Biochemistry, Biophysics, and Structural Biology Commons^™

Ceramide Induces Human Hepcidin Gene Transcription Through Jak/Stat3 Pathway, Sizhao Lu, Sathish Kumar Natarajan, Justin L. Mott, Kusum K. Kharbanda, Duygu Dee Harrison-Findik

Department of Biochemistry: Faculty Publications

Changes in lipid metabolism and iron content are observed in the livers of patients with fatty liver disease. The expression of hepcidin, an iron-regulatory and acute phase protein synthesized by the liver, is also modulated. The potential interaction of lipid and iron metabolism is largely unknown.We investigated the role of lipid intermediate, ceramide in the regulation of human hepcidin gene, HAMP. Human hepatoma HepG2 cells were treated with cell-permeable ceramide analogs. Ceramide induced significant up-regulation of HAMP mRNA expression in HepG2 cells. The effect of ceramide on HAMP expression was mediated through transcriptional mechanisms because it was completely blocked …

Engineering A Trifunctional Proline Utilization A Chimaera By Fusing A Dna-Binding Domain To A Bifunctional Puta, Benjamin W. Arentson, Erin L. Hayes, Weidong Zhu, John J. Tanner, Donald F. Becker

Department of Biochemistry: Faculty Publications

Proline utilization A (PutA) is a bifunctional flavoenzyme with proline dehydrogenase (PRODH) and Δ¹-pyrroline-5- carboxylate (P5C) dehydrogenase (P5CDH) domains that catalyses the two-step oxidation of proline to glutamate. Trifunctional PutAs also have an N-terminal ribbon–helix–helix (RHH) DNA-binding domain and moonlight as autogenous transcriptional repressors of the put regulon. A unique property of trifunctional PutA is the ability to switch functions from DNA-bound repressor to membrane-associated enzyme in response to cellular nutritional needs and proline availability. In the present study, we attempt to construct a trifunctional PutA by fusing the RHH domain of Escherichia coli PutA (EcRHH) to the …

Mechanistic Nanotherapeutic Approach Based On Sirna-Mediated Dj-1 Protein Suppression For Platinum-Resistant Ovarian Cancer, Canan Schumann, Stephanie Chan, Oleh Khalimonchuk, Shannon Khal, Vitaliya Moskal, Vidhi Shah, Adam W. G. Alani, Olena Taratula, Oleh Taratula

Department of Biochemistry: Faculty Publications

We report an efficient therapeutic modality for platinum resistant ovarian cancer based on siRNAmediated suppression of a multifunctional DJ-1 protein that is responsible for the proliferation, growth, invasion, oxidative stress and overall survival of various cancers. The developed therapeutic strategy can work alone or in concert with a low dose of the first line chemotherapeutic agent cisplatin, to elicit a maximal therapeutic response. To achieve an efficient DJ-1 knockdown, we constructed the polypropylenimine dendrimer-based nanoplatform targeted to LHRH receptors overexpressed on ovarian cancer cells. The quantitative PCR and western immunoblotting analysis, revealed that the delivered DJ-1 siRNA downregulated the expression …

Antisense Oligonucleotides: Treatment Strategies And Cellular Internalization, Colton M. Miller, Ed Harris

Department of Biochemistry: Faculty Publications

The clinical application of antisense oligonucleotides (ASOs) is becoming more of a reality as several drugs have been approved for the treatment of human disorders and many others are in various phases in development and clinical trials. ASOs are short DNA/RNA oligos which are heavily modified to increase their stability in biological fluids and retain the properties of creating RNA-RNA and DNA-RNA duplexes that knock-down or correct genetic expression. This review outlines several strategies that ASOs utilize for the treatment of various congenital diseases and syndromes that develop with aging. In addition, we discuss some of the mechanisms for specific …

Logical Modeling And Dynamical Analysis Of Cellular Networks, Wassim Abou-Jaoudé, Pauline Traynard, Pedro T. Monteiro, Julio Saez-Rodriguez, Tomáš Helikar, Denis Thieffry, Claudine Chaouiya

