Relating Metatranscriptomic Profiles to the Micropollutant
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WO 2018/009838 Al 11 January 2018 (11.01.2018) W !P O PCT
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2018/009838 Al 11 January 2018 (11.01.2018) W !P O PCT (51) International Patent Classification: Declarations under Rule 4.17: C12N 5/075 (2010.01) — as to applicant's entitlement to apply for and be granted a (21) International Application Number: patent (Rule 4.1 7(H)) PCT/US2017/041 155 — as to the applicant's entitlement to claim the priority of the earlier application (Rule 4.17(Hi)) (22) International Filing Date: 07 July 2017 (07.07.2017) Published: — with international search report (Art. 21(3)) (25) Filing Language: English — before the expiration of the time limit for amending the (26) Publication Langi English claims and to be republished in the event of receipt of amendments (Rule 48.2(h)) (30) Priority Data: — with sequence listing part of description (Rule 5.2(a)) 62/359,416 07 July 2016 (07.07.2016) US (71) Applicant: RUBIUS THERAPEUTICS, INC. [US/US]; 620 Memorial Dr #100W, Cambridge, MA 02139 (US). (72) Inventors; and (71) Applicants: HARANDI, Omid [US/US]; 39 Rowena Road, Newton, MA 02459 (US). KHANWALKAR, Ur- jeet [IN/US]; 2 11 Elm Street, Apt. 3, Cambridge, MA 02139 (US). HARIHARAN, Sneha [IN/US]; 18 Hamilton Road, Apt. 407, Arlington, MA 02472 (US). (72) Inventors: KAHVEJIAN, Avak; 2 Beverly Road, Arling ton, MA 02474 (US). MATA-FINK, Jordi; 8 Windsor Rd #1, Somerville, MA 02144 (US).DEANS, Robert, J.; 1609 Ramsgate Court, Riverside, CA 92506 (US). -
Table 2. Functional Classification of Genes Differentially Regulated After HOXB4 Inactivation in HSC/Hpcs
Table 2. Functional classification of genes differentially regulated after HOXB4 inactivation in HSC/HPCs Symbol Gene description Fold-change (mean ± SD) Signal transduction Adam8 A disintegrin and metalloprotease domain 8 1.91 ± 0.51 Arl4 ADP-ribosylation factor-like 4 - 1.80 ± 0.40 Dusp6 Dual specificity phosphatase 6 (Mkp3) - 2.30 ± 0.46 Ksr1 Kinase suppressor of ras 1 1.92 ± 0.42 Lyst Lysosomal trafficking regulator 1.89 ± 0.34 Mapk1ip1 Mitogen activated protein kinase 1 interacting protein 1 1.84 ± 0.22 Narf* Nuclear prelamin A recognition factor 2.12 ± 0.04 Plekha2 Pleckstrin homology domain-containing. family A. (phosphoinosite 2.15 ± 0.22 binding specific) member 2 Ptp4a2 Protein tyrosine phosphatase 4a2 - 2.04 ± 0.94 Rasa2* RAS p21 activator protein 2 - 2.80 ± 0.13 Rassf4 RAS association (RalGDS/AF-6) domain family 4 3.44 ± 2.56 Rgs18 Regulator of G-protein signaling - 1.93 ± 0.57 Rrad Ras-related associated with diabetes 1.81 ± 0.73 Sh3kbp1 SH3 domain kinase bindings protein 1 - 2.19 ± 0.53 Senp2 SUMO/sentrin specific protease 2 - 1.97 ± 0.49 Socs2 Suppressor of cytokine signaling 2 - 2.82 ± 0.85 Socs5 Suppressor of cytokine signaling 5 2.13 ± 0.08 Socs6 Suppressor of cytokine signaling 6 - 2.18 ± 0.38 Spry1 Sprouty 1 - 2.69 ± 0.19 Sos1 Son of sevenless homolog 1 (Drosophila) 2.16 ± 0.71 Ywhag 3-monooxygenase/tryptophan 5- monooxygenase activation protein. - 2.37 ± 1.42 gamma polypeptide Zfyve21 Zinc finger. FYVE domain containing 21 1.93 ± 0.57 Ligands and receptors Bambi BMP and activin membrane-bound inhibitor - 2.94 ± 0.62 -
Metabolic Engineering of Microbial Cell Factories for Biosynthesis of Flavonoids: a Review
molecules Review Metabolic Engineering of Microbial Cell Factories for Biosynthesis of Flavonoids: A Review Hanghang Lou 1,†, Lifei Hu 2,†, Hongyun Lu 1, Tianyu Wei 1 and Qihe Chen 1,* 1 Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China; [email protected] (H.L.); [email protected] (H.L.); [email protected] (T.W.) 2 Hubei Key Lab of Quality and Safety of Traditional Chinese Medicine & Health Food, Huangshi 435100, China; [email protected] * Correspondence: [email protected]; Tel.: +86-0571-8698-4316 † These authors are equally to this manuscript. Abstract: Flavonoids belong to a class of plant secondary metabolites that have a polyphenol structure. Flavonoids show extensive biological activity, such as antioxidative, anti-inflammatory, anti-mutagenic, anti-cancer, and antibacterial properties, so they are widely used in the food, phar- maceutical, and