Sunday 1 April Parallel Session 5: Mitochondria
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Parallel Molecular Evolution of Catalases and Superoxide Dismutases—Focus on Thermophilic Fungal Genomes
antioxidants Article Parallel Molecular Evolution of Catalases and Superoxide Dismutases—Focus on Thermophilic Fungal Genomes Katarína Chovanová 1, Miroslav Böhmer 2 , Andrej Poljovka 1, Jaroslav Budiš 2, Jana Harichová 1, Tomáš Szemeš 2 and Marcel Zámocký 1,3,* 1 Laboratory for Phylogenomic Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravska cesta 21, SK-84551 Bratislava, Slovakia; [email protected] (K.C.); [email protected] (A.P.); [email protected] (J.H.) 2 Department of Molecular Biology, Faculty of Nat. Sciences, Science Park of Comenius University, Comenius University, Ilkoviˇcova8, SK-84104 Bratislava, Slovakia; [email protected] (M.B.); [email protected] (J.B.); [email protected] (T.S.) 3 Department of Chemistry, Institute of Biochemistry, BOKU, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria * Correspondence: [email protected] Received: 24 September 2020; Accepted: 22 October 2020; Published: 27 October 2020 Abstract: Catalases (CAT) and superoxide dismutases (SOD) represent two main groups of enzymatic antioxidants that are present in almost all aerobic organisms and even in certain anaerobes. They are closely interconnected in the catabolism of reactive oxygen species because one product of SOD reaction (hydrogen peroxide) is the main substrate of CAT reaction finally leading to harmless products (i.e., molecular oxygen and water). It is therefore interesting to compare the molecular evolution of corresponding gene families. We have used a phylogenomic approach to elucidate the evolutionary relationships among these two main enzymatic antioxidants with a focus on the genomes of thermophilic fungi. Distinct gene families coding for CuZnSODs, FeMnSODs, and heme catalases are very abundant in thermophilic Ascomycota. -
Revision of Agents of Black-Grain Eumycetoma in the Order Pleosporales
Persoonia 33, 2014: 141–154 www.ingentaconnect.com/content/nhn/pimj RESEARCH ARTICLE http://dx.doi.org/10.3767/003158514X684744 Revision of agents of black-grain eumycetoma in the order Pleosporales S.A. Ahmed1,2,3, W.W.J. van de Sande 4, D.A. Stevens 5, A. Fahal 6, A.D. van Diepeningen 2, S.B.J. Menken 3, G.S. de Hoog 2,3,7 Key words Abstract Eumycetoma is a chronic fungal infection characterised by large subcutaneous masses and the pres- ence of sinuses discharging coloured grains. The causative agents of black-grain eumycetoma mostly belong to the Madurella orders Sordariales and Pleosporales. The aim of the present study was to clarify the phylogeny and taxonomy of mycetoma pleosporalean agents, viz. Madurella grisea, Medicopsis romeroi (syn.: Pyrenochaeta romeroi), Nigrograna mackin Pleosporales nonii (syn. Pyrenochaeta mackinnonii), Leptosphaeria senegalensis, L. tompkinsii, and Pseudochaetosphaeronema taxonomy larense. A phylogenetic analysis based on five loci was performed: the Internal Transcribed Spacer (ITS), large Trematosphaeriaceae (LSU) and small (SSU) subunit ribosomal RNA, the second largest RNA polymerase subunit (RPB2), and transla- tion elongation factor 1-alpha (TEF1) gene. In addition, the morphological and physiological characteristics were determined. Three species were well-resolved at the family and genus level. Madurella grisea, L. senegalensis, and L. tompkinsii were found to belong to the family Trematospheriaceae and are reclassified as Trematosphaeria grisea comb. nov., Falciformispora senegalensis comb. nov., and F. tompkinsii comb. nov. Medicopsis romeroi and Pseu dochaetosphaeronema larense were phylogenetically distant and both names are accepted. The genus Nigrograna is reduced to synonymy of Biatriospora and therefore N. -
Thermophilic Fungi: Taxonomy and Biogeography