Department of Biochemistry: Faculty Publications

The logical (or logic) formalism is increasingly used to model regulatory and signaling networks. Complementing these applications, several groups contributed various methods and tools to support the definition and analysis of logical models. After an introduction to the logical modeling framework and to several of its variants, we review here a number of recent methodological advances to ease the analysis of large and intricate networks. In particular, we survey approaches to determine model attractors and their reachability properties, to assess the dynamical impact of variations of external signals, and to consistently reduce large models. To illustrate these developments, we further …

Antisense Oligonucleotides: Treatment Strategies And Cellular Internalization, Colton M. Miller, Edward N. Harris

Department of Biochemistry: Faculty Publications

The clinical application of antisense oligonucleotides (ASOs) is becoming more of a reality as several drugs have been approved for the treatment of human disorders and many others are in various phases in development and clinical trials. ASOs are short DNA/RNA oligos which are heavily modified to increase their stability in biological fluids and retain the properties of creating RNA-RNA and DNA-RNA duplexes that knock-down or correct genetic expression. This review outlines several strategies that ASOs utilize for the treatment of various congenital diseases and syndromes that develop with aging. In addition, we discuss some of the mechanisms for specific …

Polyglycine Acts As A Rejection Signal For Protein Transport At The Chloroplast Envelope, Joshua K. Endow, Agostinho Gomes Rocha, Amy J. Baldwin, Rebecca L. Roston, Toshio Yamaguchi, Hironari Kamikubo, Kentaro Inoue

Department of Biochemistry: Faculty Publications

PolyGly is present in many proteins in various organisms. One example is found in a transmembrane β-barrel protein, translocon at the outer-envelope-membrane of chloroplasts 75 (Toc75). Toc75 requires its N-terminal extension (t75) for proper localization. t75 comprises signals for chloroplast import (n75) and envelope sorting (c75) in tandem. n75 and c75 are removed by stromal processing peptidase and plastidic type I signal peptidase 1, respectively. PolyGly is present within c75 and its deletion or substitution causes mistargeting of Toc75 to the stroma. Here we have examined the properties of polyGly-dependent protein targeting using two soluble passenger proteins, the mature portion …

Mutation In Atg5 Reduces Autophagy And Leads To Ataxia With Developmental Delay, Myungjin Kim, Erin Sandford, Damian Gatica, Yu Qiu, Xu Liu, Yumei Zheng, Brenda A. Schulman, Jishu Xu, Ian Semple, Seung-Hyun Ro, Boyoung Kim, R. Nehir Mavioglu, Aslihan Tolun, Andras Jipa, Szabolcs Takats, Manuela Karpati, Jun Z. Li, Zuhal Yapici, Gabor Juhasz, Jun Hee Lee, Daniel J. Klionsky, Margit Burmeister

Department of Biochemistry: Faculty Publications

Autophagy is required for the homeostasis of cellular material and is proposed to be involved in many aspects of health. Defects in the autophagy pathway have been observed in neurodegenerative disorders; however, no genetically-inherited pathogenic mutations in any of the core autophagy-related (ATG) genes have been reported in human patients to date. We identified a homozygous missense mutation, changing a conserved amino acid, in ATG5 in two siblings with congenital ataxia, mental retardation, and developmental delay. The subjects’ cells display a decrease in autophagy flux and defects in conjugation of ATG12 to ATG5. The homologous mutation in yeast …

Can Chilling Tolerance Of C4 Photosynthesis In Miscanthus Be Transferred To Sugarcane?, Katarzyna Glowacka, Aasifuddin Ahmed, Shailendra Sharma, Tom Abbott, Jack C. Comstock, Stephen P. Long, Erik J. Sacks

