Biochemistry, Biophysics, and Structural Biology Commons^™

Towards A Systems Approach To Understanding Plant Cell Walls, Chris R. Somerville, Stefan Bauer, Ginger Brininstool, Michelle Facette, Thorsten Hamann, Jennifer Milne, Erin Osborne, Alex Paradez, Staffan Persson, Ted K. Raab, Sonja Vorwerk, Heather Youngs

Ted K. Raab

One of the defining features of plants is a body plan based on the physical properties of cell walls. Structural analyses of the polysaccharide components, combined with highresolution imaging, have provided the basis for much of the current understanding of cell walls. The application of genetic methods has begun to provide new insights into how walls are made, how they are controlled, and how they function. However, progress in integrating biophysical, developmental, and genetic information into a useful model will require a system-based approach.

Tsc2 Modulates Actin Cytoskeleton And Focal Adhesion Through Tsc1-Binding Domain And The Rac1 Gtpase, Elena Goncharova, Dmitry Goncharov, Daniel J. Noonan, Vera P Krymskaya

Molecular and Cellular Biochemistry Faculty Publications

Tuberous sclerosis complex (TSC) 1 and TSC2 are thought to be involved in protein translational regulation and cell growth, and loss of their function is a cause of TSC and lymphangioleiomyomatosis (LAM). However, TSC1 also activates Rho and regulates cell adhesion. We found that TSC2 modulates actin dynamics and cell adhesion and the TSC1-binding domain (TSC2-HBD) is essential for this function of TSC2. Expression of TSC2 or TSC2-HBD in TSC2-/- cells promoted Rac1 activation, inhibition of Rho, stress fiber disassembly, and focal adhesion remodeling. The down-regulation of TSC1 with TSC1 siRNA in TSC2-/- cells activated Rac1 and induced loss of …

Isolation Of Cancer Stem Cells From Adult Glioblastoma Multiforme, Xianpeng Yuan, James Curtin, Yizhi Xiong, Gentao Liu, Sebastian Waschsmann-Hogiu, Daniel Farkas, Keith Black, John Yu

Articles

Glioblastoma multiforme (GBM) is the most common adult primary brain tumor and is comprised of a heterogeneous population of cells. It is unclear which cells within the tumor mass are responsible for tumor initiation and maintenance. In this study, we report that brain tumor stem cells can be identified from adult GBMs. These tumor stem cells form neurospheres, possess the capacity for self-renewal, express genes associated with neural stem cells (NSCs), generate daughter cells of different phenotypes from one mother cell, and differentiate into the phenotypically diverse populations of cells similar to those present in the initial GBM. Having a …

Structure–Function Studies Of The Yeast Saccharomyces Cerevisiae Α–Mating Factor Pheromone Receptor Ste2p, Ayça Akal–Strader

Doctoral Dissertations

G protein–coupled receptors (GPCRs) are seven transmembrane domain cell surface proteins that respond to a variety of environmental cues. Response of these receptors to their cognate stimuli on the extracellular region of the cell results in a concurrent activation of a complex series of intracellular signaling pathways that prepare the cell for the required adjustments through regulation of gene expression levels. Participation of GPCRs in such intricate signal transduction pathways renders them important players in human diseases. The GPCR family of proteins therefore represents one of the largest classes of proteins to be targeted in the development of drug design …

P14arf : A P53-Independent Tumor Suppressor, Monte W. Miller

Loma Linda University Electronic Theses, Dissertations & Projects

Many genetic alterations at the CDKN2A locus on human chromosome 9 have been shown to be at least partially responsible for transformation of cells to a cancerous phenotype. This locus encodes two proteins, p16 and p14, that play a pivotal role in tumor surveillance.

