Biochemistry Commons^™

3d Printed Microfluidic Devices For Bioanalysis, Michael J. Beauchamp

Theses and Dissertations

This work presents the development of 3D printed microfluidic devices and their application to microchip analysis. Initial work was focused on the development of the printer resin as well as the development of the general rules for resolution that can be achieved with stereolithographic 3D printing. The next stage of this work involved the characterization of the printer with a variety of interior and exterior resolution features. I found that the minimum positive and negative feature sizes were about 20 μm in either case. Additionally, micropillar arrays were printed with pillar diameters as small as 16 μm. To demonstrate one …

Dna Capture Via Magnetic Beads In A Microfluidic Platformfor Rapid Detection Of Antibiotic Resistance Genes, David Hyrum Harris

Theses and Dissertations

Antibiotic resistant infections are a growing health care concern, with many cases reported annually. Infections can cause irreversible bodily damage or death if they are not diagnosed in a timely matter. To rapidly diagnose antibiotic resistance in infections, it is important to be able to capture and isolate the DNA coding for the resistance genes. This is challenging because bacteria are present in blood in minute concentrations. To enrich the DNA to detectable levels, I modified magnetic microbeads with ssDNA sequences complementary to the target DNA to capture the DNA via hybridization. I compared DNA capture efficiency in three different …

Tracing Nutrient Sources To Lipid Production In Insects Using Stable Isotope (Δ13c, Δ2h) Tracers: Implications For Nutritional Physiology Of Migratory Species., Libesha Anparasan, Keith A. Hobson

Western Research Forum

Using stable isotope measurements of insect tissues to determine origin and migratory patterns is well established. However, isotopically determining nutritional origins of lipids, the primary fuel of migration, has not been as thoroughly researched. We explored isotopic links between diet and stored lipids in laboratory raised True armyworm moths (Mythimna unipuncta) using δ¹³C and δ²H measurements. Pupae were randomly separated into four groups (n=20) and fed isotopically distinct nectar, each consisting of a combination of high δ¹³C (C4 sugar), or low δ¹³C (C3 sugar) carbohydrate, with high δ²H (deuterium spiked), …

The Wet Bridge Transfer System: An Novel In Vitro Tool For Assessing Exogenous Surfactant As A Pulmonary Drug Delivery Vehicle, Brandon J. Baer

Western Research Forum

Background:

Due to its complex branching structure, direct drug delivery to the remote areas of the lung is a major challenge. Consequently, most therapies, such as those treating pulmonary infection and inflammation, must utilize large systemic dosing, with the potential for adverse side effects. A novel alternative strategy is to use exogenous surfactant, a material capable of distributing throughout the lung, as a pulmonary drug delivery vehicle.

Objective:

Utilize an in vitro transferring system to assess exogenous surfactant (BLES) as a pulmonary delivery vehicle for different therapeutics.

Methods:

An in vitro technique was developed to simultaneously study surfactant delivery and …

Iron-Sulfur Cluster Biosynthesis In Methanogens, Cuiping Zhao

LSU Doctoral Dissertations

Methanogens live in a syntrophic consortium with bacteria, taking advantage of the metabolic abilities of their syntrophic partners to overcome energetic barriers and break down compounds that they cannot digest by themselves. Interspecies electron transfer, which is a major type of microbial communication in syntrophic processes, improves methanogenesis and anaerobic oxidization of methane (AOM) processes involved in syntrophic consortia. These processes have a significant impact on the global carbon cycle. Most of the essential enzymes involved in methanogenesis are iron-sulfur proteins. Iron-sulfur clusters are one of the oldest and most versatile cofactors present in all domains of life. To date, …

Nepal Ambient Monitoring And Source Testing Experiment (Namaste): Emissions Of Particulate Matter And Sulfur Dioxide From Vehicles And Brick Kilns And Their Impacts On Air Quality In The Kathmandu Valley, Nepal, Min Zhong, Eri Saikawa, Alexander Avramov, Chen Chen, Boya Sun, Wenlu Ye, William C. Keene, Robert J. Yokelson, Thilina Jayarathne, Elizabeth A. Stone, Maheswar Rupakheti, Arnico K. Panday

Chemistry and Biochemistry Faculty Publications

Air pollution is one of the most pressing environmental issues in the Kathmandu Valley, where the capital city of Nepal is located. We estimated emissions from two of the major source types in the valley (vehicles and brick kilns) and analyzed the corresponding impacts on regional air quality. First, we estimated the on-road vehicle emissions in the valley using the International Vehicle Emissions (IVE) model with local emissions factors and the latest available data for vehicle registration. We also identified the locations of the brick kilns in the Kathmandu Valley and developed an emissions inventory for these kilns using emissions …

