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A Review Of Natural And Engineered Enzymes Involved In Bioethanol Production, Ines Cuesta Urena

Graduate Student Theses, Dissertations, & Professional Papers

Alternative petroleum-derived fuels, such as biofuels, is another form to decrease the dependence of non-renewable energy. The most promising alternative energy is cellulosic ethanol because of the abundance of cellulose and the overall lack of concern for the food-versus-fuel dilemma.

In order to produce ethanol from cellulosic materials, pretreatment is required to “open” the lignocellulosic matrix and make cellulose more susceptible to enzymatic degradation. Enzymatic hydrolysis of lignocellulose is an important area of research due to the absence of negative effects in downstream processes in comparison with acid hydrolysis. Both natural enzymes and engineered enzymes can be used in the …

Reduction Of Oxidative Stress And Storage Lesions (Rcsl) In Red Blood Cells - Analysis Of Ascorbic Acid (Aa), N-Acetylcysteine Amide (Ad4), And Serotonin (5-Ht), Shanmuka Gadiraju

UROP Posters

Oxidative stress is a common occurrence in red blood cell (RBC) storage in blood banks throughout the world. Typically RBC units stored under routine standard protocol (stored in SAGM-CPD additive solution) can only be kept up to 42 days for transfusion usage before being discarded. I am studying the effects of Ascorbic Acid (AA), N-acetylcysteine amide (AD4), and Serotonin (5-HT) as additives in blood bank storage because I want to find out if these additives can reduce storage-induced oxidative stress on red blood cells (RBCs), in order to help my reader understand how potential blood storage additives can affect the …

Deep Models For Brain Em Image Segmentation: Novel Insights And Improved Performance, Ahmed Fakhry, Hanchuan Peng, Shuiwang Ji

Computer Science Faculty Publications

Motivation: Accurate segmentation of brain electron microscopy (EM) images is a critical step in dense circuit reconstruction. Although deep neural networks (DNNs) have been widely used in a number of applications in computer vision, most of these models that proved to be effective on image classification tasks cannot be applied directly to EM image segmentation, due to the different objectives of these tasks. As a result, it is desirable to develop an optimized architecture that uses the full power of DNNs and tailored specifically for EM image segmentation.

Results: In this work, we proposed a novel design of DNNs for …

Inactivation Of Cytomegalovirus In Breast Milk Using Ultraviolet-C Irradiation: Opportunities For A New Treatment Option In Breast Milk Banking, Megan L. Lloyd, Nurul Hod, Jothsna Jayaraman, Elizabeth A. Marchant, Lukas Christen, Peter Chiang, Peter E. Hartmann, Geoffrey R. Shellam, Karen N. Simmer

Research outputs 2014 to 2021

Pasteurized donor human milk is provided by milk banks to very preterm babies where their maternal supply is insufficient or unavailable. Donor milk is currently processed by Holder pasteurization, producing a microbiologically safe product but significantly reducing immunoprotective components. Ultraviolet-C (UV-C) irradiation at 254 nm is being investigated as an alternative treatment method and has been shown to preserve components such as lactoferrin, lysozyme and secretory IgA considerably better than Holder pasteurization. We describe the inactivation of cytomegalovirus, a virus commonly excreted into breast milk, using UV-C irradiation. Full replication was ablated by various treatment doses. However, evidence of viral …

Investigating The Function Of Aintegumenta-Like6 (Ail6) In Arabidopsis Flower Development, Han Han

Theses and Dissertations

AINTEGUMENTA (ANT) and AINTEGUMENTA-LIKE6 (AIL6) encode related transcription factors with partially overlapping roles in floral organ development in the model plant Arabidopsis thaliana. ANT and AIL6 do not make equivalent contributions to these processes. Loss of ANT function by itself results in smaller flowers, demonstrating that the role of ANT in organ size control cannot be provided by AIL6. Loss of AIL6 function on its own has no phenotypic consequences indicating that all of its roles in flower development can be provided by ANT or some other genes. To further probe the function of AIL6 in flower development, we investigated …

