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Industrial Applications of Marine Enzymes: Innovative screening and expression platforms to discover and use the functional protein diversity from the sea

Deliverables

D8.6 Two articles on main highlights of the INMARE project in a non-scientific journal

Two articles on main highlights of the INMARE project in a non-scientific journal

D8.8 Report on the inter-disciplinary symposium on ‘Marine Biodiversity: Ownership, Sharing and intellectual Property Protection’

Report on the inter-disciplinary symposium on ‘Marine Biodiversity: Ownership, Sharing and intellectual Property Protection’

D8-15 Two articles on main highlights of the INMARE project in a non-scientific jornal

Second article on main highlights of the INMARE project in a non-scientific jornal

D8.10 At least two peer-reviewed papers in legal or inter-disciplinary journals on IP issues

At least two peer-reviewed papers in legal or inter-disciplinary journals on IP issues

D8.5 Report on INMARE Workshop on metagenomics and bioprospecting

Report on INMARE Workshop on metagenomics and bioprospecting

D8.7 Report on INMARE Bioinformatics training Workshop

Report on INMARE Bioinformatics training Workshop

D8.2 INMARE Project Website published online

INMARE Project Website published online

D8.9 INMARE Project Leaflet with summary information and noteworthy outputs for wide distribution

INMARE Project Leaflet with summary information and noteworthy outputs for wide distribution

D8.11 At least two patents filed

At least two patents filed

D8.14 Two INMARE Science Policy Briefs for management-level personnel and decision makers/advisors with a focus on the research efforts of INMARE

Second INMARE Science Policy Brief for management-level personnel and decision makers/advisors with a focus on the research efforts of INMARE

D8.1 Communication and Dissemination Strategy

Communication and Dissemination Strategy

D8.3 INMARE Project Brochure with general information for wide distribution

INMARE Project Brochure with general information for wide distribution

D8.4 Two INMARE Science Policy Briefs for management-level personnel and decision makers/advisors with a focus on the research efforts of INMARE

Two INMARE Science Policy Briefs for management-level personnel and decision makers/advisors with a focus on the research efforts of INMARE

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Publications

Degradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Data

Author(s): Rafael Bargiela, Christoph Gertler, Mirko Magagnini, Francesca Mapelli, Jianwei Chen, Daniele Daffonchio, Peter N. Golyshin, Manuel Ferrer
Published in: Frontiers in Microbiology, Issue 6, 2015, ISSN 1664-302X
DOI: 10.3389/fmicb.2015.01270

Diversity of hydrolases from hydrothermal vent sediments of the Levante Bay, Vulcano Island (Aeolian archipelago) identified by activity-based metagenomics and biochemical characterization of new esterases and an arabinopyranosidase

Author(s): Antonio Placido, Tran Hai, Manuel Ferrer, Tatyana N. Chernikova, Marco Distaso, Dale Armstrong, Alexander F. Yakunin, Stepan V. Toshchakov, Michail M. Yakimov, Ilya V. Kublanov, Olga V. Golyshina, Graziano Pesole, Luigi R. Ceci, Peter N. Golyshin
Published in: Applied Microbiology and Biotechnology, Issue 99/23, 2015, Page(s) 10031-10046, ISSN 0175-7598
DOI: 10.1007/s00253-015-6873-x

The novel extremely acidophilic, cell-wall-deficient archaeon Cuniculiplasma divulgatum gen. nov., sp. nov. represents a new family, Cuniculiplasmataceae fam. nov., of the order Thermoplasmatales

Author(s): Olga V. Golyshina, Peter N. Golyshin, Nadine I. Goldenstein, Heinrich Lünsdorf, Kai-Uwe Hinrichs, Ilya V. Kublanov
Published in: International Journal of Systematic and Evolutionary Microbiology, Issue 66/1, 2016, Page(s) 332-340, ISSN 1466-5026
DOI: 10.1099/ijsem.0.000725

Structural and Functional Characterization of a Ruminal β-Glycosidase Defines a Novel Subfamily of Glycoside Hydrolase Family 3 with Permuted Domain Topology

Author(s): Mercedes Ramírez-Escudero, Mercedes V. del Pozo, Julia Marín-Navarro, Beatriz González, Peter N. Golyshin, Julio Polaina, Manuel Ferrer, Julia Sanz-Aparicio
Published in: Journal of Biological Chemistry, Issue 291/46, 2016, Page(s) 24200-24214, ISSN 0021-9258
DOI: 10.1074/jbc.M116.747527

Metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community

Author(s): Stephan Thies, Sonja Christina Rausch, Filip Kovacic, Alexandra Schmidt-Thaler, Susanne Wilhelm, Frank Rosenau, Rolf Daniel, Wolfgang Streit, Jörg Pietruszka, Karl-Erich Jaeger
Published in: Scientific Reports, Issue 6, 2016, Page(s) 27035, ISSN 2045-2322
DOI: 10.1038/srep27035

