Biochemistry Commons^™

Two-Ply Channels For Faster Wicking In Paper-Based Microfluidic Devices, Conor K. Camplisson, Kevin M. Schilling, William L. Pedrotti, Howard A. Stone, Andres W. Martinez

Chemistry and Biochemistry

This article describes the development of porous two-ply channels for paper-based microfluidic devices that wick fluids significantly faster than conventional, porous, single-ply channels. The two-ply channels were made by stacking two single-ply channels on top of each other and were fabricated entirely out of paper, wax and toner using two commercially available printers, a convection oven and a thermal laminator. The wicking in paper-based channels was studied and modeled using a modified Lucas–Washburn equation to account for the effect of evaporation, and a paper-based titration device incorporating two-ply channels was demonstrated.

The Generation, Exploitation And Future Of Induced Pluripotent Stem Cells, Jacob Steenwyk

Scholarly Undergraduate Research Journal at Clark (SURJ)

The foundational advancements of John Gurdon and Shinya Yamanaka have improved understanding of dedifferen- tiation of cells to a pluripotent state. The seminal discovery established a novel system to study disease pathogenesis, drug screening, and toxicity, as well as sprouted the new field of regenerative medicine. In this article, the method- ology to obtain dedifferentiated cells, known as induced pluripotent stem (iPS) cells, subsequent validation, and application of which are reviewed. The experiments investigated here aim to demonstrate the capacity of iPS cells to replace the ethically-gray human embryonic cells by developing human livers and viable, healthy animals. It is …

Biochemical Effects Of Meditation: A Literature Review, William C. Daube, Charles E. Jakobsche

Scholarly Undergraduate Research Journal at Clark (SURJ)

Meditation is an activity that can help reduce stress and anxiety from daily life as well as help cultivate overall feel- ings of peacefulness, relaxation, and contentment. This review describes several studies that have been used to assess how meditation can influence the body at the molecular level. The presented results focus on small-molecule metab- olites, which are broadly defined as naturally-produced molecules that weigh less than approximately 1000 Da. The results show that meditation can significantly affect hormones and neurotransmitters such as cortisol, dehydroepi- androstrone, serotonin, melatonin, and epinephrine. Some common and modern experimental techniques that are relevant to …

Structure Based Drug Design Targeting Bacterial Antibiotic Resistance And Alzheimer's Disease, Eric Michael Lewandowski

USF Tampa Graduate Theses and Dissertations

Structure based drug design is a rapidly advancing discipline that examines how protein targets structurally interact with small molecules, or known inhibitors, and then uses this information to lead inhibitor optimization efforts. In the case of novel inhibitors, protein structural information is first obtained via X-ray crystallography, NMR studies, or a combination of both approaches. Then, computational molecular docking is often used to screen, in silico, millions of small molecules and calculate the potential interactions they may have with the target protein’s binding pocket, in hopes of identifying novel low affinity inhibitors. By examining the interactions these small, low affinity, …

Cobalt-Centred Boron Molecular Drums With The Highest Coordination Number In The Cob16− Cluster, Ivan A. Popov, Tian Jian, Gary V. Lopez, Alexander I. Boldyrev, Lai-Sheng Wang

Chemistry and Biochemistry Faculty Publications

The electron deficiency and strong bonding capacity of boron have led to a vast variety of molecular structures in chemistry and materials science. Here we report the observation of highly symmetric cobalt-centered boron drum-like structures of CoB16⁻, characterized by photoelectron spectroscopy and ab initio calculations. The photoelectron spectra display a relatively simple spectral pattern, suggesting a high symmetry structure. Two nearly degenerate isomers with D8d(I) and C4v (II) symmetries are found computationally to compete for the global minimum. These drum-like structures consist of two B8 rings sandwiching a cobalt atom, which has the highest …

Temporal Variation In Optical Properties Of Chromophoric Dissolved Organic Matter (Cdom) In Southern California Coastal Waters With Nearshore Kelp And Seagrass, Catherine D. Clark, Warren J. De Bruyn, Paige Aiona

