The Identification of Dual Protective Agents Against Cisplatin
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Effects of Mimosine Administered to a Perfused Area of Skin in Angora Goats by R
Downloaded from British Journal of Nutrition (1996), 15, 69-19 69 https://www.cambridge.org/core Effects of mimosine administered to a perfused area of skin in Angora goats BY R. PUCHALA, S. G. PIERZYNOWSKI, T. SAHLU* AND S. P. HART E. (Kika) de la Garza Institute for Goat Research, Langston University, Langston, Oklahoma 73050, USA . IP address: (Received I1 November 1994 - Revised 15 March 1995 -Accepted I1 May 1995) 170.106.34.90 The effect of mimosine on a perfused area of skin tissue was studied using an isolated perfusion technique. Four mature Angora wethers (body weight 35 (SE 2.3) kg) were cannulated bilaterally with indwelling silicone catheters in the superficial branches of the deep circumflex iliac artery and vein. Mimosine , on (40 mg/kg metabolic weight (Wo75)per d) was infused intra-arterially into one iliac artery of each goat for 3 d and saline was infused in the contralateral (control) iliac artery. Iliac venous blood samples were 27 Sep 2021 at 22:01:16 taken from both sides along with arterial samples from the carotid artery. Mimosine infusion elevated plasma mimosine in the carotid artery (52.6 (SEM19.21) pol/l) and iliac vein on the saline-treated side to 54.1 (SEM 16-31)~ol/l and in the iliac vein on the mimosine-treated side to 191.3 (SEM1914) pmol/l (P < 0.01). Mimosine decreased feed intake (2.3 v. 0.6 kg/d, ~~~0.29;P < 0.001) and water consumption (5-2 v. 1.3 litres/d, SEM 0.67; P < 0.001). -
Review on the Nutritive Value and Toxic Aspects of Leucaena Leucocephala
Trop Anim Prod 1979 4:2 113 A REVIEW ON THE NUTRITIVE VALUE AND TOXIC ASPECTS OF LEUCAENA LEUCOCEPHALA U ter Meulen1, S Struck1, E Schulke2 and E A El Harith1 1 Institut fur Tierphysiologie und Tierernahrung der Universitat Gottingen Oskar-Kellner-Weg 6, Weende 3400 Gottingen, West Germany This review discusses the nutritive value of Leucaena leucocephala and its mimosine toxicity when used as a forage for livestock. Chemical analysis and feeding trial. have indicated that Leucaena leaf-meal with its high protein, calcium, -carotene and xanthophyll contents, is potentially a valuable feed for livestock in the tropics. The symptoms of mimosine toxicity in cattle, sheep, poultry, goats horses, pigs and rats ire discussed, The chemical value of mimosine and the possible mechanism of its toxicity are reviewed. Possible solutions to the toxicity problem are presented together with the suggestion that further studies be initiated to overcome this problem. Key Words: Leucaena, mimosine toxicity, livestock, forage, feeding trials The uses of the tropical legume Leucaena leucocephala are quite versatile. These uses include its function as a source of firewood and timber,its role in soil erosion control (Dijkman 1950), its ability to provide shade for other plants as well as its function in maintaining the fertility of the soil and of serving as a nutritious forage for animal feed (Ruskln 1977). Presently the greatest use of this plant in animal nutrition is its incorporation in cattle feed. Leucaena leaf-meal, with its rich protein, minerals and vitamin content, is also becoming a popular ingredient in poultry feeds in the tropics (D'Mello and Taplin 1978). -
The ELIXIR Core Data Resources: Fundamental Infrastructure for The
Supplementary Data: The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences The “Supporting Material” referred to within this Supplementary Data can be found in the Supporting.Material.CDR.infrastructure file, DOI: 10.5281/zenodo.2625247 (https://zenodo.org/record/2625247). Figure 1. Scale of the Core Data Resources Table S1. Data from which Figure 1 is derived: Year 2013 2014 2015 2016 2017 Data entries 765881651 997794559 1726529931 1853429002 2715599247 Monthly user/IP addresses 1700660 2109586 2413724 2502617 2867265 FTEs 270 292.65 295.65 289.7 311.2 Figure 1 includes data from the following Core Data Resources: ArrayExpress, BRENDA, CATH, ChEBI, ChEMBL, EGA, ENA, Ensembl, Ensembl Genomes, EuropePMC, HPA, IntAct /MINT , InterPro, PDBe, PRIDE, SILVA, STRING, UniProt ● Note that Ensembl’s compute infrastructure