Molecular Biology Commons^™

Altering Oligomerization Of Epha2 Via Mutations In The Intracellular Domain, Ryan W. Lingerak

Honors Research Projects

Eph receptor tyrosine kinases (RTKs) are activated by membrane-bound ligands called ephrins. Eph RTKs are divided into two subclasses, each activated by a specific classes of the ligand ephrin. The overexpression of Eph receptors is correlated to cancer cell metastasis in several different types of cancers. Studies with the EphA2 extracellular domain (ECD) and ephrinA1 ligand have shown that upon binding of ephrin to the receptor, EphA2 undergoes increased oligomerization and activation. This indicates that oligomerization is intimately connected to kinase activity. High resolution crystal structures of the EphA2 ECD have revealed some details of these ligand bound oligomers, as ...

Tea Induction Of Cyp6a8 Promoter In Drosophila Melanogaster, Fiona Retzer

University of Tennessee Honors Thesis Projects

No abstract provided.

Explore Variable Potential Ion Guide For Mass Spectrometry, Curtiss D. Hanson

Curtiss D. Hanson

A variable potential ion guide for placement within the reflectron of a time-of-flight mass spectrometer includes an elongate resistive electrode placed axially within the reflectron. The electrode may be a non-conductive monofilament coated with a resistive polymer coating, with one end of the electrode coupled to a high potential source, the electrode carrying a potential gradient along its length.

Ion Trap Mass Analyzer Apparatus, Methods, And Systems Utilizing One Or More Multiple Potential Ion Guide (Mpig) Electrodes, Curtiss Dwight Hanson

Curtiss D. Hanson

In one aspect of the invention, an ion trap mass analyzer includes a variable- or multi-potential type ion guide (MPIG) assembly which has been pre-configured to produce a parabolic-type potential field. Each MPIG electrode has a resistive coating of designed characteristics. In one example the coating varies in thickness along the length of an underlying uniform substrate. The MPIG assembly can be a single MPIG electrode or an array of a plurality of MPIG electrodes. An array can facilitate delocalization for improved performance. This chemical modification of a uniform underlying substrate promotes cheaper and flexible instruments. The modified MPIG electrodes ...

Multi-Pass Reflectron Time-Of-Flight Mass Spectrometer, Curtiss D. Hanson

Curtiss D. Hanson

A novel design for a time-of-flight mass spectrometer capable of tandem mass spectrometry measurements with high resolution and high sensitivity using two variable reflectrons in a co-linear geometry. Variably switched reflectrons are oriented coaxially on opposing ends of the ion flight region allowing multiple passes of the ions along the flight region permitting high resolution, tandem mass spectrometry experiments to be performed. An electrostatic particle guide is incorporated to ensure high ion transmission efficiency in a multi-pass system. In addition to permitting the high transmission efficiency of ions, the EPG can be used in a bipolar pulsed mode to isolate ...

The N-Terminus Of Ift46 Mediates Intraflagellar Transport Of Outer Arm Dynein And Its Cargo-Adaptor Oda16, Yuqing Hou, George B. Witman

Radiology Publications and Presentations

Cilia are assembled via intraflagellar transport (IFT). The IFT machinery is composed of motors and multi-subunit particles, termed IFT-A and IFT-B, that carry cargo into the cilium. Knowledge of how the IFT subunits interact with their cargo is of critical importance for understanding how the unique ciliary domain is established. We previously reported a Chlamydomonas mutant, ift46-1, that fails to express the IFT-B protein IFT46, has greatly reduced levels of other IFT-B proteins, and assembles only very short flagella. A spontaneous suppression of ift46-1 restored IFT-B levels and enabled growth of longer flagella, but the flagella lacked outer dynein arms ...

Prtad: A Database For Protein Residue Torsion Angle Distributions, Xiaoyong Sun, Di Wu, Robert L. Jernigan, Zhijun Wu

Robert Jernigan

PRTAD is a dedicated database and structural bioinformatics system for protein analysis and modelling. The database is developed to host and analyse the statistical data for protein residue level 'virtual' bond and torsion angles obtained from their distributions in databases of known protein structures such as in the PDB Data Bank. PRTAD is capable of generating, caching, and displaying the statistical distributions of the angles of various types. The collected information can be used to extract geometric restraints or define statistical potentials for protein structure determination. PRTAD is supported with a friendly designed web interface so that users can easily ...

Host-Pathogen Protein-Protein Interaction Prediction Using An In Silico Model, John C. F. Hsieh, Robert L. Jernigan, Susan J. Lamont

Robert Jernigan

Newcastle Disease (ND) is caused by Newcastle Disease Virus (NDV) and is a major problem in developing countries where vaccination against NDV is not easily achievable. A step required for NDV infection is the cleavage of the NDV fusion (F) protein. Using structural information of the NDV F protein and the only known host protein binding partner, protein disulfide isomerase A3 (PDIA3), we computer modeled the interaction between the two proteins by looking at a docked structure of these two proteins. With our docked structure, we visualized one of the catalytic domains of PDIA3 being near the cleavage site of ...