Journal of Agricultural Technology Thermophilic Fungi: Taxonomy and Biogeography Raj Kumar Salar1* and K.R. Aneja2 1Department of Biotechnology, Chaudhary Devi Lal University, Sirsa – 125 055, India 2Department of Microbiology, Kurukshetra University, Kurukshetra – 136 119, India Salar, R. K. and Aneja, K.R. (2007) Thermophilic Fungi: Taxonomy and Biogeography. Journal of Agricultural Technology 3(1): 77-107. A critical reappraisal of taxonomic status of known thermophilic fungi indicating their natural occurrence and methods of isolation and culture was undertaken. Altogether forty-two species of thermophilic fungi viz., five belonging to Zygomycetes, twenty-three to Ascomycetes and fourteen to Deuteromycetes (Anamorphic Fungi) are described. The taxa delt with are those most commonly cited in the literature of fundamental and applied work. Latest legal valid names for all the taxa have been used. A key for the identification of thermophilic fungi is given. Data on geographical distribution and habitat for each isolate is also provided. The specimens deposited at IMI bear IMI number/s. The document is a sound footing for future work of indentification and nomenclatural interests. To solve residual problems related to nomenclatural status, further taxonomic work is however needed. Key Words: Biodiversity, ecology, identification key, taxonomic description, status, thermophile Introduction Thermophilic fungi are a small assemblage in eukaryota that have a unique mechanism of growing at elevated temperature extending up to 60 to 62°C. During the last four decades many species of thermophilic fungi sporulating at 45oC have been reported. The species included in this account are only those which are thermophilic in the sense of Cooney and Emerson (1964). -
A Comparative Study of in Vitro Susceptibility of Madurella
Original Article A comparative Study of In vitro Susceptibility of Madurella mycetomatis to Anogeissus leiocarpous Leaves, Roots and Stem Barks Extracts Ikram Mohamed Eltayeb*1, Abdel Khalig Muddathir2, Hiba Abdel Rahman Ali3 and Saad Mohamed Hussein Ayoub1 1Department of Pharmacognosy, Faculty of Pharmacy, University of Medical Sciences and Technology, P. O. Box 12810, Khartoum, Sudan 2Department of Pharmacognosy, Faculty of Pharmacy, University of Khartoum, Khartoum, Sudan 3Commission of Biotechnology and Genetic Engineering, National Center for Research, Khartoum, Sudan ABSTRACT Objective: Anogeissus leiocarpus leaves, roots and stem bark are broadly utilized as a part of African traditional medicine against numerous pathogenic microorganisms for treating skin diseases and infections. Mycetoma disease is a fungal and/ or bacterial skin infection, mainly caused by filamentous Madurella mycetomatis fungus. The objective of this study is to investigate and compare the antifungal activity of A. leiocarpus leaves, roots and stem bark against the isolated mycetoma pathogen, M. mycetomatis fungus. Methods: The alcoholic crude extracts, and their petroleum ether, chloroform and ethyl acetate fractions of A. leiocarpus leaves, roots and stem bark were prepared and their antifungal activity against the isolated M. mycetomatis fungus were assayed according to the Address for NCCLS antifungal modified method and MTT assay compared to the Correspondence Ketoconazole, standard antifungal drug. The most bioactive fractions were subjected to chemical analysis using LC-MS/MS Department of chromatographic analytical method. Pharmacognosy, Results: The results demonstrated the potent antifungal activity of A. Faculty of Pharmacy, leiocarpus extracts against the isolated pathogenic M. mycetomatis University of Medical compared to the negative and positive controls. The chloroform Sciences and fractions showed higher antifungal activity among the other extracts, Technology, P. -
A Novel Application Potential of GH6 Cellobiohydrolase Ctcel6 From
INTERNATIONAL JOURNAL OF AGRICULTURE & BIOLOGY ISSN Print: 1560–8530; ISSN Online: 1814–9596 16–768/2017/19–2–355–362 DOI: 10.17957/IJAB/15.0290 http://www.fspublishers.org Full Length Article A Novel Application Potential of GH6 Cellobiohydrolase CtCel6 from Thermophilic Chaetomium thermophilum for Gene Cloning, Heterologous Expression and Biological Characterization Qinzheng Zhou, Jianchao Jia, Peng Ji and Chao Han* Department of Mycology, Shandong Agricultural University, Taian, Shandong 271018, China *For correspondence: [email protected] Abstract Chaetomium thermophilum is a thermophilic fungus expressed a series of glycoside hydrolases. Genome sequence analysis of C. thermophilium revealed that ctcel6 gene encoded a putative cellobiohydrolase which composed of 397 amino acid residues including a