Biochemistry Commons^™

Rapid And Noncontaminating Sampling System For Trace Elements In Global Ocean Surveys, Gregory A. Cutter, Kenneth W. Bruland

OES Faculty Publications

A system for the rapid and noncontaminating sampling of trace elements with volumes of up to 36 L per depth and including the dissolved and particulate phases has been developed for ocean sections that are a crucial part of programs such as International GEOTRACES. The system uses commercially available components, including an aluminum Seabird Carousel with all titanium pressure housings for electronics and sensors to eliminate zinc sacrificial anodes and holding twenty-four 12 L GO-FLO bottles, and a 7500 m, 14 mm Vectran conducting cable (passing over an A-frame with nonmetallic sheave) spooled onto a traction winch. The GO-FLO bottles …

Interfamily Variation In Amphibian Early Life-History Traits: Raw Material For Natural Selection?, Gareth R. Hopkins, Brian G. Gall, Susannah S. French, Edmund D. Brodie Jr.

Biology Faculty Publications

The embryonic development and time to hatching of eggs can be highly adaptive in some species, and thus under selective pressure. In this study, we examined the underlying interfamily variation in hatching timing and embryonic development in a population of an oviparous amphibian, the rough-skinned newt (Taricha granulosa). We found significant, high variability in degree of embryonic development and hatching timing among eggs from different females. Patterns of variation were present regardless of temperature.We also could not explain the differences among families by morphological traits of the females or their eggs. This study suggests that the variation necessary for natural …

Dimerization And Heme Binding Are Conserved In Amphibian And Starfish Homologues Of The Microrna Processing Protein Dgcr8., Rachel Senturia, Arthur Laganowsky, Ian Barr, Brooke D. Scheidemantle, Feng Guo

Natural Sciences and Mathematics | Faculty Scholarship

Human DiGeorge Critical Region 8 (DGCR8) is an essential microRNA (miRNA) processing factor that is activated via direct interaction with Fe(III) heme. In order for DGCR8 to bind heme, it must dimerize using a dimerization domain embedded within its heme-binding domain (HBD). We previously reported a crystal structure of the dimerization domain from human DGCR8, which demonstrated how dimerization results in the formation of a surface important for association with heme. Here, in an attempt to crystallize the HBD, we search for DGCR8 homologues and show that DGCR8 from Patiria miniata (bat star) also binds heme. The extinction coefficients (ε) …

Genome, Functional Gene Annotation, And Nuclear Transformation Of The Heterokont Oleaginous Alga Nannochloropsis Oceanica Ccmp1779, Astrid Vieler, Guangxi Wu, Chia-Hong Tsai, Blair Bullard, Adam J. Cornish, Christopher Harvey, Ida-Barbara Reca, Chelsea Thornburg, Rujira Achawanantakun, Christopher J. Buehl, Michael S. Campbell, David Cavalier, Kevin L. Childs, Teresa J. Clark, Rahul Deshpande, Erika Erickson, Ann Armenia Ferguson, Witawas Handee, Que Kong, Xiaobo Li, Bensheng Liu, Steven Lundback, Cheng Peng, Rebecca Roston, Michigan State University, Jeffrey P. Simpson, Allan Terbush, Jaruswan Warakanont, Simone Zäuner, Eva M. Farre, Eric L. Hegg, Ning Jiang, Min-Hao Kuo, Yan Lu, Krishna K. Niyogi, John Ohlrogge, Katherine W. Osteryoung, Yair Shachar-Hill, Barbara B. Sears, Yanni Sun, Hideki Takahashi, Mark Yandell, Shin-Han Shiu, Christoph Benning

Department of Biochemistry: Faculty Publications

Unicellular marine algae have promise for providing sustainable and scalable biofuel feedstocks, although no single species has emerged as a preferred organism. Moreover, adequate molecular and genetic resources prerequisite for the rational engineering of marine algal feedstocks are lacking for most candidate species. Heterokonts of the genus Nannochloropsis naturally have high cellular oil content and are already in use for industrial production of high-value lipid products. First success in applying reverse genetics by targeted gene replacement makes Nannochloropsis oceanica an attractive model to investigate the cell and molecular biology and biochemistry of this fascinating organism group. Here we present the …

