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Molecular Basis For Distinct Pathways For Protein Import Into Arabidopsis Chloroplasts, Danny Schnell, C. Rounds, H. Inoue 2010 University of Massachusetts - Amherst

Molecular Basis For Distinct Pathways For Protein Import Into Arabidopsis Chloroplasts, Danny Schnell, C. Rounds, H. Inoue

Danny Schnell

The translocons at the outer envelope membrane of chloroplasts (TOCs) initiate the import of thousands of nucleus-encoded proteins into the organelle. The identification of structurally and functionally distinct TOC complexes has led to the hypothesis that the translocons constitute different import pathways that are required to coordinate the import of sets of proteins whose expression varies in response to organelle biogenesis and physiological adaptation. To test this hypothesis, we examined the molecular basis for distinct TOC pathways by analyzing the functional diversification among the Toc159 family of TOC receptors. We demonstrate that the N-terminal A-domains of the Toc159 receptors regulate ...


Enzyme-Catalyzed Hydrolysis Of Cellulose In Ionic Liquids: A Green Approach Toward The Production Of Biofuels, Sayantan Bose, Daniel W. Armstrong, Jacob W. Petrich 2010 Iowa State University

Enzyme-Catalyzed Hydrolysis Of Cellulose In Ionic Liquids: A Green Approach Toward The Production Of Biofuels, Sayantan Bose, Daniel W. Armstrong, Jacob W. Petrich

Chemistry Publications

We investigated the reactivity and stability of a commercial mixture of cellulases in eight ionic liquids by optical and calorimetric techniques. First, hydrolysis by cellulases from Tricoderma reesei in these ionic liquids was benchmarked against that in aqueous buffer. Only 1-methylimidazolium chloride (mim Cl) and tris-(2-hydroxyethyl)methylammonium methylsulfate (HEMA) provided a medium in which hydrolysis could occur. While hydrolysis at 65 °C is initially much faster in buffer than in these two liquids, it reaches a plateau after 2 h, whereas the reaction progresses monotonically in the two ionic liquids. This difference in the rate of hydrolysis is largely ...


An Integrative Study Of Gene Expression Of Pma Induced Differentiation In Hl-60 Cells By Dna Microarray Analysis, Emily Marie Swain 2010 Dickinson College

An Integrative Study Of Gene Expression Of Pma Induced Differentiation In Hl-60 Cells By Dna Microarray Analysis, Emily Marie Swain

Student Honors Theses By Year

This study seeks to elucidate the molecular mechanisms by which the acute myeloid leukemia cell line, HL-60, is induced to differentiate into macrophage-like cells following exposure to phorbol 12-myristate 13-acetate (PMA). Changes in gene expression over the time course of PMA treatment were measured by DNA microarray analysis and select genes shown to be significantly up and down-regulated were validated by quantitative real-time PCR. Functional studies of transcription factor binding activities were performed by the electrophoretic mobility shift assay (EMSA). Novel findings include the rapid and sustained induction of mRNA levels for a group of CC chemokine genes (CCL2, CCL3 ...


Probabilistic Protein Design, Comparative Modeling, And The Structure Of A Multidomain P53 Oligomer Bound To Dna, Thomas John Petty II 2010 University of Pennsylvania

Probabilistic Protein Design, Comparative Modeling, And The Structure Of A Multidomain P53 Oligomer Bound To Dna, Thomas John Petty Ii

Publicly Accessible Penn Dissertations

Proteins are the main functional components of all cellular processes, and most of them fold into unique three-dimensional shapes guided by their amino-acid sequence. Discovering the structure of a protein, or protein complexes, can provide important clues about how they perform their function. However, the chemical, physical or architectural properties of many proteins impede traditional approaches to structure determination. Two such proteins, the tumor suppressor p53 and the cholesterol processing enzyme endothelial lipase, are prime examples of problematic proteins that defy structural investigation via crystallographic methods. Therefore, new techniques must be developed to gain valuable structural insights, such as: computationally ...