Department of Biochemistry: Faculty Publications

The goal of this study was to investigate whether chilling tolerance of C₄ photosynthesis in Miscanthus can be transferred to sugarcane by hybridization. Net leaf CO₂ uptake (A_sat) and the maximum operating efficiency of photosystem II (Ф_PSII) were measured in warm conditions (25 °C/20 °C), and then during and following a chilling treatment of 10 °C/5 °C for 11 day in controlled environment chambers. Two of three hybrids (miscanes), ‘US 84-1058’ and ‘US 87-1019’, did not differ significantly from the chilling tolerant M. xgiganteus ‘Illinois’ (Mxg), for A_sat, and Φ …

Novel Acyltranserases And Methods Of Using, Edgar B. Cahoon, Umidjon Iskandarov, Hae Jin Kim, Jillian Collins-Silva

Department of Biochemistry: Faculty Publications

Provided herein are novel acyltransferases and methods of using Such novel acyltransferases in making medium-chain fatty acids.

High-Throughput Mutation, Selection, And Phenotype Screening Of Mutant Methanogenic Archaea, Mary E. Walter, Alicia Ortiz, Casey Sondgeroth, Nathan M. Sindt, Nikolas Duszenko, Jennie L. Catlett, You Zhou, Shah R. Valloppilly, Christopher Anderson, Samodha Fernando, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Bacterial and archaeal genomes can contain 30% or more hypothetical genes with no predicted function. Phylogenetically deep-branching microbes, such as methane-producing archaea (methanogens), contain up to 50% genes with unknown function. In order to formulate hypotheses about the function of hypothetical gene functions in the strict anaerobe, Methanosarcina acetivorans, we have developed high-throughput anaerobic techniques to UV mutagenize, screen, and select for mutant strains in 96-well plates. Using these approaches we have isolated 10 mutant strains that exhibit a variety of physiological changes including increased or decreased growth rate relative to the parent strain when cells use methanol and/or …

Mutual Information Upper Bound Of Molecular Communication Based On Cell Metabolism, Massimiliano Pierobon, Zahmeeth Sakkaff, Jennie L. Catlett, Nicole R. Buan

Department of Biochemistry: Faculty Publications

Synthetic biology is providing novel tools to engineer cells and access the basis of their molecular information processing, including their communication channels based on chemical reactions and molecule exchange. Molecular communication is a discipline in communication engineering that studies these types of communications and ways to exploit them for novel purposes, such as the development of ubiquitous and heterogeneous communication networks to interconnect biological cells with nano and biotechnology-enabled devices, i.e., the Internet of Bio-Nano Things. One major problem in synthetic biology stands in the development of reliable techniques to control the engineered cells from the external environment. In this …

Molecular Mechanism Of The Priming By Jasmonic Acid Of Specific Dehydration Stress Response Genes In Arabidopsis, Ning Liu, Zoya Avramova

School of Biological Sciences: Faculty Publications

Background: Plant genes that provide a different response to a similar dehydration stress illustrate the concept of transcriptional ‘dehydration stress memory’. Pre-exposing a plant to a biotic stress or a stress-signaling hormone may increase transcription from response genes in a future stress, a phenomenon known as ‘gene priming’. Although known that primed transcription is preceded by accumulation of H3K4me3 marks at primed genes, what mechanism provides for their appearance before the transcription was unclear. How augmented transcription is achieved, whether/how the two memory phenomena are connected at the transcriptional level, and whether similar molecular and/or epigenetic mechanisms regulate them are …

Suppression Of Nlrp3 Inflammasome By Γ-Tocotrienol Ameliorates Type 2 Diabetes, Yongeun Kim, Wei Wang, Meshail Okla, Inhae Kang, Regis Moreau, Soonkyu Chung

Department of Nutrition and Health Sciences: Faculty Publications

The Nod-like receptor 3 (NLRP3) inflammasome is an intracellular sensor that sets off the innate immune system in response to microbial-derived and endogenous metabolic danger signals. We previously reported that γ-tocotrienol (γT3) attenuated adipose tissue inflammation and insulin resistance in diet-induced obesity, but the underlying mechanism remained elusive. Here, we investigated the effects of γT3 on NLRP3 inflammasome activation and attendant consequences on type 2 diabetes. γT3 repressed inflammasome activation, caspase-1 cleavage, and interleukin (IL) 1β secretion in murine macrophages, implicating the inhibition of NLRP3 inflammasome in the anti-inflammatory and antipyroptotic properties of γT3. Furthermore, supplementation of leptin-receptor KO mice …

Effect Of Two-Year Caloric Restriction On Bone Metabolism And Bone Mineral Density In Non-Obese Younger Adults: A Randomized Clinical Trial, Dt Villareal, L Fontana, Sk Das, Et Al.

