C-Jun Nh2-Terminal Kinase Is Required For Lineage-Specific Differentiation But Not Stem Cell Self-Renewal, 2010 University of Massachusetts Medical School
C-Jun Nh2-Terminal Kinase Is Required For Lineage-Specific Differentiation But Not Stem Cell Self-Renewal, Ping Xu, Roger J. Davis
Davis Lab Publications
The c-Jun NH(2)-terminal kinase (JNK) is implicated in proliferation. Mice with a deficiency of either the Jnk1 or the Jnk2 genes are viable, but a compound deficiency of both Jnk1 and Jnk2 causes early embryonic lethality. Studies using conditional gene ablation and chemical genetic approaches demonstrate that the combined loss of JNK1 and JNK2 protein kinase function results in rapid senescence. To test whether this role of JNK was required for stem cell proliferation, we isolated embryonic stem (ES) cells from wild-type and JNK-deficient mice. We found that Jnk1(-/-) Jnk2(-/-) ES cells underwent self-renewal, but these cells proliferated ...
Quasispecies-Like Behavior Observed In Catalytic Rna Populations Evolving In A Test Tube, 2010 Portland State University
Quasispecies-Like Behavior Observed In Catalytic Rna Populations Evolving In A Test Tube, Carolina Diaz Arenas, Niles Lehman
Chemistry Faculty Publications and Presentations
Background: During the RNA World, molecular populations were probably very small and highly susceptible to the force of strong random drift. In conjunction with Muller's Ratchet, this would have imposed difficulties for the preservation of the genetic information and the survival of the populations. Mechanisms that allowed these nascent populations to overcome this problem must have been advantageous.
Results: Using continuous in vitro evolution experimentation with an increased mutation rate imposed by MnCl2, it was found that clonal 100-molecule populations of ribozymes clearly exhibit certain characteristics of a quasispecies. This is the first time this has been seen with ...
Reverse Genetic And Cell Biological Approaches To The Study Of Developmental Functions Of Class Xi Myosin In Arabidopsis Thaliana, 2010 University of Tennessee - Knoxville
Reverse Genetic And Cell Biological Approaches To The Study Of Developmental Functions Of Class Xi Myosin In Arabidopsis Thaliana, Eunsook Park
Myosin proteins function as molecular motors that drive the ATP-dependent movement of cellular components along actin filaments. Vascular plants encode two different types of myosin, referred to as class VIII and class XI. Although class XI myosins have been suggested to function in organelle movement and cytoplasmic streaming, little is known about their cellular function in detail.
The Arabidopsis genome encodes 13 class XI myosin genes. The reasons for the relatively large number of myosin XI isoforms present within a single plant species are unknown. To investigate the function of these gene products in the cell, we determined the spatial ...
T Cell Specific Adapter Protein (Tsad) Interacts With Tec Kinase Itk To Promote Cxcl12 Induced Migration Of Human And Murine T Cells, Tone Berge, Vibeke Sundvold-Gjerstad, Stine Granum, Thorny Cecilie Bie Andersen, Gunn B. Holthe, Lena Claesson-Welsh, Amy H. Andreotti, Marit Inngjerdingen, Anne Spurkland
Biochemistry, Biophysics and Molecular Biology Publications
The chemokine CXCL12/SDF-1α interacts with its G-protein coupled receptor CXCR4 to induce migration of lymphoid and endothelial cells. T cell specific adapter protein (TSAd) has been found to promote migration of Jurkat T cells through interaction with the G protein β subunit. However, the molecular mechanisms for how TSAd influences cellular migration have not been characterized in detail. We show that TSAd is required for tyrosine phosphorylation of the Lck substrate IL2-inducible T cell kinase (Itk). Presence of Itk Y511 was necessary to boost TSAd's effect on CXCL12 induced migration of Jurkat T cells. In addition, TSAd's ...
Fast Protein Structure Alignment, 2010 Rose-Hulman Institute of Technology
Fast Protein Structure Alignment, Yosi Shibberu, Allen Holder, Kyla Lutz
Mathematical Sciences Technical Reports (MSTR)
We address the problem of aligning the 3D structures of two proteins. Our pairwise comparisons are based on a new optimization model that is succinctly expressed in terms of linear transformations and highlights the problem’s intrinsic geometry. The optimization problem is approximately solved with a new polynomial time algorithm. The worst case analysis of the algorithm shows that the solution is bounded by a constant depending only on the data of the problem.
