Primary and Secondary Antibodies & Reagents for Laboratory Research 2017
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Comparative Chloroplast Genomes of Four Lycoris Species (Amaryllidaceae) Provides New Insight Into Interspecific Relationship and Phylogeny
biology Article Comparative Chloroplast Genomes of Four Lycoris Species (Amaryllidaceae) Provides New Insight into Interspecific Relationship and Phylogeny Fengjiao Zhang 1,2, Ning Wang 1,2, Guanghao Cheng 1,2, Xiaochun Shu 1,2, Tao Wang 1,2 , Weibing Zhuang 1,2, Ruisen Lu 1,2,* and Zhong Wang 1,2,* 1 Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China; [email protected] (F.Z.); [email protected] (N.W.); [email protected] (G.C.); [email protected] (X.S.); [email protected] (T.W.); [email protected] (W.Z.) 2 The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China * Correspondence: [email protected] (R.L.); [email protected] (Z.W.) Simple Summary: The genus Lycoris (Amaryllidaceae) comprises about 20 species with high orna- mental and medicinal value. However, germplasm identification is still difficult due to frequent interspecific hybridization and intraspecific morphological variation within this genus. Plastid genome sequencing has been proven to be a useful tool to identify closely related species and is widely used in the field of plant evolution and phylogeny. In the present study, we provided four Citation: Zhang, F.; Wang, N.; chloroplast genomes of Lycoris and retrieved seven published species in the genus for comparative Cheng, G.; Shu, X.; Wang, T.; Zhuang, genomics and phylogenetic analyses. All these chloroplast genomes possess the typical quadripartite W.; Lu, R.; Wang, Z. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Complete Chloroplast Genomes Shed Light on Phylogenetic
www.nature.com/scientificreports OPEN Complete chloroplast genomes shed light on phylogenetic relationships, divergence time, and biogeography of Allioideae (Amaryllidaceae) Ju Namgung1,4, Hoang Dang Khoa Do1,2,4, Changkyun Kim1, Hyeok Jae Choi3 & Joo‑Hwan Kim1* Allioideae includes economically important bulb crops such as garlic, onion, leeks, and some ornamental plants in Amaryllidaceae. Here, we reported the complete chloroplast genome (cpDNA) sequences of 17 species of Allioideae, fve of Amaryllidoideae, and one of Agapanthoideae. These cpDNA sequences represent 80 protein‑coding, 30 tRNA, and four rRNA genes, and range from 151,808 to 159,998 bp in length. Loss and pseudogenization of multiple genes (i.e., rps2, infA, and rpl22) appear to have occurred multiple times during the evolution of Alloideae. Additionally, eight mutation hotspots, including rps15-ycf1, rps16-trnQ-UUG, petG-trnW-CCA , psbA upstream, rpl32- trnL-UAG , ycf1, rpl22, matK, and ndhF, were identifed in the studied Allium species. Additionally, we present the frst phylogenomic analysis among the four tribes of Allioideae based on 74 cpDNA coding regions of 21 species of Allioideae, fve species of Amaryllidoideae, one species of Agapanthoideae, and fve species representing selected members of Asparagales. Our molecular phylogenomic results strongly support the monophyly of Allioideae, which is sister to Amaryllioideae. Within Allioideae, Tulbaghieae was sister to Gilliesieae‑Leucocoryneae whereas Allieae was sister to the clade of Tulbaghieae‑ Gilliesieae‑Leucocoryneae. Molecular dating analyses revealed the crown age of Allioideae in the Eocene (40.1 mya) followed by diferentiation of Allieae in the early Miocene (21.3 mya). The split of Gilliesieae from Leucocoryneae was estimated at 16.5 mya. -
