Biochemistry Commons^™

How Pakistan's Media Spreads The Message About Reproductive And Sexual Health, Syed H. Abidi, Muhammad Raees, Syed Ali

Department of Biological & Biomedical Sciences

Abstract, issue, and pagination are not provided by the author/publisher

Application Of Lipid Styryl Dye For Staining Intracytoplasmic Membranes In Gram-Negative Bacteria, Theodore J. Hammer

Williams Honors College, Honors Research Projects

Intracytoplasmic membranes are structures that form within cells which help facilitate a variety of different metabolic processes. This feature of intracellular membranes makes them particularly valuable for studying compartmentalization and cell dynamics in bacteria. In the past, transmission electron microscopy has been the primary method for imaging bacteria with intracytoplasmic membranes. Because transmission electron microscopy takes images of a cell in fixed slices, it’s impossible to follow a cell’s growth and development over time. Fluorescence microscopy is a particularly effective method of measurement that can combat these issues when evaluating live bacterial cells. Here, standard biochemical laboratory procedures were used …

Transfer Rna Comes Of Age, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

"The year the journal RNA was founded was slated by some in scientific publishing to be the year that one particular type of RNA's run in the spotlight would end. In 1995 I had recently started as a post-doc with Dieter Söll at Yale when he came into the lab to solemnly inform us all that an editor at a certain (S)cience journal had just told him “we won't be publishing any more tRNA papers.” For a post-doc who had migrated across the Atlantic for the sole purpose of furthering his career by working on tRNA this was not great …

Introduction To Fifth Special Issue On Electroporation-Based Technologies And Treatments, Damijan Miklavčič, Lluis M. Mir, P. Thomas Vernier

Bioelectrics Publications

This special issue of the Journal of Membrane Biology contains reports on recent developments in the field of electroporation by participants in the International Workshop and Postgraduate Course on Electroporation-Based Technologies and Treatments held in November 2014 in Ljubljana. This was the eighth session of what is now an annual event, first organized in 2003.

In Situ Oh Generation From O2- And H2o2 Plays A Critical Role In Plasma Induced Cell Death, Dehui Xu, Dingxing Liu, Biqing Wang, Chen Chen, Zeyu Chen, Dong Li, Yanjie Yang, Hailan Chen, Michael G. Kong

Bioelectrics Publications

Reactive oxygen and nitrogen species produced by cold atmospheric plasma (CAP) are considered to be the most important species for biomedical applications, including cancer treatment. However, it is not known which species exert the greatest biological effects, and the nature of their interactions with tumor cells remains ill-defined. These questions were addressed in the present study by exposing human mesenchymal stromal and LP-1 cells to reactive oxygen and nitrogen species produced by CAP and evaluating cell viability. Superoxide anion (O₂-) and hydrogen peroxide (H₂O₂) were the two major species present in plasma, but their …

Picosecond To Terahertz Perturbation Of Interfacial Water And Electropermeabilization Of Biological Membranes, P. Thomas Vernier, Zachary A. Levine, Ming-Chak Ho, Shu Xiao, Iurii Semenov, Andrei G. Pakhomov

Bioelectrics Publications

Non-thermal probing and stimulation with subnanosecond electric pulses and terahertz electromagnetic radiation may lead to new, minimally invasive diagnostic and therapeutic procedures and to methods for remote monitoring and analysis of biological systems, including plants, animals, and humans. To effectively engineer these still-emerging tools, we need an understanding of the biophysical mechanisms underlying the responses that have been reported to these novel stimuli. We show here that subnanosecond (≤500 ps) electric pulses induce action potentials in neurons and cause calcium transients in neuroblastoma-glioma hybrid cells, and we report complementary molecular dynamics simulations of phospholipid bilayers in electric fields in which …

Diffuse, Non-Polar Electropermeabilization And Reduced Propidium Uptake Distinguish The Effect Of Nanosecond Electric Pulses, Iurii Semenov, Christian W. Zemlin, Olga N. Pakhomova, Shu Xiao, Andrei G. Pakhomov

