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.
Replication And Active Demethylation Represent Partially Overlapping Mechanisms For Erasure Of H3k4me3 In Budding Yeast, 2010 University of Massachusetts Medical School
Replication And Active Demethylation Represent Partially Overlapping Mechanisms For Erasure Of H3k4me3 In Budding Yeast, Marta Radman-Livaja, Chih Long Liu, Nir Friedman, Stuart L. Schreiber, Oliver J. Rando
Open Access Articles
Histone modifications affect DNA-templated processes ranging from transcription to genomic replication. In this study, we examine the cell cycle dynamics of the trimethylated form of histone H3 lysine 4 (H3K4me3), a mark of active chromatin that is viewed as "long-lived" and that is involved in memory during cell state inheritance in metazoans. We synchronized yeast using two different protocols, then followed H3K4me3 patterns as yeast passed through subsequent cell cycles. While most H3K4me3 patterns were conserved from one generation to the next, we found that methylation patterns induced by alpha factor or high temperature were erased within one cell cycle ...
The Heat Capacity And Thermodynamic Properties Of The Iron Oxides And Their Relation To The Mineral Core Of The Iron Storage Protein Ferritin, 2010 Brigham Young University - Provo
The Heat Capacity And Thermodynamic Properties Of The Iron Oxides And Their Relation To The Mineral Core Of The Iron Storage Protein Ferritin, Claine Lindsey Morton Snow
All Theses and Dissertations
The iron oxides are a group of materials with geological, biological, and technological importance. A thermodynamic understanding of these materials is important because it provides information about their relative stabilities, chemical reactivity, and transformations. This study provides the heat capacity of a nanocrystalline magnetite (Fe3O4) sample, bulk hematite (α-Fe2O3), nanocrystalline hematite, akaganéite (β-FeOOH), and lepidocrocite (γ-FeOOH) at temperatures as low as 0.5 K. These measurements were fit to theoretical functions at temperatures lower than 15 K, and the respective thermophysical properties of these materials are discussed. Also the molar entropies of bulk hematite and hydrous nanocrystalline hematite as well ...
Microtensile Bond Strength Of Self-Adhesive Resin-Based Dental Cement, 2010 The Pennsilyvania State University, Department of Chemistry
Microtensile Bond Strength Of Self-Adhesive Resin-Based Dental Cement, Selda Keskin
This study investigated the effectiveness of bleaching agents on the micro tensile bond strength (mTBS) of self-adhesive luting cement and enamel. A total of 126 samples were prepared from the labial surfaces of permanent human maxillary central incisors and assigned into three groups with 42 samples each as: control, enamel bleached with 10% hydrogen peroxide (HP), and enamel bleached with 10% carbamide peroxide (CP). Rely X Unicem1 (3 M, ESPE) was used as self-adhesive resin cement. The total testing period for bleaching was selected as 14 days and the bleaching agents were applied 8 hours a day. The statistical one-way ...
A Natural Missing Link Between Activated And Downhill Protein Folding Scenarios, 2010 University of Illinois at Urbana-Champaign
A Natural Missing Link Between Activated And Downhill Protein Folding Scenarios, Feng Liu, Caroline Maynard, Gregory E. Scott, Artem Melnykov, Kathleen B. Hall, Martin Gruebele
Chemistry and Biochemistry
We propose protein PTB1:4W as a good candidate for engineering into a downhill folder. PTB1:4W has a probe-dependent thermal unfolding curve and sub-millisecond T-jump relaxation kinetics on more than one time scale. Its refolding rate in denaturant is a non-linear function of denaturant concentration (curved chevron plot). Yet at high denaturant concentration its unfolding is probe-independent, and the folding kinetics can be fitted to a single exponential decay. The domain appears to fold via a mechanism between downhill folding and activated folding over several small barriers, and when denaturant is added, one of these barriers greatly increases and ...
Abundance Of Ammonia-Oxidizing Archaea And Bacteria Along An Estuarine Salinity Gradient In Relationship To Potential Nitrification Rates, Anne E. Bernhard, Zachary C. Landry, Alison Blevins, José R. De La Torre, Anne E. Giblin, David A. Stahl
Biology Faculty Publications
Abundance of ammonia-oxidizing Archaea (AOA) was found to be always greater than that of ammonia-oxidizing Bacteria along an estuarine salinity gradient, and AOA abundance was highest at intermediate salinity. However, AOA abundance did not correlate with potential nitrification rates. This lack of correlation may be due to methodological limitations or alternative energy sources.