Faculty, Staff and Students Publications

Although caloric restriction (CR) could delay biologic aging in humans, it is unclear if this would occur at the cost of significant bone loss. We evaluated the effect of prolonged CR on bone metabolism and bone mineral density (BMD) in healthy younger adults. Two-hundred eighteen non-obese (body mass index [BMI] 25.1?±?1.7?kg/m(2) ), younger (age 37.9?±?7.2 years) adults were randomly assigned to 25% CR (CR group, n?=?143) or ad libitum (AL group, n?=?75) for 2 years. Main outcomes were BMD and markers of bone turnover. Other outcomes included body composition, bone-active hormones, nutrient intake, and physical activity. Body weight (-7.5?±?0.4 versus …

Transcriptional Regulation Of Specialized Metabolites In Arabidopsis Thaliana And Catharanthus Roseus, Craig M. Schluttenhofer

Theses and Dissertations--Plant and Soil Sciences

For millennia humans have utilized plant specialized metabolites for health benefits, fragrances, poisons, spices, and medicine. Valued metabolites are often produced in small quantities and may command high prices. Understanding when and how the plant synthesizes these compounds is important for improving their production. Phytohormone signaling cascades, such as jasmonate (JA) activate or repress transcription factors (TF) controlling expression of metabolite biosynthetic genes. TFs regulating specialized metabolite biosynthetic genes can be manipulated to engineer plants with increased metabolite production.

WRKY transcription factor are known components of both JA signaling cascades and regulation of specialized metabolism. The presence of WRKY binding …

Effect Of Quantum Dots, Novel Biological Imaging Agents, In Liver Cells In Vitro, Utshaha Maharjan

All Master's Theses

The use of Quantum dots (QDs) coated with polymer and functionalized with carboxylic acid groups in medical applications are explored. Their water solubility and exceptional stability in aqueous environments make them potentially useful for such applications as imaging and ligand attachments. However, there are concerns regarding the toxic effects of QDs and the minimal dose that can be used without producing any detrimental effects to organisms. In this study, QDs coated with the amphiphilic polymer coating tri-n-octylphosphine oxide and poly (maleic anhydride-alt-1-tetradecene (TOPO-PMAT)) which is functionalized with carboxylic acid groups were used to investigate their toxic effect in mouse liver …

Confirmation Of Emx2 Protein Binding Partners, Cody Gillman

All Master's Theses

The neocortex is a structure within mammalian brains that processes sensory input from eyes, ears, and touch receptors and mediates the conscious use of skeletal muscles. The processing of information related to each of these types of functions is localized within discrete areas of the neocortex, which are separated by sharp borders. Proper development of these functional areas is regulated during embryogenesis by several transcription factors that are expressed in distinct gradients across the progenitor layer of the neocortex, the ventricular zone. Despite the vast amount of progress that has been made in describing how these transcription factors impact the …

An Investigation Of Juvenile Alewife (Alosa Pseudoharengus) Habitat Use And Growth Using Natural Markers, Gregory Norman Labonte Ms

All Student Scholarship

This research attempts to connect patterns in growth and migration of an anadromous species. The goal of this research was to understand habitat movements and growth of juvenile alewives (Alosa pseudoharengus) in the Penobscot Estuary and Bay through the use of otolith microchemistry, otolith growth increments, and a laboratory stable isotope turnover study. Understanding the connection between growth and movement of juvenile alewives may lead to more accurate and sophisticated conservation and restoration methods for anadromous species.