A New Approach To Understanding Biological Control Of Quinone Electrochemistry, Bruce R. Lichtenstein 2010 University of Pennsylvania

A New Approach To Understanding Biological Control Of Quinone Electrochemistry, Bruce R. Lichtenstein

Publicly Accessible Penn Dissertations

Oxidoreductases play pivotal roles in energy capturing and converting processes of life. During these processes, quinones shuttle protons and reducing equivalents between membrane-bound oxidoreductases that generate the proton motive force during oxidative phosphorylation and photophosphorylation. A key mechanistic feature of these oxidoreductases is their ability to tune the reduction potentials of the hydroquinone, semiquinone and oxidized states of their substrate quinones. This level of control allows for maximization of conversion efficiency between the energy of the quinone reducing equivalents and the proton motive force, and prevents side reactions that may be fatal to cells. A half-century of experimental study and ...


Mimosa: A System For Minimotif Annotation, Jay Vyas, Ronald J. Nowling, Thomas Meusburger, David P. Sargeant, Krishna Kadaveru, Michael R. Gryk, Vamsi Kundeti, Sanguthevar Rajasekaran, Martin Schiller 2010 University of Connecticut Heath Center,

Mimosa: A System For Minimotif Annotation, Jay Vyas, Ronald J. Nowling, Thomas Meusburger, David P. Sargeant, Krishna Kadaveru, Michael R. Gryk, Vamsi Kundeti, Sanguthevar Rajasekaran, Martin Schiller

Life Sciences Faculty Publications

BACKGROUND:

Minimotifs are short peptide sequences within one protein, which are recognized by other proteins or molecules. While there are now several minimotif databases, they are incomplete. There are reports of many minimotifs in the primary literature, which have yet to be annotated, while entirely novel minimotifs continue to be published on a weekly basis. Our recently proposed function and sequence syntax for minimotifs enables us to build a general tool that will facilitate structured annotation and management of minimotif data from the biomedical literature.

RESULTS:

We have built the MimoSA application for minimotif annotation. The application supports management of ...


Dynamics Of The Toc Gtpases: Modulation By Nucleotides And Transit Peptides Reveal A Mechanism For Chloroplast Protein Import, Lovett Evan Reddick 2010 University of Tennessee - Knoxville

Dynamics Of The Toc Gtpases: Modulation By Nucleotides And Transit Peptides Reveal A Mechanism For Chloroplast Protein Import, Lovett Evan Reddick

Doctoral Dissertations

The chloroplast is the green organelle in the plant cell responsible for harvesting energy from sunlight and converting it into sugars and ATP. Origins of this organelle can be traced back to an endosymbiotic event in which a primitive eukaryotic cell capable of oxidative phosphorylation engulfed a free-living cyanobacterium capable of photosynthetic respiration (1). Immediately following this event the details are not clear, however what is known is that over the course of evolution, the engulfed cyanobacteria relinquished approximately 97% of its protein coding sequences to the host cell nucleus, thus making the newly formed chloroplast reliant on its host ...


Preeclampsia, Autoimmunity And The At1 Receptor, Roxanna A. Irani 2010 The University of Texas Graduate School of Biomedical Sciences at Houston

Preeclampsia, Autoimmunity And The At1 Receptor, Roxanna A. Irani

The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)

Preeclampsia (PE) is a disease of late pregnancy characterized by maternal hypertension and proteinuria. It is associated with preterm delivery and significant perinatal morbidity and mortality. Despite affecting ~7% of first pregnancies, there is no effective screening method to identify women at risk, nor is there a definitive treatment other than delivery of the baby and placenta. Though the pathogenesis of PE remains unclear, an imbalance in the renin-angiotensin and immune systems are thought to be major contributors. Bridging these two concepts, it has recently been shown that women with PE harbor specific autoantibodies: the angiotensin II type 1 receptor ...