Enzyme Shielding in an Enzyme-thin and Soft Organosilica Layer

Author(s): M. Rita Correro, Negar Moridi, Hansjörg Schützinger, Sabine Sykora, Erik M. Ammann, E. Henrik Peters, Yves Dudal, Philippe F.-X. Corvini, Patrick Shahgaldian
Published in: Angewandte Chemie International Edition, Issue 55/21, 2016, Page(s) 6285-6289, ISSN 1433-7851
DOI: 10.1002/anie.201600590

Metaproteomics and metabolomics analyses of chronically petroleum-polluted sites reveal the importance of general anaerobic processes uncoupled with degradation

Author(s): Rafael Bargiela, Florian-Alexander Herbst, Mónica Martínez-Martínez, Jana Seifert, David Rojo, Simone Cappello, María Genovese, Francesca Crisafi, Renata Denaro, Tatyana N. Chernikova, Coral Barbas, Martin von Bergen, Michail M. Yakimov, Manuel Ferrer, Peter N. Golyshin
Published in: PROTEOMICS, Issue 15/20, 2015, Page(s) 3508-3520, ISSN 1615-9853
DOI: 10.1002/pmic.201400614

Reversible Supramolecular Surface Attachment of Enzyme-Polymer Conjugates for the Design of Biocatalytic Filtration Membranes

Author(s): Negar Moridi, Philippe F.-X. Corvini, Patrick Shahgaldian
Published in: Angewandte Chemie International Edition, Issue 54/49, 2015, Page(s) 14800-14804, ISSN 1433-7851
DOI: 10.1002/anie.201507020

Bacterial population and biodegradation potential in chronically crude oil-contaminated marine sediments are strongly linked to temperature

Author(s): Rafael Bargiela, Francesca Mapelli, David Rojo, Bessem Chouaia, Jesús Tornés, Sara Borin, Michael Richter, Mercedes V. Del Pozo, Simone Cappello, Christoph Gertler, María Genovese, Renata Denaro, Mónica Martínez-Martínez, Stilianos Fodelianakis, Ranya A. Amer, David Bigazzi, Xifang Han, Jianwei Chen, Tatyana N. Chernikova, Olga V. Golyshina, Mouna Mahjoubi, Atef Jaouanil, Fatima Benzha, Mirk
Published in: Scientific Reports, Issue 5, 2015, Page(s) 11651, ISSN 2045-2322
DOI: 10.1038/srep11651

Biodiversity for biocatalysis: A review of the α/β-hydrolase fold superfamily of esterases-lipases discovered in metagenomes

Author(s): Manuel Ferrer, Rafael Bargiela, Mónica Martínez-Martínez, Jaume Mir, Rainhard Koch, Olga V. Golyshina, Peter N. Golyshin
Published in: Biocatalysis and Biotransformation, Issue 33/5-6, 2015, Page(s) 235-249, ISSN 1024-2422
DOI: 10.3109/10242422.2016.1151416

Whole cell biocatalysts: essential workers from Nature to the industry

Author(s): Carla C. C. R. de Carvalho
Published in: Microbial Biotechnology, 2016, ISSN 1751-7915
DOI: 10.1111/1751-7915.12363

Supramolecular enzyme engineering in complex nanometer-thin biomimetic organosilica layers

Author(s): M. Rita Correro, Michael Takacs, Sabine Sykora, Philippe F.-X. Corvini, Patrick Shahgaldian
Published in: RSC Adv., Issue 6/92, 2016, Page(s) 89966-89971, ISSN 2046-2069
DOI: 10.1039/C6RA17775A

High Throughput Screening of Esterases, Lipases and Phospholipases in Mutant and Metagenomic Libraries: A Review

Author(s): Carlina Peña-García, Mónica Martínez-Martínez, Dolores Reyes-Duarte, Manuel Ferrer
Published in: Combinatorial Chemistry & High Throughput Screening, Issue 19/8, 2016, Page(s) 605-615, ISSN 1386-2073
DOI: 10.2174/1386207319666151110123927

Activity screening of environmental metagenomic libraries reveals novel carboxylesterase families

Author(s): Ana Popovic, Tran Hai, Anatoly Tchigvintsev, Mahbod Hajighasemi, Boguslaw Nocek, Anna N. Khusnutdinova, Greg Brown, Julia Glinos, Robert Flick, Tatiana Skarina, Tatyana N. Chernikova, Veronica Yim, Thomas Brüls, Denis Le Paslier, Michail M. Yakimov, Andrzej Joachimiak, Manuel Ferrer, Olga V. Golyshina, Alexei Savchenko, Peter N. Golyshin, Alexander F. Yakunin
Published in: Scientific Reports, Issue 7, 2017, Page(s) 44103, ISSN 2045-2322
DOI: 10.1038/srep44103

Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote-Eukaryote Interactions within the Pseudovibrio Genus

Author(s): Stefano Romano, Antonio Fernàndez-Guerra, F. Jerry Reen, Frank O. Glöckner, Susan P. Crowley, Orla O'Sullivan, Paul D. Cotter, Claire Adams, Alan D. W. Dobson, Fergal O'Gara
Published in: Frontiers in Microbiology, Issue 7, 2016, ISSN 1664-302X
DOI: 10.3389/fmicb.2016.00387

Cultivation-based strategies to find efficient marine biocatalysts

Author(s): Carlos J. C. Rodrigues, Ricardo F.S. Pereira, Pedro Fernandes, Joaquim M.S. Cabral, Carla C. C. R. de Carvalho
Published in: Biotechnology Journal, Issue 12/7, 2017, Page(s) 1700036, ISSN 1860-6768
DOI: 10.1002/biot.201700036

Harnessing Bacterial Signals for Suppression of Biofilm Formation in the Nosocomial Fungal Pathogen Aspergillus fumigatus

Author(s): F. Jerry Reen, John P. Phelan, David F. Woods, Rachel Shanahan, Rafael Cano, Sarah Clarke, Gerard P. McGlacken, Fergal O’Gara
Published in: Frontiers in Microbiology, Issue 7, 2016, ISSN 1664-302X
DOI: 10.3389/fmicb.2016.02074

Synthesis and electrochemical detection of a thiazolyl-indole natural product isolated from the nosocomial pathogen Pseudomonas aeruginosa

Author(s): Alyah Buzid, Eoin Ó Muimhneacháin, F. Jerry Reen, Phyllis E. Hayes, Leticia M. Pardo, Fengjun Shang, Fergal O’Gara, Jonathan Sperry, John H. T. Luong, Jeremy D. Glennon, Gerard P. McGlacken
Published in: Analytical and Bioanalytical Chemistry, Issue 408/23, 2016, Page(s) 6361-6367, ISSN 1618-2642
DOI: 10.1007/s00216-016-9749-8

Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats

Author(s): Dimitry Y Sorokin, Enzo Messina, Francesco Smedile, Pawel Roman, Jaap S Sinninghe Damsté, Sergio Ciordia, Maria Carmen Mena, Manuel Ferrer, Peter N Golyshin, Ilya V Kublanov, Nazar I Samarov, Stepan V Toshchakov, Violetta La Cono, Michail M Yakimov
Published in: The ISME Journal, Issue 11/5, 2017, Page(s) 1245-1260, ISSN 1751-7362
DOI: 10.1038/ismej.2016.203

Dissecting the regulation of bile-induced biofilm formation in Staphylococcus aureus

Author(s): Dulantha Ulluwishewa, Liang Wang, Callen Pereira, Stephanie Flynn, Elizabeth Cain, Stephen Stick, F. Jerry Reen, Joshua P. Ramsay, Fergal O’Gara
Published in: Microbiology, Issue 162/8, 2016, Page(s) 1398-1406, ISSN 1350-0872
DOI: 10.1099/mic.0.000317

Bile signalling promotes chronic respiratory infections and antibiotic tolerance

Author(s): F. Jerry Reen, Stephanie Flynn, David F. Woods, Niall Dunphy, Muireann Ní Chróinín, David Mullane, Stephen Stick, Claire Adams, Fergal O’Gara
Published in: Scientific Reports, Issue 6/1, 2016, ISSN 2045-2322
DOI: 10.1038/srep29768

Direct and Rapid Electrochemical Detection of Pseudomonas aeruginosa Quorum Signaling Molecules in Bacterial Cultures and Cystic Fibrosis Sputum Samples through Cationic Surfactant-Assisted Membrane Disruption

Author(s): Alyah Buzid, F. Jerry Reen, Victor K. Langsi, Eoin Ó Muimhneacháin, Fergal O'Gara, Gerard P. McGlacken, John H. T. Luong, Jeremy D. Glennon
Published in: ChemElectroChem, Issue 4/3, 2017, Page(s) 533-541, ISSN 2196-0216
DOI: 10.1002/celc.201600590

The requirements at the C-3 position of alkylquinolones for signalling in Pseudomonas aeruginosa

Author(s): Rachel Shanahan, F. Jerry Reen, Rafael Cano, Fergal O'Gara, Gerard P. McGlacken
Published in: Org. Biomol. Chem., Issue 15/2, 2017, Page(s) 306-310, ISSN 1477-0520
DOI: 10.1039/C6OB01930G

Bile acids destabilise HIF-1α and promote anti-tumour phenotypes in cancer cell models

