Physical Sciences and Mathematics Commons^™

The Bioaccessibility Of Methylmercury In Rice And Fish, Michael Angelo Ojeda

Undergraduate Research at FIU (URFIU) Conference

Traditionally, fish is considered as the major source for humans exposed to methylmercury (MeHg), which is a highly toxic contaminant,-however recent study has shown that consumption of rice could be another MeHg exposure pathway to human beings. To evaluate the potential health risk caused by consumption of rice and rice product contraining MeHg, not only amount but also the bioaccessibility of MeHg in rice and rice products are required, because the amounts of methylmercury in samples is an overestimate and does not provide the accurate fraction that is mobilized from the food source. An in vitro digestive method was used …

Investigation Of The Hydrophobic Sites Of Dream, Daniel Rapado

Undergraduate Research at FIU (URFIU) Conference

DREAM (downstream regulatory element antagonist modulator) also known as calsenilin or KChIP-3 is a calcium binding protein that has been associated with memory retention, pain sensing, calcium homeostasis and Alzheimer’s disease. It has two EF hands that bind Ca2+ and change the conformation of the protein. DREAM has two hydrophobic cavities in both the N- and C- terminus. These hydrophobic sites act as important binding sites with Kv channels, presenilin and other small molecules. Previously our group has showed that hydrophobic molecules such as NS5806 and 1,8- ANS can bind to the hydrophobic cavities in the C-terminus. The aim of …

Targeting Transcription-Coupled Dna Supercoiling For Discovery Of Bacterial Dna Gyrase Inhibitors, Alex Capaldo

Undergraduate Research at FIU (URFIU) Conference

Antibiotic production has been stagnant in the recent decade in comparison to the 30-years before that. The emergence of multidrug resistant bacteria is of mounting importance and a universal problem. The stagnation of antibiotic production, in part, is due to the lack of innovation in creating highly specific screening tools. Bacterial DNA gyrase is a type II topoisomerase that introduces negative supercoils into DNA, an essential mechanism for bacteria but absent from eukaryotes, making it an ideal target for identifying antibacterial compounds. In this study, we have constructed an E. coli strain FL#1181 that contains a pair of divergently coupled …

Crude Oil Characterization Using Sara Fractionation And Gc-Ms, Nicholas Hernandez

Undergraduate Research at FIU (URFIU) Conference

Crude oil is a naturally-occurring liquid mixture, composed of hydrocarbons as well as oxygen, nitrogen and sulfur-containing compounds. While previous research has been able to identify broad differences between classes of crude oil, the elucidating the structure of compounds within oils remains elusive, especially for heavier compounds. To determine the composition of Boscan, a heavy crude oil, SARA fractionation was performed to separate the sample into 4 different classes of chemical compounds: saturated hydrocarbons, aromatic compounds, resins, and asphaltenes. A sample of oil was chromatographically separated on activated alumina using solvents of increasing polarity. Each fraction was analyzed using gas …

Break Junction Technique For Studying Individual Biological Molecules, Brian Mayorga

Undergraduate Research at FIU (URFIU) Conference

Single molecule biophysics is a rapidly growing field that has great implications in the broader area of nanotechnology. The quantum properties of complex biological molecules can also be studied through the use of advanced techniques that examine molecules on an individual scale. Current methods for studying individual molecules often lack the accuracy needed to yield satisfactory data. In our experiments, we attempted to use a Scanning Tunneling Microscope (STM) based break junction method to study the quantum tunneling current through small biomolecules. By probing the currents changes through these molecules on an individual scale under external gating and in a …

Surface-Enhanced Raman Spectroscopy Study Of Arsenic Speciation Under Cellular Matrix Influence, Mingwie Yang, Afia Anjuman

Undergraduate Research at FIU (URFIU) Conference

Arsenic is an environmentally consequential metalloid which has various species based on its oxidation states and methyl substituents. In this study, Surface-Enhanced Raman Spectroscopy was utilized to explore Arsenic speciation under the cellular matrix influence using physiological buffers (sodium bicarbonate, phosphate etc.). Four common existing arsenicals were used: arsenite, arsenate, monomethylarsonic acid, and dimethylarsinic acid. Liquid droplets of arsenical solutions were dropped onto the Silver nanoparticle coated films and strong signals were generated by Raman spectroscopy. Signals were regenerated for the dried droplets after water evaporated from the solutions. Arsenicals were closer to the surface of the films and in …

Molecular Modeling Of Conformational Space Of The Knot Protein Yibk, Daniel Gimeno

Undergraduate Research at FIU (URFIU) Conference

Structurally, proteins follow entropy favorable layouts that have high stability while performing their function. Knots are typically not observed due the amount of energy needed to form this structure outweighed the stability of the protein. Despite this, there are several rare proteins whose polypeptide backbone form knotted configurations. YibK is one such protein with a trefoil knot (e.g., 3-1 knot) in its carboxy terminus. These proteins reveal interesting topographies with less entropy than if the protein were compressed. In the present work, we studied the main interactions involved in the folding pathway of YibK, based on molecular dynamics (MD) simulations …