Divergent Transcriptional Regulation Of Suppressors Of Cytokine Signaling Genes In Adipocytes, Paula Mota De Sa

LSU Doctoral Dissertations

The Janus Kinase - Signal Transducer and Activator of Transcription (JAK-STAT) signaling pathway transduces several signals crucial for development and homeostasis. Suppressors of cytokine signaling (SOCS) proteins control JAK-STAT signaling via a negative feedback loop. The transcription factor STAT5 is known to play a significant role in fat cell development and function, and several studies suggest that acetylation may affect STAT5 transcriptional activity. To test this hypothesis, we treated 3T3-L1 adipocytes with growth hormone (GH) to activate STAT5 in the presence or absence of histone deacetylase (HDAC) inhibitors. STAT5 acetylation levels were low in adipocytes and mostly unchanged by the …

In Vitro Evaluation Of Ovarian Cancer Tumorigenesis As A Function Of Quinone Oxidoreducatse-1 And Cell Phenotype, Milcah S. Jackson

LSU Doctoral Dissertations

In vitro multicellular spheroids are attractive model systems for assessing genetic and epigenetic changes that occur in diseased tissues. Understanding how such alterations in gene and subsequent protein expression affect disease progression and metastasis, drug resistance, and recurrence is of great interest in cancer research. In this regard, examining expression and activity of proteins, such as those with cytoprotective ability that are overexpressed in cancer cells, in addition to cell phenotype (i.e., stem-like, epithelial, mesenchymal, or mixed), are two ways to evaluate genetic and epigenetic changes. Moreover, determining the impact that cytoprotective proteins and cell phenotype have on tumor formation …

Consumption Of Black Raspberries Altered The Composition Of The Fecal Microbiome In Mice Fed A Western Type Diet (Or04-01-19), Abby D. Benninghoff, Sumira Phatak, Korry Hintze

Chemistry and Biochemistry Faculty Publications

Dietary strategies to reduce colonic inflammation and promote gut homeostasis may markedly reduce the risk of colitis-associated colorectal cancer. Previously, we showed that dietary supplementation with black raspberries significantly suppressed colitis and colon tumorigenesis promoted by the consumption a Western type diet in mice. In this study, our goal was to assess the impact of consumption of the TWD with and without black raspberry supplementation on the composition of the fecal microbiome over the course of disease development.

Dietary Intervention With Black Raspberries To Reduce Colitis Symptoms In Mice Fed Either Standard Ain93g Diet Or The Total Western Diet (P05-021-19), Daphne Michelle Rodriguez Jimenez, Michaela Brubaker, Elizabeth Park, Canyon Neal, Korry Hintze, Abby D. Benninghoff

Chemistry and Biochemistry Faculty Publications

Approximately 1.4 million people suffer from inflammatory bowel disease, which is a major risk factor for developing colitis associated colorectal cancer (CAC). Dietary interventions with the goal to reduce colon inflammation and encourage gut microbiome homeostasis may be a strategy to reduce the risk of CAC. The antioxidants and anti-inflammatory compounds present in black raspberries (BRB) have demonstrated protective effects in the colon epithelium and may alter the composition of the gut microbiome. Previously, we showed that dietary supplementation with black raspberries significantly suppressed colitis and colon tumorigenesis promoted by the consumption of a Western type diet in mice. The …

Application Of Single Particle Electron Microscopy To Native Lens Gap Junctions And Intrinsically Disordered Signaling Complexes, Janette Bernadette Myers

Dissertations and Theses

Gap junctions are a class of membrane proteins that facilitate cell-to-cell communication by forming channels that directly couple the cytoplasm of neighboring cells. The channels are composed of monomers called connexins. Humans express 21 connexin isoforms in a cell-type specific fashion, and each isoform has distinct mechanisms of permeation and regulation. Co-assembly of multiple isoforms into a single intercellular channel can change channel properties, such as conductance and selectivity to substrates (e.g., ions, metabolites and signaling molecules). However, the mechanistic basis for this functional diversity has remained poorly understood. This lack of mechanistic insight has been due in large part …

Maximizing And Modeling Malonyl-Coa Production In Escherichia Coli, Tatiana Thompson Silveira Mello