Bioelectrics Publications

Ca²⁺ activation and membrane electroporation by 10-ns and 4-ms electric pulses (nsEP and msEP) were compared in rat embryonic cardiomyocytes. The lowest electric field which triggered Ca²⁺ transients was expectedly higher for nsEP (36 kV/cm)than forms EP (0.09 kV/cm) but the respective doses were similar (190 and460 mJ/g). At higher intensities, both stimuli triggered prolonged firing in quiescent cells. An increase of basal Ca²⁺ level by N10 nM in cells with blocked voltage-gated Ca²⁺ channels and depleted Ca²⁺ depot occurred at 63 kV/cm (nsEP) or 0.14 kV/cm (msEP) and was regarded as electroporation threshold. These …

Connecting Proline Metabolism And Signaling Pathways In Plant Senescence, Lu Zhang, Donald F. Becker

Department of Biochemistry: Faculty Publications

The amino acid proline has a unique biological role in stress adaptation. Proline metabolism is manipulated under stress by multiple and complex regulatory pathways and can profoundly influence cell death and survival in microorganisms, plants, and animals. Though the effects of proline are mediated by diverse signaling pathways, a common theme appears to be the generation of reactive oxygen species (ROS) due to proline oxidation being coupled to the respiratory electron transport chain. Considerable research has been devoted to understand how plants exploit proline metabolism in response to abiotic and biotic stress. Here, we review potential mechanisms by which proline …

Chloroplast Lipid Transfer Processes In Chlamydomonas Reinhardtii Involving A Trigalactosyldiacylglycerol 2 (Tgd2) Ortholog, Jaruswan Warakanont, Chia-Hong Tsai, Elena J.S. Michel, George R. Murphy Iii, Peter Y. Hsueh, Rebecca L. Roston, Barbara B. Sears, Christoph Benning

Department of Biochemistry: Faculty Publications

In plants, lipids of the photosynthetic membrane are synthesized by parallel pathways associated with the endoplasmic reticulum (ER) and the chloroplast envelope membranes. Lipids derived from the two pathways are distinguished by their acyl-constituents. Following this plant paradigm, the prevalent acyl composition of chloroplast lipids suggests that Chlamydomonas reinhardtii (Chlamydomonas) does not use the ER pathway; however, the Chlamydomonas genome encodes presumed plant orthologs of a chloroplast lipid transporter consisting of TGD (TRIGALACTOSYLDIACYLGLYCEROL) proteins that are required for ER-tochloroplast lipid trafficking in plants. To resolve this conundrum, we identified a mutant of Chlamydomonas deleted in the TGD2 gene and characterized …

Phenotypic Screening Identifies Brefeldin A/Ascotoxin As An Inducer Of Lipid Storage In The Algae Chlamydomonas Reinhardtii, Nishikant Wase, Boqiang Tu, Paul N. Black, Concetta C. Dirusso

Department of Biochemistry: Faculty Publications

The use of microalgae as a biofuel feedstock is highly desired, but current methods to induce lipid accumulation cause severe stress responses that limit biomass and, thus oil yield. To address these issues, a high throughput screening (HTS) method was devised to identify chemical inducers of growth and lipid accumulation. Optimization was performed to determine the most effective cell density, DMSO and Nile Red (NR) concentrations to monitor growth and lipid accumulation. The method was tested using 1717 compounds from National Cancer Institute (NCI) Diversity Set III and Natural Products Set II in Chlamydomonas reinhardtii. Cells were inoculated at …

Cytotoxic Activity Of Triazole-Containing Alkyl Β-D-Glucopyranosides On A Human T-Cell Leukemia Cell Line, E. Davis Oldham, Larissa M. Nunes, Armando Varela-Ramirez, Stephen E. Rankin, Barbara L. Knutson, Renato J. Aguilera, Hans-Joachim Lehmler

Chemistry and Physics

Simple glycoside surfactants represent a class of chemicals that are produced from renewable raw materials. They are considered to be environmentally safe and, therefore, are increasingly used as pharmaceuticals, detergents, and personal care products. Although they display low to moderate toxicity in cells in culture, the underlying mechanisms of surfactant-mediated cytotoxicity are poorly investigated.