Author(s): J. P. Phelan, F. J. Reen, N. Dunphy, R. O’Connor, F. O’Gara
Published in: BMC Cancer, Issue 16/1, 2016, ISSN 1471-2407
DOI: 10.1186/s12885-016-2528-2

Integrated (Meta) Genomic and Synthetic Biology Approaches to Develop New Biocatalysts

Author(s): María Parages, José Gutiérrez-Barranquero, F. Reen, Alan Dobson, Fergal O’Gara
Published in: Marine Drugs, Issue 14/3, 2016, Page(s) 62, ISSN 1660-3397
DOI: 10.3390/md14030062

Molecular Signature of Pseudomonas aeruginosa with Simultaneous Nanomolar Detection of Quorum Sensing Signaling Molecules at a Boron-Doped Diamond Electrode

Author(s): Alyah Buzid, Fengjun Shang, F. Jerry Reen, Eoin Ó Muimhneacháin, Sarah L. Clarke, Lin Zhou, John H. T. Luong, Fergal O’Gara, Gerard P. McGlacken, Jeremy D. Glennon
Published in: Scientific Reports, Issue 6/1, 2016, ISSN 2045-2322
DOI: 10.1038/srep30001

Exploiting Interkingdom Interactions for Development of Small-Molecule Inhibitors of Candida albicans Biofilm Formation

Author(s): F. Jerry Reen, John P. Phelan, Lorna Gallagher, David F. Woods, Rachel M. Shanahan, Rafael Cano, Eoin Ó Muimhneacháin, Gerard P. McGlacken, Fergal O'Gara
Published in: Antimicrobial Agents and Chemotherapy, Issue 60/10, 2016, Page(s) 5894-5905, ISSN 0066-4804
DOI: 10.1128/AAC.00190-16

Is There Potential for Repurposing Statins as Novel Antimicrobials?

Author(s): Emma Hennessy, Claire Adams, F. Jerry Reen, Fergal O'Gara
Published in: Antimicrobial Agents and Chemotherapy, Issue 60/9, 2016, Page(s) 5111-5121, ISSN 0066-4804
DOI: 10.1128/AAC.00192-16

Analysis of defence systems and a conjugative IncP-1 plasmid in the marine polyaromatic hydrocarbons-degrading bacterium Cycloclasticus sp. 78-ME

Author(s): Michail M. Yakimov, Francesca Crisafi, Enzo Messina, Francesco Smedile, Anna Lopatina, Renata Denaro, Dietmar H. Pieper, Peter N. Golyshin, Laura Giuliano
Published in: Environmental Microbiology Reports, Issue 8/4, 2016, Page(s) 508-519, ISSN 1758-2229
DOI: 10.1111/1758-2229.12424

Screening for Enantioselective Lipases

Author(s): Thomas Classen, Filip Kovacic, Benjamin Lauinger, Jörg Pietruszka, Karl-Erich Jaeger
Published in: Springer Protocols Handbooks, 2016
DOI: 10.1007/8623_2016_218

Metagenomics and the Search for Industrial Enzymes

Author(s): Mónica Martínez-Martínez, Rafael Bargiela, Manuel Ferrer
Published in: Biotechnology of Microbial Enzymes, 2017, Page(s) 167-184
DOI: 10.1016/b978-0-12-803725-6.00007-8

Mining microbial signals for enhanced biodiscovery of secondary metabolites

Author(s): F. Jerry Reen, Jose A. Gutiérrez-Barranquero, Fergal O’Gara
Published in: Methods in Molecular Biology, 2016, Page(s) 287-300
DOI: 10.1007/978-1-4939-6691-2_19

Bile Aspiration; a host factor modulating chronic respiratory infection.

Author(s): Flynn, S., Woods, D., Ní Chróinín, M., Mullane, D., Adams, C., Reen, F.J. & F O’Gara.
Published in: Bile Aspiration; a host factor modulating chronic respiratory infection., Issue Bile Acids: Biosynthesis, Metabolic Regulation and Biological Functions, 2016

Novel Tools for the Functional Expression of Metagenomic DNA

Author(s): Nadine Katzke, Andreas Knapp, Anita Loeschcke, Thomas Drepper, Karl-Erich Jaeger
Published in: Novel Tools for the Functional Expression of Metagenomic DNA, Issue Meth. Mol. Biol, 2016, Page(s) 159-196
DOI: 10.1007/978-1-4939-6691-2_10

The Marine Microbiome

Author(s): Lucas J. Stal, Mariana Silvia Cretoiu
Published in: Metagenomics as a tool for biodiscovery and enhancement of production of bioactives, Issue The marine microbiome – an untold resource of biodiversity and biotechnological potential, 2016
DOI: 10.1007/978-3-319-33000-6