Predicting Dna-Binding Sites Of Proteins From Amino Acid Sequence, Changhui Yan, Michael Terribilini, Feihong Wu, Robert L. Jernigan, Drena Dobbs, Vasant Honavar

Robert Jernigan

Background

Understanding the molecular details of protein-DNA interactions is critical for deciphering the mechanisms of gene regulation. We present a machine learning approach for the identification of amino acid residues involved in protein-DNA interactions.

Results

We start with a Naïve Bayes classifier trained to predict whether a given amino acid residue is a DNA-binding residue based on its identity and the identities of its sequence neighbors. The input to the classifier consists of the identities of the target residue and 4 sequence neighbors on each side of the target residue. The classifier is trained and evaluated (using leave-one-out cross-validation) on ...

Amelioration Of Prenatal Alcohol Effects By Environmental Enrichment In A Mouse Model Of Fasd, Aniruddho Chokroborty-Hoque

Electronic Thesis and Dissertation Repository

Maternal alcohol consumption during pregnancy results in a spectrum of behavioural and cognitive deficits collectively known as Fetal Alcohol Spectrum Disorders (FASD). Currently, little is know about if and how the external environment may modulate these deficits. I have used C57BL/6 mice to study this interaction between prenatal alcohol exposure and the postnatal environment. Alcohol exposure during synaptogenesis produces high levels of anxiety-like traits and decreased memory performance. Alcohol-exposed mice (and matched unexposed controls) were put in 'environmentally-enriched' conditions of voluntary exercise, physical activities and cognitive stimulation to ascertain the effects of a positive postnatal environment. The results show ...

Engaging Medical Students In Problem-Based Search And Study Of The Biomedical Literature., Zhiyong Han, Samantha L Margulies, Divya Kurian, Joshua M Jabaut, Akshita Mehta, Ramzi Dudum, Huberta Koudoro, Ria S Roberts, Jay Lee, Jonathan Li, Hieu T Nguyen, Mark Elliott

Biochemistry and Molecular Medicine Faculty Publications

No abstract provided.

Dietary Phytochemicals As Inhibitors Of Primary Amine Oxidase, Padraig Shanahan, Jeffrey O'Sullivan, Keith F. Tipton, Gemma Kinsella, Barry J. Ryan, Gary T. Henehan

Articles

Phytochemicals such as methylxanthines, catechins and polyphenols show health benefits in a range of diseases although their mechanism of action is not fully understood. Primary Amine Oxidase (PrAO) is widely recognised as a therapeutic drug target for the treatment of inflammatory, vascular and neurodegenerative diseases. Previous work in our laboratories showed that caffeine inhibited bovine PrAO activity with a Ki of 1.0mM. In the present study we examined a range of methylxanthines and catechins as inhibitors of bovine PrAO. The methylxanthines tested were caffeine, paraxanthine, theophylline, theobromine and 7-methylxanthine. Of these, only theobromine was an inhibitor with an IC50 ...

Expression And Purification Of Dna Polymerase 1 (Klenow Fragment) For Single-Molecule Nanotube Dna Sequencing, Chanelle Hunter

Chanelle Hunter

Sh2-Dependent Autophosphorylation Within The Tec Family Kinase Itk, Raji E. Joseph, Andrew Severin, Lie Min, D. Bruce Fulton, Amy H. Andreotti

Andrew Severin

The Tec family kinase, Itk (interleukin-2 tyrosine kinase), undergoes an in cis autophosphorylation on Y180 within its Src homology 3 (SH3) domain. Autophosphorylation of the Itk SH3 domain by the Itk kinase domain is strictly dependent on the presence of the intervening Src homology 2 (SH2) domain. A direct docking interaction between the Itk kinase and SH2 domains brings the Itk SH3 domain into the active site where Y180 is then phosphorylated. We now identify the residues on the surface of the Itk SH2 domain responsible for substrate docking and show that this SH2 surface mediates autophosphorylation in the full-length ...

Metastasis-Associated Protein 1 Deficiency Results In Compromised Pulmonary Alveolar Capillary Angiogenesis In Mice., Jun-Hui Qin, Zhen-Yu Ke, Qiang Zhou, Li Wang, Yuan Liang, Ying-Mei Wang, Tong Yang, Xing Gao, Jing Ye, Rekesh Kumar, Rui-An Wang

Biochemistry and Molecular Medicine Faculty Publications

Background

The aim of this study was to investigate the effects of metastasis-associated protein 1 (MTA1) deficiency during angiogenesis of pulmonary alveolar capillaries in mice and to determine the molecular mechanisms involved.