physically relocated in 2016, so “Users/IP address” data are not available for that year. In this case, the 2015 numbers were rolled forward to 2016. ● Note that STRING makes only minor releases in 2014 and 2016, in that the interactions are re-computed, but the number of “Data entries” remains unchanged. The major releases that change the number of “Data entries” happened in 2013 and 2015. So, for “Data entries” , the number for 2013 was rolled forward to 2014, and the number for 2015 was rolled forward to 2016. The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences 1 Figure 2: Usage of Core Data Resources in research The following steps were taken: 1. API calls were run on open access full text articles in Europe PMC to identify articles that mention Core Data Resource by name or include specific data record accession numbers. -
PLK-1 Promotes the Merger of the Parental Genome Into A
RESEARCH ARTICLE PLK-1 promotes the merger of the parental genome into a single nucleus by triggering lamina disassembly Griselda Velez-Aguilera1, Sylvia Nkombo Nkoula1, Batool Ossareh-Nazari1, Jana Link2, Dimitra Paouneskou2, Lucie Van Hove1, Nicolas Joly1, Nicolas Tavernier1, Jean-Marc Verbavatz3, Verena Jantsch2, Lionel Pintard1* 1Programme Equipe Labe´llise´e Ligue Contre le Cancer - Team Cell Cycle & Development - Universite´ de Paris, CNRS, Institut Jacques Monod, Paris, France; 2Department of Chromosome Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria; 3Universite´ de Paris, CNRS, Institut Jacques Monod, Paris, France Abstract Life of sexually reproducing organisms starts with the fusion of the haploid egg and sperm gametes to form the genome of a new diploid organism. Using the newly fertilized Caenorhabditis elegans zygote, we show that the mitotic Polo-like kinase PLK-1 phosphorylates the lamin LMN-1 to promote timely lamina disassembly and subsequent merging of the parental genomes into a single nucleus after mitosis. Expression of non-phosphorylatable versions of LMN- 1, which affect lamina depolymerization during mitosis, is sufficient to prevent the mixing of the parental chromosomes into a single nucleus in daughter cells. Finally, we recapitulate lamina depolymerization by PLK-1 in vitro demonstrating that LMN-1 is a direct PLK-1 target. Our findings indicate that the timely removal of lamin is essential for the merging of parental chromosomes at the beginning of life in C. elegans and possibly also in humans, where a defect in this process might be fatal for embryo development. *For correspondence: [email protected] Introduction Competing interests: The After fertilization, the haploid gametes of the egg and sperm have to come together to form the authors declare that no genome of a new diploid organism. -
Learning Protein Constitutive Motifs from Sequence Data Je´ Roˆ Me Tubiana, Simona Cocco, Re´ Mi Monasson*
TOOLS AND RESOURCES Learning protein constitutive motifs from sequence data Je´ roˆ me Tubiana, Simona Cocco, Re´ mi Monasson* Laboratory of Physics of the Ecole Normale Supe´rieure, CNRS UMR 8023 & PSL Research, Paris, France Abstract Statistical analysis of evolutionary-related protein sequences provides information about their structure, function, and history. We show that Restricted Boltzmann Machines (RBM), designed to learn complex high-dimensional data and their statistical features, can efficiently model protein families from sequence information. We here apply RBM to 20 protein families, and present detailed results for two short protein domains (Kunitz and WW), one long chaperone protein (Hsp70), and synthetic lattice proteins for benchmarking. The features inferred by the RBM are biologically interpretable: they are related to structure (residue-residue tertiary contacts, extended secondary motifs (a-helixes and b-sheets) and intrinsically disordered regions), to function (activity and ligand specificity), or to phylogenetic identity. In addition, we use RBM to design new protein sequences with putative properties by composing and ’turning up’ or ’turning down’ the different modes at will. Our work therefore shows that RBM are versatile and practical tools that can be used to unveil and exploit the genotype–phenotype relationship for protein families. DOI: https://doi.org/10.7554/eLife.39397.001 Introduction In recent years, the sequencing of many organisms’ genomes has led to the collection of a huge number of protein sequences, which are catalogued in databases such as UniProt or PFAM Finn et al., 2014). Sequences that share a common ancestral origin, defining a family (Figure 1A), *For correspondence: are likely to code for proteins with similar functions and structures, providing a unique window into [email protected] the relationship between genotype (sequence content) and phenotype (biological features). -