The Evolutionary Rewiring Of Ubiquitination Targets Has Reprogrammed The Regulation Of Carbon Assimilation In The Pathogenic Yeast Candida Albicans, Doblin Sandai, Zhikang Yin, Laura Selway, David Stead, Janet Walker, Michelle D. Leach, Iryna Bohovych, Iuliana V. Ene, Stavroula Kastora, Susan Budge, Carol A. Munro, Frank C. Odds, Neil A.R. Gow, Alistair J.P. Brown

Department of Biochemistry: Faculty Publications

Microbes must assimilate carbon to grow and colonize their niches. Transcript profiling has suggested that Candida albicans, a major pathogen of humans, regulates its carbon assimilation in an analogous fashion to the model yeast Saccharomyces cerevisiae, repressing metabolic pathways required for the use of alterative nonpreferred carbon sources when sugars are available. However, we show that there is significant dislocation between the proteome and transcriptome in C. albicans. Glucose triggers the degradation of the ICL1 and PCK1 transcripts in C. albicans, yet isocitrate lyase (Icl1) and phosphoenolpyruvate carboxykinase (Pck1) are stable and are retained. Indeed, numerous …

Proline Dehydrogenase Is Essential For Proline Protection Against Hydrogen Peroxide Induced Cell Death, Sathish Kumar Natarajan, Weidong Zhu, Xinwen Liang, Lu Zhang, Andrew Demers, Matthew C. Zimmerman, Melanie A. Simpson, Donald F. Becker

Department of Biochemistry: Faculty Publications

Proline metabolism has an underlying role in apoptotic signaling that impacts tumorigenesis. Proline is oxidized to glutamate in the mitochondria with the rate limiting step catalyzed by proline dehydrogenase (PRODH). PRODH expression is inducible by p53 leading to increased proline oxidation, reactive oxygen species (ROS) formation, and induction of apoptosis. Paradoxical to its role in apoptosis, proline also protects cells against oxidative stress. Here we explore the mechanism of proline protection against hydrogen peroxide stress in melanoma WM35 cells. Treatment of WM35 cells with proline significantly increased cell viability, diminished oxidative damage of cellular lipids and proteins, and retained ATP …

Late-Stage Maturation Of The Rieske Fe/S Protein: Mzm1 Stabilizes Rip1 But Does Not Facilitate Its Translocation By The Aaa Atpase Bcs1, Tie-Zhong Cui, Pamela M. Smith, Jennifer L. Fox, Oleh Khalimonchuk, Dennis R. Winge

Department of Biochemistry: Faculty Publications

The final step in the assembly of the ubiquinol-cytochrome c reductase or bc₁ complex involves the insertion of the Rieske Fe/S cluster protein, Rip1. Maturation of Rip1 occurs within the mitochondrial matrix prior to its translocation across the inner membrane (IM) in a process mediated by the Bcs1 ATPase and subsequent insertion into the bc₁ complex. Here we show that the matrix protein Mzm1 functions as a Rip1 chaperone, stabilizing Rip1 prior to the translocation step. In the absence of Mzm1, Rip1 is prone to either proteolytic degradation or temperature-induced aggregation. A series of Rip1 truncations were engineered …

Bio-Logic Builder: A Non-Technical Tool For Building Dynamical, Qualitative Models, Tomáš Helikar, Bryan Kowal, Alex Madrahimov, Manish Shrestha, Jay Pedersen, Kahani Limbu, Ishwor Thapa, Thaine Rowley, Rahul Satalkar, Naomi Kochi, John Konvalina, Jim A. Rogers

Department of Biochemistry: Faculty Publications

Computational modeling of biological processes is a promising tool in biomedical research. While a large part of its potential lies in the ability to integrate it with laboratory research, modeling currently generally requires a high degree of training in mathematics and/or computer science. To help address this issue, we have developed a web-based tool, Bio- Logic Builder, that enables laboratory scientists to define mathematical representations (based on a discrete formalism) of biological regulatory mechanisms in a modular and non-technical fashion. As part of the user interface, generalized ‘‘biologic’’ modules have been defined to provide users with the building blocks for …

Development Of Mass Spectrometric Methods For The Analysis Of Serotonin And Related Compounds In Biological Matrices, Merisa Moriarty

Theses

Serotonin is a major neurotransmitter in the brain and affects various functions both in the brain and in the rest of the body. It has been linked to depression, migraines, and aggression, as well as many psychiatric disorders including schizophrenia, dementia and anorexia nervosa. It also has been associated with conditions like Alzheimer’s disease along with other neurotransmitters such as dopamine.