nutraceutical industries. However, traditional sources of flavonoids are no longer sufficient to meet current demands. In recent years, with the clarification of the biosynthetic pathway of flavonoids and the development of synthetic biology, it has become possible to use synthetic metabolic engineering methods with microorganisms as hosts to produce flavonoids. This article mainly reviews the biosynthetic pathways of flavonoids and the development of microbial expression systems for the production of flavonoids in order to provide a useful reference for further research on synthetic metabolic engineering of flavonoids. Meanwhile, the application of co-culture systems in the biosynthesis of flavonoids is emphasized in this review. Citation: Lou, H.; Hu, L.; Lu, H.; Wei, Keywords: flavonoids; metabolic engineering; co-culture system; biosynthesis; microbial cell factories T.; Chen, Q. -
Grapes for the Desert: Salt Stress Signaling in Vitis
Grapes for the Desert: Salt Stress Signaling in Vitis Zur Erlangung des akademischen Grades eines DOKTORS DER NATURWISSENSCHAFTEN (Dr. rer. Nat.) der Fakultät für Chemie und Biowissenschaften des Karlsruher Instituts für Technologie (KIT) genehmigte DISSERTATION von Ahmed Abd Alkarim Mohammed Ismail aus Damanhour, Ägypten Die vorliegende Dissertation wurde in der Abteilung Molekulare Zellbiologie, am Botanischen Institut des Karlsruher Instituts für Technologie (KIT) im Zeitraum von April 2010 bis Juli 2013 angefertigt. Dekan: Prof. Dr. M. Bastmeyer Referent: Prof. Dr. P. Nick Korreferent: Prof. Dr. H. Puchta Prof. Dr. Natalia Requena Dr. Christoph Basse Tag der mündlichen Prüfung: 19. Juli 2013 Hiermit erkläre ich, dass ich die vorliegende Dissertation, abgesehen von der Benutzung der angegebenen Hilfsmittel, selbstständig verfasst habe. Alle Stellen, die gemäß Wortlaut oder Inhalt aus anderen Arbeiten entnommen sind, wurden durch Angabe der Quelle als Entlehnungen kenntlich gemacht. Diese Dissertation liegt in gleicher oder ähnlicher Form keiner anderen Prüfungsbehörde vor. Karlsruhe, den 19. Juli 2013 Ahmed Abd Alkarim Mohammed Ismail Table of Contents Table of Contents Abbreviations ........................................................................... IV Summary / Zusammenfassung ............................................... XI 1 Introduction ............................................................................. 1 1.1 What does stress mean for a plant? .............................................. 1 1.2 Environmental -
Chapter 5 High-Pressure Stopped-Flow Kinetic Studies of Nnos
Probing the dynamics and conformational landscape of neuronal nitric oxide synthase A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Life Sciences 2013 Anna Sobolewska-Stawiarz Contents Contents ...................................................................................................................... 2 List of Figures ............................................................................................................. 6 List of Tables ............................................................................................................ 10 Abstract ..................................................................................................................... 12 Declaration ................................................................................................................ 13 Copyright Statement ................................................................................................ 13 Acknowledgements ................................................................................................... 14 List of Abbreviations ............................................................................................... 15 List of Amino Acids Abbreviations ........................................................................ 17 CHAPTER 1. INTRODUCTION ........................................................................... 18 1.1 Nitric oxide synthase ......................................................................................... -
Carbon Monoxide Prevents TNF-Α-Induced Enos Downregulation by Inhibiting NF-Κb-Responsive Mir-155-5P Biogenesis