(12) United States Patent (10) Patent No.: US 8,962,619 B2 Ashwell Et Al
USOO8962619B2 (12) United States Patent (10) Patent No.: US 8,962,619 B2 Ashwell et al. (45) Date of Patent: *Feb. 24, 2015 (54) SUBSTITUTED (58) Field of Classification Search MIDAZOPYRIDINYL-AMNOPYRIDINE None COMPOUNDS See application file for complete search history. (71) Applicant: ArCule, Inc., Woburn, MA (US) (56) References Cited U.S. PATENT DOCUMENTS (72) Inventors: Mark A. Ashwell, Carlisle, MA (US); Chris Brassard, Somerville, MA (US); 4,522,811 A 6/1985 Eppstein et al. Anton Filikov, Rockville, MD (US); 33. R: ck 3. RileyShWell f et alal. ............... 514,303 ason Hill. Auburndale, MA (US); Steffi 8,609.688 B2 * 12/2013 Ashwell et al. ............... 514,303 Koerner, Medford, MA (US); 2002/0151549 A1 10/2002 Hayakawa et al. Jean-Marc Lapierre, Pelham, NH (US); 2006/0035921 A1 2/2006 Castelhano et al. Yanbin Liu, Acton, MA (US); Nivedita 2007. O142369 A1 6/2007 van Heek et al. 2007,0254.868 A1 11/2007 Lauffer et al. Namdev, Westford, MA (US); Robert 2009/0253734 A1 10/2009 Kelly, III et al. Nicewonger, Tyngsboro, MA (US); 2011/0059936 A1 3/2011 Lauffer et al. Rocio Palma, North Andover, MA (US); 2011/0172203 A1 7, 2011 Ashwell et al. Manish Tandon, Framingham, MA 2012/0329793 A1* 12/2012 Ashwell et al. ............ 514,234.2 (US); David Vensel, Brookline, MA (US); Akihisa Matsuda, Tokyo (JP); FOREIGN PATENT DOCUMENTS Shin Iimura, Tokyo (JP); Kenichi CN 1824665 A 8, 2006 Yoshida, Tokyo (JP); Takanori DE 3722.992 A1 1, 1989 Yamazaki, Tokyo (JP); Takahiro P 12: A. 3. E. Kitamura, Tokyo (JP); Takeshi JP 200034.4780 A 12/2000 Isoyama, Tokyo (JP) KR 20090007347 U 7, 2009 WO WO-96.19991 A1 T 1996 (73) Assignee: ArCule, Inc., Woburn, MA (US) WO WO-99.57 103 A1 11, 1999 WO WO-03.08.0125 A2 10/2003 (*) Notice: Subject to any disclaimer, the term of this WO WO-03080610 A1 10, 2003 WO WO-03O88967 A1 10, 2003 patent is extended or adjusted under 35 WO WO-20050117OO A1 2/2005 U.S.C. -
Annual Scientific Report 2013 on the Cover Structure 3Fof in the Protein Data Bank, Determined by Laponogov, I
EMBL-European Bioinformatics Institute Annual Scientific Report 2013 On the cover Structure 3fof in the Protein Data Bank, determined by Laponogov, I. et al. (2009) Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases. Nature Structural & Molecular Biology 16, 667-669. © 2014 European Molecular Biology Laboratory This publication was produced by the External Relations team at the European Bioinformatics Institute (EMBL-EBI) A digital version of the brochure can be found at www.ebi.ac.uk/about/brochures For more information about EMBL-EBI please contact: [email protected] Contents Introduction & overview 3 Services 8 Genes, genomes and variation 8 Molecular atlas 12 Proteins and protein families 14 Molecular and cellular structures 18 Chemical biology 20 Molecular systems 22 Cross-domain tools and resources 24 Research 26 Support 32 ELIXIR 36 Facts and figures 38 Funding & resource allocation 38 Growth of core resources 40 Collaborations 42 Our staff in 2013 44 Scientific advisory committees 46 Major database collaborations 50 Publications 52 Organisation of EMBL-EBI leadership 61 2013 EMBL-EBI Annual Scientific Report 1 Foreword Welcome to EMBL-EBI’s 2013 Annual Scientific Report. Here we look back on our major achievements during the year, reflecting on the delivery of our world-class services, research, training, industry collaboration and European coordination of life-science data. The past year has been one full of exciting changes, both scientifically and organisationally. We unveiled a new website that helps users explore our resources more seamlessly, saw the publication of ground-breaking work in data storage and synthetic biology, joined the global alliance for global health, built important new relationships with our partners in industry and celebrated the launch of ELIXIR. -
