Biological and Chemical Physics Commons^™

Laser-Induced Breakdown Spectroscopy For Elemental Analysis In Bioarchaeology And Forensic Anthropology, Kelsi N. Kuehn

USF Tampa Graduate Theses and Dissertations

Within bioarchaeology and forensic anthropology, the current processes of differentiating between individual human skeletal remains are imprecise, costly, and inefficient. A novel analytical technique within anthropology, laser-induced breakdown spectroscopy (LIBS) can aid in the identification of human remains using rapid laser ablation occurring at the micro-scale, making the technique virtually non-destructive to the sample. Considering this, LIBS could offer a superior method for materials discrimination and human identification. This research sought to examine whether LIBS can be used to obtain elemental signatures within bones to distinguish individuals from one another in a rapid, non-destructive manner. Seven human skeletal donors and …

Similarities Between Insect Swarms And Isothermal Globular Clusters, Dan Gorbonos, Kasper Van Der Vaart, Michael Sinhuber, James G. Puckett, Andrew M. Reynolds, Nicholas T. Ouellette, Nir S. Gov

Physics and Astronomy Faculty Publications

Previous work has suggested that disordered swarms of flying insects can be well modeled as self-gravitating systems, as long as the “gravitational” interaction is adaptive. Motivated by this work, we compare the predictions of the classic, mean-field King model for isothermal globular clusters to observations of insect swarms. Detailed numerical simulations of regular and adaptive gravity allow us to expose the features of the swarms' density and velocity profiles that are due to long-range interactions and are captured by the King model phenomenology, and those that are due to adaptivity and short-range repulsion. Our results provide further support for adaptive …

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 …

Sensitivity Of Radical Sam Enzyme Mftc To Molecular Oxygen, Vishnu Govindarajan

Electronic Theses and Dissertations

MftC is a radical S-adenosyl L-methionine (SAM) enzyme that catalyzes the first step in the production of mycofactocin. It is a ribosomally synthesized post-translationally modified (RiPP) redox cofactor shown to be essential for the survival of bacteria in the Mycobacterium genus in the presence of cholesterol as a carbon source and for the sequestration of ethanol. MftC catalyzes the C – terminal decarboxylation of tyrosine and the subsequent cross-linking of tyrosine to the penultimate valine on the precursor peptide MftA. The product formed out of the reaction is processed into mycofactocin in downstream processes. The bacteria in the Mycobacterium tuberculosis …

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 …

Size And Density Of Upside-Down Jellyfish, Cassiopea Sp., And Their Impact On Benthic Fluxes In A Caribbean Lagoon, Chester B. Zarnoch, Noshin Hossain, Erika Fusco, Mary Alldred, Timothy J. Hoellein, Sophia Perdikaris

School of Global Integrative Studies: Faculty Publications

Anthropogenic disturbances may be increasing jellyfish populations globally. Epibenthic jellyfish are ideal organisms for studying this phenomenon due to their sessile lifestyle, broad geographic distribution, and prevalence in near-shore coastal environments. There are few studies, however, that have documented epibenthic jellyfish abundance and measured their impact on ecological processes in tropical ecosystems. In this study, the density and size of the upside-down jellyfish (Cassiopea spp.) were measured in Codrington Lagoon, Barbuda. A sediment core incubation study, with and without Cassiopea, also was performed to determine their impact on benthic oxygen and nutrient fluxes. Densities of Cassiopea were 24–168 …

Crystal Structure Of Thermus Thermophilus Methylenetetrahydrofolate Dehydrogenase And Determinants Of Thermostability, Fernando Maiello, Gloria Gallo, Camila Coelho, Fernanda Sucharski, Leon Hardy, Martin Würtele

USF St. Petersburg Campus Faculty Publications

The elucidation of mechanisms behind the thermostability of proteins is extremely important both from the theoretical and applied perspective. Here we report the crystal structure of methylenetetrahydrofolate dehydrogenase (MTHFD) from Thermus thermophilus HB8, a thermophilic model organism. Molecular dynamics trajectory analysis of this protein at different temperatures (303 K, 333 K and 363 K) was compared with homologous proteins from the less temperature resistant organism Thermoplasma acidophilum and the mesophilic organism Acinetobacter baumannii using several data reduction techniques like principal component analysis (PCA), residue interaction network (RIN) analysis and rotamer analysis. These methods enabled the determination of important residues for …

