree of life, explored in this review, stresses the importance of vesicle-mediated processes throughout biology.

AbstractUbiquitously acting chromatin opening elements (UCOEs) consist of methylation-free CpG islands encompassing dual divergently transcribed promoters of housekeeping genes that have been shown to confer resistance to transcriptional silencing and to produce consistent and stable transgene expression in tissue culture systems. To develop improved strategies for hematopoietic cell gene therapy, we have assessed the potential of the novel human HNRPA2B1-CBX3 UCOE (A2UCOE) within the context of a self-inactivating (SIN) lentiviral vector. Unlike viral promoters, the enhancer-less A2UCOE gave rise to populations of cells that expressed a reporter transgene at a highly reproducible level. The efficiency of expression per vector genome was also markedly increased in vivo compared with vectors incorporating either spleen focus-forming virus (SFFV) or cytomegalovirus (CMV) promoters, suggesting a relative resistance to silencing. Furthermore, an A2UCOE-IL2RG vector fully restored the IL-2 signaling pathway within IL2RG-deficient human cells in vitro and successfully rescued the X-linked severe combined immunodeficiency (SCID-X1) phenotype in a mouse model of this disease. These data indicate that the A2UCOE displays highly reliable transcriptional activity within a lentiviral vector, largely overcoming insertion-site position effects and giving rise to therapeutically relevant levels of gene expression. These properties are achieved in the absence of classic enhancer activity and therefore may confer a high safety profile.

The absolute clarity of the lens of the eye is vital in the visual system. The unique structural and physiological properties of the lens are tightly integrated with highly ordered protein content to allow the lens to remain transparent. Consequently, any alteration or disturbance of these highly ordered proteins can affect the optical properties of the lens. In humans, cataracts are the major cause of blindness, yet the exact aetiology of cataract formation (cataractogenesis) is not fully understood. The purpose of the current research was to investigate whether deregulation of the Ca²⁺-dependent enzyme, calpains, following changes in lens Ca²⁺ homeostasis, is a key mechanism leading to undesired cleavage of a number of proteins that are linked with maintaining lens transparency and contributing to cataractogenesis. An ovine lens culture (in vitro) system and the heritable ovine cataract (in vivo) model were used to test the research hypothesis. The Ca²⁺ ionophore, ionomycin, was used to induce a Ca²⁺ overload and in vitro opacification during lens culture. Opacity in the lens was graded by a computer image analysis program. Protein profile (SDS-PAGE, 2-DE and Western detection), calpain activity (casein zymography), lens structure (microscopic view) and cytotoxicity level (LDH leakage assay) were analysed in Ca²⁺-induced opaque lenses. The involvement of calpain during opacification was further examined by applying synthetic exogenous calpain inhibitors to the in vitro system. Two novel exogenous calpain inhibitors were also assessed for their therapeutic potential in preventing the progression of cataracts in the in vivo cataract model by topical administration of the inhibitor direct to the sheep's eye over a 11 week period. HPLC was used to detect the penetration of these compounds into ocular tissues. Sustained Ca²⁺ influx into cultured lenses caused dense opacification. The opacity was characterised by formation of a turbid fraction and cell death in the outer cortex of the ovine lens. There was increased calpain autolysis associated with the progress of opacification, indicating increased calpain activity. Major degradation of the cytoskeletal proteins, spectrin and vimentin, was observed whilst there was limited degradation of the lens structural soluble proteins, crystallins, in response to a Ca²⁺ flux. Lens proteins were protected from degradation by adding synthetic calpain inhibitors to the culture medium. Topical administration of novel anti-calpain molecules failed to retard the progression of cataractogenesis in the ovine inherited cataract model. Further investigation of drug penetration showed that efficacy of inhibitory compounds was limited by permeability of these molecules across the cornea and the ability of the molecules to reach and penetrate into the lens. The ovine lens Ca²⁺-induced opacification (OLCO) model in this thesis has provided a model to understand the role of Ca²⁺ homeostasis in lens transparency. With sustained intracellular Ca²⁺ level, the degradation of cytoskeletal elements is highly correlated with calpain activity. Cataractogenesis is the pathological response to the loss of lens Ca²⁺ homeostasis in this model. The current results support the hypothesis that the deregulation of calpain activity is a trigger for a series of cascading events, leading to death of the cells in the lens.

The prevalence and incidence of obesity and related co-morbidities such as insulin resistance and type two diabetes mellitus (T2DM) are rapidly increasing world-wide. These health burdens negatively impact individuals, families, the community and the government, for a multitude of reasons. The search for suitable therapeutic targets for obesity, in combination with a healthy diet and increased physical activity is a strategy for weight management and associated co-morbidities such as T2DM. The endocannabinoid system is a lipid derived signalling system that is modulated by different dietary fatty acids and has a role in regulating energy homeostasis. Modulation of cannabinoid receptor 1 (CB1) reduces whole body adiposity and increases oxidative capacity within the skeletal muscle. The skeletal muscle is a major contributor to whole body energy metabolism through the oxidation of fatty acids, insulin signalling and glucose uptake, therefore understanding the impact that endocannabinoid pharmaceutics have on this tissue is essential. Putative endocannabinoid receptors including G Protein- Coupled Receptor (GPR55) and G Protein-Coupled Receptor 18 (GPR18) may potentially be beneficial pharmaceutical targets for obesity and associated co-morbidities. GPR55 expression is upregulated in visceral adipose tissue in obesity and T2DM. Surprisingly GPR55 knockout mice have increased adiposity and reduced physical activity. While GPR18 has been shown to be expressed in adipose tissue, its role in obesity is unknown. Furthermore the role that atypical cannabinoid compounds, O-1602 or O-1918 (which have/ are hypothesised to have affinities for these receptors and therefore modulate these putative cannabinoid receptors) have in obesity and skeletal muscle homeostasis, following chronic treatment has yet to be determined. The dietary intake of specific fatty acids can also alter circulating endocannabinoid concentrations depending on the type of fatty acid consumed. The effect that different dietary fatty acids have on the putative cannabinoid receptors GPR55 and GPR18 and whole body energy homeostasis in obesity is unknown. Therefore the overall focus for this thesis was to determine the role that atypical cannabinoids have on homeostatic skeletal muscle signalling and whole body energy metabolism in obesity. In addition to this, the effect that different dietary fatty acids have in obesity and whole body energy metabolism were also determined, which may partially be attributed to GPR55 and GPR18 signalling.