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Optical properties of chromophoric dissolved organic matter (CDOM) were measured in surf zone waters in diurnal field studies at a Southern California beach with nearshore kelp and seagrass beds and intertidal plant wrack. Absorption coefficients (aCDOM(300 nm)) ranged from 0.35 m21 to 3.7 m21 with short-term variability<1 h, increases at ebb and flood tides and higher values (6 m21) during an offshore storm event. Spectral slopes (S) ranged from 0.0028 nm21 to 0.017 nm21, with higher values after the storm; S was generally inversely correlated with aCDOM(300 nm). 3-D excitation–emission matrix spectra (EEMs) for samples with lower S values had humic-type peaks associated with terrestrial material (A, C), marine microbial material (M) and protein peaks, characteristic of freshly produced organic material. Samples with high S values had no or reduced protein peaks, consistent with aged material. Fluorescent indexes (f450/f500 >2.5, BIX>1.1) were consistent with microbial aquatic sources. Leachates of senescent kelp and seagrass had protein and humic-type EEM peaks. After solar simulator irradiation (4 h), protein peaks rapidly photochemically degraded, humic-type peak C increased in intensity and peak M disappeared. Optical characteristics of kelp leachates were most similar to field samples, …

Multi-Dimensional Glycan Microarrays With Glyco-Macroligands, Satya Nandana Narla, Huan Nie, Yu Li, Xue-Long Sun

Chemistry Faculty Publications

Glycan microarray has become a powerful high-throughput tool for examining binding interactions of carbohydrates with the carbohydrate binding biomolecules like proteins, enzymes, antibodies etc. It has shown great potential for biomedical research and applications, such as antibody detection and profiling, vaccine development, biomarker discovery, and drug screening. Most glycan microarrays were made with monovalent glycans immobilized directly onto the array surface via either covalent or non-covalent bond, which afford a multivalent glycans in two dimensional (2D) displaying. A variety of glyco-macroligands have been developed to mimic multivalent carbohydrate-protein interactions for studying carbohydrate-protein interactions and biomedical research and applications. Recently, a …

Characterization Of Inhibitors Of Fatty Acid Transport Protein-2 In Cell And Animal Models, Nipun Saini

Department of Biochemistry: Dissertations, Theses, and Student Research

Obesity is correlated with insulin resistance and elevated levels of glucose, triglycerides and free fatty acids in blood. This affects overall metabolism and leads to disease. In the obese state, fat also accumulates in non-adipose tissue including liver, muscle and pancreas, where it can lead to cellular dysfunction and death. Currently, only a limited number of drugs are available to combat obesity and it is clear that new drugs, which more narrowly target the metabolic pathways involved, are required. Fatty Acid Transport Proteins (FATPs) are bifunctional proteins involved in the uptake and activation of fatty acids by esterification with coenzyme …

Ligand Frameworks For Transition-Metal Complexes That Model Metalloenzyme Active, Denan Wang

Dissertations (1934 -)

Advances in the field of biomimetic inorganic chemistry require the design of sophisticated ligand frameworks that reflect the amazing complexity of metalloenzyme active sites. For instance, most active sites feature extensive hydrogen-bonding interactions between ligands bound to the metal center (the “first” coordination sphere) and nearby units in the outer (or “second”) sphere. Since these interactions modify the structural and electronic properties of the active sites, a number of inorganic chemists have sought to design ligands that permit outer-sphere functional groups to interact with first-sphere donors. This dissertation describes our contribution to these broader efforts to model the second coordination …

Image-Charge Detection €“ Novel Instrumentation And Applications, Brandon Lee Barney

Theses and Dissertations

Image-charge detection is an analytical technique in which a highly-charged particle is detected by the magnitude of the image current that it generates in a detecting electrode. This current is represented as a voltage between the charged particle and the sensing electrode. It is a single particle detection method, ideal for the analysis of large, variable mass particles such as biological cells. Some of the physical properties of Bacillus subtilis spores were explored using different applications of image-charge detection. B. subtilis is a gram-negative spore-forming bacteria that has been shown to exhibit extremophile behavior. The particular extremophile behavior that was …

The Role Of Atp And Cleavage Factor Phosphorylation In Pre-Mrna 3' Cleavage Reaction, Asya Khleborodova