Ndhf Sequence Evolution and the Major Clades in the Sunflower Family KI-JOONG KIM* and ROBERT K
Proc. Natl. Acad. Sci. USA Vol. 92, pp. 10379-10383, October 1995 Evolution ndhF sequence evolution and the major clades in the sunflower family KI-JOONG KIM* AND ROBERT K. JANSENt Department of Botany, University of Texas, Austin, TX 78713-7640 Communicated by Peter H. Raven, Missouri Botanical Garden, St. Louis, MO, June 21, 1995 ABSTRACT An extensive sequence comparison of the either too short or too conserved to provide adequate numbers chloroplast ndhF gene from all major clades of the largest of characters in recently evolved families. A number of alter- flowering plant family (Asteraceae) shows that this gene native genes have been suggested as potential candidates for provides -3 times more phylogenetic information than rbcL. phylogenetic comparisons at lower taxonomic levels (9). The This is because it is substantially longer and evolves twice as phylogenetic utility of one of these, matK, has been recently fast. The 5' region (1380 bp) ofndhF is very different from the demonstrated (10). Comparison of sequences of two chloro- 3' region (855 bp) and is similar to rbcL in both the rate and plast genomes (rice and tobacco), however, revealed only two the pattern of sequence change. The 3' region is more A+T- genes, rpoCl and ndhF, that are considerably longer and evolve rich, has higher levels of nonsynonymous base substitution, faster than rbcL (9, 11). We selected ndhF because it is longer and shows greater transversion bias at all codon positions. and evolves slightly faster than rpoCl (11), because rpoCl has These differences probably reflect different functional con- an intron that may require additional effort in DNA amplifi- straints on the 5' and 3' regions of nduhF. -
Table S2.Up Or Down Regulated Genes in Tcof1 Knockdown Neuroblastoma N1E-115 Cells Involved in Differentbiological Process Anal
Table S2.Up or down regulated genes in Tcof1 knockdown neuroblastoma N1E-115 cells involved in differentbiological process analysed by DAVID database Pop Pop Fold Term PValue Genes Bonferroni Benjamini FDR Hits Total Enrichment GO:0044257~cellular protein catabolic 2.77E-10 MKRN1, PPP2R5C, VPRBP, MYLIP, CDC16, ERLEC1, MKRN2, CUL3, 537 13588 1.944851 8.64E-07 8.64E-07 5.02E-07 process ISG15, ATG7, PSENEN, LOC100046898, CDCA3, ANAPC1, ANAPC2, ANAPC5, SOCS3, ENC1, SOCS4, ASB8, DCUN1D1, PSMA6, SIAH1A, TRIM32, RNF138, GM12396, RNF20, USP17L5, FBXO11, RAD23B, NEDD8, UBE2V2, RFFL, CDC GO:0051603~proteolysis involved in 4.52E-10 MKRN1, PPP2R5C, VPRBP, MYLIP, CDC16, ERLEC1, MKRN2, CUL3, 534 13588 1.93519 1.41E-06 7.04E-07 8.18E-07 cellular protein catabolic process ISG15, ATG7, PSENEN, LOC100046898, CDCA3, ANAPC1, ANAPC2, ANAPC5, SOCS3, ENC1, SOCS4, ASB8, DCUN1D1, PSMA6, SIAH1A, TRIM32, RNF138, GM12396, RNF20, USP17L5, FBXO11, RAD23B, NEDD8, UBE2V2, RFFL, CDC GO:0044265~cellular macromolecule 6.09E-10 MKRN1, PPP2R5C, VPRBP, MYLIP, CDC16, ERLEC1, MKRN2, CUL3, 609 13588 1.859332 1.90E-06 6.32E-07 1.10E-06 catabolic process ISG15, RBM8A, ATG7, LOC100046898, PSENEN, CDCA3, ANAPC1, ANAPC2, ANAPC5, SOCS3, ENC1, SOCS4, ASB8, DCUN1D1, PSMA6, SIAH1A, TRIM32, RNF138, GM12396, RNF20, XRN2, USP17L5, FBXO11, RAD23B, UBE2V2, NED GO:0030163~protein catabolic process 1.81E-09 MKRN1, PPP2R5C, VPRBP, MYLIP, CDC16, ERLEC1, MKRN2, CUL3, 556 13588 1.87839 5.64E-06 1.41E-06 3.27E-06 ISG15, ATG7, PSENEN, LOC100046898, CDCA3, ANAPC1, ANAPC2, ANAPC5, SOCS3, ENC1, SOCS4, -
Sequencing of Cdna