predicted signal peptide sequence. Ctcel6 gene was cloned, heterologously expressed in Pichia pastoris and purified by Ni2+ affinity chromatography. Sequence alignment indicated that CtCel6 enzyme belonged to glycoside hydrolase family 6 (GH6) and the molecular mass of purified recombinant enzyme CtCel6 was 42 kDa by SDS-PAGE analysis. Characterization of recombinant CtCel6 exhibited high hydrolysis activity and excellent thermostability. The optimum reaction temperature and pH was 70oC and pH 5, respectively. The bivalent metallic cations Mg2+ and Ca2+ significantly enhanced the activity of CtCel6. The specific activity of CtCel6 enzyme was 1.27 U/mg and Km value was 0.38 mM on β-D- glucan. The substrate specificity and hydrolysis products insisted that CtCel6 was an exo-/endo-type cellobiohydrolase. The biochemical properties of recombinant CtCel6 made it potentially effective for bioconversion of biomass and had tremendous potential in industrial applications such as enzyme preparation industry and feed processing industry. -
Utilization of the Internal Transcribed Spacer Regions As Molecular Targets
Medical Mycology 2002, 40, 87±109 Accepted 9July 2001 Review article Utilizationof the internaltranscribed spacer regions as molecular targets to detect andidentify human fungal pathogens P.C.IWEN*, S.H.HINRICHS* & M.E.RUPP Downloaded from https://academic.oup.com/mmy/article/40/1/87/961355 by guest on 29 September 2021 y *Department ofPathology and Microbiology,University ofNebraska MedicalCenter, Omaha, Nebraska, USA; Internal Medicine, y University ofNebraska MedicalCenter, Omaha, Nebraska, USA Advancesin molecular technology show greatpotential for the rapiddetection and identication of fungifor medical,scienti c andcommercial purposes. Numerous targetswithin the fungalgenome have been evaluated, with much of the current work usingsequence areas within the ribosomalDNA (rDNA) gene complex. This sectionof the genomeincludes the 18S,5 8Sand28S genes which codefor ribosomal ¢ RNA(rRNA) andwhich havea relativelyconserved nucleotide sequence among fungi.It alsoincludes the variableDNA sequence areas of the interveninginternal transcribedspacer (ITS) regionscalled ITS1 and ITS2. Although not translatedinto proteins,the ITScoding regions have a criticalrole in the developmentof functional rRNA,with sequencevariations among species showing promiseas signature regionsfor molecularassays. This review of the current literaturewas conducted to evaluateclinical approaches for usingthe fungalITS regions as molecular targets. Multipleapplications using the fungalITS sequences are summarized here including those for cultureidenti cation, phylogenetic -
New Species of Madurella, Causative Agents of Black-Grain Mycetoma
New Species of Madurella, Causative Agents of Black-Grain Mycetoma G. Sybren de Hoog,a,b,c,d Anne D. van Diepeningen,a El-Sheikh Mahgoub,e and Wendy W. J. van de Sandef Centraalbureau voor Schimmelcultures KNAW Fungal Biodiversity Centre, Utrecht, The Netherlandsa; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlandsb; Peking University Health Science Center, Research Center for Medical Mycology, Beijing, Chinac; Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Chinad; Mycetoma Research Centre, University of Khartoum, Khartoum, Sudane; and Erasmus Medical Center, Department of Medical Microbiology and Infectious Diseases, Rotterdam, The Netherlandsf Downloaded from A new species of nonsporulating fungus, isolated in a case of black-grain mycetoma in Sudan, is described as Madurella fahalii. The species is characterized by phenotypic and molecular criteria. Multigene phylogenies based on the ribosomal DNA (rDNA) internal transcribed spacer (ITS), the partial -tubulin gene (BT2), and the RNA polymerase II subunit 2 gene (RPB2) indicate that M. fahalii is closely related to Madurella mycetomatis and M. pseudomycetomatis; the latter name is validated according to the rules of botanical nomenclature. Madurella ikedae was found to be synonymous with M. mycetomatis. An isolate from Indo- nesia was found to be different from all known species based on multilocus analysis and is described as Madurella tropicana. Madurella is nested within the order Sordariales, with Chaetomium as its nearest neighbor. Madurella fahalii has a relatively low optimum growth temperature (30°C) and is less susceptible to the azoles than other Madurella species, with voriconazole http://jcm.asm.org/ and posaconazole MICs of 1 g/ml, a ketoconazole MIC of 2 g/ml, and an itraconazole MIC of >16 g/ml. -