The Effect Of Muscle Cell Differentiation On Ire1a Activation And The Unfolded Protein Response, Marco Zamora Bulla

Undergraduate Research at FIU (URFIU) Conference

The endoplasmic reticulum (ER), one of the base structures of a cell, is the site in which newly synthesized proteins are folded. This process is tightly regulated to ensure that the cell is working at optimal capacity and homeostasis, balance, is maintained. When the folding capacity of new proteins is surpassed, cells enter a state of stress called endoplasmic reticular stress (ER stress), which triggers the Unfolded Protein Response (UPR). The UPR is regulated by three main proteins inositol requiring enzyme 1 α (IRE1α), protein kinase RNA-like endoplasmic reticulum kinase (PERK), and activating transcription factor 6 (ATF 6), providing different …

Software Assisted Molecular Elucidation Based On Timsft- Icr Ms/Ms Analysis Of Complex Mixtures, Carlos Acosta

Undergraduate Research at FIU (URFIU) Conference

The determination of the chemical structure of a molecule within a complex mixture is a challenging analytical problem. In the present work, we describe a workflow based on the analytical characterization of complex mixtures using complementary Trapped Ion Mobility Separation and ultra-high resolution FT-ICR mass separation (TIMS-FT-ICR MS/MS) for the analysis of complex mixtures (e.g., crude oils and dissolved organic matter). In particular, we take advantage of the high mobility resolution and high mass accuracy of TIMS-FT-ICR MS/MS to generate candidate structures using a custom developed theoretical workflow for Software Assisted Molecular Elucidation (SAME) based on the ion-neutral collision cross …

Determination Of Effector Binding Affinities Using Pac, David Butcher, Jovany J. Betancourt

Undergraduate Research at FIU (URFIU) Conference

Determination of binding affinity and thermodynamic parameters of interactions between two molecules is a common procedure in biochemical contexts. Steady-state fluorescence titration is one of the most commonly used techniques to determine the binding affinity of small effector compounds and ligands to large biomolecules such as proteins. This method, however requires 1) the ligand to be fluorescent and exhibit a measureable change in fluorescence intensity between the bound and free states or 2) a fluorescent residue (e.g. tryptophan) near the ligand binding site whose fluorescence changes as a result of ligand binding. The new technique presented here utilizes photoacoustic calorimetry …

Terpene Adsorption Analysis In Tedlar Air Sampling Bags, Jeremy B. Guedes, Alison G. Simon

Undergraduate Research at FIU (URFIU) Conference

Tedlar® air sampling bags, which are composed of a polyvinyl fluoride polymer, are the EPA recommended bags used in several whole-air sampling and analytical methods for determining the presence of volatiles. Recent studies suggest that compounds which exhibit hydrogen bonding, as well as those that have a low vapor pressure, will tend to adsorb to the Tedlar® bags at a high rate. Furthermore, alkenes seem to display significant adsorption rates. For example, terpenes are a type of volatile organic compound (VOC) which contain the alkene functional group, and are found in oils produced by plants and some insects. In the …

Calculating Vsin(I) Of Planet-Hosting Young Stars, Jennifer Medina

Undergraduate Research at FIU (URFIU) Conference

Constraining the spin-orbit alignment of close-in planets in young systems can provide insight on their migratory history. We can combine Vsin(i) with measurements of the stellar rotation period and radius to determine the star's orbital inclination, which we can compare to that of the planet as determined from the transit. Vsin(i) is determined from the rotational broadening on the star's spectral lines, so it is ideal to work with young, fast-rotating stars where broadening is more easily measured. We measure Vsin(i) of seven planet-hosting stars within the Praesepe star cluster by using high-resolution spectra from the Immersion Grating INfrared Spectrometer …

Differences In Use Of Metaphor Between Narrative And Non-Narrative Texts, Armando J. Ochoa

Undergraduate Research at FIU (URFIU) Conference

Metaphors are widespread in human language and are used in all types of text. One of the most common text types are narratives, which share a number of unique structural traits which distinguish them from non-narrative types. We investigate if there is any difference in the use of metaphor between narrative and non-narrative texts. We first created a Java API to interface with the Vienna University Annotated Metaphor Corpus (VUAMC), which provides four different types of text (three non-narrative and one narrative) with word-by-word annotations of metaphor occurrences. We then contrasted narrative and non-narrative texts by calculating several similarity measures, …

Investigation Of The Properties Of Acid- Contaminated Sediment And Its Effect On Contaminant Mobility, Awmna K. Rana