Dissertations, Theses, and Capstone Projects

The 3' end cleavage/polyadenylation (3' processing) is important in generating a functional messenger RNA (mRNA) transcript. It is long-known that ATP can significantly stimulate the in vitro cleavage of adenovirus type 2 L3 (Ad2L3) RNA substrate. Here, we used ATP analogs in structure-activity assays to show that the structural features of ATP and its analogs determine in vitro 3' cleavage efficiency. More specifically, we demonstrate that the structure of the nitrogenous base, the nucleotide sugar and the triphosphate group contribute to the efficiency of the nucleotide-stimulated in vitro 3' cleavage reaction.

It was found that AppNp, an analog of ATP …

Knowledge Discovery And Prediction Modeling Of Protein-Drug Binding Kinetic By Integrating Machine Learning, Normal Mode Analysis And Molecular Dynamics Simulation, See Hong Chiu

Dissertations, Theses, and Capstone Projects

One of the unaddressed challenges in drug discovery is that drug potency measured by protein-ligand binding affinity, such as IC₅₀ and K_d in vitro, is not correlated with drug activity in vivo. Computational modeling is playing an increasing role in designing efficient therapeutics. However, existing computational methods for the high-throughput study of protein-ligand interactions (PLI) mainly focus on the prediction of the binding affinity. This is the combined effect of association (k_on) and dissociation (k_off) rate constants. Few works have been produced to predict koff or its reciprocal, residence time, which is a key …

Characterizing Migratory Signaling Pathways Of Transplantable Retinal Progenitor Cells And Photoreceptor Precursor Cells Toward Restoration Of Degenerative Retina ' A Systems Biology Approach, Uchenna John Unachukwu

Dissertations, Theses, and Capstone Projects

A common feature of several heterogeneous diseases that result in retinal degeneration (RD) is photoreceptor loss, leading to an irreversible decline in visual function [15-17]. There are no cell replacement treatments available for RD diseases such as age-related macular degeneration (AMD) and retinitis pigmentosa (RP). Although many RD cases are of a genetic origin, a promising strategy to treat diseased phenotypes is by replacing lost photoreceptor cells, for synaptic integration and restoration of visual function. To advance photoreceptor-replacement strategies as a practical therapy, in light of highly restricted integration rates reported across studies, this body of research focused on defining …

Exploiting Cancer Cell Signaling And Metabolism: Implications For Therapeutic Approach, Suman Mukhopadhyay

Dissertations, Theses, and Capstone Projects

Over the last decade, metabolic dysregulation in cancer cells has stimulated a significant amount of interest in basic research. It has been established that cancer cells increase glucose uptake and alter the fate of glycolytic and tricarboxylic acid (TCA) cycle intermediates for the synthesis of biological molecules to accommodate high rates of cellular growth and proliferation. Moreover, it is more prominent that some metabolic dysregulations are specific to particular oncogenes. Exploiting the dysregulated metabolic dependency of cancer cells with therapeutic means could represent a novel approach for clinical aspect.

To meet the need of increased anabolic metabolism cancer cells engage …

Heterogeneous Oxidation Of Catechol, Elizabeth A. Pillar, Ruixin Zhou, Marcelo I. Guzman

Chemistry Faculty Publications

Natural and anthropogenic emissions of aromatic hydrocarbons from biomass burning, agro-industrial settings, and fossil fuel combustion contribute precursors to secondary aerosol formation (SOA). How these compounds are processed under humid tropospheric conditions is the focus of current attention to understand their environmental fate. This work shows how catechol thin films, a model for oxygenated aromatic hydrocarbons present in biomass burning and combustion aerosols, undergo heterogeneous oxidation at the air–solid interface under variable relative humidity (RH = 0–90%). The maximum reactive uptake coefficient of O₃(g) by catechol γ_O3 = (7.49 ± 0.35) × 10^–6 occurs for …

Fatty Acid Transport Protein-2 Inhibitor Grassofermata/Cb5 Protects Cells Against Lipid Accumulation And Toxicity, Nipun Saini, Paul N. Black, David Montefusco, Concetta Dirusso