Development Of "Inside-Out" Pegylated Crosslinked Hemoglobin Polymers: Novel Hemoglobin-Based Oxygen Carriers (Hboc), Kyle Douglas Webster

Dissertations

The development of an effective blood substitute is urgent due to increasingly common blood shortages, the need to type-match donated blood, and communicable diseases (e.g. HIV) posing risks for blood transfusions around the world. There have been many attempts at creating hemoglobin-based oxygen carriers (HBOC) using a variety of techniques centered around the use of polyethylene glycol (PEG) conjugated to hemoglobin (Hb) tetramers. A novel method, “Inside-Out” PEGylation, has been developed by our lab to produce a polyethylene glycol crosslinked hemoglobin (PEG XL-Hb) polymer. This method utilizes a single PEG backbone that is surrounded by multiple proteins, instead of covering …

Role Of Pkc Delta In Uv Radiation Dna Damage Repair, Gargi Patil

Master's Theses

DNA damage caused by ultraviolet radiation (UV), such as cyclobutane pyrimidine dimers (CPD), is repaired by the nucleotide excision repair (NER) pathway. When NER is defective, DNA damage is not repaired, leading to mutations and skin cancer. After DNA damage, the cell cycle is halted at various checkpoints to allow time for repair of the damage and maintain genomic integrity, however little is known about the coordination between NER DNA damage repair and cell cycle halting at checkpoints after DNA damage. Protein kinase C δ (PKCδ) plays major role in apoptosis and maintains the G2/M checkpoint in response to UV …

The Role Of C-Abl Kinase In Hcc Development, Lennox Chitsike

Master's Theses

Hepatocellular Carcinoma is the second most lethal cancer after pancreatic cancer. Unresectable HCC tumors carry a poor prognosis and few treatment options are available. The dismal prognosis is mainly due to limited therapy options and molecularly targeted therapy is deemed as solution. Here, we report a novel role of c-Abl in HCC development. We provide evidence of c-Abl activation in human HCC samples compared to normal liver. Using genetic and pharmacological tools, we show that c-Abl plays a vital role in HCC progression in vitro and in vivo. We have identified Axl as an effector in processes mediated by c-Abl. …

A Bioluminescence Sensor Of Nlrp3 Inflammasome Activation, Michael Alexander Winek

Master's Theses

The innate immune system is many organisms first line of defense against pathogenic insult or tissue damage. This defense strategy is intent on restoring homeostasis upon perturbation. Upon activation of the innate immune system in humans, an oligomeric protein complex termed the “Inflammasome” forms in myeloid cells. The canonical output of activation of any subset of inflammasome is Caspase-1-mediated secretion of pro-inflammatory cytokines IL1β and IL18. Chronic or uncontrolled inflammasome activation is at the core of myriad economically burdening diseases. In many of these diseases, endogenous factors chronically engage the innate immune system. To study these diseases in in vivo, …

Attempted Identification Of The Calcium-Dependent Sodium Channel Gene In Paramecium Tetraurelia Using Rnai, Gwendolyn Kuzmishin

Senior Independent Study Theses

Ion channels play an important role in the swimming behavior of Paramecium tetraurelia. Electrophysiological experiments indicate that a calcium-dependent sodium channel exists in Paramecium, but a gene has not been identified for this channel. It is hypothesized that this channel evolved from a voltage-dependent sodium channel after a whole genome duplication event. In this paper, 13 candidate genes were identified from the Paramecium genome based on their similarity to a reference human voltage-dependent sodium channel. Bioinformatics analysis of the selectivity filter of these putative ion channel genes suggested that at least 8 of the candidate genes were sodium channels …

High Borate Glasses For The Controlled Release Of Therapeutic Metal Ions, Kathleen O'Connell