Thermophiles and Thermozymes
Thermophiles and Thermozymes Edited by María-Isabel González-Siso Printed Edition of the Special Issue Published in Microorganisms www.mdpi.com/journal/microorganisms Thermophiles and Thermozymes Thermophiles and Thermozymes Special Issue Editor Mar´ıa-Isabel Gonz´alez-Siso MDPI • Basel • Beijing • Wuhan • Barcelona • Belgrade Special Issue Editor Mar´ıa-Isabel Gonzalez-Siso´ Universidade da Coruna˜ Spain Editorial Office MDPI St. Alban-Anlage 66 4052 Basel, Switzerland This is a reprint of articles from the Special Issue published online in the open access journal Microorganisms (ISSN 2076-2607) from 2018 to 2019 (available at: https://www.mdpi.com/journal/ microorganisms/special issues/thermophiles) For citation purposes, cite each article independently as indicated on the article page online and as indicated below: LastName, A.A.; LastName, B.B.; LastName, C.C. Article Title. Journal Name Year, Article Number, Page Range. ISBN 978-3-03897-816-9 (Pbk) ISBN 978-3-03897-817-6 (PDF) c 2019 by the authors. Articles in this book are Open Access and distributed under the Creative Commons Attribution (CC BY) license, which allows users to download, copy and build upon published articles, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. The book as a whole is distributed by MDPI under the terms and conditions of the Creative Commons license CC BY-NC-ND. Contents About the Special Issue Editor ...................................... vii Mar´ıa-Isabel Gonz´alez-Siso Editorial for the Special Issue: Thermophiles and Thermozymes Reprinted from: Microorganisms 2019, 7, 62, doi:10.3390/microorganisms7030062 ........ -
The Discovery of Fenarimols As Novel Drug
bioRxiv preprint doi: https://doi.org/10.1101/258905; this version posted February 2, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Full title: Addressing the Most Neglected Diseases through an Open Research Model: the Discovery of Fenarimols as Novel Drug Candidates for Eumycetoma. Short title: Eumycetoma Open Research Model Drug discovery 1 bioRxiv preprint doi: https://doi.org/10.1101/258905; this version posted February 2, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Addressing the Most Neglected Diseases through an Open Research Model: the Discovery of 2 Fenarimols as Novel Drug Candidates for Eumycetoma. 3 4 Wilson Lim1, Youri Melse1, Mickey Konings1, Hung Phat Duong2, Kimberly Eadie1, Benoît Laleu3, Ben 4 2 4 1 5 Perry , Matthew H. Todd , Jean-Robert Ioset , Wendy W.J. van de Sande * 6 7 8 1Erasmus MC, Department of Medical Microbiology and Infectious Diseases, Rotterdam, The 9 Netherlands 10 2School of Chemistry, The University of Sydney, Sydney, Australia 11 3Medicines for Malaria Venture (MMV), Geneva, Switzerland 12 4DNDi, Geneva, Switzerland 13 14 15 16 Corresponding author: Wendy W.J. van de Sande 17 * [email protected] (WvdS) 2 bioRxiv preprint doi: https://doi.org/10.1101/258905; this version posted February 2, 2018. -
Niclosamide Is Active in Vitro Against Mycetoma Pathogens
molecules Article Niclosamide Is Active In Vitro against Mycetoma Pathogens Abdelhalim B. Mahmoud 1,2,3,† , Shereen Abd Algaffar 4,† , Wendy van de Sande 5, Sami Khalid 4 , Marcel Kaiser 1,2 and Pascal Mäser 1,2,* 1 Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland; [email protected] (A.B.M.); [email protected] (M.K.) 2 Faculty of Science, University of Basel, 4001 Basel, Switzerland 3 Faculty of Pharmacy, University of Khartoum, Khartoum 11111, Sudan 4 Faculty of Pharmacy, University of Science and Technology, Omdurman 14411, Sudan; [email protected] (S.A.A.); [email protected] (S.K.) 5 Erasmus Medical Center, Department of Medical Microbiology and Infectious Diseases, 3000 Rotterdam, The Netherlands; [email protected] * Correspondence: [email protected]; Tel.: +41-61-284-8338 † These authors contributed equally to this work. Abstract: Redox-active drugs are the mainstay of parasite chemotherapy. To assess their repurposing potential for eumycetoma, we have tested a set of nitroheterocycles and