An Investigation Of Bag3 Knockdown And Its Effects On The Cytotoxicity Of Laromustine, Colin Sheehan

Honors Theses

Laromustine is a sulfonylhydrazine anticancer prodrug whose main cytotoxic arises from its ability to interfere with DNA replication of dividing cells. Multiple studies have suggested that Laromustine induces a form of cell death known as apoptosis. In a previous study investigating the mechanism of apoptosis, bcl2-associated athanogene 3 (BAG3) demonstrated significant upregulation in the presence of Laromustine. Given its anticancer ability, we selected BAG3 as a target for further investigation. BAG3 knockdown through transient shRNA transfections was performed in U138 glioblastoma multiforme cells and verified using qRT-PCR analysis. Finally, cell death assays were used to assess Laromustine’s cytotoxic effect on …

Divergent Responses Of Atlantic Coastal And Oceanic Synechococcus To Iron Limitation, Katherine R. M. Mackey, Anton F. Post, Matthew R. Mcilvin, Gregory A. Cutter, Seth G. John, Mak A. Saito

OES Faculty Publications

Marine Synechococcus are some of the most diverse and ubiquitous phytoplankton, and iron (Fe) is an essential micronutrient that limits productivity in many parts of the ocean. To investigate how coastal and oceanic Atlantic Synechococcus strains acclimate to Fe availability, we compared the growth, photophysiology, and quantitative proteomics of two Synechococcus strains from different Fe regimes. Synechococcus strain WH8102, from a region in the southern Sargasso Sea that receives substantial dust deposition, showed impaired growth and photophysiology as Fe declined, yet used few acclimation responses. Coastal WH8020, from the dynamic, seasonally variable New England shelf, displayed a multitiered, hierarchical cascade …

The Relative Importance Of Methanogenesis In The Decomposition Of Organic Matter In Northern Peatlands, J. Elizabeth Corbett, Malak M. Tfaily, David J. Burdige, Paul H. Glaser, Jeffrey P. Chanton

OES Faculty Publications

Using an isotope-mass balance approach and assuming the equimolar production of CO₂ and CH₄ from methanogenesis (e.g., anaerobic decomposition of cellulose), we calculate that the proportion of total CO₂ production from methanogenesis varies from 37 to 83% across a variety of northern peatlands. In a relative sense, methanogenesis was a more important pathway for decomposition in bogs (80 ± 13% of CO₂ production) than in fens (64 ± 5.7% of CO₂ production), but because fens contain more labile substrates they may support higher CH4 production overall. The concentration of CO₂ produced from methanogenesis (CO …

The Geotraces Intermediate Data Product 2014, Edward Mawji, Reiner Schlitzer, Elena M. Dodas, Cyril Abadie, Wafa Abouchami, Robert F. Anderson, Gregory A. Cutter

OES Faculty Publications

The GEOTRACES Intermediate Data Product 2014 (IDP2014) is the first publicly available data product of the international GEOTRACES programme, and contains data measured and quality controlled before the end of 2013. It consists of two parts: (1) a compilation of digital data for more than 200 trace elements and isotopes (TEls) as well as classical hydrographic parameters, and (2) the eGEOTRACES Electronic Atlas providing a strongly inter-linked on-line atlas including more than 300 section plots and 90 animated 3D scenes. The IDP2014 covers the Atlantic, Arctic, and Indian oceans, exhibiting highest data density in the Atlantic. The TEI data in …

Genetic Indicators Of Iron Limitation In Wild Populations Of Thalassiosira Oceanica From The Northeast Pacific Ocean, P. Dreux Chappell, Leann P. Whitney, Joselynn R. Wallace, Adam I. Darer, Samua Jean-Charles, Bethany D. Jenkins