Breakdowns in the p14 pathway have been estimated to be present in approximately 40% of human cancers and only recently have its binding partners and effects begun to be defined. Its interaction with the p53 pathway, which is estimated to be inactivated or mutated in 50% of all cancers, makes it difficult to determine its own …

Enterotoxin B Subunit Lectins As Adjuvants For Improvement Of Mucosal Vaccine, Nak-Won Choi

Loma Linda University Electronic Theses, Dissertations & Projects

In comparison with whole organism vaccines, subunit vaccines may be safer for immunization but may lack sufficient immunogenicity to provide complete immunity to the pathogen. To resolve this problem, bacterial and plant enterotoxin B subunit adjuvants containing a variety of receptor-binding properties were used to enhance the immunogenicity of rotavirus subunit vaccines. Enterotoxin B subunit adjuvants were employed to enhance protection against virus infection. Pentameric cholera toxin B subunit (CTB), shiga toxin-1 B subunit (STB) and monomeric ricin toxin B subunit (RTB) molecules were genetically linked to a 90 amino acid peptide from the simian rotavirus (SA11) nonstructural protein NSP4 …

Lateral Hypothalamic Signaling Mechanisms Underlying Feeding Stimulation: Differential Contributions Of Src Family Tyrosine Kinases To Feeding Triggered Either By Nmda Injection Or By Food Deprivation, Arshad Khan, Herman H. Cheung, Elizabeth R. Gillard, Jennifer A. Palarca, Derek S. Welsbie, James W. Gurd, B. Glenn Stanley

Arshad M. Khan, Ph.D.

No abstract provided.

Rhodobacter Capsulatus Porphobilinogen Synthase, A High Activity Metal Ion Independent Hexamer, David Bollivar

Scholarship

No abstract provided.

Structural Mimicry In Class A G Protein-Coupled Receptor Rotamer Toggle Switches, Sean D. Mcallister, Dow P. Hurst, Judy Barnett-Norris, Diane L. Lynch, Patricia H. Reggio, Mary E. Abood

Faculty and Research Publications

In this study, we tested the hypothesis that a CB₁ TMH3-4-5-6 aromatic microdomain, which includes F3.25(190), F3.36(201), W5.43(280), and W6.48(357), is centrally involved in CB₁ receptor activation, with the F3.36(201)/W6.48(357) interaction key to the maintenance of the CB₁-inactive state. We have shown previously that when F3.36(201), W5.43(280), and W6.48(357) are individually mutated to alanine, a significant reduction in ligand binding affinity is observed in the presence of WIN 55,212-2 and SR141716A but not CP55,940 and anandamide. In the work presented here, we report a detailed functional analysis of the F3.36(201)A, F3.25(190)A, W5.43(280)A, and W6.48(357)A mutant receptors …

Gene Markers And Complex Disorders: A Review, M S. Mahmood, N Kureshi, P M. Frossard

Department of Biological & Biomedical Sciences

No abstract provided.

High-Resolution Serum Proteomic Patterns For Ovarian Cancer Detection, Keith A. Baggerly, Sarah R. Edmonson, Jeffrey S. Morris, Kevin R. Coombes

Jeffrey S. Morris

No abstract provided.

Variability In Lipid Profile In Patients With Acute Myocardial Infarction From Two Tertiary Care Hospitals In Pakistan, M P. Iqbal, M Shafiq, N Mehboobali, S P. Iqbal, K Abbasi

Department of Biological & Biomedical Sciences

Objective: To investigate changes in total cholesterol, high density lipoprotein (HDL)-cholesterol, low density lipoprotein (LDL)-cholesterol and triglycerides in serum of Pakistani patients with AMI due to age, gender, body mass index (BMI), diabetes, hypertension, and smoking, and also find out the prevalence of hypercholesterolemia, hypertriglyceridemia, "low HDL-cholesterol" and "isolated low-HDL cholesterol" in them.
Patients and Methods: Serum samples from 451 consecutive AMI patients (250 from National Institute of Cardiovascular Diseases, Karachi and 201 from Armed Forces Institute of Cardiology, Rawalpindi) were analyzed for total cholesterol, HDL-cholesterol and triglycerides using kit methods. LDL-cholesterol was determined using the Friedewald formula.
Results: Mean …

Modeling The Tertiary Structure Of A Maize (Zea Mays Ssp. Mays) Non-Symbiotic Hemoglobin, Juán Sáenz-Rivera, Gautam Sarath, Raul Peter-Arredondo