Role Of The Hypothalamic-Pituitary-Thyroid Axis In Metabolic Regulation By Jnk1, 2010 University of Massachusetts Medical School
Role Of The Hypothalamic-Pituitary-Thyroid Axis In Metabolic Regulation By Jnk1, Guadalupe Sabio, Julie Cavanagh-Kyros, Tamera Barrett, Dae Young Jung, Hwi Jin Ko, Helena Ong, Caroline Morel, Alfonso Mora, Judith Reilly, Jason K. Kim, Roger J. Davis
Davis Lab Publications
The cJun N-terminal kinase 1 (JNK1) is implicated in diet-induced obesity. Indeed, germline ablation of the murine Jnk1 gene prevents diet-induced obesity. Here we demonstrate that selective deficiency of JNK1 in the murine nervous system is sufficient to suppress diet-induced obesity. The failure to increase body mass is mediated, in part, by increased energy expenditure that is associated with activation of the hypothalamic-pituitary-thyroid axis. Disruption of thyroid hormone function prevents the effects of nervous system JNK1 deficiency on body mass. These data demonstrate that the hypothalamic-pituitary-thyroid axis represents an important target of metabolic signaling by JNK1.
Increasing Diterpene Yield With A Modular Metabolic Engineering System In E. Coli: Comparison Of Mev And Mep Isoprenoid Precursor Pathway Engineering, Dana Morrone, Luke Lowry, Mara K. Determan, David M. Hershey, Meimei Xu, Reuben J. Peters
Biochemistry, Biophysics and Molecular Biology Publications
Engineering biosynthetic pathways in heterologous microbial host organisms offers an elegant approach to pathway elucidation via the incorporation of putative biosynthetic enzymes and characterization of resulting novel metabolites. Our previous work in Escherichia coli demonstrated the feasibility of a facile modular approach to engineering the production of labdane-related diterpene (20 carbon) natural products. However, yield was limited (<0.1 mg/L), presumably due to reliance on endogenous production of the isoprenoid precursors dimethylallyl diphosphate and isopentenyl diphosphate. Here, we report incorporation of either a heterologous mevalonate pathway (MEV) or enhancement of the endogenous methyl erythritol phosphate pathway (MEP) with our modular metabolic engineering system. With MEP pathway enhancement, it was found that pyruvate supplementation of rich media and simultaneous overexpression of three genes (idi, dxs, and dxr) resulted in the greatest increase in diterpene yield, indicating distributed metabolic control within this pathway. Incorporation of a heterologous MEV pathway in bioreactor grown cultures resulted in significantly higher yields than MEP pathway enhancement. We have established suitable growth ...0.1>
Large Scale Reverse Genetics In Arabidopsis: Case Studies From The Chloroplast 2010 Project, 2010 Western Michigan University
Large Scale Reverse Genetics In Arabidopsis: Case Studies From The Chloroplast 2010 Project, Imad Ajjawi, Yan Lu, Linda Savage, Shannon Bell, Robert Last
No abstract provided.
Nmr Assignments Of A Stable Processing Intermediate Of Human Frataxin, 2010 Wayne State University
Nmr Assignments Of A Stable Processing Intermediate Of Human Frataxin, Kalyan C. Kondapalli, Krisztina Z. Bencze, Eric Dizin, James A. Cowan, Timothy L. Stemmler
Biochemistry and Molecular Biology Faculty Publications
Frataxin, a nuclear encoded protein targeted to the mitochondrial matrix, has recently been implicated as an iron chaperone that delivers ferrous iron to the iron-sulfur assembly enzyme IscU. During transport across the mitochondrial membrane, the N-terminal mitochondrial targeting sequence of frataxin is cleaved in a two-step process to produce the mature protein found in the matrix, however N-terminal extended forms of the protein have also been observed in vivo. The recent structural characterization studies of the human frataxin ortholog were performed on a truncated variant of the protein. Here we report the NMR spectral assignment of an extended form of ...
The Globin Gene Family Of The Cephalochordate Amphioxus: Implications For Chordate Globin Evolution, 2010 Institute of Molecular Genetics, Johannes Gutenberg-University
The Globin Gene Family Of The Cephalochordate Amphioxus: Implications For Chordate Globin Evolution, Bettina Ebner, Georgia Panopoulou, Serge N. Vinogradov, Laurent Kiger, Michael C. Marden, Thorsten Burmester, Thomas Hankeln
Wayne State University Associated BioMed Central Scholarship
The lancelet amphioxus (Cephalochordata) is a close relative of vertebrates and thus may enhance our understanding of vertebrate gene and genome evolution. In this context, the globins are one of the best studied models for gene family evolution. Previous biochemical studies have demonstrated the presence of an intracellular globin in notochord tissue and myotome of amphioxus, but the corresponding gene has not yet been identified. Genomic resources of Branchiostoma floridae now facilitate the identification, experimental confirmation and molecular evolutionary analysis of its globin gene repertoire.
We show that B. floridae harbors at least fifteen paralogous globin genes ...