Theses

Within the biomaterial community significant effort has been directed towards engineering materials that induce precise host responses, which are tailored to specific applications. However, this has also seen an increase in the complexity of some biomaterials, which is being increasingly criticised within the literature, as it is attributed to hindering their clinical utility. In this context the release of therapeutic metal ions from glass-based biomaterials have been shown to promote hard tissue repair and regeneration through angiogenesis and osteogenesis processes. Within this thesis project two separate quaternary high borate glass systems were prepared containing the therapeutic metal ions strontium and …

A Five Residue Insertion Between Codons 28 And 29 Of The Hiv-1 Protease Gene Reduces The Replicative Capacity Of The Virus, Cathy Mcleod

Wayne State University Theses

HIV-1 protease (PR) is a 99 amino acid protein responsible for cleavage of the viral polyprotein. We have identified a novel clinical isolate, MDR/28, which contains a five residue insertion between codons 28 and 29 of a multi-drug resistant (MDR) PR. This clinical isolate displays reduced viral replicative capacity compared to the wild-type. As opposed to drug-resistance mutations, studies on insertions remain largely underrepresented in the literature, and the consequences of such insertions are largely unknown. To understand the mechanism leading to reduced replicative capacity, three PR models were created and subjected to 40ns molecular dynamics simulations: MDR/28, wild type, …

Probing Allosteric, Partial Inhibition Of Thrombin Using Novel Anticoagulants, Stephen S. Verespy Iii

Theses and Dissertations

Thrombin is the key protease that regulates hemostasis; the delicate balance between procoagulation and anticoagulation of blood. In clotting disorders, like deep vein thrombosis or pulmonary embolism, procoagulation is up-regulated, but propagation of clotting can be inhibited with drugs targeting the proteases involved, like thrombin. Such drugs however, have serious side effects (e.g., excessive bleeding) and some require monitoring during the course of treatment. The reason for these side effects is the mechanism by which the drugs’ act. The two major mechanisms are direct orthosteric and indirect allosteric inhibition, which will completely abolish the protease’s activity. Herein we sought an …

High Affinity Block Of Icl,Swell By Thiol-Reactive Small Molecules, Sung H. Park

Theses and Dissertations

Ebselen (Ebs) is considered as a glutathione peroxidase (GPx) mimetic and primarily thought to function by scavenging intracellular reactive oxygen species (ROS). Previous to our work, Deng et al. (2010a) demonstrated complete block of I_Cl,swell with 15 microM Ebs following endothelin-1 (ET-1) induced activation of the current in cardiomyocytes. This block was presumed to take effect mainly via the quenching of ROS. Nonetheless, our work with DI TNC1 astrocytes strongly emphasizes that Ebs might function by an alternative mechanism based on its kinetic profile in blocking I_Cl,swell. Our experiments showed that 45 nM Ebs can fully block …

Investigating The Mechanism Of The Compartmentalized Cbp (Creb-Binding Protein) Ubiquitin Ligase Activities, Oluwatoyin E. Akande

Theses and Dissertations

CBP (CREB Binding Protein) is global transcriptional co-activator and histone acetyltransferase. CBP is involved in the modulation of the transcription of many genes via histone acetylation at the promoter regions of the target genes. Also, non-histone proteins and transcription factors can be acetylated by CBP to promote their transcriptional activation. In addition to its transcription co-activator role, CBP is involved in many other pathological and physiological cellular processes such as cell growth and differentiation, cell transformation and development, response to stress, cell cycle regulation and apoptosis.