ORIGINAL RESEARCH ARTICLE published: 07 March 2011 doi: 10.3389/fmicb.2011.00041 Transcription profiling of the model cyanobacterium Synechococcus sp. strain PCC 7002 by Next-Gen (SOLiD™) sequencing of cDNA Marcus Ludwig and Donald A. Bryant* Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA Edited by: The genome of the unicellular, euryhaline cyanobacterium Synechococcus sp. PCC 7002 encodes Thomas E. Hanson, University of about 3200 proteins. Transcripts were detected for nearly all annotated open reading frames Delaware, USA by a global transcriptomic analysis by Next-Generation (SOLiD™) sequencing of cDNA. In the Reviewed by: Martin Hagemann, University Rostock, cDNA samples sequenced, ∼90% of the mapped sequences were derived from the 16S and Germany 23S ribosomal RNAs and ∼10% of the sequences were derived from mRNAs. In cells grown Jack Meeks, University of California, photoautotrophically under standard conditions [38°C, 1% (v/v) CO2 in air, 250 μmol photons USA m−2 s−1], the highest transcript levels (up to 2% of the total mRNA for the most abundantly *Correspondence: transcribed genes; e.g., cpcAB, psbA, psaA) were generally derived from genes encoding Donald A. Bryant, Department of Biochemistry and Molecular Biology, structural components of the photosynthetic apparatus. High-light exposure for 1 h caused The Pennsylvania State University, changes in transcript levels for genes encoding proteins of the photosynthetic apparatus, Type-1 S-235 Frear Building, University Park, NADH dehydrogenase complex and ATP synthase, whereas dark incubation for 1 h resulted PA 16802, USA. in a global decrease in transcript levels for photosynthesis-related genes and an increase in e-mail: [email protected] transcript levels for genes involved in carbohydrate degradation. -
Electronic Supplementary Material (ESI) for Metallomics
Electronic Supplementary Material (ESI) for Metallomics. This journal is © The Royal Society of Chemistry 2018 Uniprot Entry name Gene names Protein names Predicted Pattern Number of Iron role EC number Subcellular Membrane Involvement in disease Gene ontology (biological process) Id iron ions location associated 1 P46952 3HAO_HUMAN HAAO 3-hydroxyanthranilate 3,4- H47-E53-H91 1 Fe cation Catalytic 1.13.11.6 Cytoplasm No NAD biosynthetic process [GO:0009435]; neuron cellular homeostasis dioxygenase (EC 1.13.11.6) (3- [GO:0070050]; quinolinate biosynthetic process [GO:0019805]; response to hydroxyanthranilate oxygenase) cadmium ion [GO:0046686]; response to zinc ion [GO:0010043]; tryptophan (3-HAO) (3-hydroxyanthranilic catabolic process [GO:0006569] acid dioxygenase) (HAD) 2 O00767 ACOD_HUMAN SCD Acyl-CoA desaturase (EC H120-H125-H157-H161; 2 Fe cations Catalytic 1.14.19.1 Endoplasmic Yes long-chain fatty-acyl-CoA biosynthetic process [GO:0035338]; unsaturated fatty 1.14.19.1) (Delta(9)-desaturase) H160-H269-H298-H302 reticulum acid biosynthetic process [GO:0006636] (Delta-9 desaturase) (Fatty acid desaturase) (Stearoyl-CoA desaturase) (hSCD1) 3 Q6ZNF0 ACP7_HUMAN ACP7 PAPL PAPL1 Acid phosphatase type 7 (EC D141-D170-Y173-H335 1 Fe cation Catalytic 3.1.3.2 Extracellular No 3.1.3.2) (Purple acid space phosphatase long form) 4 Q96SZ5 AEDO_HUMAN ADO C10orf22 2-aminoethanethiol dioxygenase H112-H114-H193 1 Fe cation Catalytic 1.13.11.19 Unknown No oxidation-reduction process [GO:0055114]; sulfur amino acid catabolic process (EC 1.13.11.19) (Cysteamine -
82167915.Pdf