TOOLS and RESOURCES: a Mammalian Enhancer Trap
1 TOOLS AND RESOURCES: 2 3 A Mammalian Enhancer trap Resource for Discovering and Manipulating Neuronal Cell Types. 4 Running title 5 Cell Type Specific Enhancer Trap in Mouse Brain 6 7 Yasuyuki Shima1, Ken Sugino2, Chris Hempel1,3, Masami Shima1, Praveen Taneja1, James B. 8 Bullis1, Sonam Mehta1,, Carlos Lois4, and Sacha B. Nelson1,5 9 10 1. Department of Biology and National Center for Behavioral Genomics, Brandeis 11 University, Waltham, MA 02454-9110 12 2. Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive 13 Ashburn, VA 20147 14 3. Current address: Galenea Corporation, 50-C Audubon Rd. Wakefield, MA 01880 15 4. California Institute of Technology, Division of Biology and Biological 16 Engineering Beckman Institute MC 139-74 1200 East California Blvd Pasadena CA 17 91125 18 5. Corresponding author 19 1 20 ABSTRACT 21 There is a continuing need for driver strains to enable cell type-specific manipulation in the 22 nervous system. Each cell type expresses a unique set of genes, and recapitulating expression of 23 marker genes by BAC transgenesis or knock-in has generated useful transgenic mouse lines. 24 However since genes are often expressed in many cell types, many of these lines have relatively 25 broad expression patterns. We report an alternative transgenic approach capturing distal 26 enhancers for more focused expression. We identified an enhancer trap probe often producing 27 restricted reporter expression and developed efficient enhancer trap screening with the PiggyBac 28 transposon. We established more than 200 lines and found many lines that label small subsets of 29 neurons in brain substructures, including known and novel cell types. -
A Unicellular Relative of Animals Generates a Layer of Polarized Cells
RESEARCH ARTICLE A unicellular relative of animals generates a layer of polarized cells by actomyosin- dependent cellularization Omaya Dudin1†*, Andrej Ondracka1†, Xavier Grau-Bove´ 1,2, Arthur AB Haraldsen3, Atsushi Toyoda4, Hiroshi Suga5, Jon Bra˚ te3, In˜ aki Ruiz-Trillo1,6,7* 1Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain; 2Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom; 3Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Oslo, Norway; 4Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan; 5Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Hiroshima, Japan; 6Departament de Gene`tica, Microbiologia i Estadı´stica, Universitat de Barcelona, Barcelona, Spain; 7ICREA, Barcelona, Spain Abstract In animals, cellularization of a coenocyte is a specialized form of cytokinesis that results in the formation of a polarized epithelium during early embryonic development. It is characterized by coordinated assembly of an actomyosin network, which drives inward membrane invaginations. However, whether coordinated cellularization driven by membrane invagination exists outside animals is not known. To that end, we investigate cellularization in the ichthyosporean Sphaeroforma arctica, a close unicellular relative of animals. We show that the process of cellularization involves coordinated inward plasma membrane invaginations dependent on an *For correspondence: actomyosin network and reveal the temporal order of its assembly. This leads to the formation of a [email protected] (OD); polarized layer of cells resembling an epithelium. We show that this stage is associated with tightly [email protected] (IR-T) regulated transcriptional activation of genes involved in cell adhesion. -
Evolution of Gene Dosage on the Z-Chromosome of Schistosome
RESEARCH ARTICLE Evolution of gene dosage on the Z-chromosome of schistosome parasites Marion A L Picard1, Celine Cosseau2, Sabrina Ferre´ 3, Thomas Quack4, Christoph G Grevelding4, Yohann Coute´ 3, Beatriz Vicoso1* 1Institute of Science and Technology Austria, Klosterneuburg, Austria; 2University of Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, University Montpellier, Perpignan, France; 3Universite´ Grenoble Alpes, CEA, Inserm, BIG-BGE, Grenoble, France; 4Institute for Parasitology, Biomedical Research Center Seltersberg, Justus- Liebig-University, Giessen, Germany Abstract XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes. DOI: https://doi.org/10.7554/eLife.35684.001 *For correspondence: [email protected] Introduction In species with separate sexes, genetic sex determination is often present in the form of differenti- Competing interests: The ated sex chromosomes (Bachtrog et al., 2014). -