Department of Biochemistry: Faculty Publications

The inhibition of the fatty acid uptake into non-adipose tissues provides an attractive target for prevention of lipotoxicity leading to obesity-associated non-alcoholic fatty liver disease and type 2 diabetes. Fatty acid transport proteins (FATPs) are bifunctional proteins involved in the uptake and activation of fatty acids by esterification with coenzyme A. Here we characterize Grassofermata/CB5, previously identified as a fatty acid uptake inhibitor directed against HsFATP2. The compound was effective in inhibiting the uptake of fatty acids in the low micro-molar range (IC₅₀ 8–11μM) and prevented palmitate-mediated lipid accumulation and cell death in cell lines that are models for …

Elongation Factor-P At The Crossroads Of The Host-Endosymbiont Interface, Andrei Rajkovic, Anne Witzky, William Navarre, Andrew J. Darwin, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Elongation factor P (EF-P) is an ancient bacterial translational factor that aids the ribosome in polymerizing oligo-prolines. EF-P structurally resembles tRNA and binds in-between the exit and peptidyl sites of the ribosome to accelerate the intrinsically slow reaction of peptidyl-prolyl bond formation. Recent studies have identified in separate organisms, two evolutionarily convergent EF-P post-translational modification systems (EPMS), split predominantly between gammaproteobacteria, and betaproteobacteria. In both cases EF-P receives a post-translational modification, critical for its function, on a highly conserved residue that protrudes into the peptidyl-transfer center of the ribosome. EPMSs are comprised of a gene(s) that synthesizes the precursor molecule …

Characterizing The Rogfp2-Orp1 Fluorescent Biosensor For Detecting Oxidative Stress In Mammalian Cells, Sara A. Doan, Stevie Norcross, Mathew Tantama

The Summer Undergraduate Research Fellowship (SURF) Symposium

Parkinson’s disease is a neurodegenerative disease involving the death of neurons in the substantia nigra and loss of the neurotransmitter, dopamine. The disease leads to progressive loss of motor control. Exact causes and mechanisms by which Parkinson’s disease proceeds are unknown, however, previous experiments determine oxidative stress in mitochondria as a factor that results in cell death. Strategies have been implemented to generate fluorescent biosensors to monitor reactive oxygen species (ROS) concentrations while simultaneously measuring the spatiotemporal distribution and correlation between the ROS, cellular function and organelle. Orp1, an enzyme found in yeast, is a sensitive oxidizing species and when …

Short Communication: Lack Of Association Between Mthfr Gene Polymorphisms And Response To Methotrexate Treatment In Pakistani Patients With Rheumatoid Arthritis, Mohammad Perwaiz Iqbal, Azra Arif Ali, Naseema Mehboobali, Khalida Iqbal

Department of Biological & Biomedical Sciences

Methylenetetrahydrofolate reductase (MTHFR) gene polymorphisms have been reported to be associated with response to methotrexate (MTX) in certain populations of patients with rheumatoid arthritis (RA). This study aims at investigating any relationship of two single nucleotide polymorphisms (SNPs) in MTHFR gene, C677T and A1298C with response to therapy with MTX in Pakistani RA patients. Allelic frequencies of the two polymorphisms (C677T and A1298C) were determined in 67 RA patients (9 males and 58 females; mean age 42.87 ± 13.5 years) who had previously participated in a prospective clinical trial. Fifty-one patients had received MTX and were followed up for response …

Coastal Sediment Elevation Change Following Anthropogenic Mangrove Clearing, Heather Lyn Hayden, Elise F. Granek

Environmental Science and Management Faculty Publications and Presentations

Coastal mangrove forests along tropical shorelines serve as an important interface between land and sea. They provide a physical buffer protecting the coastline from erosion and act as sediment “traps” catching terrestrial sediment, thus preventing smothering of subtidal coral reefs. Coastal development that removes mangrove habitat may impact adjacent nearshore coral reefs through sedimentation and nutrient loading. We examined differences in sediment elevation change between patches of open-coast intact and anthropogenically cleared red mangroves (Rhizophora mangle) on the east side of Turneffe Atoll, Belize, to quantify changes following mangrove clearing. Samples were collected over a 24 month period at five …