Biochemistry, Biophysics, and Structural Biology Commons^™

Using Ammonium Pore Water Profiles To Assess Stoichiometry Of Deep Remineralization Processes In Methanogenic Continental Margin Sediments, David J. Burdige, Tomoko Komada

OES Faculty Publications

In many continental margin Sediments, a deep reaction zone exists which is separated from remineralization processes near the sediment surface. Here, methane diffuses upward to a depth where it is oxidized by downwardly diffusing sulfate. However, the methane sources that drive this anaerobic oxidation of methane (AOM) in the sulfate-methane transition zone (SMT) may vary among sites. In particular, these sources can be thought of as either (i) "internal" sources from in situ methanogenesis (regardless of where it occurs in the sediment column) that are ultimately coupled to organic matter deposition and burial, or (ii) "external" sources such as hydrocarbon …

Distributions Of Particulate Heme B In The Atlantic And Southern Oceans- Implications For Electron Transport In Phytoplankton, Martha Gledhill, Eric P. Achterberg, David J. Honey, Maria C. Nielsdottir, Micha J.A. Rijkenberg

OES Faculty Publications

Concentrations of heme b, the iron-containing component of b-type hemoproteins, ranged from b concentrations were enhanced in the photic zone and decreased with depth. Heme b concentrations correlated positively with chlorophyll a (chl a) in the TNA (r=0.41, pb did not correlate with chl a in the IB or SS. In the IB and SS, stations with high-chlorophyll and low-nutrient (Fe and/or Si) concentrations exhibited low heme bconcentrations relative to particulate organic carbon (< 0.1 μmolmol^-1, and high chl a:heme b ratios (> 500). High chl a:heme b ratios resulted from relative decreases in …

Membrane Surface Charges Attracted Protons Are Not Relevant To Proton Motive Force, James Weifu Lee

Chemistry & Biochemistry Faculty Publications

[First Paragraph] Only a half-century ago, British scientist Peter Mitchell proposed the conceptual scheme known as "chemiosmotic theory" that identified the role of proton coupling in the formation of ATP in cells [1,2]. Mitchell's delocalized proton-coupling chemiosmotic theory was initially quite controversial. But it would win for him the Nobel Prize in Chemistry in 1978. However, questions about Mitchell's chemiosmotic hypothesis have never gone away and a number of credible studies indicated the full extent of Mitchell's idea didn't always hold up to experience.

Solid-Phase Organic Matter Reduction Regulates Anaerobic Decomposition In Bog Soil, Jason K. Keller, Kimberly K. Takagi

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Peatlands store globally significant amounts of carbon and are important sources of the greenhouse gas methane (CH4) to the atmosphere. However, for reasons which are not well understood, many peatland soils produce smaller amounts of CH4 than theoretically predicted, and carbon dioxide (CO2) produced during anaerobic decomposition in peatland soils cannot be accounted for by commonly measured microbial processes. Here we show that the reduction of solid-phase organic matter (i.e., humic substances) suppresses CH4 production in a bog soil and can be responsible for 33–61% of the total carbon mineralization in this soil. These results demonstrate that the reduction of …

Enzymatic Characterization Of The Ammonia Tunnel In Helicobacter Pylori Asp-Trnaasn/Glu-Trnagln Amidotransferase, Liangjun Zhao

Wayne State University Dissertations

The Helicobacter pylori (H. pylori) Asp-tRNA^Asn/Glu-tRNA^Gln amidotransferase (AdT) plays important roles in indirect aminoacylation and translational fidelity; however, its inter-domain communication and ammonia delivery mechanisms are not well understood. In the present study, we investigated the three activities of H. pylori AdT (glutaminase, kinase and transamidase) and used these reactions as probes to examine the inter-domain communication and ammonia delivery mechanisms between this enzyme's two isolated active sites. We adapted and optimized an assay to kinetically characterize a series of mutations at conserved positions throughout the putative AdT ammonia tunnel. The kinase assay enabled us …