Functional Cooperation Of The Proapoptotic Bcl2 Family Proteins Bmf And Bim In Vivo, 2010 University of Massachusetts Medical School
Functional Cooperation Of The Proapoptotic Bcl2 Family Proteins Bmf And Bim In Vivo, Anette Hubner, Julie Cavanagh-Kyros, Mercedes Rincon, Richard Flavell, Roger J. Davis
Davis Lab Publications
Bcl2-modifying factor (Bmf) is a member of the BH3-only group of proapoptotic proteins. To test the role of Bmf in vivo, we constructed mice with a series of mutated Bmf alleles that disrupt Bmf expression, prevent Bmf phosphorylation by the c-Jun NH(2)-terminal kinase (JNK) on Ser(74), or mimic Bmf phosphorylation on Ser(74). We report that the loss of Bmf causes defects in uterovaginal development, including an imperforate vagina and hydrometrocolpos. We also show that the phosphorylation of Bmf on Ser(74) can contribute to a moderate increase in levels of Bmf activity. Studies of compound mutants ...
Probing Local Structural Fluctuations In Myoglobin By Size-Dependent Thiol-Disulfide Exchange, 2010 University of Massachusetts Amherst
Probing Local Structural Fluctuations In Myoglobin By Size-Dependent Thiol-Disulfide Exchange, Margaret M. Stratton, S N. Loh, T A. Cutler, J H. Ha
Biochemistry & Molecular Biology Department Faculty Publication Series
All proteins undergo local structural fluctuations (LSFs) or breathing motions. These motions are likely to be important for function but are poorly understood. LSFs were initially defined by amide hydrogen exchange (HX) experiments as opening events, which expose a small number of backbone amides to (1)H/(2)H exchange, but whose exchange rates are independent of denaturant concentration. Here, we use size-dependent thiol-disulfide exchange (SX) to characterize LSFs in single cysteine-containing variants of myoglobin (Mb). SX complements HX by providing information on motions that disrupt side chain packing interactions. Most importantly, probe reagents of different sizes and chemical properties ...
Role Of Muscle C-Jun Nh2-Terminal Kinase 1 In Obesity-Induced Insulin Resistance, 2010 University of Massachusetts Medical School
Role Of Muscle C-Jun Nh2-Terminal Kinase 1 In Obesity-Induced Insulin Resistance, Guadalupe Sabio, Norman J. Kennedy, Julie Cavanagh-Kyros, Dae Young Jung, Hwi Jin Ko, Helena Ong, Tamera Barrett, Jason K. Kim, Roger J. Davis
Davis Lab Publications
Obesity caused by feeding of a high-fat diet (HFD) is associated with an increased activation of c-Jun NH(2)-terminal kinase 1 (JNK1). Activated JNK1 is implicated in the mechanism of obesity-induced insulin resistance and the development of metabolic syndrome and type 2 diabetes. Significantly, Jnk1(-)(/)(-) mice are protected against HFD-induced obesity and insulin resistance. Here we show that an ablation of the Jnk1 gene in skeletal muscle does not influence HFD-induced obesity. However, muscle-specific JNK1-deficient (M(KO)) mice exhibit improved insulin sensitivity compared with control wild-type (M(WT)) mice. Thus, insulin-stimulated AKT activation is suppressed in muscle, liver, and ...
In Vivo Labeling Of A Model Β-Clam Protein With A Fluorescent Amino Acid, 2010 University of Massachusetts Amherst
In Vivo Labeling Of A Model Β-Clam Protein With A Fluorescent Amino Acid, Mangayarkarasi Periasamy
Masters Theses 1911 - February 2014
Proteins can be labeled with different tags to enable their structural and functional investigations. In addition, labeling proteins at specific sites helps in studying the conformational dynamics of these molecules. A plethora of methods is available to facilitate labeling, choice of which largely depends on the requirements and the anticipated end results. In general, the various labeling methods can be classified into four different classes based on the stage at which labeling is performed, namely post translational labeling, non-ribosomal synthesis, in vitro translation and in vivo translation. Interestingly all these techniques use different unnatural amino acids for this purpose.
Myosin Xi Is Essential For Tip Growth In Physcomitrella Patens, 2010 University of Massachusetts - Amherst
Myosin Xi Is Essential For Tip Growth In Physcomitrella Patens, L Vidali, Gm Burkart, Rc Augustine, E Kerdavid, E Tuzel, M Bezanilla
Class XI myosins are plant specific and responsible for cytoplasmic streaming. Because of the large number of myosin XI genes in angiosperms, it has been difficult to determine their precise role, particularly with respect to tip growth. The moss Physcomitrella patens provides an ideal system to study myosin XI function. P. patens has only two myosin XI genes, and these genes encode proteins that are 94% identical to each other. To determine their role in tip growth, we used RNA interference to specifically silence each myosin XI gene using 5′ untranslated region sequences. We discovered that the two myosin XI ...