The Minor Envelope Glycoproteins Gp2a And Gp4 Of Porcine Reproductive And Respiratory Syndrome Virus Interact With The Receptor Cd163, 2010 University of Nebraska-Lincoln
The Minor Envelope Glycoproteins Gp2a And Gp4 Of Porcine Reproductive And Respiratory Syndrome Virus Interact With The Receptor Cd163, Phani B. Das, Phat X. Dinh, Israrul H. Ansari, Marcelo De Lima, Fernando A. Osorio, Asit K. Pattnaik
Papers in Veterinary and Biomedical Science
Porcine reproductive and respiratory syndrome virus (PRRSV) contains the major glycoprotein, GP5, as well as three other minor glycoproteins, namely, GP2a, GP3, and GP4, on the virion envelope, all of which are required for generation of infectious virions. To study their interactions with each other and with the cellular receptor for PRRSV, we have cloned each of the viral glycoproteins and CD163 receptor in expression vectors and examined their expression and interaction with each other in transfected cells by coimmunoprecipitation (co-IP) assay using monospecific antibodies. Our results show that a strong interaction exists between the GP4 and GP5 proteins, although ...
The Scale Of Population Structure In Arabidopsis Thaliana, 2010 University of Southern California
The Scale Of Population Structure In Arabidopsis Thaliana, Alexander Platt, Matthew Horton, Yu S. Huang, Yan Li, Alison E. Anastasio, Ni Wayan Mulyati, Jon Agren, Oliver Bossdorf, Diane Byers, Kathleen Donohue, Megan Dunning, Eric B. Holub, Andrew Hudson, Valerie Le Corre, Olivier Loudet, Fabrice Roux, Norman Warthmann, Detlef Weigel, Luz Rivero, Randy Scholl, Magnus Nordborg, Joy Bergelson, Justin O. Borevitz
Faculty Publications – Biological Sciences
The population structure of an organism reflects its evolutionary history and influences its evolutionary trajectory. It constrains the combination of genetic diversity and reveals patterns of past gene flow. Understanding it is a prerequisite for detecting genomic regions under selection, predicting the effect of population disturbances, or modeling gene flow. This paper examines the detailed global population structure of Arabidopsis thaliana. Using a set of 5,707 plants collected from around the globe and genotyped at 149 SNPs, we show that while A. thaliana as a species self-fertilizes 97% of the time, there is considerable variation among local groups. This ...
Cytotoxicity Of Bacterial-Derived Toxins To Immortal Lung Epithelial And Macrophage Cells, 2010 University of Arizona, Tucson
Cytotoxicity Of Bacterial-Derived Toxins To Immortal Lung Epithelial And Macrophage Cells, Dianne E. Peterson, Jayne M. Collier, Matthew E. Katterman, Rachel A. Turner, Mark R. Riley
Biological Systems Engineering: Papers and Publications
Health risks associated with inhalation and deposition of biological materials have been a topic of great concern due to highly publicized cases of inhalation anthrax, of new regulations on the release of particulate matter, and to increased concerns on the hazards of indoor air pollution. Here, we present an evaluation of the sensitivity of two immortal cell lines (A549, human lung carcinoma epithelia) and NR8383 (rat alveolar macrophages) to a variety of bacterial-derived inhalation hazards and simulants including etoposide, gliotoxin, streptolysin O, and warfarin. The cell response is evaluated through quantification of changes in mitochondrial succinate dehydrogenase activity, release of ...
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>
Preparation Of Drosophila Polytene Chromosome Squashes For Antibody Labeling, 2010 Iowa State University
Preparation Of Drosophila Polytene Chromosome Squashes For Antibody Labeling, Weili Cai, Ye Jin, Jack Girton, Jorgen Johansen, Kristen M. Johansen
Biochemistry, Biophysics and Molecular Biology Publications
Drosophila has long been a favorite model system for studying the relationship between chromatin structure and gene regulation due to the cytological advantages provided by the giant salivary gland polytene chromosomes of third instar larvae. In this tissue the chromosomes undergo many rounds of replication in the absence of cell division giving rise to approximately 1000 copies. The DNA remains aligned after each replicative cycle resulting in greatly enlarged chromosomes that provide a unique opportunity to correlate chromatin morphology with the localization of specific proteins. Consequently, there has been a high level of interest in defining the epigenetic modifications present ...