Development Of Peptide Inhibitors Targeting Clostridium Difficile Toxins A/B And Characterizing The Regulatory Role Of A Putative Negative Regulator Tcdc In Clostridium Difficile Toxin Gene Expression, Sanofar Jainul Abdeen

Wayne State University Dissertations

Clostridium difficile infections cause one of the most common and vital hospitalacquired

diseases often associated with broad-spectrum antibiotic usage. TcdA and TcdB

are the key virulence factors involved in major patho-physiology. While standard

antibiotics provide some respite, due to the high relapse rates and the emergence of more

severe disease presentations, antibiotics alone have often proven to be suboptimal.

Therefore there is a desperate need to develop an effective non-antimicrobial

therapeutics. Part of this work focuses on identification and further characterization of

peptide therapeutic that target the major virulence factor TcdA/TcdB. Towards

development of mechanistic-based anti-toxin agent, phage display was …

Regulation Of The Glycine Transporter 1 (Glyt1) By Pkca-Dependent Ubiquitination, Susana Barrera

Open Access Theses & Dissertations

Glycine is one of the major inhibitory neurotransmitters in the central nervous system. It is implicated in the regulation of motor-sensory function such as; pain perception, reflex responses, and is essential for early development of the CNS. In addition to its inhibitory actions, it acts as an obligatory co-agonist for the activation of glutamatergic NMDARs, which are of pivotal importance in the process of learning and memory, its dysfunction leads to several neurodegenerative diseases. Two high affinity Na+/Cl- dependent transporters GlyT1 and GlyT2 tightly regulate the availability of glycine present at the synapse for the activation of NMDARs and GlyRs. …

Electric Field Standing Wave Effects In Ft-Ir Transflection Spectra Of Biological Tissue Sections: Simulated Models Of Experimental Variability, Tomasz P. Wrobel, Barbara Wajnchold, Hugh Byrne, Malgorzata Baranska

Articles

The so-called electric field standing wave effect (EFSW) has recently been demonstrated to significantly distort FT-IR spectra acquired in a transflection mode, both experimentally and in simulated models, bringing into question the appropriateness of the technique for sample characterization, particularly in the field of spectroscopy of biological materials. The predicted effects are most notable in the regime where the sample thickness is comparable to the source wavelength. In this work, the model is extended to sample thicknesses more representative of biological tissue sections and to include typical experimental factors which are demonstrated to reduce the predicted effects. These include integration …

Aβ Alters The Dna Methylation Status Of Cell-Fate Genes In An Alzheimer’S Disease Model, Gary D. Isaacs, Noor Taher, Courtney Mckenzie, Rebecca Garrett, Matthew Baker, Nena Fox

Faculty Publications and Presentations

Alzheimer’s disease (AD) is characterized by neurofibrillary tangles and extracellular amyloid-β plaques (Aβ). Despite ongoing research, some ambiguity remains surrounding the role of Aβ in the pathogenesis of this neurodegenerative disease. While several studies have focused on the mutations associated with AD, our understanding of the epigenetic contributions to the disease remains less clear. To that end, we determined the changes in DNA methylation in differentiated human neurons with and without Aβ treatment. We isolated the DNA from neurons treated with Aβ or vehicle, and digested the two samples with either a methylation-sensitive (HpaII) or a methylation-insensitive (MspI) restriction endonuclease. …

Development Of A Starch-Based Mussel-Mimetic Adhesive Polymer, Jeffrey Kazimir De Kozlowski