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Biochimica et Biophysica Acta 1837 (2014) 954–963 Contents lists available at ScienceDirect Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbabio Characterization of the type 2 NADH:menaquinone oxidoreductases from Staphylococcus aureus and the bactericidal action of phenothiazines☆ Lici A. Schurig-Briccio a, Takahiro Yano b,HarveyRubinb,RobertB.Gennisa,⁎ a Department of Biochemistry, University of Illinois, 600 S. Mathews Street, Urbana, IL 61801, USA b Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA article info abstract Article history: Methicillin-resistant Staphylococcus aureus (MRSA) is currently one of the principal multiple drug resistant Received 21 March 2014 bacterial pathogens causing serious infections, many of which are life-threatening. Consequently, new therapeutic Received in revised form 27 March 2014 targets are required to combat such infections. In the current work, we explore the type 2 Nicotinamide adenine Accepted 28 March 2014 dinucleotide reduced form (NADH) dehydrogenases (NDH-2s) as possible drug targets and look at the effects Available online 5 April 2014 of phenothiazines, known to inhibit NDH-2 from Mycobacterium tuberculosis. NDH-2s are monotopic fl Keywords: membrane proteins that catalyze the transfer of electrons from NADH via avin adenine dinucleotide (FAD) to + Bioenergetics/electron transfer complex the quinone pool. They are required for maintaining the NADH/Nicotinamide adenine dinucleotide (NAD ) Enzyme inhibitor redox balance and contribute indirectly to the generation of proton motive force. NDH-2s are not present in Respiratory chain mammals, but are the only form of respiratory NADH dehydrogenase in several pathogens, including S. -
Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in -
Molecular and Functional Analysis of Nicotinate Catabolism in Eubacterium Barkeri
Molecular and functional analysis of nicotinate catabolism in Eubacterium barkeri Ashraf Alhapel, Daniel J. Darley, Nadine Wagener, Elke Eckel, Nora Elsner, and Antonio J. Pierik* Laboratorium fu¨r Mikrobielle Biochemie, Fachbereich Biologie, Philipps Universita¨t, D-35032 Marburg, Germany Edited by Perry A. Frey, University of Wisconsin, Madison, WI, and approved June 29, 2006 (received for review March 1, 2006) The anaerobic soil bacterium Eubacterium barkeri catabolizes nic- complex (see Fig. 1). Based on the identified intermediates, otinate to pyruvate and propionate via a unique fermentation. A several anticipated enzymes were purified and characterized: full molecular characterization of nicotinate fermentation in this nicotinate dehydrogenase (12), 6-hydroxynicotinate reductase organism was accomplished by the following results: (i) A 23.2-kb (7), 2-methyleneglutarate mutase, and 3-methylitaconate DNA segment with a gene cluster encoding all nine enzymes was isomerase (13, 14). These findings outlined the nicotinate fer- cloned and sequenced, (ii) two chiral intermediates were discov- mentation pathway and placed the identified intermediates in an ered, and (iii) three enzymes were found, completing the hitherto enzymatic framework. unknown part of the pathway. Nicotinate dehydrogenase, a (non- The nicotinate dehydrogenase contains [2Fe-2S] clusters (15), selenocysteine) selenium-containing four-subunit enzyme, is en- FAD and molybdopterin cytosine dinucleotide (16), and has an coded by ndhF (FAD subunit), ndhS (2 x [2Fe-2S] subunit), and by unusual subunit composition [50, 37, 33, and 23 kDa (17)]. It has the ndhL͞ndhM genes. In contrast to all enzymes of the xanthine labile (nonselenocysteine) selenium (18) also identified in pu- dehydrogenase family, the latter two encode a two-subunit mo- rine dehydrogenase from Clostridium purinolyticum and xanthine lybdopterin protein. -
Metabolic Targets of Coenzyme Q10 in Mitochondria