OPEN Experimental & Molecular Medicine (2017) 49, e403; doi:10.1038/emm.2017.193 Official journal of the Korean Society for Biochemistry and Molecular Biology www.nature.com/emm ORIGINAL ARTICLE Carbon monoxide prevents TNF-α-induced eNOS downregulation by inhibiting NF-κB-responsive miR-155-5p biogenesis Seunghwan Choi1, Joohwan Kim1, Ji-Hee Kim1, Dong-Keon Lee1, Wonjin Park1, Minsik Park1, Suji Kim1, Jong Yun Hwang2, Moo-Ho Won3, Yoon Kyung Choi1,4, Sungwoo Ryoo5, Kwon-Soo Ha1, Young-Guen Kwon6 and Young-Myeong Kim1 Heme oxygenase-1-derived carbon monoxide prevents inflammatory vascular disorders. To date, there is no clear evidence that HO-1/CO prevents endothelial dysfunction associated with the downregulation of endothelial NO synthesis in human endothelial cells stimulated with TNF-α. Here, we found that the CO-releasing compound CORM-2 prevented TNF-α-mediated decreases in eNOS expression and NO/cGMP production, without affecting eNOS promoter activity, by maintaining the functional activity of the eNOS mRNA 3′-untranslated region. By contrast, CORM-2 inhibited MIR155HG expression and miR-155-5p biogenesis in TNF-α-stimulated endothelial cells, resulting in recovery of the 3′-UTR activity of eNOS mRNA, a target of miR-155-5p. The beneficial effect of CORM-2 was blocked by an NF-κB inhibitor, a miR-155-5p mimic, a HO-1 inhibitor and siRNA against HO-1, indicating that CO rescues TNF-α-induced eNOS downregulation through NF-κB-responsive miR-155-5p expression via HO-1 induction; similar protective effects of ectopic HO-1 expression and bilirubin were observed in endothelial cells treated with TNF-α. -
Carnitine Metabolism to Trimethylamine by an Unusual Rieske-Type Oxygenase from Human Microbiota
Carnitine metabolism to trimethylamine by an unusual Rieske-type oxygenase from human microbiota Yijun Zhua,1, Eleanor Jamesona,1, Marialuisa Crosattib,1, Hendrik Schäfera, Kumar Rajakumarb, Timothy D. H. Buggc, and Yin Chena,2 aSchool of Life Sciences and cDepartment of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom; and bDepartment of Infection, Immunity, and Inflammation, University of Leicester, Leicester LE1 9HN, United Kingdom Edited by David W. Russell, University of Texas Southwestern Medical Center, Dallas, TX, and approved January 29, 2014 (received for review September 5, 2013) Dietary intake of L-carnitine can promote cardiovascular diseases in (14, 15). Assigning functions encoded in the human microbiome humans through microbial production of trimethylamine (TMA) using existing databases can be problematic. For example, the and its subsequent oxidation to trimethylamine N-oxide by hepatic Pfam protein database currently contains over 25% of protein flavin-containing monooxygenases. Although our microbiota are re- families with no assigned functions (release 26.0) (19). sponsible for TMA formation from carnitine, the underpinning mo- Lack of functional characterization of key microbial functions lecular and biochemical mechanisms remain unclear. In this study, in our microbiota is exemplified by very recent studies on car- using bioinformatics approaches, we first identified a two-component diovascular diseases (20–23). These studies have shown that the Rieske-type oxygenase/reductase (CntAB) and associated gene human microbiota is responsible for the production of trime- cluster proposed to be involved in carnitine metabolism in repre- thylamine N-oxide (TMAO), which is believed to promote ath- sentative genomes of the human microbiota. CntA belongs to a erogenesis through its interaction with macrophages and lipid group of previously uncharacterized Rieske-type proteins and has metabolism (20–23). -
Bioinorganic Chemistry of Nickel