The Role Of A2b Adenosine Receptor Signaling In Adenosine Dependent Lung Disease, Yang Zhou 2010 University of Texas Graduate School of Biomedical Sciences at Houston

The Role Of A2b Adenosine Receptor Signaling In Adenosine Dependent Lung Disease, Yang Zhou

The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)

Chronic lung diseases and acute lung injuries are two distinctive pulmonary disorders that result in significant morbidity and mortality. Adenosine is a signaling nucleoside generated in response to injury and can serve both protective and destructive functions in tissues and cells through interaction with four G-protein coupled adenosine receptors: A1R, A2AR, A2BR, and A3R. However, the relationship between these factors is poorly understood. Recent findings suggest the A2BR has been implicated in the regulation of both chronic lung disease and acute lung injury. The work presented in this dissertation utilized the adenosine deaminase-deficient mouse model and the bleomycin-induced pulmonary injury ...


Host-Pathogen Interactions Of Secreted And Surface Staphylococcus Aureus Factors, Vanessa Vazquez 2010 University of Texas Graduate School of Biomedical Sciences at Houston

Host-Pathogen Interactions Of Secreted And Surface Staphylococcus Aureus Factors, Vanessa Vazquez

The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)

Staphylococcus aureus is an opportunistic bacterial pathogen that can infect humans and other species. It utilizes an arsenal of virulence factors to cause disease, including secreted and cell wall anchored factors. Secreted toxins attack host cells, and pore-forming toxins destroy target cells by causing cell lysis. S. aureus uses cell-surface adhesins to attach to host molecules thereby facilitating host colonization. The Microbial Surface Components Recognizing Adhesive Matrix Molecules (MSCRAMMs) are a family of cell-wall anchored proteins that target molecules like fibronectin and fibrinogen. The Serine-aspartate repeat (Sdr) proteins are a subset of staphylococcal MSCRAMMs that share similar domain organization. Interestingly ...


De Novo Truncating Fus Gene Mutation As A Cause Of Sporadic Amyotrophic Lateral Sclerosis, Mariely DeJesus-Hernandez, Jannet Kocerha, NiCole Finch, Richard Crook, Matt Baker, Pamela Desaro, Amelia Johnston, Nicola Rutherford, Aleksandra Wojtas 2010 Mayo Clinic

De Novo Truncating Fus Gene Mutation As A Cause Of Sporadic Amyotrophic Lateral Sclerosis, Mariely Dejesus-Hernandez, Jannet Kocerha, Nicole Finch, Richard Crook, Matt Baker, Pamela Desaro, Amelia Johnston, Nicola Rutherford, Aleksandra Wojtas

Jannet Kocerha

Mutations in the gene encoding fused in sarcoma (FUS) were recently identified as a novel cause of amyotrophic lateral sclerosis (ALS), emphasizing the genetic heterogeneity of ALS. We sequenced the genes encoding superoxide dismutase (SOD1), TAR DNA-binding protein 43 (TARDBP) and FUS in 99 sporadic and 17 familial ALS patients ascertained at Mayo Clinic. We identified two novel mutations in FUS in two out of 99 (2.0%) sporadic ALS patients and established the de novo occurrence of one FUS mutation. In familial patients, we identified three (17.6%) SOD1 mutations, while FUS and TARDBP mutations were excluded. The de ...


Overexpression And Partial Purification Of Recombinant Human Serine Hydroxymethyltransferase: A Potential Anticancer Target, Suprit Singh Deol 2010 California Polytechnic State University, San Luis Obispo

Overexpression And Partial Purification Of Recombinant Human Serine Hydroxymethyltransferase: A Potential Anticancer Target, Suprit Singh Deol

Chemistry and Biochemistry

Serine Hydroxymethyltransferase (SHMT) is a member of the thymidylate synthase cycle that provides pyrimidine nucleotides to actively dividing cells, including cancer cells. The other two enzymes involved in this cycle have been targets for clinical anticancer drugs, suggesting that inhibitors of SHMT may also be used as clinical anticancer drugs. In order to test potential inhibitors against SHMT, human SHMT has been overexpressed in E. coli and partially purified by selective ammonium sulfate fractionation followed by anion-exchange fast protein liquid chromatography. A coupled assay using L-allo-threonine and alcohol dehydrogenase was used to identify active fractions, which were analyzed ...