OES Faculty Publications

Assessing the iron (Fe) nutritional status of natural diatom populations has proven challenging as physiological and molecular responses can differ in diatoms of the same genus. We evaluated expression of genes encoding flavodoxin (FLDA1) and an Fe-starvation induced protein (ISIP3) as indicators of Fe limitation in the marine diatom Thalassiosira oceanica. The specificity of the response to Fe limitation was tested in cultures grown under Fe-and macronutrient-deficient conditions, as well as throughout the diurnal light cycle. Both genes showed a robust and specific response to Fe limitation in laboratory cultures and were detected in small volume samples collected from …

Elucidation Of A Novel Pathway In Staphylococcus Aureus: The Essential Site-Specific Processing Of Ribosomal Protein L27, Erin A. Wall

Theses and Dissertations

Ribosomal protein L27 is a component of the eubacterial large ribosomal subunit that has been shown to play a critical role in substrate stabilization during protein synthesis. This function is mediated by the L27 N-terminus, which protrudes into the peptidyl transferase center where it interacts with both A-site and P-site tRNAs as well as with 23S rRNA. We observed that L27 in S. aureus and other Firmicutes is encoded with a short N-terminal extension that is not present in most Gram-negative organisms, and is absent from mature ribosomes. The extension contains a conserved cleavage motif; nine N-terminal amino acids are …

Regulation Of Tie2 Extracellular Complex Formation In Angiogenesis, Annamarie Dalton

Theses and Dissertations

Pathological angiogenesis is an essential component of tumor growth, development, and metastasis for which few effective therapeutic options exist. Though many cancer therapies target the function of cell surface receptors, mechanisms regulating membrane receptor crosstalk remain unclear. Two important families of receptors in angiogenesis, the Ties and Integrins, respond to the extracellular environment via outside-in and, in the case of Integrins, also inside- out signaling. Recent reports showed that the endothelial specific tyrosine kinase receptor, Tie2, forms complexes with two of the endothelial Integrin heterodimers, α₅β₁ and α_Vβ₃, providing a convenient mechanism for …

Characterization Of A Novel Protease In Staphylococcus Aureus, Adam L. Johnson

Theses and Dissertations

A newly discovered cysteine protease, Prp, has been shown to perform an essential, site-specific cleavage of ribosomal protein L27 in Staphylococcus aureus. In Firmicutes and related bacteria, ribosomal protein L27 is encoded with a conserved N-terminal extension that must be removed to expose residues critical for ribosome function. Uncleavable and pre-cleaved variants were unable to complement an L27 deletion in S. aureus, indicating that this N-terminal processing event is essential and likely plays an important regulatory role. The gene encoding the responsible protease (prp) has been shown to be essential, and is found in all organisms …

Numerical Geometry Of Map And Model Assessment, Willy Wriggers, Jing He

Mechanical & Aerospace Engineering Faculty Publications

We are describing best practices and assessment strategies for the atomic interpretation of cryo-electron microscopy (cryo-EM) maps. Multiscale numerical geometry strategies in the Situs package and in secondary structure detection software are currently evolving due to the recent increases in cryo-EM resolution. Criteria that aim to predict the accuracy of fitted atomic models at low (worse than 8 angstrom) and medium (4-8 angstrom) resolutions remain challenging. However, a high level of confidence in atomic models can be achieved by combining such criteria. The observed errors are due to map-model discrepancies and due to the effect of imperfect global docking strategies. …

The Role Of Rnai In Downregulation Of Physcomitrella Patens Defense Genes And The Preliminary Steps Of Peg Mediated Transformation Of Mosses, Adam Beswick