A Framework Of Multi-Dimensional And Multi-Scale Modeling With Applications, Zilong Li

Doctoral Dissertations

In this dissertation, a framework for multi-dimensional and multi-scale modeling is proposed. The essential idea is based on oriented space curves, which can be represented as a 3D slender object or 1D step parameters. SMILES and Masks provide functionalities that extend slender objects into branched and other objects. We treat the conversion between 1D, 2D, 3D, and 4D representations as data unification. A mathematical analysis of different methods applied to helices (a special type of space curves) is also provided. Computational implementation utilizes Model-ViewController design principles to integrate data unification with graphical visualizations to create a dashboard. Applications of multi-dimensional …

Magneto-Driven Gradients Of Diamagnetic Objects For Engineering Complex Tissues, Hannah M. Zlotnick, Andy T. Clark, Sarah E. Gullbrand, James L. Carey, Xuemei Cheng, Robert L. Mauck

Physics Faculty Research and Scholarship

Engineering complex tissues represents an extraordinary challenge and, to date, there have been few strategies developed that can easily recapitulate native‐like cell and biofactor gradients in 3D materials. This is true despite the fact that mimicry of these gradients may be essential for the functionality of engineered graft tissues. Here, a non‐traditional magnetics‐based approach is developed to predictably position naturally diamagnetic objects in 3D hydrogels. Rather than magnetizing the objects within the hydrogel, the magnetic susceptibility of the surrounding hydrogel precursor solution is enhanced. In this way, a range of diamagnetic objects (e.g., polystyrene beads, drug delivery microcapsules, and living …

A Vibrational Spectroscopic Based Approach For Diagnosing Babesia Bovis Infection, Anja Ruther, David Perezguaita, William Poole, Brian Cooke, Carlos Suarez, Philip Heraud, Bayden Wood

Articles

Babesia bovis parasites present a serious and significant health concern for the beef and dairy industries in many parts of the world. Difficulties associated with the current diagnostic techniques include they are prone to human error (microscopy) or expensive and time consuming (Polymerase Chain Reaction) to perform. Little is known about the biochemical changes in blood that are associated with Babesia infections. The discovery of new biomarkers will lead to improved diagnostic outcomes for the cattle industry. Vibrational spectroscopic technologies can record a chemical snapshot of the entire organism and the surrounding cell thereby providing a phenotype of the organism …

Application Of Optical Trapping To Obtain Single-Source Str Profiles From Forensically Relevant Body Fluid Mixtures With Modified Dna Analysis Workflow, Benjamin J. O'Brien

Master of Science in Forensic Science Directed Research Projects

Current methods of mixture separation in forensic DNA laboratories typically deconvolute the mixture after analysis using statistical analysis or probabilistic genotyping. To save time and effort of labs already backlogged, a method to separate mixtures on a cellular level before analysis needs to be developed. Optical trapping is a method that uses a focused 1064 nm laser to manipulate cells. Previous research has shown that approximately 50 spermatozoa or 15 leukocytes from a liquid sample are required to produce a full STR DNA profile. It was found that the number of spermatozoa required remains constant when the method of sample …

Consciousness As A Factor In Evolution, Kenneth A. Augustyn

Michigan Tech Publications, Part 1

What I call the mind began as a non-conscious robotic biochemical process control system in the very earliest forms of life. As life evolved, problems in control became more difficult and exceeded the computational capabilities of the organisms. Nature discovered a means of transcending computable physical processes resulting in non-computational subjective mental capabilities that, while still not conscious, had a degree of genuine autonomy from the physical world. These autonomous subjective wants and goals now affected the course of (but not the mechanism of) evolution. The integrated amalgam of robotic and transrobotic unconscious capabilities eventually gave rise to consciousness, which …

Effect Of Non-Thermal Atmospheric Pressure Plasma On Wound Bacteria And Cell Proliferation, Mohd Nasir Norhayati

Student Works (2020-2029)