Global Cellular Response to Chemotherapy- Induced
RESEARCH ARTICLE elife.elifesciences.org Global cellular response to chemotherapy- induced apoptosis Arun P Wiita1,2, Etay Ziv3,4, Paul J Wiita5, Anatoly Urisman1,6, Olivier Julien1, Alma L Burlingame1, Jonathan S Weissman3,7, James A Wells1,3* 1Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, United States; 2Department of Laboratory Medicine, University of California, San Francisco, San Francisco, United States; 3Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States; 4Department of Radiology, University of California, San Francisco, San Francisco, United States; 5Department of Physics, The College of New Jersey, Ewing, United States; 6Department of Pathology, University of California, San Francisco, San Francisco, United States; 7Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States Abstract How cancer cells globally struggle with a chemotherapeutic insult before succumbing to apoptosis is largely unknown. Here we use an integrated systems-level examination of transcription, translation, and proteolysis to understand these events central to cancer treatment. As a model we study myeloma cells exposed to the proteasome inhibitor bortezomib, a first-line therapy. Despite robust transcriptional changes, unbiased quantitative proteomics detects production of only a few critical anti-apoptotic proteins against a background of general translation inhibition. Simultaneous ribosome profiling further reveals potential translational regulation of stress response genes. Once the apoptotic machinery is engaged, degradation by caspases is largely independent of upstream bortezomib effects. Moreover, previously uncharacterized non-caspase proteolytic events also participate in cellular deconstruction. Our systems-level data also support co-targeting the anti-apoptotic regulator HSF1 to promote cell death by bortezomib. -
Mimosine Concentration in Leucaena Leucocephala Under Various Environmental Conditions
Tropical Grasslands-Forrajes Tropicales (2019) Vol. 7(2):164–172 164 DOI: 10.17138/TGFT(7)164-172 ILC2018 Keynote paper* Mimosine concentration in Leucaena leucocephala under various environmental conditions Concentración de mimosina en Leucaena leucocephala bajo diferentes condiciones ambientales MICHAEL D.H. HONDA AND DULAL BORTHAKUR Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI, USA. manoa.hawaii.edu Abstract Leucaena leucocephala (leucaena) is a multipurpose tropical tree-legume that is highly resistant to many biotic and abiotic stresses. Leucaena is used primarily as an animal fodder owing to its protein-rich foliage. However, leucaena foliage also contains mimosine, a toxic non-protein amino acid that can cause alopecia, goiter and other thyroid problems, infertility and fetal death. Considering its toxicity and abundance in leucaena, it is important to quantify the mimosine concentrations in leucaena under different environmental conditions. Mimosine was extracted from various types of leucaena tissue exposed to a range of environmental conditions and then quantified by HPLC. The mimosine concentrations in leucaena treated with NaCl increased after 6 days of treatment and remained relatively high when treatment continued for 18 days. Interestingly, leucaena exposed to complete darkness for up to 5 days had a higher mimosine concentration than control plants exposed to normal light/dark photoperiods. On the other hand, drying leucaena leaflets or macerating them in an alkaline buffer significantly lowered their mimosine concentration. Mature leaflets that had fallen off the plant and dried out also contained significantly less mimosine than fresh leaflets. The results of this study indicate that mimosine concentrations in leucaena are affected by environmental conditions and this knowledge can assist in managing to prevent toxicity.