CBP and its paralogue p300, play double-edged roles in the regulation of p53, a …

Celecoxib Enhances Sorafenib/Sildenafil Lethality In Cancer Cells And Reverts Platinum Chemotherapy Resistance, Timothy A. Webb

Theses and Dissertations

The present studies sought to determine whether the lethality of the drug combination [sorafenib + sildenafil] could be enhanced by the anti-inflammatory agent celecoxib, using ovarian cancer and other tumor cell lines as models. Also, in a dose dependent fashion celecoxib enhanced [sorafenib + sildenafil] lethality in multiple ovarian cancer cell lines. In a dose dependent fashion celecoxib enhanced the ability of [sorafenib + sildenafil] to reduce expression of multiple chaperone proteins in parallel with lower levels of the drug efflux pumps ABCB1 and ABCG2. Over-expression of GRP78 and HSP27 maintained pump expression in the presence of drugs. Cell killing …

The Study Of The Regulon Of Oxyr In Escherichia Coli And Porphyromonas Gingivalis, Christopher K. Pham

Theses and Dissertations

The facultative anaerobe, Escherichia coli and the obligate anaerobe, Porphyromonas gingivalis are two bacteria that reside in our body. Although they reside in separate environments, they are both subject to hydrogen peroxide stress and have mechanisms to regulate the stress. OxyR is the primary transcriptional regulator/sensor of oxidative stress response caused by hydrogen peroxide. OxyR in P. gingivalis is not well-characterized compared to OxyR in E. coli. We sought to characterize and compare the two forms of OxyR in order to gain a better understanding of the protein. We determined the oligomeric state of both proteins: primarily a tetramer for …

Resolution Of Inflammation Rescues Axon Initial Segment Disruption, Nicholas M. George

Theses and Dissertations

Axonal domains are required for proper neuron function. These domains are unstable and degenerate concurrent with the inflammation in multiple sclerosis (MS) and the inflammatory disease models experimental autoimmune encephalomyelitis (EAE) and lipopolysaccharide (LPS) induced inflammation. Previous studies from our laboratory have shown that the axon initial segment (AIS) is maintained independently of the presence of myelin, but that AIS disruption is seen in MS as well as EAE and LPS-mediated inflammation. AIS loss can be interrupted in the early stage of EAE using the anti-inflammatory drug Didox. However, the potential for Didox directed repair of the AIS in later …

Conditional Cardiac-Specific Akap13 Knockout Induces Sex Dependent Biventricular Dilated Cardiomyopathy With Sarcomeric And Mitochondrial Defects, Kimberlyn M. Baig-Ward

Theses and Dissertations

Heart disease is a complex and heterogeneous disease. Notably, studies have demonstrated gender differences in the expression and types of cardiovascular disease, such as dilated cardiomyopathy (DCM), a major underlying cause of heart failure. Previously we showed that loss of A-Kinase Anchoring Protein 13 (Akap13), a unique proto-oncogene and estrogen receptor modulator, resulted in enlarged embryonic hearts, defective cardiac sarcomere formation, and embryonic lethality in mice. Data have also shown cAMP-dependent Protein Kinase A (PKA) to be involved in DCM pathophysiology. Given the established role of AKAP13 in cell signaling, its ability to bind and modulate ligand-activated nuclear hormone …

Role Of Vav2 In Podocyte Inflammasome Activation And Glomerular Injury During Hyperhomocysteinemia, Sabena Conley

Theses and Dissertations

Hyperhomocysteinemia (hHcys) is a widely known pathogenic factor in the progression of end-stage renal disease (ESRD) and it is also associated with an increased risk for injurious cardiovascular pathologies during ESRD. HHcys is linked to the formation and activation of the NOD-like receptor protein 3 (NLRP3) inflammasome, characterized as a critical early mechanism initiating the inflammatory response. NADPH oxidase (NOX)-derived reactive oxygen species (ROS) mediate the activation of the NLRP3 inflammasome in podocytes in response to elevated levels of homocysteine (Hcys) in vitro and in vivo. However, it remains unknown how NLRP3 inflammasome activation is triggered by NOX. The …

Atm Phosphorylates Subunit A Of Pp2a Resulting In Its Nuclear Export And Spatiotemporal Regulation Of The Dna Damage Response, Amrita D. Sule