Gautam Sarath Publications

The tertiary structure of a maize (Zea mays ssp. mays) non-symbiotic hemoglobin (Hbm) was modeled using computer tools and the known tertiary structure of rice Hb1 as a template. This method was tested by predicting the tertiary structure of soybean leghemoglobin a (Lba) using rice Hb1 as a template. The tertiary structures of the predicted and native Lba were similar, indicating that our computer methods could reliably predict the tertiary structures of plant Hbs. We next predicted the tertiary structure of Hbm. Hbm appears to have a long pre-helixA and a large CD-loop. The positions of the distal …

Dynamics Of Dissolved Organic Carbon, Nitrogen And Phosphorus In A Seagrass Meadow Of Laguna Madre, Texas, Susan Ziegler, Edith Kaiser, Ronald Benner

Faculty Publications

No abstract provided.

Phylogenetic Analysis Of The Formin Homology 2 Domain, Henry N. Higgs, Kevin J. Peterson

Dartmouth Scholarship

Formin proteins are key regulators of eukaryotic actin filament assembly and elongation, and many species possess multiple formin isoforms. A nomenclature system based on fundamental features would be desirable, to aid the rapid identification and characterization of novel formins. In this article, we attempt to systematize the formin family by performing phylogenetic analyses of the formin homology 2 (FH2) domain, an independently folding region common to all formins, which alone can influence actin dynamics. Through database searches, we identify 101 FH2 domains from 26 eukaryotic species, including 15 in mice. Sequence alignments reveal a highly conserved yeast-specific insert in the …

A Subset Of Liver Nk T Cells Is Activated During Leishmania Donovani Infection By Cd1d-Bound Lipophosphoglycan, Joseph L. Amprey, Jin S. Im, Salvatore J. Turco, Henry W. Murray, Petr A. Illarionov, Gurdyal S. Besra, Steven A. Porcelli, Gerald F. Späth

Molecular and Cellular Biochemistry Faculty Publications

Natural killer (NK) T cells are activated by synthetic or self-glycolipids and implicated in innate host resistance to a range of viral, bacterial, and protozoan pathogens. Despite the immunogenicity of microbial lipoglycans and their promiscuous binding to CD1d, no pathogen-derived glycolipid antigen presented by this pathway has been identified to date. In the current work, we show increased susceptibility of NK T cell–deficient CD1d^−/− mice to Leishmania donovani infection and Leishmania-induced CD1d-dependent activation of NK T cells in wild-type animals. The elicited response was Th1 polarized, occurred as early as 2 h after infection, and was independent from …

Thermal And Sodium Dodecylsulfate Induced Transitions Of Streptavidin, Mark J. Waner, Irina Navrotskaya, Amanda Bain, Edward D. Oldham, David P. Mascotti

Chemistry

The strong specific binding of streptavidin (SA) to biotin is utilized in numerous biotechnological applications. The SA tetramer is also known to exhibit significant stability, even in the presence of sodium dodecylsulfate (SDS). Despite its importance, relatively little is known about the nature of the thermal denaturation pathway for SA. This work uses a homogeneous SA preparation to expand on the data of previous literature reports, leading to the proposal of a model for temperature induced structural changes in SA. Temperature dependent data were obtained by SDS and native polyacrylamide gel electrophoresis (PAGE), differential scanning calorimetry (DSC), and fluorescence and …

Cystic Breast Lymphangioma, S N. Waqar, H Khan, S F. Mekan, N Kayani, A J. Raja

Department of Biological & Biomedical Sciences

No abstract provided.

Layer-By-Layer Self -Assembly For Enzyme And Dna Encapsulation And Delivery, Amish Patel

Doctoral Dissertations

Thin wall microcapsules were formed via Layer-by-Layer Self-Assembly of alternate adsorption of oppositely charged polyelectrolyte on microcores. After the core dissolution, empty polymeric shells with 20–25 nm thick walls were obtained. These microcapsules were loaded with Myoglobin, Hemoglobin and Glucose Oxidase by opening capsule pores at low pH and closing them at higher pH. The native structure of the enzyme was not affected due to different treatments. Biocompatible nanoshells were also prepared for encasing DNA. Using the same Layer-by-Layer Self-Assembly approach nanoparticle were constructed containing DNA as one of the layers. The nanoparticles of different architecture were used to deliver …