Piperlongumine (Piplartine) And Analogues: Antiproliferative Microtubule-Destabilising Agents, Mary J. Meegan, Seema M. Nathwani, Brendan Twamley, Daniela M. Zisterer, Niamh O'Boyle

Articles

Piperlongumine (piplartine, 1) is a small molecule alkaloid that is receiving intense interest due to its antiproliferative and anticancer activities. We investigated the effects of 1 on tubulin and microtubules. Using both an isolated tubulin assay, and a combination of sedimentation and Western blotting, we demonstrated that 1 is a tubulin-destabilising agent. This result was confirmed by immunofluorescence and confocal microscopy, which showed that microtubules in MCF-7 breast cancer cells were depolymerised when treated with 1. We synthesised a number of analogues of 1 to explore structure-activity relationships. Compound 13 had the best cytotoxic profile of this series, …

A Fret Investigation Into Molecular Mechanisms Of Cardiac Troponin Activation In Reconstituted Thin Filaments, Maria Eleni Moutsoglou

Electronic Theses and Dissertations

Cardiomyopathies (CM) are the leading cause of death in America, and can develop from mutations in sarcomeric proteins, leading to altered protein structure and function. Current therapies target upstream signaling pathways to treat the symptoms of heart failure, but are associated with increased mortality by affecting downstream signaling pathways and other muscle types. Rational drug design can develop therapies to treat CM at the protein level. However, a detailed knowledge of how sarcomeric proteins regulate muscle contraction is required. Muscle contraction occurs through a cyclic interaction between actin thin and myosin thick filaments, regulated by intracellular Ca2+ concentration. Troponin (Tn), …

Epigenetic Response To Habitat Change: Changes Variation In Dna Methylation Frequencies And Generational Transmission Vary With Invasion Status, Aaron W. Schrey, Travis R. Robbins, Jacob D. Lee, David W. Dukes, Alexandria K. Ragsdale, Christopher J. Thawley, Tracy Langkilde

Biology: Faculty Publications

Epigenetic mechanisms may be important for a native species’ response to rapid environmental change. Red Imported Fire Ants (Solenopsis invicta Santschi, 1916) were recently introduced to areas occupied by the Eastern Fence Lizard (Sceloporus undulatus Bosc & Daudin, 1801). Behavioral, morphological and physiological phenotypes of the Eastern Fence Lizard have changed following invasion, creating a natural biological system to investigate environmentally induced epigenetic changes. We tested for variation in DNA methylation patterns in Eastern Fence Lizard populations associated with different histories of invasion by Red Imported Fire Ants. At methylation sensitive amplified fragment length polymorphism loci, we detected a higher …

Novel Regulatory Mechanisms Of Inositol Biosynthesis In Saccharomyces Cerevisiae And Mammalian Cells, And Implications For The Mechanism Underlying Vpa-Induced Glucose 6-Phosphate Depletion, Wenxi Yu

Wayne State University Dissertations

Myo-inositol is the precursor of all inositol containing molecules, including inositol phosphates, phosphoinositides and glycosylphosphatidylinositols, which are signaling molecules involved in many critical cellular functions. Perturbation of inositol metabolism has been linked to neurological disorders. Although several widely-used anticonvulsants and mood-stabilizing drugs have been shown to exert inositol depletion effects, the mechanisms of action of the drugs and the role of inositol in these diseases are not understood. Elucidation of the molecular control of inositol synthesis will shed light on the pathologies of inositol related illnesses.

In Saccharomyces cerevisiae, deletion of the four glycogen synthase kinase-3 genes, MCK1, MRK1, MDS1, …

Cardiolipin Is Required For Optimal Acetyl-Coa Metabolism, Vaishnavi Raja

Wayne State University Dissertations

The phospholipid cardiolipin (CL) is crucial for many cellular functions and signaling pathways, both inside and outside of mitochondria. My thesis focuses on the role of CL in energy metabolism. Many reactions of electron transport and oxidative phosphorylation, the transport of metabolites needed for these processes, and the stabilization of electron transport chain supercomplexes, require CL. Recent studies indicate that CL is required for the synthesis of iron-sulfur (Fe-S) co-factors, which are essential for numerous metabolic pathways. Activation of carnitine-acetylcarnitine translocase, which transports acetyl-CoA into the mitochondria, is CL dependent. The presence of substantial amounts of CL in the peroxisomal …