Theses and Dissertations

Ataxia telangiectasia mutated (ATM) is a serine-threonine protein kinase and major regulator of the DNA damage response (DDR). One critical ATM target is protein phosphatase 2A (PP2A) known to regulate diverse cellular processes such as mitosis and cell growth as well as dephosphorylation of many proteins during the recovery from the DDR while returning the cell to normalcy. Interestingly, ATM and PP2A are known to form an auto-regulatory yin-yang kinase-phosphatase relationship. Herein, we show that the phosphorylation of the PP2A-Aα structural subunit at S401 by ATM results in nuclear export, which regulates the DDR at multiple levels and affects genomic …

Artemisinin Production By Plant Hairy Root Cultures In Gas- And Liquid-Phase Bioreactors, Nivedita Patra, Ashok K. Srivastava

Articles

Key message

Alternative biotechnological protocol for large-scale artemisinin production was established. It featured enhanced growth and artemisinin production by cultivation of hairy roots in nutrient mist bioreactor (NMB) coupled with novel cultivation strategies.

Artemisinin is used for the treatment of cerebral malaria. Presently, its main source is from seasonal plant Artemisia annua. This study featured investigation of growth and artemisinin production by A. annua hairy roots (induced by Agrobacterium rhizogenes-mediated genetic transformation of explants) in three bioreactor configurations—bubble column reactor, NMB and modified NMB particularly to establish their suitability for commercial production. It was observed that cultivation of …

Quantitative Comparison Of A Nanoengineered Alumina Coated Cnt Arrays To Sio2 Coated Cnts And Solution Based Delivery System, Shree Aier

Maseeh Summer Undergraduate Research Experience

To meet the growing need for nanoengineered biocompatible materials to serve as drug delivery platforms, in this research, carbon nanotube arrays were fabricated by chemical vapor deposition, followed by an alumina coating by the high yielding, tightly controlled atomic layer deposition. This nanoengineered vertically aligned alumina nanowire array serves as a platform for delivering antigens, which act as cancer adjuvants. The physicochemical characteristics of the nanowires (NWs) can significantly influence the delivery of a biomolecule to immune cells. To investigate the material characteristics, the delivery efficiency of the antigen using NWs was quantitatively assessed by flow cytometry. Further, the mechanism …

Small Molecule Disruption Of Ros-Regulating Pathways In Human Carcinoma, Rebecca E. Mccall

College of Graduate Studies: Theses & Dissertations

Gold (I) coordinated N-heterocyclic carbenes containing appended redox cycling moieties were designed and analyzed for their ability to target the antioxidant network via multiple mechanisms in various human cancer cell models. Complexes containing either ferrocene or naphthoquinone redox cycling moieties were screened for inhibition of cell growth, inhibition of thioredoxin reductase (TrxR), and accentuation of exogenous ROS. The cell death pathway employed was determined by flow cytometry via detection of Annexin-V FITC. Furthermore, differential gene expression between treated cells and untreated cells revealed the induction of endoplasmic reticulum stress and unfolded protein response pathways.

Identification And Characterization Of Small Molecules Targeting Fkbp52 As A Novel Treatment For Prostate Cancer, Naihsuan C. Guy

Open Access Theses & Dissertations

Prostate cancer (PCa) is one of the most commonly diagnosed diseases and the second leading cause of cancer deaths among men worldwide. Its growth is dependent upon androgen receptor (AR) signaling and the mainstay for treatment is hormone-ablation therapy using antiandrogens and/or androgen-deprivation therapies (ADT). Treatment of PCa with antiandrogens and/or ADT are initially effective; they act to repress the AR by directly competing with androgens for the ligand binding domain (LBD) and prevent activation of the receptor resulting in tumor regression. Unfortunately, the resistance to these treatments invariably emerges and results in a much more aggressive form of tumor …

A Requirement For Y841 In Jak3 Enzymatic Activity And Hematopoietic Cancers, George Steven Martinez