Bacterial Degradation Of Disinfection By-Products In Drinking Water, Laura Inga Fauntleroy

Chemistry & Biochemistry Theses & Dissertations

Chlorine became a major disinfectant for the removal of microbial contaminants in 1914. Current water chlorination procedures yield halogenated disinfection byproducts (DBPs), such as haloalkanes and haloacetic acids (HAAs), due to the reaction of chlorine with naturally occurring organic compounds. Various water utilities have observed decreased HAAs levels in maximum residence time locations (MRTLs), where they were expected to be higher. These MRTLs have low free chlorine residual and high heterotrophic bacteria plate counts. Xanthobacter autotrophicus, GJ-10, is a bacterium that has been shown to contain dehalogenase enzymes and, therefore, can biodegrade HAAs. A number of water-system bacteria were …

Waccnes Containing Bovine Herpe Svirus 1 Attenuated By Mutation In Latency-Related Gene, Clinton J. Jones

School of Veterinary and Biomedical Sciences: Faculty Publications

Vaccines for pathogenic Strains of bovine herpesvirus 1 (BHV-1) which are based on attenuated BHV-1 having a mutation in the latency-related gene are provided. Live, attenuated vaccines are also provided which express anti gens from other viral or bacterial pathogens and thus form the basis of a variety of vaccines.

Rapid And Convenient Method For Preparing Masters For Microcontact Printing With 1–12 Μm Features, Lloyd W. Zilch, Ghaleb A. Husseini, Yit-Yian Lua, Michael V. Lee, Kevin R. Gertsch, Bennion R. Cannon, Robert M. Perry, Eric T. Sevy, Matthew C. Asplund, Adam T. Woolley, Matthew R. Linford

Faculty Publications

Mechanical scribing can be employed to create surfaces with recessed features. Through replica molding elastomeric copies of these scribed surfaces are created that function as stamps for microcontact printing. It is shown that this new method for creating masters for microcontact printing can be performed with a computer-controlled milling machine (CNC), making this method particularly straightforward and accessible to a large technical community that does not need to work in a particle free environment. Thus, no clean room, or other specialized equipment is required, as is commonly needed to prepare masters. Time-of-flight secondary ion mass spectrometry confirms surface pattering by …

Evidence Of Linear Lattice Expansion And Covalency Enhancement In Rutile Tio2 Nanocrystals, Guangshe Li, Juliana Boerio-Goates, Brian F. Woodfield, Liping Li

Faculty Publications

Lattice variations and bonding characteristics in rutile TiO2 nanocrystals were examined by x-ray diffraction and x-ray photoelectron spectroscopy. With a reduction in the physical dimensions, rutile TiO2 nanocrystals show a linear lattice expansion and an anomalous covalency enhancement in apparent contradiction to the ionicity increase in BaTiO3 and CuO nanocrystals as reported recently by S. Tsunekawa et al. [Phys. Rev. Lett. 2000, 85, 3440] and V. R. Palkar et al. [Phys. Rev. B 1996, 53, 2167]. A surface defect dipole model is proposed to explain these physical phenomena in terms of the strong interactions among the surface dipoles that produce …

Immunity In Medicine, M Saeed

Department of Biological & Biomedical Sciences

No abstract provided.

Identification And Characterization Of Phosphoseryl-Trna [Ser]Sec Kinase, Bradley A. Carlson, Xue-Ming Xu, Gregory V. Kryukov, Mahadev Rao, Marla J. Berry, Vadim N. Gladyshev, Dolph L. Hatfield

Vadim Gladyshev Publications

In 1970, a kinase activity that phosphorylated a minor species of seryl-tRNA to form phosphoseryl-tRNA was found in rooster liver [Maenpaa, P. H. & Bernfield, M. R. (1970) Proc. Natl. Acad. Sci. USA 67, 688–695], and a minor seryl-tRNA that decoded the nonsense UGA was detected in bovine liver. The phosphoseryl-tRNA and the minor UGA-decoding seryl-tRNA were subsequently identified as selenocysteine (Sec) tRNA ^[Ser]Sec, but the kinase activity remained elusive. Herein, by using a comparative genomics approach that searched completely sequenced archaeal genomes for a kinase-like protein with a pattern of occurrence similar to that of components of Sec …