Undergraduate Research at FIU (URFIU) Conference

The Savannah River Site (SRS), is a hazardous waste management facility responsible for nuclear storage and remediation of contaminated soil and groundwater. Underground vitrified clay pipes were used to transport acid radioactive effluents to the basins and allowed to evaporate and seep into the underlying soil. Over time the acidic nature of the basin influent caused mobilization of metals and radionuclides resulting in localized groundwater contaminant plumes. The main objective of this study is to assess the impact of prolonged contact between soil and the acidic waste stream and more specifically, the change in specific surface area and pore distribution …

Analysis Of Small Molecule Antagonist Binding With Relaxin Receptor, Briana Cervantes

Undergraduate Research at FIU (URFIU) Conference

Increased relaxin (RLN) peptide expression has been found in prostrate, breast, and endometrial cancers. The proliferative and anti-apoptotic effects of relaxin contribute to cancer growth, and thus a small-molecule antagonist of relaxin signaling may inhibit these cancer-promoting effects. We have identified several antagonists, which suppress activation of the G protein-coupled relaxin receptor, relaxin/insulin like family peptide receptor 1 (RXFP1), and are completely or partially ineffective against the closely related receptor RXFP2. The goal of this study is to define the region of relaxin receptor responsible for antagonist response. Comparison of amino acid sequences between RXFP1 and RXFP2 revealed 14 differences …

A Review Of Data Repositories For The Long Tail Of Computer Science, Pachev Joseph

Undergraduate Research at FIU (URFIU) Conference

Computer scientists undertaking research often find themselves struggling to find or generate the right data to formulate or test hypotheses, validate models, or test algorithms – which in turn leads to greater time and effort allocated to searching for or producing data, rather than using it to perform scientific research. This data barrier is a significant impediment to scientific progress, because most of the progress occurs in the long tail of computer science: in many smaller, silo-like laboratories that rarely share data. This paper surveys nineteen existing data repositories based on their respective feature sets. Out of the nineteen reviewed …

Examining The Relationship Between Career Outcome Expectations And Physics Identity, Camila Monslave

Undergraduate Research at FIU (URFIU) Conference

A small percentage of physics degrees are awarded each year. Previous studies about career outcome expectations, or what students hope to achieve in their careers, have revealed strong relationships between outcome expectations and STEM career choice. Drawing from a US national survey with responses from 15,847 students in mandatory College English courses (Outreach Programs and Science Career Intentions, NSF # 1161052), we examined the relationship between student’s outcome expectations and physics identity. It has previously been found that students with certain outcome expectations are more likely to develop a physics identity. Expanding beyond prior work, we focus on how outcome …

Molecular Modeling Of The Conformational Space Of The Knot Protein Dehl, Virgilio Velasco

Undergraduate Research at FIU (URFIU) Conference

Knot conformations in proteins are folding patterns in the amino acid chain that lead to the formation of a knot via pathways that are not yet understood. The bacteria Pseudomonas putida expresses a protein known as DehI, that serves as a halo acid dehalogenase. The tertiary conformation of DehI in the native state is a Stevedore 6-1 knot, making it one of the most complex of its kind. In the present work, we studied the influence of the charge state on the folding dynamics of the knot protein DehI. Briefly, the conformational space of DehI was sampled by coarse molecular …

Labeling Of Genetically Modified Organisms, Melissa Isoba

Undergraduate Research at FIU (URFIU) Conference

Advancements in transgenic technologies have led to the widespread use of genetically modified organisms (GMOs). Recent criticism of the use of GMOs due to health hazards has brought attention to whether or not these items should be mandatorily labeled. Due to the controversy regarding the safety of consuming GMOs, the public has differing views on labeling GMOs.

This study explored how accurately the public’s opinions regarding the labeling of GMOs are reflected in the United States’ biotechnological and agricultural policies. A qualitative analysis of eight primary sources was conducted, half were surveys and the other half were documents from the …

What Are The Implications Of One-To-One Technology Implementation?, Kevin Nguyen

Undergraduate Research at FIU (URFIU) Conference

This research study was used to examine my research question, “What are the implications of one-t- -one technology implementation?” This study specifically focused on the implications of one-to-one technology, one-to-one technology efficiency, and how teachers/students interact and feel about oneto- one technology. The study also describes these implications and future suggestions regarding one-to-one technology implementation and research. The study was conducted at a suburban high school located in Miami Dade County Public Schools and the tenth grade students would be surveyed through their English classes with the teacher’s consent. A census of tenth grade English teachers was taken and their …

Ethics Of Cystic Fibrosis Gene Therapies, Michelle Rojas

Undergraduate Research at FIU (URFIU) Conference

While knowledge of genetics originated centuries ago, the field had difficulty progressing until the Human Genome Project (HGP) expanded this topic of study by offering new insights on human genetics. The HGP was created to organize and lay out the complete set of genetic material in a species otherwise known as the genome, this project also aided in the discovery of diseasecausing genes. The recognition of disease-causing genes led to the formulation of gene therapies to treat specific disorders such as cystic fibrosis. This study analyzes not only how ethics are impacting the development of cystic fibrosis gene therapies but …