Advanced bioinformatics for genome and metagenome analyses and discovery of novel biocatalists from extremophiles: implications for improving industrial bioprocesses

Deliverables

Documents, reports (10)

metagenome sequence and annotation

Publication of sequenced and annotated metagenomes obtained with already available and new bioinformatics tools. Publication of metagenome data banks.

Improved bioinformatics tools

Publication of new pipelines to assist genome annotation of unknown sequences.On-line open source softwares.

patenting and industrial applications

Patents and preliminary tests of newly characterized enzymes and new metabolic pathways in industrial application

reports on new biocatalists

Publications on new characterized biocatalists and their potential applications

Joint publications concerning WP1-WP5

"Joint publications concerning WP1-WP5. The editor of ""Computational biology and chemistry"" (impact factor 1.7), Wentian Li, invited dr. Pietro Liò (Cambridge) to organize a special issues on this matter."

proposals for new projects

New proposals for EU projects.

Web page ,Twitter and Facebook account

"Publlished web pages ,Twitter and Facebook accounts. Participation to the followung workshops for dissemination: http://www3.unil.ch/wpmu/eseb2015/ http://sbg.org.br/Evolution2015/ http://www.smbe.org/ eccsb/icsb http://www.iscb.org/about-ismb masamb https://twitter.com/theosysbio/status/454249905088114688 cmsb http://cmsb2015.sciencesconf.org/ http://www.physoc.org/suggest-symposium#Physiology_2015 We would like to apply to EMBO (http://applications.embo.org/01/register.php?reg=L06Q). for the organization of a workshop. "

E. focardii genome database and identification of sequences encoding molecules of interest for industrial applications.

Publication of an E. focardii genome database. Identified genomic sequences encoding molecules of interest for industrial applications

New insight on the molecular mechanisms responsible for cold-adaptation and/or environmental adaptation

Publications on the characterized new insights on the molecular mechanisms responsible for cold and/or environmental adaptation. The coordinator the project has been invited to organize a special issue on Frontiers in Bioengineering and Biotechnology , that will focus on this topic.

New rules for system biology

Pubblications of improved bionformatic competence and that defines new rules for system biology.

Other (8)

genome annotations

Annotated genome to be analysed for discovering biomolecules of interest. Publications of data banks.

Characterized new metabolic pathways

Characterized new metabolic pathways that may be of interest for bioremediation processes and industrial application

characterization of biocatalysts of interest

characterized new biocatalysts from extreme microorganisms that may be of interest for industrial applications

Optimized biomolecules

production of biomolecules with optimized properties at extreme conditions, such as improved catalytic activity, catalytic specificity, thermostability and many others.

Isolation of microbes that can survive to extreme environments for cultivation when possible that can survive to extreme environments for cultivation when possibles

Isolated and cultivated microbes able to survive to extreme environments, in particular psychrophilic microbes. These microbes can be the source of new enzymes and/or metabolic pathways that can be exploited in industrial applications and for bioremediation.

trained researchers on bioinformatics

Trained ESR on bioinformatics able to analyse genomic and metagenomic sequences.

optimized molecules for bioremediation

Optimized molecules for bioremediation with improved degradation activity of pollutants.

Characterized new biocatalists

Characterizaed biomolecules that may be involved in adaptation to cold and/or extreme environment able to produce compound at low temperatures (with saving of energy) and other extreme conditions (high salt concentration, extreme pH conditions), that may be of interest for industrial applications.

Websites, patent fillings, videos etc. (2)

patent on optimized biomolecules

patent on optimized biomolecules that can be provided for industrial applications

Patents

Patent of new softwares, tools and algorithms for system biology.