Open Access Theses & Dissertations

A medical need exists for successfully treating people afflicted with leukemia, especially those who develop drug resistant forms. Relapse leukemia cases are particularly high within Hispanic populations where this disease is among the most frequently occurring cancer. Fourteen somatic mutations have been reported in Janus tyrosine kinase 3 (Jak3), including M511I and A573V, from patients with various forms of leukemia. To monitor drug sensitivity, a model system was developed. Indeed, many of these mutations have been shown to possess transforming ability in cell lines such as the IL-3 dependent pro-B cell line Ba/F3. As such, Ba/F3 cells were transformed to …

Structure And Biological Activity Of A D3g Mutation In The Human Mitochondrial Chaperonin Hsp60, Jihui Li

Open Access Theses & Dissertations

Proteins are essential components in all cellular activities, including signal transduction, gene expression regulation, immune response, structural support and many others. Following their synThesis on the ribosome, proteins need to fold into their precise three-dimensional structure to obtain functionality. If they fold incorrectly they are prone to aggregation and cause a wide range of neurodegenerative diseases. Some proteins are capable of folding without assistance but others need help from protein complexes known as chaperonins. Chaperonins are a family of proteins that assemble into barrel-shaped cages the create a protected chamber for misfolded proteins to refold into their biologically active state. …

Comparative Proteomic Analysis Of Extracellular Vesicles From Prostate Cancer-Derived Cell Lines, Gloria Polanco

Open Access Theses & Dissertations

Prostate cancer (PCa) is the leading non-cutaneous malignancy and the second deadliest among American men. PCa mortality rates among African American men are much higher than any other ethnic group, and the same is true for men of African ancestry world-wide. There is also a lack of reliable diagnostic markers and effective treatment options. Extracellular vesicles (EVs) have been observed to play an important role in cancer processes such as promotion of tumor growth and metastasis. They are also a promising source of diagnostic markers. This study addresses these problems by studying the proteome of EVs derived from PCa cells …

Local Corticotropin Releasing Hormone (Crh) Signals To Its Receptor Crhr1 During Postnatal Development Of The Mouse Olfactory Bulb, Isabella Garcia, Paramjit K Bhullar, Burak Tepe, Joshua Ortiz-Guzman, Longwen Huang, Alexander M Herman, Lesley Chaboub, Benjamin Deneen, Nicholas J Justice, Benjamin R Arenkiel

Faculty, Staff and Students Publications

Neuropeptides play important physiological functions during distinct behaviors such as arousal, learning, memory, and reproduction. However, the role of local, extrahypothalamic neuropeptide signaling in shaping synapse formation and neuronal plasticity in the brain is not well understood. Here, we characterize the spatiotemporal expression profile of the neuropeptide corticotropin-releasing hormone (CRH) and its receptor CRHR1 in the mouse OB throughout development. We found that CRH-expressing interneurons are present in the external plexiform layer, that its cognate receptor is expressed by granule cells, and show that both CRH and CRHR1 expression enriches in the postnatal period when olfaction becomes important towards olfactory-related …

Novel Cell Penetrating Peptide-Adaptors Effect Intracellular Delivery And Endosomal Escape Of Protein Cargos, John C. Salerno, Verra M. Ngwa, Scott J. Nowak, Carol A. Chrestensen, Allison N. Healey, Jonathan L. Mcmurry

Faculty Articles

The use of cell penetrating peptides (CPPs) as biomolecular delivery vehicles holds great promise for therapeutic and other applications, but development has been stymied by poor delivery and lack of endosomal escape. We have developed a CPP-adaptor system capable of efficient intracellular delivery and endosomal escape of user-defined protein cargos. The cell penetrating sequence of HIV transactivator of transcription was fused to calmodulin, which binds with subnanomolar affinity to proteins containing a calmodulin binding site. Our strategy has tremendous advantage over prior CPP technologies because it utilizes high affinity noncovalent, but reversible coupling between CPP and cargo. Three different cargo …