Undergraduate Honors Thesis Collection

When attacked by a pathogen, the moss Physcomitrella patens will undergo both a hypersensitive response (HR) as well as a systematic acquired resistance (SAR) response. The SAR response turns on genes that ready the plant for future pathogen attacks. The hormone jasmonic acid (JA) is one of the products of SAR response in P. patens. In this study interference RNA (RNAi) was used to decrease gene expression of the allene oxide cyclase (ACe) gene, a key gene in the production pathway of JA. Using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), RNAi was found to significantly lower ACC gene levels …

Design And Synthesis Of Isatin-Based Caspase Inhibitors For Ruthenium Caging Applications, Kasun Chinthaka Ratnayake

Wayne State University Theses

ABSTRACT

DESIGN AND SYNTHESIS OF ISATIN BASED CASPASE INHIBITORS FOR RUTHENIUM CAGING APPLICATIONS

by

KASUN CHINTHAKA RATNAYAKE

August 2015

Advisor: Jeremy J. Kodanko, Ph.D.

Major: Chemistry (Organic)

Degree: Master of Science

Apoptosis is the energy dependent programmed cell death. Improper function of apoptosis could lead to diseases such as cancers, strokes, Alziemer’s disease. Caspases are the enzymes involved in the later stage of this process. Peptidyl and non-peptidyl caspase inhibitors have been synthesized recently. These non-peptidyl compound classes which consist of pyrrolidinyl-5-sulfo isatins have showed a greater potency against executioner caspases, caspase-3 and -7. According to literature and for further …

The Structural Heterogeneity And Dynamics Of Base Stacking And Unstacking In Nucleic Acids, Ada Anna Sedova

Legacy Theses & Dissertations (2009 - 2024)

Base stacking provides stability to nucleic acid duplexes, and base unstacking is involved in numerous biological functions related to nucleic acids, including replication, repair, transcription, and translation. The patterns of base stacking and unstacking in available nucleic acid crystal structures were classified after separation into their individual single strand dinucleotide components and clustering using a k-means-based ensemble clustering method. The A- and B-form proximity of these dinucleotide structures were assessed to discover that RNA dinucleotides can approach B-form-like structures. Umbrella sampling molecular dynamics simulations were used to obtain the potential of mean force profiles for base unstacking at 5'-termini for …

Rna Aptamer Mediated Manipulation Of The 70 Kilodalton Heat Shock Protein Chaperone Machinery, Deepak Thirunavukarasu

Legacy Theses & Dissertations (2009 - 2024)

Protein quality control involves refolding of damaged proteins and facilitating degradation of irreparable proteins. Understanding the protein quality control mechanism is critical, since defects in it has been implicated in a number of age-related diseases like neurodegenerative diseases and also in cancer. A vast network of molecular chaperones and proteolytic systems collaborate to maintain protein quality control. The 70 kilodalton Heat shock protein (Hsp70) is a highly conserved and ubiquitous chaperone, which interacts with a variety of protein substrates including newly synthesized polypeptides, unfolded, partially misfolded and native proteins to maintain protein quality control. Hsp70 chaperone function is coupled to …

Novel Nmr Based Technologies To Study Macromolecular Structures, Subhabrata Majumder

Legacy Theses & Dissertations (2009 - 2024)

Nuclear Magnetic Resonance Spectroscopy (NMR) is one of the principle tools in structural biology to probe macromolecular structures and interactions. The atomic resolution afforded by this technique has been widely used to probe protein-protein, and protein-ligand interactions in-vitro. However, the natural milieu of the proteins is the living cell and the cellular cytoplasm is extremely heterogeneous. The NMR studies of folded protein in-cell, till now, have been limited by non-specific interactions of the cytosol. This thesis outlays a general methodology to study protein structure/interactions inside the living cells using NMR. In a closely related objective, it also describes the use …

Systematic Study Of The Biological Effects Of Nitric Oxide (No) Using Innovative No Measurement And Delivery Systems, Weilue He

Dissertations, Master's Theses and Master's Reports

Nitric oxide (NO) is recognized as the most important small signaling molecule in the human body. An imbalance of NO is closely associated with many serious diseases such as neurological disorders, cardiovascular diseases, chronic inflammations and cancers. Herein two chemiluminescence-based devices (a real-time NO measurement device and a controllable NO delivery device) were developed to facilitate the NO quantitative study and obtain information for NO related drug design.