The aim of this research project is to develop various mass spectrometric methods for the analysis of serotonin, dopamine and similar indoles in both urine and serum matrices. This thesis provides extensive reviews detailing a general overview of serotonin …

Signals From Intraventricular Depth Electrodes Can Control A Brain-Computer Interface, Jerry J. Shih, Dean J. Krusienski

Electrical & Computer Engineering Faculty Publications

A Brain-Computer Interface (BCI) is a device that enables severely disabled people to communicate and interact with their environments using their brain waves. Most research investigating BCI in humans have used scalp-recorded electroencephalography (EEG). We have recently demonstrated that signals from intracranial electrocorticography (ECoG) and stereotactic depth electrodes (SDE) in the hippocampus can be used to control a BCI P300 Speller paradigm. We report a case in which stereotactic depth electrodes positioned in the ventricle were able to obtain viable signals for a BCI. Our results demonstrate that event-related potentials from intraventricular electrodes can be used to reliably control the …

Design, Synthesis, And Anticancer Activity Of Ruthenium Complexes, Brock S. Howerton

Theses and Dissertations--Chemistry

Ruthenium complexes show promise as light activated photodynamic therapy (PDT) prodrugs. Strained octahedral complexes were synthesized that produce a cytotoxic species upon light activation. pUC19 DNA damage in vitro experiments were carried out to determine the type of damage observed. In vivo cell experiments were carried out on the non-small lung cancer A549 cell line to determine the phototherapeutic window of the synthesized complexes. One mechanism of drug resistance via elevated levels of glutathione was addressed through in vitro binding studies carried out with UV-Vis spectroscopy and in vivo glutathione titrations in the A549 cell line. Several complexes were shown …

Electric Field Exposure Triggers And Guides Formation Of Pseudopod-Like Blebs In U937 Monocytes, Mikhail A. Rassokhin, Andrei G. Pakhomov

Bioelectrics Publications

We describe a new phenomenon of anodotropic pseudopod-like blebbing in U937 cells stimulated by nanosecond pulsed electric field (nsPEF). In contrast to "regular," round-shaped blebs, which are often seen in response to cell damage, pseudopod-like blebs (PLBs) formed as longitudinal membrane protrusions toward anode. PLB length could exceed the cell diameter in 2 min of exposure to 60-ns, 10-kV/cm pulses delivered at 10-20 Hz. Both PLBs and round-shaped nsPEF-induced blebs could be efficiently inhibited by partial isosmotic replacement of bath NaCl for a larger solute (sucrose), thereby pointing to the colloid-osmotic water uptake as the principal driving force for bleb …

Molecular Characterization And Tissue-Specific Gene Expression Of Dermacentor Variabilis Α-Catenin In Response To Rickettsial Infection, Piyanate Sunyakumthorn, Natthida Petchampai, Michael T. Kearney, Daniel E. Sonenshine, Kevin R. Macaluso

Biological Sciences Faculty Publications

Alpha catenin is a cytoskeleton protein that acts as a regulator of actin rearrangement by forming an E-cadherin adhesion complex. In Dermacentor variabilis, a putative α-catenin (Dvα-catenin) was previously identified as differentially regulated in ovaries of ticks chronically infected with Rickettsia montanensis. To begin characterizing the role(s) of Dvα-catenin during rickettsial infection, the full-length Dvα-catenin cDNA was cloned and analysed. Comparative sequence analysis demonstrates a 3069-bp cDNA with a 2718-bp open reading frame with a sequence similar to Ixodes scapularis α-catenin. A portion of Dvα-catenin is homologous to the vinculin-conserved domain containing a putative …

Development Of An In-Cell Förster Resonance Energy Transfer Technique To Study Protein Structure Inside Living Cells, Victoria Lynn Murray

Wayne State University Dissertations

The goal of my thesis is to develop an in-cell fluorescence technique that allows for measurement of the distances between fluorescence acceptors and donors within a protein or between two proteins inside the correct intracellular compartment of living cells. The successful achievement of this goal will allow us to obtain high-resolution structural information from a protein, one key step towards high-resolution structural biology of proteins inside the living cell.

