Fuzziness in Protein Interactions: a Historical Perspective

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Determining the population structures of cubozoan jellyfishes with biophysical modelling

Jodie Schlaefer studied box jellyfish. She found that self-contained stocks were separated by only tens of kilometers, challenging the paradigm that jellyfish populations are well mixed over large distances. The occurrence of box jellyfish is unpredictable because their abundance is influenced by conditions at the small spatial scale of stocks

The role of transcription factor dFoxO in regulating tracheal terminal cell plasticity of the fruit fly Drosophila melanogaster

Plasticity is a fundamental biological process that ensures that individuals' morphology, behavior, and physiology adapt to match their environment. Understanding the mechanisms that regulate trait plasticity is important because knowledge of how phenotypic plasticity is regulated has significant consequences for the study of diseases that result from changes in plasticity. Reduced O2 levels—or hypoxia, can lead to irreversible cellular damage in organisms, and therefore, organisms have evolved adaptive responses to compensate for the lack of O2. Drosophila melanogaster is highly resistant to oxygen deficiency and its respiratory (tracheal) system has features in common with the vertebrate vascular system. The tracheal terminal cells (TTCs) are plastic in nature, and they respond to hypoxia and different dietary conditions by sprouting out new branches, a process that can be compared to angiogenesis in mammals. Here we elucidate the role of the transcription factor, Forkhead box protein O(dFoxO) in regulating TTC plasticity. Deregulation of FoxO activity in the TTCs achieved by deficiency and overexpression of FoxO led to the loss of plasticity of the terminal cells. However, partial reduction of expression of FoxO via RNAi led to hyperbranching phenotype, suggesting that FoxO need to be expressed at a physiologically relevant level to maintain plasticity of the terminal cells. Suppressing JNK activity in the terminal cells did not affect the plasticity of the terminal cells, suggesting that the FoxO regulation in the terminal cells is independent of JNK activity. On the other hand, the induced release of Insulin from the insulin producing cells positively regulated the terminal branching, implying dFoxO might be regulated via IIS signaling

Semidefinite programming and linear equations vs. homomorphism problems

We introduce a relaxation for homomorphism problems that combines semidefinite programming with linear Diophantine equations, and propose a framework for the analysis of its power based on the spectral theory of association schemes. We use this framework to establish an unconditional lower bound against the semidefinite programming + linear equations model, by showing that the relaxation does not solve the approximate graph homomorphism problem and thus, in particular, the approximate graph colouring problem

RNA interference in Lepidoptera: an overview of successful and unsuccessful studies and implications for experimental design

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Glycosylation in Tribolium castaneum : composition, physiological significance and exploitation for pest control

The majority of all the proteins undergoes glycosylation. This post-translational modification of proteins is involved in numerous biological processes and an erroneous glycosylation is often lethal. Following this logic interference with insect glycosylation is likely to be an effective way to control insect pests. Unfortunately, most of the knowledge on insect glycobiology comes from the research on Drosophila which lacks relevance in the context of pest insect control. This work focused on the discovery of the physiological importance of N-glycosylation in the red flour beetle, Tribolium castaneum, which is a pest and a model insect. Additionally, this PhD thesis investigates the use of glycan-binding proteins (lectins) and the disruption of N-glycosylation as control strategies against pest beetles. Lectins have high insecticidal activity against insect cells but when fed to the red flour beetle their efficiency was greatly impaired by susceptibility to proteolysis, low efficiency of passing through the peritrophic matrix and inefficient transport to the hemolymph. These factors restricting the insecticidal properties of lectins could be generalized to virtually all insecticidal proteins. Therefore these data can be used for a more rational selection of novel insecticidal toxins and enhancement of the activity of the currently used ones. By studying glycan composition, gene expression analysis and functional genomics it was determined that N-glycosylation is involved in insect metamorphosis. Regulated production of N-glycans was crucial for larval growth, progression of the life stages and development of adult appendages. Finally, disruption of the early stages of the N-glycosylation pathway appears to be promising strategy for future control of insect pests