Structural Characterization And Therapeutic Utility Of The Proton-Coupled Folate Transporter, Michael Roy Wilson

Wayne State University Dissertations

Folate is a B9 vitamin essential to DNA synthesis. The proton-coupled folate transporter (PCFT) is a newly discovered proton/folate symporter with an acidic pH optimum and broad expression across a variety of solid tumor types, with limited expression in normal tissues. Several antifolate molecules have been developed as cancer therapeutics, although these classical antifolates display numerous off-target effects due to transport by the ubiquitous reduced folate carrier (RFC). In this dissertation, we determine the roles of multiple PCFT structure/function domains, and develop PCFT-specific antifolates to target solid tumors. We utilize substituted cysteine accessibility methods (SCAM) to identify a novel reentrant …

From Seed To Sky: Impacts Of Explosive Compounds On Vegetation Across Spatial And Developmental Scales, Stephen M. Via

Theses and Dissertations

Explosive compounds are broadly distributed across the globe as a result of nearly two centuries of munitions use in warfare and military activities. Two explosive compounds have seen disproportionate use; RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) and TNT (2-methyl- 1,3,5-trinitrobenzene), being the most commonly found explosives in the environment. The effects of explosives on biota have been studied in great detail; however, there is a general lack of understanding with regard to broader ecological impacts of these contaminants. My dissertation objective was to follow the impacts of explosive compounds on vegetation across scales. Impacts on vegetation at the species scale alter community composition via …

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 …

Understanding Dna Condensation By Low Generation (G0/G1) And Zwitterionic G4 Pamam Dendrimers, Min An

Theses and Dissertations--Chemistry

Cationic polymers have shown potential as gene delivery vectors due to their ability to condense DNA and protect it from cellular and restriction nucleases. Dendrimers are hyperbranched macromolecules with precisely defined molecular weights and highly symmetric branches stemming from a central core. The nanosize, tunable surface chemistries and ease of surface functionalization has made dendrimers an attractive alternative to conventional linear polymers for DNA delivery applications. The commercially available, cationic dendrimer poly(amidoamine) or PAMAM is the most widely studied dendrimer for use as a gene delivery vector. The aim of this dissertation is to provide an increased understanding of the …

The Development Of Colorimetric Assays To Determine The Identity And Frequency Of Specific Nucleobases In Dna Oligomers, Elizabeth Marie Thomas

Theses and Dissertations--Chemistry

Colorimetric methods combined with color-changing chemical probes are widely used as simple yet effective tools for identifying and quantifying a wide variety of molecules in solution. For nucleic acids (DNA and RNA), perhaps the most commonly used colorimetric probe is potassium permanganate, which can be used to identify single-stranded pyrimidines (thymine and cytosine) in polymers. Unfortunately, permanganate is not an effective probe for identifying purines (adenine and guanine), especially in the presence of the more reactive pyrimidines. Therefore, robust methods for discriminating between the purines remain elusive, thereby creating a barrier toward developing more complex colorimetric applications. In this dissertation, …

Assembly And Degradation Of A Trimeric Membrane Protein Acrb, Qian Chai

Theses and Dissertations--Chemistry

Multidrug efflux pumps are membrane proteins that actively transport foreign objects out of cells. The active efflux of these pumps is a critical self-defense mechanism that enables the survival of bacteria under hostile environments. Efflux pump AcrB is a member of the Resistance-Nodulation-Division (RND) super family. In E. coli, it associates with periplasmic protein AcrA and outer membrane channel TolC to extrude a variety of noxious compounds out of cell from both the cytoplasm and the periplasm. My dissertation research focused on two aspects of this multidrug efflux pump: the oligomerization process during the biogenesis of AcrB and its …