LSU Master's Theses

In E. coli, fatty acid synthesis is catalyzed by the enzyme acetyl-CoA carboxylase (ACC), which converts acetyl-CoA into malonyl-CoA. Malonyl-CoA is a major building block for numerous of bioproducts. Multiple parameters regulate the homeostatic cellular concentration of malonyl-CoA, keeping it at a very low level. Understanding how these parameters affect the bacterial production of malonyl-CoA is fundamental to maximizing it and its bioproducts. To this end, competing pathways consuming malonyl-CoA can be eliminated, and optimal nutritional and environmental conditions can be provided to the fermentation broth. Most previous studies utilized genetic modifications, expensive consumables, and high-cost quantification methods, making …

Compositional Optimization Of Amyloid-Graphene Oxide Nanohybrids For Biomaterials, Claire L. Drewery

Materials Engineering

Amyloid nanofibrils are natural materials capable of self-assembling into precise structures with tunable functionalities, while exhibiting excellent mechanical properties. In combination with highly conductive graphene oxide (GO), the 1-D amyloid nanofibrils and 2-D nanosheets of GO can produce a robust and bio-functional nanohybrid, hypothesized to exhibit multi-domain functional properties useful for enzyme sensing, water purification, drug delivery, and tissue scaffolding applications. Here, we examine the properties of an amyloid-graphene oxide nanohybrid film made with amyloids derived from hen egg white lysozymes in an attempt to explore the diverse toolbox of amyloid derivatives and establish ideal fabrication methods and formulations of …

Arachidin 3 Modulation Of Lipid Metabolism In Rotavirus Infections, Stormey Wisdom

Electronic Theses and Dissertations

Rotavirus (RV) can cause severe and deadly gastroenteritis in young children, infants, and immunocompromised individuals. Previous studies have shown that arachidin 3 (A3) inhibits RV replication, and that RV replication is dependent on the presence of lipids. This study investigated the alteration of lipid metabolism by A3 in RV infected HT29.f8 cells. A decrease in the RV regulation of lipid biosynthesis genes was observed with the addition of A3 using qRT-PCR. Also, immunofluorescent and histochemical staining for neutral fats, a major component of cellular lipid droplets, revealed an increased accumulation with both RV and RV+A3 when compared to no virus …

Modulation Of Biological Responses To 2 Ns Electrical Stimuli By Field Reversal, Esin B. Sözer, P. Thomas Vernier

Bioelectrics Publications

Nanosecond bipolar pulse cancellation, a recently discovered Phenomenon, is modulation of the effects of a unipolar electric pulse exposure by a second pulse of opposite polarity. This attenuation of biological response by reversal of the electric field direction has been reported with pulse durations from 60 ns to 900 ns for a wide range of endpoints, and it is not observed with conventional electroporation pulses of much longer duration (> 100 mu s) where pulses are additive regardless of polarity. The most plausible proposed mechanisms involve the field-driven migration of ions to and from the membrane interface (accelerated membrane discharge). …

Electrochemically Reactive Membranes For Efficient Biomass Recovery, Pollutant Degradation And Commercialization, Likun Hua

Dissertations

Micropollution in natural waters such as rivers and groundwater aquifers is a widespread problem that prevents these potentially potable sources from being used as drinking water. In the United States, approximately two-thirds of the over 1,200 most serious hazardous waste sites in the nation are contaminated with trichloroethylene (TCE), a potentially carcinogenic compound. Other emerging and environmentally persistent organic micropollutants include polyromantic hydrocarbons (PAHs), organophosphate flame retardants, endocrine disrupting compounds (EDCs), pesticides, herbicides, pharmaceuticals and personal care products (PPCPs). Membrane filtration is one of the most efficient separation processes widely used for water treatment and pollutant removal. However, traditional membrane …

Nf-Κb In Biomphalaria Glabrata: A Genetic Fluke?, Paige Stocker

Lawrence University Honors Projects

Biomphalaria glabrata is the intermediate host to the disease causing parasitic worm, Schistosoma mansoni. Previous work has identified homologs of NF-κB, a known immune related transcription factor, in B. glabrata and work has also been done to establish putative κB sites. It has also been observed that the p65 homologous subunit has an extended N-terminal region not present in other homologs. The goal of the present study is twofold: investigate DNA binding affinity of two NF-κB subunits, Bg-p65 and Bg-p50, and characterize the nature of the N-terminal extension of Bg-p65. In the current work, it is shown through the …

Understanding How Map Kinases Influence Endothelial Nitric-Oxide Synthase Activity, Xzaviar Solone

