Viscoelastic finite element modeling of deformation transients of single cells

The objective of this thesis is to use computational modeling to study the deformation of single cells subjected to mechanical stresses. Our motivation stems from experimental observations that cells are subjected to mechanical stresses arising from their environment throughout their lifetime, and that such stresses can regulate many important biological processes. While the exact mechanotransduction mechanisms involved are not well understood, quantitative models for cell deformation can yield important insights. In this thesis, we developed an axisymmetric finite element model to study the deformation of suspended fibroblasts in the optical stretcher and neutrophils in tapered micropipettes. The key feature of our model is the use of a viscoelastic constitutive equation whose parameters can be varied both spatially and temporally so as to mimic the experimentally-observed spatio-temporal heterogeneity of cellular material properties. Our model suggested that cellular remodeling, in the form of an increased cellular viscosity, occurred during optical stretching of fibroblasts. The increase would have to be approximately 20-fold to explain the experimental data for different loading time-scales. We also showed that cell size is a more important factor in determining the strain response of the optically-stretched fibroblasts compared to the thickness of the actin cortical region. This result can explain the higher optical deformability observed experimentally for malignant fibroblasts. In addition, our simulations showed that maximal stress propagates into the nuclear region for malignant fibroblasts whereas for normal fibroblasts, the maximal stress does not. Finally, results from modeling the tapered micropipette experiments also suggested that cellular remodeling, in the form of a decreased cellular elasticity and viscosity, occurred during the process of neutrophil aspiration. Taken together, our simulation results on optically-stretched fibroblasts and aspirated neutrophils suggested that cells in general are able to sense mechanical stresses and respond by varying their material properties during deformation

On the straight and narrow: how cultural beliefs about sex/gender manifest in college biology learning environments.

This dissertation focused on the ways that social beliefs about sex/gender and sexuality manifest in biology classrooms. Especially for health science students, classes include topics like sex, sexuality, sexual behaviors, or sex determination that forms the foundation of their understanding of human forms and behaviors. If the information they receive does not include the LGBTQIA+ community, their education will fail to adequately prepare them for the reality of healthcare practice where they will be expected to treat all patients with dignity and respect. There are three chapters in this dissertation. In chapter one, I asked what beliefs about and conceptions of sex/gender are present in undergraduate students. I found that students with more academic experience view sex/gender characteristics as occurring along a continuum rather than discrete traits and that health science students were more likely to conflate sex and gender along dichotomous male/female lines, with innate and essential characteristics defining these groups. This led me to analyze the ways that college-level nursing anatomy/physiology textbooks represent sex/gender and LGBTQIA+ populations. For chapter two, I conducted a qualitative content analysis of four common nursing textbooks and found that the books either excluded LGBTQIA+ healthcare needs and history or only mentioned LGBTQIA+ people in the context of disease or pathology, and they promoted social norms as scientifically validated. In an effort to counter these representations, I challenged the binary ‘two sex’ model using intersex case studies. Chapter three also assessed the phobias, attitudes, and cultural competence (ability to treat patients in a culturally sensitive manner) of biology students. I found that students still hold binary views of the sexes even after reading an intersex case study, and that case study had minimal impact on phobia, attitudes, or competence. However, there was evidence of a paradigm shift toward a sex model that sees the similarities between humans rather than the differences. Future directions should consider common misconceptions related to the ‘two sex’ model and how best to address these in biology curricula

Determine the parameters for photoelectric effect data using correlation and simple linear regression

Pearson's correlation coefficient, otherwise known as the product-moment correlation coefficient, a non-parametric process, is a very important concept in statistics, data science, and even in machine learning. It has gained tremendous acceptance in almost all fields and industries where data analysis is the business of the day. It helps to highlight the affinity between two variables whose behaviour might be entirely different, correlation coefficient is an indicator that shows whether such affinity is positive, negative, or none, when no linear relationship can be established between the variables. It is characterized by a numerical value that ranges between -1 and 1. These values serve as the indicators that determine the status of the relationship. In this research, we utilized the idea of correlation coefficient and simple linear regression on experimental data of photoelectric effects to determine the Planck constant, work function, and threshold frequency using MATLAB code

Structural insights into the production of 3-hydroxypropionic acid by aldehyde dehydrogenase from Azospirillum brasilense

3-Hydroxypropionic acid (3-HP) is an important platform chemical to be converted to acrylic acid and acrylamide. Aldehyde dehydrogenase (ALDH), an enzyme that catalyzes the reaction of 3-hydroxypropionaldehyde (3-HPA) to 3-HP, determines 3-HP production rate during the conversion of glycerol to 3-HP. To elucidate molecular mechanism of 3-HP production, we determined the first crystal structure of a 3-HP producing ALDH, alpha-ketoglutarate-semialdehyde dehydrogenase from Azospirillum basilensis (AbKGSADH), in its apo-form and in complex with NAD(+). Although showing an overall structure similar to other ALDHs, the AbKGSADH enzyme had an optimal substrate binding site for accepting 3-HPA as a substrate. Molecular docking simulation of 3-HPA into the AbKGSADH structure revealed that the residues Asn159, Gln160 and Arg163 stabilize the aldehyde-and the hydroxyl-groups of 3-HPA through hydrogen bonds, and several hydrophobic residues, such as Phe156, Val286, Ile288, and Phe450, provide the optimal size and shape for 3-HPA binding. We also compared AbKGSADH with other reported 3-HP producing ALDHs for the crucial amino acid residues for enzyme catalysis and substrate binding, which provides structural implications on how these enzymes utilize 3-HPA as a substrate

Characterisation of a 3-hydroxypropionic acid-inducible system from Pseudomonas putida for orthogonal gene expression control in Escherichia coli and Cupriavidus necator

3-hydroxypropionic acid (3-HP) is an important platform chemical used as a precursor for production of added-value compounds such as acrylic acid. Metabolically engineered yeast, Escherichia coli, cyanobacteria and other microorganisms have been developed for the biosynthesis of 3-HP. Attempts to overproduce this compound in recombinant Pseudomonas denitrificans revealed that 3-HP is consumed by this microorganism using the catabolic enzymes encoded by genes hpdH, hbdH and mmsA. 3-HP-inducible systems controlling the expression of these genes have been predicted in proteobacteria and actinobacteria. In this study, we identify and characterise 3-HP-inducible promoters and their corresponding LysR-type transcriptional regulators from Pseudomonas putida KT2440. A newly-developed modular reporter system proved possible to demonstrate that PpMmsR/PmmsA and PpHpdR/PhpdH are orthogonal and highly inducible by 3-HP in E. coli (12.3- and 23.3-fold, respectively) and Cupriavidus necator (51.5- and 516.6-fold, respectively). Bioinformatics and mutagenesis analyses revealed a conserved 40-nucleotide sequence in the hpdH promoter, which plays a key role in HpdR-mediated transcription activation. We investigate the kinetics and dynamics of the PpHpdR/PhpdH switchable system in response to 3-HP and show that it is also induced by both enantiomers of 3-hydroxybutyrate. These findings pave the way for use of the 3-HP-inducible system in synthetic biology and biotechnology applications

Cross-reactive dengue human monoclonal antibody prevents severe pathologies and death from Zika virus infections

10.1172/jci.insight.92428JCI insight2