Florence Computational Biology Group
Funded projects
Period: 3/2020 - 3/2022
Project title: Transcriptional Regulatory Networks in Antarctic bacteria as a proxy for global warming effects on microbial life in the Polar Oceans.
Funding agency: PNRA (Programma Nazionale di Ricerche in Antartide) - PNRA18_00335
Budget Unifi: 25100 €
PI: Maria Luisa Tutino, University of Naples Federico II
Unifi PI: Alessio Mengoni
Topic:
The advent of next-generation sequencing techniques resulted in the accumulation of bacterial genome sequences, also from Antarctica and its Oceans. Comparative genomics analyses contributed to unravelling some molecular mechanisms involved in the adaptation to cold lifestyles, but our comprehension on how the genome expression is modulated over the growth and by the changes of environmental parameters is still fragmentary. Bacteria are very effective in fine-tuning their transcription to always adapt the metabolic setup to changing life conditions. This plasticity is obtained by modulating global Transcription Factors, which interact with specific DNA sequences coordinates and controls the expression of many genes/operons (collectively known as regulons). Knowing the regulons number, regulon composition, and the environmental factors which influence the expression of the global TF controlling each regulon is the starting point to construct a 3D model of bacterial cell functioning. Besides enhancing our comprehension of bacterial functioning, this 3D model will help us in highlight the limits, if any, of bacterial adaptation to a changing environment, such as the global warming of seawater, contributing precious information to the prediction of future scenarios of the entire marine ecosystem functions. The main objective of the AnTReN project is the study of global transcriptional regulatory networks in Antarctic marine bacteria, especially in terms of the potential impact of global warming of Antarctic sea water. The project will use mainly genomic data and bacterial strains collected in previous PNRA-funded projects. It will be carried out by a multidisciplinary team, which can account for numerous joint publications rising also from the participation to previous PNRA funded projects. This publication record also testifies the intense and ongoing international collaborations of the team, which put together needed the expertise to achieve project ambitious aims.
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Period: 4/2018 - 4/2020
Project title: Future Antarctic microbial communities: predicting the impact of global climate changes on aquatic microbial communities through guided evolution and multi-omics integration.
Funding agency: PNRA (Programma Nazionale di Ricerche in Antartide) - PNRA16_00246
Budget: 76800 €
Topic: The distribution and function of Antarctic microorganisms are of crucial importance for the flow of matter in the Earth's biogeochemical cycles. The effects of microbial communities on the carbon and nitrogen cycles are particularly important for producing and balancing climate gases such as CO2, CH4, or N2O. This precious balance is put at risk by global climate changes, the most serious threat for the entire microbial ecosystem and, more in general, for the major biogeochemical cycles. Indeed, global change is altering species distributions and thus interactions among organisms, leading to altered biodiversity and impaired functioning of terrestrial ecosystems. Here we propose a guided evolution-based approach to experimentally simulate changes in environmental parameters (e.g. temperature, CO2 concentration, pH, pollutants concentration etc.) and investigate at different cellular levels (i.e. gene expression, genomic variants, and metabolism) the effect of such variations on Antarctic microbes. More specifically, we will combine experimental evolution, -omics data and mathematical metabolic modelling to provide an outlook on the structure and functioning of the future Antarctic microbial representatives, evaluating the impact of projected changes in some key environmental chemico-physical parameters (and/or combination thereof) and describing the molecular, evolutionary and ecological strategies that members of such community may adopt to face such conditions. Long term growth experiments will be set up and an incremental perturbation to chemico-physical parameters will be applied to microbes.
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Project title:
Exploiting Antarctica biotechnological potential: metabolic modelling for optimization of bioactive molecules biosynthesis from Antarctic bacteria
Project title: Exploiting Antarctica biotechnological potential: metabolic modelling for optimization of bioactive molecules biosynthesis from Antarctic bacteria
Funding agency: PNRA (Programma Nazionale di Ricerche in Antartide) - 2013/B4.02
Budget: 90000 €
Topic: The study of microbes inhabiting extreme environments (Antarctica) offers an irreplaceable resource for the elucidation of antagonistic relationships inside complex ecological niches and for the individuation of metabolic traits of valuable biotechnological potential. Biosynthesis of antibiotics and other interesting bioactive compounds (e.g. antitumor molecules) has been documented for bacterial strains isolated from Antarctica. Our project aims at exploiting the huge biotechnological potential of bioactive molecules obtained from Antarctic strains. Indeed the biosynthesis of these compounds in vivo is often sub-optimal and is largely dependent on growth conditions, such as temperature and medium composition. Accordingly, methods for bioactive compounds biosynthesis optimization are highly needed since they may bridge microbiological knowledge to large scale, industrial production of clinically and/or technological compounds. To this purpose, we will integrate “-omics” data with methodologies for modeling biological systems and we will implement computational and statistical models to elucidate the biosynthetic circuits responsible for the production of bioactive molecules and to gain a complete knowledge on the metabolisms of Antarctic strains for their possible biotechnological use.
Publications supported by this grant:
PMID: 24889559
PMID: 25810435
PMID: 27881075
PMID: 28095778