Master of Science in Integrative Biology Theses

Mitogen activated protein kinases (MAPK) p38 and ERK have both been reported to bind endothelial nitric oxide synthase (eNOS) with submicromolar affinity via proposed interactions with a pentabasic non-canonical MAPK binding sequence in the autoinhibitory insertion of eNOS. The neuronal isoform, which lacks the pentabasic motif, did not bind either MAPK significantly. In the present study, the pentabasic motif was validated using predictive modeling programming, and eNOS phosphorylation by MAPKs (P38, ERK and JNK) was examined using in vitro kinase assays and immunoblotting. JNK phosphorylation at Ser¹¹⁴ contrasts with ERK, which phosphorylated Ser⁶⁰⁰, and p38, which phosphorylated …

Expanding The Toolbox With Site-Specific Methods Of Bioconjugation, Tiauna S. Howard

Seton Hall University Dissertations and Theses (ETDs)

Bioconjugation is an important tool for studying complex biological systems, with site-specificity being the major challenge. Reactions based on amino acid derived organocatalysts have been widely used in organic synthesis, particularly for the asymmetric synthesis of small molecules but this concept has not been vastly explored on biomolecules. To combat these limitations, two chemical strategies are developed to effectively attach synthetic molecules site specifically to proteins. First, a protein modification technique based on conjugation at a non-native functional handle, an aldehyde or ketone, is developed. This functional handle is chemically introduced onto the biomolecules before undergoing the organocatalyzed aldol reaction, …

Analysis Of Septum Defects In Arabidopsis Organ Boundary Mutants, Katherine T. Anderson

Honors Theses

Arabidopsis thaliana, a model plant species, has been heavily studied to determine the genetic contributions that lead to gynoecium development. The Arabidopsis fruit is created from two carpels that form a gynoecium, which contains the stigma, style, and ovary. The ovary is divided into two sub-compartments by a septum, and the ovules develop within the ovary. The fruit’s purpose is to protect, nurture, and eventually disperse the mature ovules, or seeds, and if the septum does not fuse properly, the plant’s fertility will be impacted. SHOOT MERISTEMLESS (STM) and ARABIDOPSIS THALIANA HOMEOBOX GENE1 (ATH1) are two genes that are known …

Molecular Signatures Of Calpain 10 Isoforms Sequences, Envisage Functional Similarity And Therapeutic Potential, Bushra Chaudhry, Farina Hanif, Kausar Saboohi

Department of Biological & Biomedical Sciences

Calpain 10 plays a role in insulin secretion, action and susceptibility to type 2 diabetes. The mechanism through which it influences the insulin secretion and action is not completely defined. A structural bioinformatics approach is applied to envision its mechanism of action using available tools on NCBI (blastp and blastn), EMBL-EBI, Ensembl, Swiss Model Repository websites, I-TASSER, PROCHECK program and Discovery Studio software. Homology of domain I and II of calpain10 (isoform a) was established with super family cysteine proteinase domains (II a and II b, e=1.30e-77, 1.00e-20). Remaining sequences of domain III and T from (isoform a and c) …

Molecular Characterization Of The Putative Nucleotide- Binding And Hydrolyzing Activities Of The Ellis Van Creveld (Evc) Protein, Giang Nguyen

Electronic Theses and Dissertations

Ellis–van Creveld (EvC) syndrome is a rare autosomal recessive disorder that is characterized by short-limb dwarfism, extra fingers or toes, malformed teeth and nails, and congenital heart defects. Mutations in two genes, EVC and EVC2, which are located on chromosome 4, have been shown to be responsible for EvC syndrome. The protein products of these genes, EVC and EVC2 physically interact and together, they are tethered to the base of the primary cilium of cells. This multi-protein assembly positively regulates the Sonic and Indian hedgehog signaling pathways by promoting downstream processes after activation of the smoothened receptor (Smo), by the …

Generation Of Full-Length Wild-Type Gata4 Protein And Characterization Of Its Binding To Unc-45 Domains, Morgan Anderson

Electronic Theses and Dissertations

Striated muscle UNC-45 (SM UNC-45) protein acts as a chaperone for cardiac and skeletal muscle myosins; regulating their folding, assembly into thick filaments, interaction with other sarcomeric proteins, and degradation. GATA4 is an important transcription factor that regulates the expression of several cardiac muscle proteins, including myosin. A previous study demonstrated for the first time that SM UNC-45 (also known as UNC-45B) physically interacted with GATA4. The major revelation from this study is that SM UNC-45 has the potential to exert both short-term (protein level) and long-term (gene level) controls over myosin and therefore muscle structure and function. The aim …

Synthesis, Stabilization, And Modification Of Zinc Oxide Nanoparticles For Biological Applications, Allison Kimberly Freese