Non-thermal plasma produced in the plasma jet at atmospheric pressure consists of many reactive species and free radicals. The use of the atmospheric plasma jet has been expanded from surface treatment on polymers and biomaterials to the application as plasma medicine. It has been studied as a tools for wound sterilizations, enhance wound healing, topical treatment of skin diseases caused by bacteria infection and cancer therapy in recent research. The current study aims to investigate the effect of plasma on chronic wound bacteria as a supplementary to wound management particularly for compromised patients. The common practice in wound management is …

Special Issue On The Third Workshop On Biological Mentality, Kenneth A. Augustyn

Michigan Tech Publications, Part 1

The Third Workshop on Biological Mentality was held from September 23, 2019 to March 2, 2020 as a series of twenty-one Monday online conferencing sessions, each consisting of a talk followed by a Q&A discussion. Like the two previous workshops [1, 2], the objective of this workshop was to seek a deeper level of understanding the physical foundations of biological mentality (whether conscious or nonconscious).

Development Of A Comsol Microdialysis Model, Towards Creation Of Microdialysis On A Chip With Improved Geometries And Recovery, Patrick Pysz

Graduate Theses and Dissertations

Microdialysis (µD) sampling is a diffusion-limited sampling method that has been widely used in different biomedical fields for greater than 35 years. Device calibration for in vivo studies is difficult for current non-steady state analytes of interest correlated with both inflammatory response and microbial signaling molecules (QS); which exist in low ng/mL to pg/mL with molecular weights over a wide range of 170 Da to 70 kDa. The primary performance metric, relative recovery (RR), relating the collected sample to the extracellular space concentration varies from 10% to 60% per analyte even under controlled bench-top conditions. Innovations in microdialysis device design …

Analog Implementation Of The Hodgkin-Huxley Model Neuron, Zachary D. Mobille, George H. Rutherford, Jordan Brandt-Trainer, Rosangela Follmann, Epaminondas Rosa

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Period Drift In A Neutrally Stable Stochastic Oscillator, Kevin Sanft

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Odx: A Fitness Tracker-Based Device For Continuous Bacterial Growth Monitoring, Venkata V.B. Yallapragada, Uday Gowda, David Wong, Liam O'Faolain, Mark Tangney, Ganga C.R. Devarapu

Cappa Publications

Continuous monitoring of bacterial growth in aqueous media is a crucial process in academic research as well as in the biotechnology industry. Bacterial growth is usually monitored by measuring the optical density of bacteria in liquid media, using benchtop spectrophotometers. Due to the large form factor of the existing spectrophotometers, they cannot be used for live monitoring of the bacteria inside bacterial incubation chambers. Additionally, the use of benchtop spectrometers for continuous monitoring requires multiple samplings and is labour intensive. To overcome these challenges, we have developed an optical density measuring device (ODX) by modifying a generic fitness tracker. The …

Effective Statistical Energy Function Based Protein Un/Structure Prediction, Avdesh Mishra

LSU New Orleans Theses and Dissertations

Proteins are an important component of living organisms, composed of one or more polypeptide chains, each containing hundreds or even thousands of amino acids of 20 standard types. The structure of a protein from the sequence determines crucial functions of proteins such as initiating metabolic reactions, DNA replication, cell signaling, and transporting molecules. In the past, proteins were considered to always have a well-defined stable shape (structured proteins), however, it has recently been shown that there exist intrinsically disordered proteins (IDPs), which lack a fixed or ordered 3D structure, have dynamic characteristics and therefore, exist in multiple states. Based on …

Impact Of Excitation-Inhibition Balance/Imbalance On Dynamics Of Cortical Neural Networks, Vidit Agrawal

Graduate Theses and Dissertations

The purpose of this research is to study the implications of Excitation/Inhibition balance and imbalance on the dynamics of ongoing (spontaneous) neural activity in the cerebral cortex region of the brain.

The first research work addresses the question that why among the continuum of Excitation-Inhibition balance configurations, particular configuration should be favored? We calculate the entropy of neural network dynamics by studying an analytically tractable network of binary neurons. Our main result from this work is that the entropy maximizes at regime which is neither excitation-dominant nor inhibition-dominant but at the boundary of both. Along this boundary we see there …