antioxidants Review Metabolic Targets of Coenzyme Q10 in Mitochondria Agustín Hidalgo-Gutiérrez 1,2,*, Pilar González-García 1,2, María Elena Díaz-Casado 1,2, Eliana Barriocanal-Casado 1,2, Sergio López-Herrador 1,2, Catarina M. Quinzii 3 and Luis C. López 1,2,* 1 Departamento de Fisiología, Facultad de Medicina, Universidad de Granada, 18016 Granada, Spain; [email protected] (P.G.-G.); [email protected] (M.E.D.-C.); [email protected] (E.B.-C.); [email protected] (S.L.-H.) 2 Centro de Investigación Biomédica, Instituto de Biotecnología, Universidad de Granada, 18016 Granada, Spain 3 Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA; [email protected] * Correspondence: [email protected] (A.H.-G.); [email protected] (L.C.L.); Tel.: +34-958-241-000 (ext. 20197) (L.C.L.) Abstract: Coenzyme Q10 (CoQ10) is classically viewed as an important endogenous antioxidant and key component of the mitochondrial respiratory chain. For this second function, CoQ molecules seem to be dynamically segmented in a pool attached and engulfed by the super-complexes I + III, and a free pool available for complex II or any other mitochondrial enzyme that uses CoQ as a cofactor. This CoQ-free pool is, therefore, used by enzymes that link the mitochondrial respiratory chain to other pathways, such as the pyrimidine de novo biosynthesis, fatty acid β-oxidation and amino acid catabolism, glycine metabolism, proline, glyoxylate and arginine metabolism, and sulfide oxidation Citation: Hidalgo-Gutiérrez, A.; metabolism. Some of these mitochondrial pathways are also connected to metabolic pathways González-García, P.; Díaz-Casado, in other compartments of the cell and, consequently, CoQ could indirectly modulate metabolic M.E.; Barriocanal-Casado, E.; López-Herrador, S.; Quinzii, C.M.; pathways located outside the mitochondria. -
Physiological and Proteomic Responses of Diploid and Tetraploid Black Locust (Robinia Pseudoacacia L.) Subjected to Salt Stress
Int. J. Mol. Sci. 2013, 14, 20299-20325; doi:10.3390/ijms141020299 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms Article Physiological and Proteomic Responses of Diploid and Tetraploid Black Locust (Robinia pseudoacacia L.) Subjected to Salt Stress Zhiming Wang 1,†, Mingyue Wang 1,†, Likun Liu2 and Fanjuan Meng 1,* 1 College of Life Science, Northeast Forestry University, Harbin 150040, China; E-Mails: [email protected] (Z.W.); [email protected] (M.W.) 2 Department of Medical Biotechnology, College of Biomedical Science, Kangwon National University, Chuncheon, Gangwon-do 200-701, Korea; E-Mail: [email protected] † These authors contributed equally to this work. * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +86-451-8219-2170; Fax: +86-451-8643-3905. Received: 17 June 2013; in revised form: 31 August 2013 / Accepted: 9 September 2013 / Published: 14 October 2013 Abstract: Tetraploid black locust (Robinia pseudoacacia L.) is adaptable to salt stress. Here, we compared morphological, physiological, ultrastructural, and proteomic traits of leaves in tetraploid black locust and its diploid relatives under salt stress. The results showed that diploid (2×) plants suffered from greater negative effects than those of tetraploid (4×) plants. After salt treatment, plant growth was inhibited, photosynthesis was reduced, reactive oxygen species, malondialdehyde content, and relative electrolyte leakage increased, and defense-related enzyme activities decreased in 2× compared to those in 4×. In addition, salt stress resulted in distorted chloroplasts, swollen thylakoid membranes, accumulation of plastoglobules, and increased starch grains in 2× compared to those in 4×.