Ethylene Receptors Function As Components Of High-Molecular-Mass Protein Complexes In Arabidopsis, 2010 University of Tennessee - Knoxville
Ethylene Receptors Function As Components Of High-Molecular-Mass Protein Complexes In Arabidopsis, Yi-Feng Chen, Zhiyong Gao, Robert J. Kerriss Iii, Wuyi Wang, Brad M. Binder, G. Eric Schaller
Faculty Publications and Other Works -- Biochemistry, Cellular and Molecular Biology
The gaseous plant hormone ethylene is perceived in Arabidopsis thaliana by a five-member receptor family composed of ETR1, ERS1, ETR2, ERS2, and EIN4. Methodology/Principal Findings
Gel-filtration analysis of ethylene receptors solubilized from Arabidopsis membranes demonstrates that the receptors exist as components of high-molecular-mass protein complexes. The ERS1 protein complex exhibits an ethylene-induced change in size consistent with ligand-mediated nucleation of protein-protein interactions. Deletion analysis supports the participation of multiple domains from ETR1 in formation of the protein complex, and also demonstrates that targeting to and retention of ETR1 at the endoplasmic reticulum only requires the first 147 amino acids ...
Expression, Purification, And Analysis Of Unknown Translation Factors From Escherichia Coli: A Synthesis Approach, 2010 Western Washington University
Expression, Purification, And Analysis Of Unknown Translation Factors From Escherichia Coli: A Synthesis Approach, Justin D. Walter, Peter Littlefield, Scott P. Delbecq, Gerry Prody, P. Clint Spiegel
Chemistry Faculty and Staff Publications
New approaches are currently being developed to expose biochemistry and molecular biology undergraduates to a more interactive learning environment. Here, we propose a unique project-based laboratory module, which incorporates exposure to biophysical chemistry approaches to address problems in protein chemistry. Each of the experiments described herein contributes to the stepwise process of isolating, identifying, and analyzing a protein involved in a central biological process, prokaryotic translation. Students are provided with expression plasmids that harbor an unknown translation factor, and it is their charge to complete a series of experiments that will allow them to develop hypotheses for discovering the identity ...
Lysine Specific Demethylase-1 And The Brahma Chromatin Remodeling Complex Regulate Conserved Signaling Pathways During Drosophila Wing Development, Brenda Jean Curtis
The conserved SWI/SNF chromatin remodeling complex uses the energy from ATP hydrolysis to alter local chromatin environments by disrupting DNA-histone contacts. The Drosophila SWI/SNF counterpart, the Brahma complex, has been shown to have an essential role in regulating the proper expression of many developmentally important genes, including those required for eye and wing tissue morphogenesis. A temperature sensitive mutation in one of the core subunits, SNR1 (SNF5/Ini1/SMARC B1), results in reproducible wing patterning phenotypes that can be enhanced and suppressed by extragenic mutations. SNR1 functions as a regulatory subunit to modulate chromatin remodeling activities of the ...
Developmental Characterization Of Cara Mitad: A Drosophila Nuclear Receptor Co-Regulator, 2010 Loyola University Chicago
Developmental Characterization Of Cara Mitad: A Drosophila Nuclear Receptor Co-Regulator, Chhavi Chauhan
In insects and vertebrates, hormone titers drive cellular proliferation and differentiation events that guide proper development. Nuclear receptors (NR) respond to these hormone signals by activating cascades of gene expression, along with coregulator protein complexes. In Drosophila melanogaster, fluctuating titers of the steroid hormone ecdysone are responsible for coordinating the timing of organismal development. Despite major advances in our understanding of Drosophila NR activities, we lack essential knowledge of the coregulators that are required for their proper function.
We have recently identified the Drosophila cara mitad (cmi) (`dear half') gene. The deduced CMI protein is closely related to the N-terminal ...
The Role Of Igf-1 And Notch Signaling In Thoracic Malignancies., 2010 Loyola University Chicago
The Role Of Igf-1 And Notch Signaling In Thoracic Malignancies., Sandra Eliasz
Thoracic malignancies are one of the deadliest of all cancers, being the leading cause of cancer death in the Western world. Thoracic malignancies arise from different tissues; however the most common are of epithelial (commonly referred to as non-small cell lung cancer, or NSCLC), neuroendocrine (small cell lung cancer, or SCLC) and mesothelial origin (malignant mesothelioma, or MM). The DNA oncogenic virus Simian Virus 40 (SV40) has been shown to cooperate with environmental oncogenic fibers in the onset of MM. Insulin like growth factor-1 (IGF-1) signaling plays a central role in all thoracic malignancies and in the process of SV40-mediated ...