peroxides in vitro against two isolates of Madurella mycetomatis, the main causative agent of eumycetoma in Sudan. All the tested compounds were inactive except for niclosamide, which had minimal inhibitory concentrations of around 1 µg/mL. Further tests with niclosamide and niclosamide ethanolamine demonstrated in vitro activity not only against M. mycetomatis but also against Actinomadura spp., causative agents of actinomycetoma, with minimal inhibitory concentrations below 1 µg/mL. The experimental compound MMV665807, a related salicylanilide without a nitro group, was as active as niclosamide, indicating that the antimycetomal action of niclosamide is independent of its redox chemistry (which Citation: Mahmoud, A.B.; Abd Algaffar, S.; van de Sande, W.; Khalid, is in agreement with the complete lack of activity in all other nitroheterocyclic drugs tested). -
Deep Transcriptome-Sequencing and Proteome Analysis of the Hydrothermal Vent Annelid Alvinella Pompejana Identifies the Cvp-Bias
Deep transcriptome-sequencing and proteome analysis of the hydrothermal vent annelid Alvinella pompejana identifies the CvP-bias as a robust measure of eukaryotic thermostability Thomas Holder, Claire Basquin, Judith Ebert, Nadine Randel, Didier Jollivet, Elena Conti, Gáspár Jékely, Fulvia Bono To cite this version: Thomas Holder, Claire Basquin, Judith Ebert, Nadine Randel, Didier Jollivet, et al.. Deep transcriptome-sequencing and proteome analysis of the hydrothermal vent annelid Alvinella pom- pejana identifies the CvP-bias as a robust measure of eukaryotic thermostability. Biology Direct, BioMed Central, 2013, 8, pp.2. 10.1186/1745-6150-8-2. hal-01250913 HAL Id: hal-01250913 https://hal.archives-ouvertes.fr/hal-01250913 Submitted on 11 Jan 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License Holder et al. Biology Direct 2013, 8:2 http://www.biology-direct.com/content/8/1/2 RESEARCH Open Access Deep transcriptome-sequencing and proteome analysis of the hydrothermal vent annelid Alvinella pompejana identifies the CvP-bias as a robust measure of eukaryotic thermostability Thomas Holder1, Claire Basquin3, Judith Ebert3, Nadine Randel1, Didier Jollivet2, Elena Conti3, Gáspár Jékely1* and Fulvia Bono1* Abstract Background: Alvinella pompejana is an annelid worm that inhabits deep-sea hydrothermal vent sites in the Pacific Ocean. -
The Development of a Novel Diagnostic PCR for Madurella Mycetomatis Using a Comparative Genome Approach
PLOS NEGLECTED TROPICAL DISEASES RESEARCH ARTICLE The development of a novel diagnostic PCR for Madurella mycetomatis using a comparative genome approach 1 1,2 1 1 Wilson LimID , Emmanuel SiddigID , Kimberly Eadie , Bertrand NyuykongeID , 3¤a¤b 2 1 4 Sarah Ahmed , Ahmed Fahal , Annelies Verbon , Sandra SmitID , Wendy WJ van de 1 SandeID * 1 Erasmus MC, University Medical Center Rotterdam, Department of Microbiology and Infectious Diseases, a1111111111 Rotterdam, The Netherlands, 2 Mycetoma Research Centre, University of Khartoum, Khartoum, Sudan, a1111111111 3 Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands, 4 Wageningen University & Research, a1111111111 Department of Plant Science, Wageningen, The Netherlands a1111111111 ¤a Current address: Center of Expertise in Mycology of Radboud University Medical Center / Canisius a1111111111 Wilhelmina Hospital, Nijmegen, The Netherlands ¤b Current address: Faculty of medical laboratory sciences, University of Khartoum, Sudan * [email protected] OPEN ACCESS Abstract Citation: Lim W, Siddig E, Eadie K, Nyuykonge B, Ahmed S, Fahal A, et al. (2020) The development of a novel diagnostic PCR for Madurella mycetomatis using a comparative genome approach. PLoS Negl Background Trop Dis 14(12): e0008897. https://doi.org/ Eumycetoma is a neglected tropical disease most commonly caused by the fungus Madur- 10.1371/journal.pntd.0008897 ella mycetomatis. Identification of eumycetoma causative agents can only be reliably per- Editor: Husain Poonawala, Lowell General Hospital, formed by molecular identification, most commonly by species-specific PCR. The current M. UNITED STATES mycetomatis specific PCR primers were recently discovered to cross-react with Madurella Received: June 18, 2020 pseudomycetomatis. Here, we used a comparative genome approach to develop a new M.