Material/Methods

The expressions of MTA1, CD34, vascular endothelial growth factor (VEGF), alpha smooth muscle actin (α-SMA), and HIF-1α were analyzed in the lungs of MTA1-knockout (KO) and wild-type mice at embryonic day 18.5 and 2 months by quantitative PCR, immunoblotting, and immunohistochemistry. The morphological changes were investigated during pulmonary alveolar capillary formation. The heart weight/body weight (HW/BW) ratio and the size of the ...

Fluorescent Protein Biosensor For Use In Parkinson's Research, Piper R. Miller, Keelan Trull, Mathew Tantama

The Summer Undergraduate Research Fellowship (SURF) Symposium

Purinergic signaling is a type of extracellular communication that occurs between cells, mediated by adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine. In Parkinson’s Disease, purinergic signaling is disrupted, which contributes to neurodegeneration. In order to monitor this change in cell-to-cell signaling, there is a need for the development of a fluorescent protein (FP) biosensor to study the changes in the concentration of the signaling molecule ATP and its decomposition bioproduct ADP. This summer a genetically encoded ADP sensor that measures changes in ADP concentration was developed. This sensor utilizes Forster Resonance Energy Transfer (FRET) which is a sensing ...

Performing A Genetic Screen To Identify Factors That Promote Lncrna-Dependent Gene Repression, Chrishan Fernando, Cecilia Yiu, Sara Cloutier, Siwen Wang, Elizabeth Tran

The Summer Undergraduate Research Fellowship (SURF) Symposium

Long non-coding RNAs (lncRNAs) were once thought not to have useful functions in organisms but rather to be products of aberrant transcription. However, roles are being found for lncRNAs in beneficial processes such as controlling gene expression. In some of these cases, lncRNAs form R-loops in vivo. R-loops are nucleic acid structures consisting of hybridized strands of single-stranded DNA (ssDNA) and single-stranded RNA (ssRNA) as well as the displaced strand of ssDNA. Formation of these R-loops is important for gene regulation by the lncRNAs. However, factors that promote formation of lncRNA R-loops are not known. The gene PHO84 is being ...

Fret Biosensors: Engineering Fluorescent Proteins As Biological Tools For Studying Parkinson’S Disease, Nathan J. Leroy, Jacob R. Norley, Saranya Radhakrishnan, Mathew Tantama

The Summer Undergraduate Research Fellowship (SURF) Symposium

Parkinson’s Disease (PD) is a common neurodegenerative disease with over 200,000 new cases each year. In general, the cause of the disease is unknown, but oxidative stress inside of neurons has been associated with the disease’s pathology for some time. Currently, techniques to study the onset of PD inside of neurons are limited. This makes treatments and causes difficult to discover. One solution to this has been fluorescent protein biosensors. In short, these proteins can be engineered to glow when a certain state is achieved inside a cell. The present research discusses the engineering of a genetically-encoded ...

Cross-Sectional Relations Of Whole-Blood Mirna Expression Levels And Hand Grip Strength In A Community Sample, Joanne M. Murabito, Jian Rong, Kathryn L. Lunetta, Tianxiao Huan, Honghuang Lin, Qiang Zhao, Jane E. Freedman, Kahraman Tanriverdi, Daniel Levy, Martin G. Larson

UMass Metabolic Network Publications

MicroRNAs (miRNAs) regulate gene expression with emerging data suggesting miRNAs play a role in skeletal muscle biology. We sought to examine the association of miRNAs with grip strength in a community-based sample. Framingham Heart Study Offspring and Generation 3 participants (n = 5668 54% women, mean age 55 years, range 24, 90 years) underwent grip strength measurement and miRNA profiling using whole blood from fasting morning samples. Linear mixed-effects regression modeling of grip strength (kg) versus continuous miRNA 'Cq' values and versus binary miRNA expression was performed. We conducted an integrative miRNA-mRNA coexpression analysis and examined the enrichment of biologic pathways ...

Molecular And Biochemical Studies Of Several Novel Estrogen Receptor Alpha-Interacting Proteins In Breast Cancer Cells, Ahmed Edan Dhamad

Theses and Dissertations

Breast cancer is the second leading cause of cancer-related death in women, and approximately 70% of incidences are estrogen receptor (ER)-positive breast cancer. ERα and its interacting proteins play a key role in the development and progression of breast cancer. However, how ERα regulates its target gene expression and hence cell proliferation is not fully understood. To enhance our understanding of the molecular mechanism by which ERα regulates gene expression, we used a quantitative proteomic method to identify cellular proteins that interact with ERα. The first group of proteins that were identified to associate with ERα are heat shock ...