The first device used for real-time measuring NO(g) flux from living cells was developed and validated. The principle was to use a two-chamber design, with a cell culture chamber and a gaseous …

Hiv Integrase Mechanisms Of Resistance To Raltegravir, Elvitegravir, And Dolutegravir, Kyla Nicole Ross

Wayne State University Theses

ABSTRACT

HIV INTEGRASE MECHANISMS OF RESISTANCE TO RALTEGRAVIR, ELVITEGRAVIR, AND DOLUTEGRAVIR

by

KYLA ROSS

December 2015

Advisor: Dr. Ladislau Kovari

Major: Biochemistry and Molecular Biology

Degree: Master of Science

HIV-1 integrase (HIV-1 IN or IN) is a multimeric enzyme that integrates the HIV-1 genome into the chromosomes of infected CD4+ T-cells. Currently there are three FDA approved HIV-1 IN strand transfer inhibitors (INSTIs) used in clinical practice: raltegravir (RAL), elvitegravir (ELV), and dolutegravir (DTG). The [Q148H], [Q148H, G140S], [Q148R], [Q148R, G140A] and [N155H, E92Q] mutations decrease IN susceptibility to RAL and ELV and may result in therapeutic failure. As an …

Expression And Functional Analysis Of Lipids And Glycolipids From The Mammal-Dwelling Stages Of Trypanosoma Cruzi, Felipe Gazos Lopes

Open Access Theses & Dissertations

Trypanosoma cruzi is the causative agent of the life-threatening Chagas disease, in which increased platelet aggregation related to myocarditis is observed. Platelet-activating factor (PAF) is a potent intercellular lipid mediator and second messenger that exerts its activity through a PAF-specific receptor (PAFR). Previous data from our group suggested that T. cruzi synthesizes a phospholipid with PAF-like activity. The structure of T. cruzi PAF-like molecule, however, remains elusive. Here, we have purified and structurally characterized the putative T. cruzi PAF-like molecule by electrospray ionization-tandem mass spectrometry (ESI-MS/MS). Our ESI-MS/MS data demonstrated that the T. cruzi PAF-like molecule is actually a lysophosphatidylcholine …

Role Of Small Molecules In Rescuing Protein Folding Under Oxidative Stress, Mahmoud Fawzi Megahed Helal Khalil

Open Access Theses & Dissertations

Increased levels of nitrosative stress intracellularly within the endoplasmic reticulum is a key factor involvled in the pathogenesis of both Parkinson's (PD) and Alzheimer's (AD) diseases. Previous in-vitro studies in our lab showed that increased levels of nitrosative stress lead to aggregation of misfolded proteins and formation of Lewy Bodies, the main biomarker of PD and AD diseases. Although this was mainly through nitrosylation of Protein Disulfide Isomerase (PDI), the chief endoplasmic reticulum (ER) resident oxidoreductase chaperone responsible for maturation of disulfide-bond-containing proteins, we demonstrate in this project that increased levels of nitrosative stress has an additional direct effect on …

Using Antenna Tile-Assisted Substrate Delivery To Improve Detection Limits Of Deoxyribozyme, Amanda J. Cox

HIM 1990-2015

One common limitation of enzymatic reactions is the diffusion of a substrate to the enzyme active site and/or the release of the reaction products. These reactions are known as diffusion –controlled. Overcoming this limitation may enable faster catalytic rates, which in the case of catalytic biosensors can potentially lower limits of detection of specific analyte. Here we created an artificial system to enable deoxyribozyme (Dz) 10-23 based biosensor to overcome its diffusion limit. The sensor consists of the two probe strands, which bind to the analyzed nucleic acid by Watson-Crick base pairs and, upon binding re-form the catalytic core of …