inorganics Editorial Bioinorganic Chemistry of Nickel Michael J. Maroney 1,* and Stefano Ciurli 2,* 1 Department of Chemistry and Program in Molecular and Cellular Biology, University of Massachusetts Amherst, 240 Thatcher Rd. Life Sciences, Laboratory Rm N373, Amherst, MA 01003, USA 2 Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, I-40127 Bologna, Italy * Correspondence: [email protected] (M.J.M.); [email protected] (S.C.) Received: 11 October 2019; Accepted: 11 October 2019; Published: 30 October 2019 Following the discovery of the first specific and essential role of nickel in biology in 1975 (the dinuclear active site of the enzyme urease) [1], nickel has become a major player in bioinorganic chemistry,particularly in microorganisms, having impacts on both environmental settings and human pathologies. At least nine classes of enzymes are now known to require nickel in their active sites, including catalysis of redox [(Ni,Fe) hydrogenases, carbon monoxide dehydrogenase, methyl coenzyme M reductase, acetyl coenzyme A synthase, superoxide dismutase] and nonredox (glyoxalase I, acireductone dioxygenase, lactate isomerase, urease) chemistries. In addition, the dark side of nickel has been illuminated in regard to its participation in microbial pathogenesis, cancer, and immune responses. Knowledge gleaned from the investigations of inorganic chemists into the coordination and redox chemistry of this element have boosted the understanding of these biological roles of nickel in each context. In this issue, eleven contributions, including four original research articles and seven critical reviews, will update the reader on the broad spectrum of the role of nickel in biology. -
Protein S-Nitrosylation: Methods of Detection and Cellular Regulation
Protein S-Nitrosylation: Methods of Detection and Cellular Regulation by Michael Tcheupdjian Forrester Department of Biochemistry Duke University Date:_______________________ Approved: ___________________________ Jonathan S. Stamler, MD (Supervisor) ___________________________ Irwin Fridovich, PhD ___________________________ K. V. Rajagopalan, PhD ___________________________ Dennis J. Thiele, PhD ___________________________ Eric J. Toone, PhD Dissertation submitted in partial fulfillment of the requirements for the degree of doctor of philosophy in the Department of Biochemistry in the Graduate School of Duke University 2009 i v ABSTRACT Protein S-Nitrosylation: Methods of Detection and Cellular Regulation by Michael Tcheupdjian Forrester Department of Biochemistry Duke University Date:_______________________ Approved: ___________________________ Jonathan S. Stamler, MD (Supervisor) ___________________________ Irwin Fridovich, PhD ___________________________ K. V. Rajagopalan, PhD ___________________________ Dennis J. Thiele, PhD ___________________________ Eric J. Toone, PhD An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of doctor of philosophy in the Department of Biochemistry in the Graduate School of Duke University 2009 i v Copyright by Michael T. Forrester 2009 Abstract Protein S-nitrosylation—the post-translational modification of cysteine thiols into S-nitrosothiols—is a principle mechanism of nitric oxide-based signaling. Studies have demonstrated myriad roles for S-nitrosylation in organisms from bacteria to humans, and recent efforts have begun to elucidate how this redox-based modification is regulated during physiological and pathophysiological conditions. This doctoral thesis is focused on the 1) analysis of existing methodologies for the detection of protein S-nitrosylation; 2) development of new methodologies for the detection of protein S-nitrosylation and 3) discovery of novel enzymatic mechanisms by which S-nitrosylation is regulated in vivo. -
L.) Leaves Tao Jiang1,3, Kunyuan Guo2,3, Lingdi Liu1, Wei Tian1, Xiaoliang Xie1, Saiqun Wen1 & Chunxiu Wen1*
www.nature.com/scientificreports OPEN Integrated transcriptomic and metabolomic data reveal the favonoid biosynthesis metabolic pathway in Perilla frutescens (L.) leaves Tao Jiang1,3, Kunyuan Guo2,3, Lingdi Liu1, Wei Tian1, Xiaoliang Xie1, Saiqun Wen1 & Chunxiu Wen1* Perilla frutescens (L.) is an important medicinal and edible plant in China with nutritional and medical uses. The extract from leaves of Perilla frutescens contains favonoids and volatile oils, which are mainly used in traditional Chinese medicine. In this study, we analyzed the transcriptomic and metabolomic data of the leaves of two Perilla frutescens varieties: JIZI 1 and JIZI 2. A total of 9277 diferentially expressed genes and 223 favonoid metabolites were identifed in these varieties. Chrysoeriol, apigenin, malvidin, cyanidin, kaempferol, and their derivatives were abundant in the leaves of Perilla frutescens, which were more than 70% of total