To achieve this goal, we will apply the fluorescence resonance energy transfer (FRET) technique to the specifically labeled proteins inside the cells. Our rationale is to specifically label the protein(s) of …

Modes And Mechanisms Of Hfq Mediated Stress Regulation In Bacteria, Nilshad Nilam Salim

Wayne State University Dissertations

To survive bacteria must be able to respond to its ever-changing environmental conditions. sRNAs have been implicated in a variety of stress-response pathways that help bacterial systems modulate gene expression. The RNA binding protein Hfq facilities this process by, helping sRNA to base pair with its target mRNAs to initiate gene regulation. A common feature of Hfq-mediated gene regulation is the network-based organization where a single sRNA can control multiple messages to promote integrated response to stress. Current mechanistic models that are present to describe Hfq functions cannot explain the complexity at which Hfq performs gene regulation. In this work …

Prevalence And Physiological Significance Of Gene Looping In Saccharomyces Cerevisiae, Banupriya Mukundan

Wayne State University Dissertations

My Ph.D. dissertation work is focused on studying the role of promoter-bound transcription initiation factors involved in gene looping. In this study we showed that the RNAP II subunit Rpb4 has a significant effect on termination of transcription. Gene looping is disrupted in the absence of Rpb4. Rpb4 shows a strong physical interaction with the Mediator subunit Srb5. Mediator subunit Srb5 crosslinked to the 5' and 3' ends of INO1 and CHA1 genes and is required for proper termination of transcription of these genes. Srb5 affected termination of transcription through its interaction with the CF1 complex. Srb5 interaction with the …

Genetic And Biochemical Studies Of Human Apobec Family Of Proteins, Priyanga Wijesinghe

Wayne State University Dissertations

The AID/APOBEC family of proteins in higher vertebrates converts cytosines in DNA or RNA into uracil. These proteins have essential roles in either innate immunity or adaptive immunity. Recently, AID has also been implicated in DNA demethylation in the context of early embryogenesis in mammals. This is partly based on the reported ability of AID to deaminate 5-methyl cytosine to thymine (5mC to T). I reexamined this proposed new role of AID (5mC deamination) with two members of the APOBEC family in a novel Escherichia coli based genetic system. My results confirmed that while all three enzymes are strong cytosine …

Bifunctional Bisphosphonates For Delivering Biomolecules To Bone, Jivan N. Yewle

Theses and Dissertations--Chemistry

Active targeting with controlled delivery of therapeutic agents to bone is an ideal approach for treatment of several bone diseases. Since bisphosphonates (BPs) are known to have high affinity to bone mineral and are being widely used in treatment of osteoporosis, they are well-suited for drug targeting to bone. For this purpose, bifunctional hydrazine-bisphosphonates (HBPs) with spacers of various lengths and lipophilicity were synthesized and studied. Crystal growth inhibition assays demonstrated that the HBPs with shorter spacers bound more strongly to bone mineral, hydroxyapatite (HA), than did alendronate. HBPs were also demonstrated to be non-toxic to MC3T3-E1 pre-osteoblasts. The targeted …

Investigations Into Modulation Of Brain Oxidative Stress By Various Interventions, Jessica Lynn Harris

Theses and Dissertations--Chemistry

In this thesis study we examined glycogen synthase kinase-3β (GSK-3β) and its effects over Nrf2 and Pin 1 as it relates to Alzheimer’s disease (AD). AD is a neurodegenerative disease characterized by a prolonged high oxidative environment. Transcription factor Nrf2 is vital in the brain’s defense against oxidative insults through its up-regulation of over 100 antioxidants. Depletion of the brain’s antioxidant defense system results in intolerance to an oxidative environment, contributing to the progression of AD. The regulatory Pin 1 protein promotes cellular homeostasis, and when down-regulated results in increased deposits of neurofibrillary tangles (NFTs) and amyloid-β (Aβ) plaques, the …

Hydrogen/Deuterium Exchange Studies Of Protein And Non-Protein Amino Acids Using Electrospray Ionization Mass Spectrometry, Justine Victoria Arrington

Dissertations, Theses, and Masters Projects

No abstract provided.