Publications

Book chapters (1)

Bioinformatics Challenges and Potentialities in Studying Extreme Environments

Author(s): Claudio Angione, Pietro Liò, Sandra Pucciarelli, Basarbatu Can, Maxwell Conway, Marina Lotti, Habib Bokhari, Alessio Mancini, Ugur Sezerman, Andrea Telatin
Published in: Computational Intelligence Methods for Bioinformatics and Biostatistics, Issue 9874, 2016, Page(s) 205-219
DOI: 10.1007/978-3-319-44332-4_16

Peer reviewed articles (9)

Structure of a bacterial ice binding protein with two faces of interaction with ice

Author(s): Marco Mangiagalli, Guy Sarusi, Aleksei Kaleda, Maya Bar Dolev, Valentina Nardone, Vittoria Federica Vena, Ido Braslavsky, Marina Lotti, Marco Nardini
Published in: The FEBS Journal, Issue 285/9, 2018, Page(s) 1653-1666, ISSN 1742-464X
DOI: 10.1111/febs.14434

Antarctic marine ciliates under stress: superoxide dismutases from the psychrophilic Euplotes focardii are cold-active yet heat tolerant enzymes

Author(s): Alessandro Pischedda, Kesava Priyan Ramasamy, Marco Mangiagalli, Federica Chiappori, Luciano Milanesi, Cristina Miceli, Sandra Pucciarelli, Marina Lotti
Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322
DOI: 10.1038/s41598-018-33127-1

Antibiotic activity of the antioxidant drink effective Microorganism-X (EM-X) extracts against common nosocomial pathogens: an in vitro study

Author(s): Alessio Mancini, Sandra Pucciarelli
Published in: Natural Product Research, 2018, Page(s) 1-6, ISSN 1478-6419
DOI: 10.1080/14786419.2018.1517344

CiliateGEM: an open-project and a tool for predictions of ciliate metabolic variations and experimental condition design

Author(s): Alessio Mancini, Filmon Eyassu, Maxwell Conway, Annalisa Occhipinti, Pietro Liò, Claudio Angione, Sandra Pucciarelli
Published in: BMC Bioinformatics, Issue 19/S15, 2018, Page(s) 1-11, ISSN 1471-2105
DOI: 10.1186/s12859-018-2422-9

Enzymes and ice binding proteins from Antarctic organisms

Author(s): M. Lotti, S. Brocca, M. Mangiagalli, A. Pischedda, M. Orlando, S. Maione, D. De Pascale, S. Pucciarelli, M. Nardini, I. Braslavsky
Published in: New Biotechnology, Issue 44, 2018, Page(s) S43-S44, ISSN 1871-6784
DOI: 10.1016/j.nbt.2018.05.091

Saturn-Shaped Ice Burst Pattern and Fast Basal Binding of an Ice-Binding Protein from an Antarctic Bacterial Consortium

Author(s): Aleksei Kaleda, Lotem Haleva, Guy Sarusi, Tova Pinsky, Marco Mangiagalli, Maya Bar Dolev, Marina Lotti, Marco Nardini, Ido Braslavsky
Published in: Langmuir, 2018, ISSN 0743-7463
DOI: 10.1021/acs.langmuir.8b01914

Mechanisms of toxic action of silver nanoparticles in the protozoan Tetrahymena thermophila : From gene expression to phenotypic events

Author(s): Katre Juganson, Monika Mortimer, Angela Ivask, Sandra Pucciarelli, Cristina Miceli, Kaja Orupõld, Anne Kahru
Published in: Environmental Pollution, 2017, ISSN 0269-7491
DOI: 10.1016/j.envpol.2017.03.013

Rational engineering of a cold-adapted α-amylase from the Antarctic ciliate Euplotes focardii for simultaneous improvement of thermostability and catalytic activity

Author(s): Guang Yang, Hua Yao, Matteo Mozzicafreddo, Patrizia Ballarini, Sandra Pucciarelli, Cristina Miceli
Published in: Applied and Environmental Microbiology, 2017, Page(s) AEM.00449-17, ISSN 0099-2240
DOI: 10.1128/AEM.00449-17

Ice-binding proteins and the ‘domain of unknown function’ 3494 family

Author(s): Tyler D.R. Vance, Maddalena Bayer-Giraldi, Peter L. Davies, Marco Mangiagalli
Published in: The FEBS Journal, 2019, ISSN 1742-464X
DOI: 10.1111/febs.14764