The Ubiquitin Ligase Ube4b Is Required For Efficient Epidermal Growth Factor Receptor Degradation, Natalie Sirisaengtaksin 2010 University of Texas Graduate School of Biomedical Sciences at Houston

The Ubiquitin Ligase Ube4b Is Required For Efficient Epidermal Growth Factor Receptor Degradation, Natalie Sirisaengtaksin

The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)

The length of time that integral membrane proteins reside on the plasma membrane is regulated by endocytosis, a process that can inactivate these proteins by removing them from the membrane and may ultimately result in their degradation. Proteins are internalized and pass through multiple distinct intracellular compartments where targeting decisions determine their fate. Membrane proteins initially enter early endosomes, and subsequently late endosomes/multivesicular bodies (MVBs), before being degraded in the lysosome. The MVB is a subset of late endosomes characterized by the appearance of small vesicles in its luminal compartment. These vesicles contain cargo proteins sorted from the limiting ...


Non-Natural Nucleotides As Probes For The Mechanism And Fidelity Of Dna Polymerases, Irene Lee, Anthony J. Berdis 2010 Case Western Reserve University

Non-Natural Nucleotides As Probes For The Mechanism And Fidelity Of Dna Polymerases, Irene Lee, Anthony J. Berdis

Chemistry Faculty Publications

DNA is a remarkable macromolecule that functions primarily as the carrier of the genetic information of organisms ranging from viruses to bacteria to eukaryotes. The ability of DNA polymerases to efficiently and accurately replicate genetic material represents one of the most fundamental yet complex biological processes found in nature. The central dogma of DNA polymerization is that the efficiency and fidelity of this biological process is dependent upon proper hydrogen-bonding interactions between an incoming nucleotide and its templating partner. However, the foundation of this dogma has been recently challenged by the demonstration that DNA polymerases can effectively and, in some ...


Analysis Of Apoptosis Of Memory T Cells And Dendritic Cells During The Early Stages Of Viral Infection Or Exposure To Toll-Like Receptor Agonists, Kapil Bahl, Anette Hubner, Roger J. Davis, Raymond M. Welsh 2010 Yale University

Analysis Of Apoptosis Of Memory T Cells And Dendritic Cells During The Early Stages Of Viral Infection Or Exposure To Toll-Like Receptor Agonists, Kapil Bahl, Anette Hubner, Roger J. Davis, Raymond M. Welsh

Davis Lab Publications

Profound type I interferon (IFN-I)-dependent attrition of memory CD8 and CD4 T cells occurs early during many infections. It is dramatic at 2 to 4 days following lymphocytic choriomeningitis virus (LCMV) infection of mice and can be elicited by the IFN-inducing Toll receptor agonist poly(I:C). We show that this attrition occurs in many organs, indicating that it is due to T cell loss rather than redistribution. This loss correlated with elevated intracellular staining of T cells ex vivo for activated caspases but with only low levels of ex vivo staining with annexin V, probably due to the ...


Microtubule Stabilization By Bone Morphogenetic Protein Receptor-Mediated Scaffolding Of C-Jun N-Terminal Kinase Promotes Dendrite Formation, Monika Podkowa, Xin Zhao, Chi-Wing Chow, Eleanor T. Coffey, Roger J. Davis, Liliana Attisano 2010 University of Toronto

Microtubule Stabilization By Bone Morphogenetic Protein Receptor-Mediated Scaffolding Of C-Jun N-Terminal Kinase Promotes Dendrite Formation, Monika Podkowa, Xin Zhao, Chi-Wing Chow, Eleanor T. Coffey, Roger J. Davis, Liliana Attisano

Davis Lab Publications

Neuronal outgrowth occurs via coordinated remodeling of the cytoskeleton involving both actin and microtubules. Microtubule stabilization drives the extending neurite, yet little is known of the molecular mechanisms whereby extracellular cues regulate microtubule dynamics. Bone morphogenetic proteins (BMPs) play an important role in neuronal differentiation and morphogenesis, and BMP7 in particular induces the formation of dendrites. Here, we show that BMP7 induces stabilization of microtubules in both a MAP2-dependent neuronal cell culture model and in dendrites of primary cortical neurons. BMP7 rapidly activates c-Jun N-terminal kinases (JNKs), known regulators of microtubule dynamics, and we show that JNKs associate with the ...