Open Access Theses

Mussel-mimetic adhesive polymers have gained lots of attention for their strong adhesive strength, moisture resistance, and unique ability to crosslink. These properties are mainly attributed to the high content of catecholic 3,4-dihydroxyphenylalanine (DOPA) in mussel adhesive proteins. While there has been success in creating mussel-mimetic synthetic polymers, less effort has been given to create a renewable, green, biocompatible counterpart. This thesis explores the possibilities of starch-based mussel-mimetic adhesives. Carboxymethyl starch of various molecular weights and degree of substitution was synthesized and subsequent conjugation of dopamine to these polymers by 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide was investigated. The polymers suffered from very low substitution (DScatechol …

Interaction Between Maltose Binding Protein And Escherichia Coli Maltose Transporter, Yan Huang

Open Access Theses

The ATP-binding cassette (ABC) transporter superfamily is one of the largest families of transport proteins. The ABC transporters are responsible for selective permeability of solute across membranes energized by ATP hydrolysis, which occurs in all domains of life. Maltose transporter is an ABC importer that mediates maltose/maltodextrin uptake in bacteria and archaea. It is identified as an essential virulence factor in pathogenic species of Streptococcis pyogenes and Vibrio cholera (1, 2). Escherichia coli maltose transporter is a well-characterized system with crystal structures and exclusive biochemical studies available. Knowledge of the E. coli maltose transport mechanism will lead to a better …

Interaction Between Centromeric Histone H3 Variant And Shugoshin, Visarut Buranasudja

Open Access Theses

Precise and faithful segregation of chromosome segregation during mitosis depends on the ability of the cell to regulate chromosome bi-orientation on the mitotic spindle. Shugoshin (Sgo1), the protector of meiotic centromeric cohesin, is required for proper establishment of chromosome bi-orientation. Sgo1 plays a crucial role as part of a mitotic tension sensor between sister chromatids. Recently, Sgo1 has been reported to interact with histone H3 at the pericentromere region, as an important factor for tension sensing and chromosome segregation. However, the role of Sgo1 in tension sensing at centromere is still elusive. The centromere is the region of attachment of …

Force Generation By Kinesin And Myosin Cytoskeletal Motor Proteins, F. Jon Kull, Sharyn A. Endow

Dartmouth Scholarship

Kinesins and myosins hydrolyze ATP, producing force that drives spindle assembly, vesicle transport and muscle contraction. How do motors do this? Here we discuss mechanisms of motor force transduction, based on their mechanochemical cycles and conformational changes observed in crystal structures. Distortion or twisting of the central β-sheet - proposed to trigger actin-induced Pi and ADP release by myosin, and microtubule-induced ADP release by kinesins - is shown in a movie depicting the transition between myosin ATP-like and nucleotide-free states. Structural changes in the switch I region form a tube that governs ATP hydrolysis and Pi release by the motors, …

Sir2 Is Required For Clr4 To Initiate Centromeric Heterochromatin Assembly In Fission Yeast, Benjamin J. Alper, Godwin Job, Rajesh K. Yadav, Sreenath Shanker, Brandon R. Lowe, Janet F. Partridge

Chemistry & Physics Faculty Publications

Heterochromatin assembly in fission yeast depends on the Clr4 histone methyltransferase, which targets H3K9. We show that the histone deacetylase Sir2 is required for Clr4 activity at telomeres, but acts redundantly with Clr3 histone deacetylase to maintain centromeric heterochromatin. However, Sir2 is critical for Clr4 function during de novo centromeric heterochromatin assembly. We identified new targets of Sir2 and tested if their deacetylation is necessary for Clr4-mediated heterochromatin establishment. Sir2 preferentially deacetylates H4K16Ac and H3K4Ac, but mutation of these residues to mimic acetylation did not prevent Clr4-mediated heterochromatin establishment. Sir2 also deacetylates H3K9Ac and H3K14Ac. Strains bearing H3K9 or H3K14 …

Investigating The Metal Binding Affinity Of Bacterial Zinc Transporters: Zupt And Truncated Znta (Znta-Pina), Fei Nie