favonoid contents. A total of 77 unigenes encoding 15 enzymes were identifed as candidate genes involved in favonoid biosynthesis in the leaves of Perilla frutescens. High expression of the CHS gene enhances the accumulation of favonoids in the leaves of Perilla frutescens. Our results provide valuable information on the favonoid metabolites and candidate genes involved in the favonoid biosynthesis pathways in the leaves of Perilla frutescens. Perilla frutescens (L.), which is a self-compatible annual herb, belongs to the family Lamiaceae. Tis species has been widely cultivated in China, Japan, and Korea for centuries. Perilla frutescens is an important medicinal and edible plant in China with medical and nutritional uses 1. Its leaves can be utilized as a transitional medicinal herb, as a vegetable, and as a spice, and its seeds can be processed into foods and nutritional edible oils 2. -
Rhodococcus Jostii Strain 8
Functional characterisation of alkane-degrading monooxygenases in Rhodococcus jostii strain 8 Jindarat Ekprasert A thesis submitted to the School of Environmental Sciences in fulfilment of the requirements for the degree of Doctor of Philosophy September 2014 University of East Anglia Norwich, UK i Contents List of figures viii List of tables xiii Declaration xv Acknowledgements xvi Abbreviations xvii Abstract xxi Chapter 1 introduction 1 1.1. Significance of alkanes in the environment 2 1.1.1. Chemistry of alkanes 2 1.2. The Rhodococcus genus 3 1.2.1. Common characteristics of Rhodococcus spp. 3 1.2.2. Rhodococcus spp. are capable of degrading gaseous alkanes 4 1.2.3. Potential applications of Rhodococcus in biotechnology 5 1.3. Bacterial enzymes responsible for alkane degradation 6 1.3.1. Integral membrane, non-heme iron alkane hydroxylases (AlkB) 6 1.3.2. Soluble di-iron monooxygenases (SDIMO) 8 1.3.2.1. SDIMO classification 10 1.3.2.2. Molecular genetics of SDIMOs 13 1.3.2.3. Mutagenesis of soluble methane monooxygenase 13 1.3.3. Cytochrome P450 alkane hydroxylases 14 3.3.1. Class I P450 14 3.3.2. Class II P450 (CYP52) 15 3.3.3. Class II P450 (CYP2E, CYP4B) 15 1.3.4. Membrane bound copper-containing (and possibly iron-containing) monooxygenases 15 1.4. Alkane metabolisms in Rhodococcus spp. 16 1.4.1. Aerobic metabolism of C2-C4 gaseous alkanes in bacteria 16 1.4.1.1. Ethane (C2H6) metabolism 16 1.4.1.2. Propane (C3H8) metabolism 17 ii 1.4.1.3. -
Bioluminescent Properties of Semi-Synthetic Obelin and Aequorin Activated by Coelenterazine Analogues with Modifications of C-2, C-6, and C-8 Substituents
International Journal of Molecular Sciences Article Bioluminescent Properties of Semi-Synthetic Obelin and Aequorin Activated by Coelenterazine Analogues with Modifications of C-2, C-6, and C-8 Substituents 1, 2,3, 1 2, Elena V. Eremeeva y , Tianyu Jiang y , Natalia P. Malikova , Minyong Li * and Eugene S. Vysotski 1,* 1 Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk 660036, Russia; [email protected] (E.V.E.); [email protected] (N.P.M.) 2 Key Laboratory of Chemical Biology (MOE), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China; [email protected] 3 State Key Laboratory of Microbial Technology, Shandong University–Helmholtz Institute of Biotechnology, Shandong University, Qingdao 266237, China * Correspondence: [email protected] (M.L.); [email protected] (E.S.V.); Tel.: +86-531-8838-2076 (M.L.); +7-(391)-249-44-30 (E.S.V.); Fax: +86-531-8838-2076 (M.L.); +7-(391)-290-54-90 (E.S.V.) These authors contributed equally to this work. y Received: 23 June 2020; Accepted: 27 July 2020; Published: 30 July 2020 Abstract: Ca2+-regulated photoproteins responsible for bioluminescence of a variety of marine organisms are single-chain globular proteins within the inner cavity of which the oxygenated coelenterazine, 2-hydroperoxycoelenterazine, is tightly bound. Alongside with native coelenterazine, photoproteins can also use its synthetic analogues as substrates to produce flash-type bioluminescence. However, information on the effect of modifications of various groups of coelenterazine and amino acid environment of the protein active site on the bioluminescent properties of the corresponding semi-synthetic photoproteins is fragmentary and often controversial.