The Role Of Cuticular Hydrocarbons In The Pre-Mating Isolation Of Two Pissodes Species, Stephanie L. Teale 2010 Syracuse University

The Role Of Cuticular Hydrocarbons In The Pre-Mating Isolation Of Two Pissodes Species, Stephanie L. Teale

Syracuse University Honors Program Capstone Projects

Pissodes strobi and P. nemorensis are weevils (Coleoptera, Curculionidae) that infest pines (Pinus spp.) and spruces (Picea spp.). Previous studies indicate that they are able to hybridize. In the spring, breeding site specificity maintains reproductive isolation, but in the late summer, both species occupy lateral branches of host trees. Aggregation pheromones for P. nemorensis have been identified but the mechanism for late summer isolation is unknown. Cuticular hydrocarbons have been shown to play a role in the chemical recognition of species, sex, kin, and caste in many groups of insects. The large number of possible compounds and the even larger ...


Role Of Secondary Interactions (Π, Agostic) As Well As Solvent Influence On Alkali Metal Complexes, Elizabeth D. Nagle 2010 Syracuse University

Role Of Secondary Interactions (Π, Agostic) As Well As Solvent Influence On Alkali Metal Complexes, Elizabeth D. Nagle

Syracuse University Honors Program Capstone Projects

We here attempt to synthesize heterobimetallic alkali metal complexes with bulky phenolate ligands via solid state direct metallation. The solid state route may offer a facile method of producing these heterobimetallic species. Synthesis of heterobimetallic alkali metal compounds remains a challenge, as the homometallic complexes are generally favored over formation of the heterobimetallic species. Previous work has shown that the alkali metals have a strong solvent dependency; the recrystallization of heterobimetallic products from toluene yields the heterobimetallic, while recrystallization from THF yields the homometallic. However, the ability for phenolate ligands to stabilize metal centers through secondary interactions, such as M ...


Understanding The Genetic And Molecular Mechanisms Of The Shl3 Phenotype In Arabidopsis Thaliana, Sukeerti Kesar 2010 Syracuse University

Understanding The Genetic And Molecular Mechanisms Of The Shl3 Phenotype In Arabidopsis Thaliana, Sukeerti Kesar

Syracuse University Honors Program Capstone Projects

The study of plant genetics and the molecular mechanisms regulating plant-pathogen interactions is an intensely studied area of research in molecular genetics. Gaining an understanding of the defense mechanisms of plants has proven highly useful in the construction of transgenic plants for increased crop yield. The focus of my research was on the defense mechanisms of Arabidopsis thaliana, a plant in the mustard family. Several features of Arabidopsis make it an excellent model plant for molecular genetic studies. A few of these include a short life cycle (approximately 8 weeks), a completely sequenced genome, high fecundity, and the availability of ...


The Effect Of Exogenous Estrogens On Primordial Follicle Assembly In Vivo, Jenna Rose Karavan 2010 Syracuse University

The Effect Of Exogenous Estrogens On Primordial Follicle Assembly In Vivo, Jenna Rose Karavan

Syracuse University Honors Program Capstone Projects

During embryogenesis in the mouse, primordial germ cells develop, move to the genital ridge of the embryo, and form germline cysts as the ovary develops. The cells in these cysts are linked by intercellular bridges. The cysts then undergo a breakdown process which ultimately results in primordial follicles, each of which consists of a single oocyte surrounded by somatic cells called granulosa cells. During this cyst breakdown process, approximately one-third of the original oocytes become enclosed in primordial follicles, the amount of which is representative of the number of eggs a female will have available to her during her reproductive ...


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