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Full-Text Articles in Physical Sciences and Mathematics
Modeling Disorder In Proteins Yields Insights Into The Evolution Of Stability And Function, Jonathan Huihui
Modeling Disorder In Proteins Yields Insights Into The Evolution Of Stability And Function, Jonathan Huihui
Electronic Theses and Dissertations
The central dogma of molecular biology dictates that a DNA sequence codes for an RNA sequence, which in turn codes for a sequence of amino acids that comprises a protein. Proteins are responsible with performing myriad functions within living organisms and most proteins require a folded structure in order to perform their function. The protein's structure is the direct link from sequence to function. This is known as the sequence - structure - function paradigm. However, this does not mean that the unfolded state is unimportant. In order to properly model the stability of the folded state, one needs to …
Examining Artifacts Of The Watershed Segmentation, Emily Jo Armitage
Examining Artifacts Of The Watershed Segmentation, Emily Jo Armitage
Electronic Theses and Dissertations
The watershed segmentation is an algorithm used to systematically track cell intercalary behaviors during germ band extension of the Drosophila embryo. Neighboring cells share a contracting vertical interface, called a T1, which continues contracting to a single point, a T2, and extending in the horizontal direction to create what is called a T3 interface (Fig. 1). Additionally, higher order vertices called rosettes occur when five or more cells meet at a common vertex. Simulated T2 events demonstrate that cell angle and not noise level in the image contributes to the incorrect detection of artifactual T1s in more acute angled cells …
Quantification Of Dynamic Epithelial Sheet Architecture In Botryllus Schlosseri Using 2-D & 3-D Image Analysis, Roopa Madhu
Quantification Of Dynamic Epithelial Sheet Architecture In Botryllus Schlosseri Using 2-D & 3-D Image Analysis, Roopa Madhu
Electronic Theses and Dissertations
Epithelial tubules form critical structures in various body tissues; how- ever, since they are difficult to access experimentally, their architecture and dynamics are not well understood. Here we examine the dynamic remodeling of epithelial tubes in vivo using a novel and uniquely accessible model system: the extracorporeal vasculature of Botryllus schlosseri (sea squirt). In Botryllus, massive retraction of blood vessels can be triggered without loss of barrier function, through (i) disrupting collagen crosslinking in the basement membrane using β-aminopropionitrile (BAPN); or (ii) disrupting the integrin pathway through inhibition of focal adhesion kinase (FAK). We performed stereographic projections of 3-dimensional …
Quantitative Aspects Of Interface Remodeling During Germband Extension, Timothy E. Vanderleest
Quantitative Aspects Of Interface Remodeling During Germband Extension, Timothy E. Vanderleest
Electronic Theses and Dissertations
Oriented cell intercalation is an essential developmental process that shapes tissue morphologies through the directional insertion of cells between their neighbors. Intercalary behaviors in the early Drosophila embryo occur through a remodeling of cell topologies, with cells contracting shared AP interfaces to a single point, followed by newly juxtaposed DV cells constructing horizontally-oriented interfaces between them. Previous research has focused on properties of cell-cell interfaces, and led to a model in which actomyosin networks mediate higher line tensions at AP interfaces to direct contraction. However, the contribution of tricellular vertices to tissue elongation remains unclear. This study shows that cell …
Learning From Disorder And Noise In Physical Biology, Taylor Emil Firman
Learning From Disorder And Noise In Physical Biology, Taylor Emil Firman
Electronic Theses and Dissertations
Stochasticity, disorder, and noise play crucial roles in the functioning of many biological systems over many different length scales. On the molecular scale, most proteins are envisioned as pristinely folded structures, but intrinsically disordered proteins (IDPs) have no such folded state and still serve distinct purposes within the cell. At the scale of gene regulation, realistic in vivo conditions produce stochastic fluctuations in gene expression that can lead to advantageous bet-hedging strategies, but can be difficult to characterize using a deterministic framework. Even at the organismal scale, germband extension (GBE) in Drosophila melanogaster embryos systematically elongates the epithelial tissue using …
Molecular Mechanisms Of Protein Thermal Stability, Lucas Sawle
Molecular Mechanisms Of Protein Thermal Stability, Lucas Sawle
Electronic Theses and Dissertations
Organisms that thrive under extreme conditions, such as high salt concentration, low pH, or high temperature, provide an opportunity to investigate the molecular and cellular strategies these organisms have adapted to survive in their harsh environments. Thermophilic proteins, those extracted from organisms that live at high temperature, maintain their structure and function at much higher temperatures compared to their mesophilic counterparts, found in organisms that live near room temperature. Thermophilic and mesophilic homolog protein pairs have identical functionality, and show a high degree of structural and sequential similarity, but differ significantly in their response to high temperature. Addressing the principles …