Graduate Theses/Dissertations

Nanoparticles have become very useful as delivery systems in biomedicine. The nanoparticles can be layered with different compounds to produce a vessel for transport of biological materials. Specifically, gold nanoparticles layered with a reducing agent, lysozyme, and polyelectrolytes can be synthesized to transport lysozyme into a cell. However, zinc oxide nanoparticles are cheaper, biocompatible nanoparticles that can be used for the same process. Here in, zinc oxide nanoparticle conjugates were synthesized, modified, and analyzed to be used as a biological material delivery system. The zinc oxide nanoparticles were synthesized using zinc chloride and sodium hydroxide. The particles were then layered …

Role Of The Drosophila Beaf Protein In Chromatin Domain Insulator And Promoter Function, Mukesh Maharjan

LSU Doctoral Dissertations

Proper folding of eukaryotic genomes is required to allow correct interactions between different parts of chromosomes. Precise and timely interactions among different parts of a chromosome allow proper functioning inside a nucleus, including gene regulation, DNA replication and DNA repair. Eukaryotic regulatory elements that facilitate folding and interactions include enhancers, promoters and insulator elements. Insulator elements and their binding proteins play an important role in regulating correct chromatin structure and function. The Drosophila melanogaster special chromatin structure (scs’) is one such insulator. The Boundary Element Associated Factor (BEAF) binds to scs’. BEAF is a 32 kDa protein that has two …

The Effect Of Simulated Storm Passage On The Behavior Of Whitespotted Bamboo Sharks, Chiloscyllium Plagiosum And Golden Shiners, Notemigonus Chrysoleucas, Jordan A. Healy

Honors Theses

Environmental changes during a storm can affect animal behavior; for example, tagged sharks leave shallow waters during tropical storms. While changes in shark behavior during storm passage have been documented, there have been no experimental tests to determine which environmental parameters are responsible. In this study, we experimentally manipulated two environmental cues: barometric pressure, and thunder sounds, to determine their effect on whitespotted bamboo sharks, Chiloscyllium plagiosum, and golden shiners, Notemigonus crysoleucas. Elasmobranchs do not have a swim bladder to detect pressure change; therefore, we used golden shiners to compare the reaction of a fish with a swim bladder. The …

Studies On Luminescent Gold And Platinum Nanoclusters For Biological Sensing And Catalysis, Richard Covington

Honors Theses

Nanoclusters are small nanoparticles that usually range around a micrometer in diameter. Gold Nanoclusters are known for their unique size and surface qualities and do not share metallic properties with nanoparticles or their respective bulk material. Some metal nanoclusters show high fluorescence and can be synthesized with protein mediation. Nanocluster formation depends on a number of variables, including temperature, pH, and type of reducing agent. This experiment was done to begin to understand how these variables may affect synthesis and what exactly they are. Pure Wild Type CSP-1 protein was induced, transformed, and purified in order to mediate gold and …

Investigations Of The Mechanism Of Action For Lung Cancer Cell Death By A 4-Trifluoromethoxy Substituted Chalcone, Trevor M. Stantliff

Undergraduate Theses

Chalcones are a diphenyl compound that serves as a natural precursor to flavonoids in plants. Chalcones have been shown to have anticancer and antimicrobial activities. Chemoprevention activity of chalcones are of high interest in medicinal chemistry because of the simple laboratory synthesis and modification via Claisen-Schmidt condensation. Previously this lab created and screened a library of synthetic chalcones against A549 lung adenocarcinoma cell line for antiproliferation properties. We identified a strong drug candidate (4-trifluoromethoxy substituted chalcone) for A549 growth inhibition. However, the cause of inhibition by the substituted chalcone remains to be identified We began to explore the mechanism of …

Identification Of Pathways Required For The Survival Of Inversion(16) Acute Myeloid Leukemia, Yiqian Wang

Theses & Dissertations

Inversion of chromosome 16 [inv(16)] acute myeloid leukemia (AML) generates a fusion gene CBFB-MYH11. Approximately half of inv(16) AML patients eventually relapse mainly due to the existence of leukemia stem cells (LSCs). Previous work using a Cbfb-MYH11 knockin mouse model showed that the LSCs are enriched within CSF2RB^- population. Another gene upregulated by Cbfb-MYH11 encodes the cytokine receptor IL1RL1. Using Cbfb-MYH11 knockin mice, we showed that LSCs exist in multiple sub-populations defined by their immunophenotype, and IL1RL1 is expressed by cell populations with high LSC activity. We also found that treatment of IL-33, the ligand for IL1RL1, promoted …

Developing Targeted Therapy Against Pancreatic Cancer, Garima Kaushik

Theses & Dissertations

Not available.