Resolution Of Organelle Docking And Fusion Kinetics In A Cell-Free Assay, Alexey J. Merz, William T. Wickner

Dartmouth Scholarship

In vitro assays of compartment mixing have been key tools in the biochemical dissection of organelle docking and fusion. Many such assays measure compartment mixing through the enzymatic modification of reporter proteins. Homotypic fusion of yeast vacuoles is measured with a coupled assay of proteolytic maturation of pro-alkaline phosphatase (pro-ALP). A kinetic lag is observed between the end of docking, marked by the acquisition of resistance to anti-SNARE reagents, and ALP maturation. We therefore asked whether the time taken for pro-ALP maturation adds a kinetic lag to the measured fusion signal. Prb1p promotes ALP maturation; overproduction of Prb1p accelerates ALP …

The Kini Kinesin Kif2a Is Required For Bipolar Spindle Assembly Through A Functional Relationship With Mcak, Neil J. Ganem, Duane A. Compton

Dartmouth Scholarship

Although the microtubule-depolymerizing KinI motor Kif2a is abundantly expressed in neuronal cells, we now show it localizes to centrosomes and spindle poles during mitosis in cultured cells. RNAi-induced knockdown of Kif2a expression inhibited cell cycle progression because cells assembled monopolar spindles. Bipolar spindle assembly was restored in cells lacking Kif2a by treatments that altered microtubule assembly (nocodazole), eliminated kinetochore–microtubule attachment (loss of Nuf2), or stabilized microtubule plus ends at kinetochores (loss of MCAK). Thus, two KinI motors, MCAK and Kif2a, play distinct roles in mitosis, and MCAK activity at kinetochores must be balanced by Kif2a activity at poles for spindle …

Central Role For Liver X Receptor In Insulin-Mediated Activation Of Srebp-1c Transcription And Stimulation Of Fatty Acid Synthesis In Liver., Guoxun Chen

Nutrition Publications and Other Works

Transcription of the gene encoding sterol regulatory element-binding protein 1c (SREBP-1c) is known to be activated by insulin in the liver. The resultant SREBP-1c protein activates transcription of the genes required for fatty acid synthesis. Here, we use SREBP-1c promoter reporter constructs to dissect the mechanism of insulin activation in freshly isolated rat hepatocytes. The data show that a complete insulin response (increase of 6- to 11-fold) requires two binding sites for liver X receptors (LXRs), which are nuclear receptors that are activated by oxygenated sterols. Disruption of these binding sites did not lower basal transcription but severely reduced the …

Examination Of Technologies For Student-Generated Work In A Peer-Led, Peer-Review Instructional Environment, Brian P. Coppola, Alan L. Kiste

Chemistry and Biochemistry

There is a growing literature demonstrating the effectiveness of using computer environments to assist students’ in visualizing science and mathematics concepts. However, with many of these computerized learning environments, students do not have the option of manipulating the environment. Instead, they are presented with pre-made visualizations. Enabling students to display their understanding through multiple representational forms is more interesting. In our peer-led, peer-review environment, students generate a complex, literature-based, multimedia text on which their final examination is based. However, there are great time and personnel costs in this design. Collaborating with SRI Inc., we are addressing these demands via the …

Nrage Regulates Life And Death Of Neural Progenitors, Stephen E. Kendall

Electronic Theses and Dissertations

The development of the central nervous system requires the orchestration of numerous instructive and permissive cues. These factors are secreted from signaling centers and function in a concentration dependent manner that effects the proliferation, survival and differentiation of neural progenitors (NP) and their differentiated progeny. The family including bone morphogenetic proteins (BMPs) are key regulators of NP expansion and survival. However, once NP become committed to a neuronal fate and begin to differentiate they compete for limited amounts of neurotrophin that facilitate further growth and survival. Here we show that the p75 neurotrophin receptor interacting protein NRAGE is expressed in …