Porcine Reproductive And Respiratory Syndrome Virus Nonstructural Protein 1Β Modulates Host Innate Immune Response By Antagonizing Irf3 Activation, 2010 University of Nebraska-Lincoln
Porcine Reproductive And Respiratory Syndrome Virus Nonstructural Protein 1Β Modulates Host Innate Immune Response By Antagonizing Irf3 Activation, Lalit Beura, Saumendra Sarkar, Byungjoon Kwon, Sakthivel Subramaniam, Clinton J. Jones, Asit K. Pattnaik, Fernando A. Osorio
Papers in Veterinary and Biomedical Science
Porcine reproductive and respiratory syndrome virus (PRRSV) infection of swine leads to a serious disease characterized by a delayed and defective adaptive immune response. It is hypothesized that a suboptimal innate immune response is responsible for the disease pathogenesis. In the study presented here we tested this hypothesis and identified several nonstructural proteins (NSPs) with innate immune evasion properties encoded by the PRRS viral genome. Four of the total ten PRRSV NSPs tested were found to have strong to moderate inhibitory effects on beta interferon (IFN-β) promoter activation. The strongest inhibitory effect was exhibited by NSP1 followed by, NSP2, NSP11 ...
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 ...
Antispasmodic And Vasodilator Activities Of Morinda Citrifolia Root Extract Are Mediated Through Blockade Of Voltage Dependent Calcium Channels, Anwarul Hassan Gilani, Saf-Ur-Rehman Mandukhail, Javeid Iqbal, Masoom Yasinzai, Nauman Aziz, Aslam Khan, Najeeb-Ur-Rehman
Department of Biological & Biomedical Sciences
Background: Morinda citrifolia (Noni) is an edible plant with wide range of medicinal uses. It occurs exclusively in tropical climate zone from India through Southeast Asia and Australia to Eastern Polynesia and Hawaii. The objective of this study was to explore the possible mode(s) of action for its antispasmodic, vasodilator and cardio-suppressant effects to rationalize its medicinal use in gut and cardiovascular disorders. Methods: Isolated tissue preparations such as, rabbit jejunum, rat and rabbit aorta and guinea pig atria were used to test the antispasmodic and cardiovascular relaxant effects and the possible mode of action(s) of the 70 ...
Effect Of Au And Au@Ag Core-Shell Nanoparticles On The Sers Of Bridging Organic Molecules., 2010 The Pennsilyvania State University, Department of Chemistry
Effect Of Au And Au@Ag Core-Shell Nanoparticles On The Sers Of Bridging Organic Molecules., Remziye Guzel Dr., Zafer Ustundag Dr., Haslet Eksi, Selda Keskin Dr., Bilge Taner, Zeynep Durgun, Ali Osman Solak Prof. Dr.
No abstract provided.
Theoretical Description Of A Dna-Linked Nanoparticle Self-Assembly, 2010 Wesleyan University
Theoretical Description Of A Dna-Linked Nanoparticle Self-Assembly, Chia Wei Hsu, Francesco Sciortino, Francis Starr
No abstract provided.
Laboratory Measurements Of Trace Gas Emissions From Biomass Burning Of Fuel Types From The Southeastern And Southwestern United States, 2010 University of Montana - Missoula
Laboratory Measurements Of Trace Gas Emissions From Biomass Burning Of Fuel Types From The Southeastern And Southwestern United States, I. R. Burling, Robert J. Yokelson, David W. T. Griffith, T. J. Johnson, P. Veres, J. M. Roberts, C. Warneke, S. P. Urbanski, J. Reardon, D. R. Weise, Wei Min Hao, J. De Gouw
Chemistry and Biochemistry Faculty Publications
Vegetation commonly managed by prescribed burning was collected from five southeastern and southwestern US military bases and burned under controlled conditions at the US Forest Service Fire Sciences Laboratory in Missoula, Montana. The smoke emissions were measured with a large suite of state-of-the-art instrumentation including an open-path Fourier transform infrared (OP-FTIR) spectrometer for measurement of gas-phase species. The OP-FTIR detected and quantified 19 gas-phase species in these fires: CO2, CO, CH4, C2H2, C2H4, C3H6, HCHO, HCOOH, CH3OH, CH3COOH, furan, H2O, NO, NO2, HONO, NH3, HCN, HCl, and SO2. Emission factors for these species are presented for each vegetation type burned ...
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 ...