Wayne State University Theses

Zinc is essential trace elements for all living organisms and serves as cofactor and structural cofactors for more than 300 enzymes. ZupT is one of the members of ZIP super family of transporter proteins, which were identified as iron and zinc transporter in Eukaryotes at first. However, recent evidence showed that some of members can also transport other metal ions, such as manganese or cadmium, and ZIP proteins also exist in bacteria. ZupT is responsible for zinc uptake in E. coli; however, its full metal selectivity is not yet characterized. In addition, the mechanism of transport is also unknown. Therefore, …

Effect Of Estrogen On Manganese-Induced Toxicity On Embryonic Astrocytes, Tyler T. Huynh, Kimberly J. Baker, Harold L. Komiskey

PCOM Scholarly Works

Manganese (Mn) is a natural trace metal that is essential for many physiological functions in the human body. Astrocytes in the central nervous system are susceptible reservoirs for Mn accumulation. Estrogen, a steroidal hormone, has been shown to mitigate Mn-induced toxicity in cultures of postnatal astrocytes. However, differences in expression/inducibility of glutamate transporters and glutamine synthetase, transmitters, and the natural gonadal steroids and their receptors are known to occur in astrocyte cultures derived from various stages of fetal and postnatal development. Cultures of embryonic (E18) hippocampal astrocytes were examined in this study for the ability of 17 β-estradiol (E2) to …

Decoration Of Graphene With Metal Nanoparticles And Its Application For Bioanalysis, Keun Soo Kwon

Theses, Dissertations and Culminating Projects

Graphene is a two-dimensional monolayer of tightly packed sp² hybridized Carbon atoms. Formed from graphite, the theoretical surface area of the monolayer is about 2630 m²/g, and the initial formation of graphene oxide from graphite oxide introduces a variety o f functional groups, such as -COOH, -C=0, and -OH, on its surface. The high surface area and the rich presence of functional groups, along with the potential formation o f sp² bonding networks within graphene oxide, all serve as critical factors allowing for additional chemical modifications. There are extensive research attempts being performed to explore and …

The Genetic Engineering Of Motor Proteins, Rachael M. Hartz

Legacy Theses & Dissertations (2009 - 2024)

Molecular motors are a remarkable feature within living organisms that are responsible for directional mechanical motion, which is driven by adenosine triphosphate (ATP) hydrolysis. Actin-binding molecular motors are of specific interest in the field of nanotechnology as filamentous actin is capable of carrying cargo, such as quantum dots, while it is translocated along a motor coated surface. The binding regions of motor proteins, which are known to interact with actin, such as Myosin, have been thoroughly examined and identified. Rapid genetic engineering of the ATP-hydrolyzing enzyme, adenosine kinase, to incorporate these binding regions is possible through the use of site- …

Protein Structures Under Physiological Conditions, Karl Michael Bertrand

Legacy Theses & Dissertations (2009 - 2024)

My research focused on the evaluation of protein structures and protein dynamics inside eukaryotic cells under physiological conditions. The primary analyses of my research involved the use of in-cell Nuclear Magnetic Resonance spectroscopy using Heteronuclear Single Quantum Coherence experiments. This allowed me to visualize protein structures at an atomic resolution level, as well as, study the interactions of these proteins with small molecules.

Molecular Biochemical Study Of The Cataract-Associated Mutants In Human Gammad-Crystallin, Cindy Yeung

Legacy Theses & Dissertations (2009 - 2024)

Cataract is a vision impairment disease that leads to light scattering and opacity of the eye lens. It is recognized as the most prevalent cause of blindness. Most cataracts occur due to aging, but those that occur in childhood or in young adults are typically of genetic origin. In the young (developing) eye, post–surgical complications such as glaucoma are common after cataract surgery. Hence there is a great need to develop non-surgical intervention strategies for the treatment of cataract. Here, two cataract-associated mutants of human γD-crystallin (HGD): i) Arg76 to Ser (R76S) and ii) a truncation mutation at Trp156 (W156X …