Remo Sanges

Stazione Zoologica Anton Dohrn Napoli, Animal Physiology and Evolution, Faculty Member

Stazione Zoologica Anton Dohrn Napoli, Dept. of Biology and Evolution of Marine Organisms (BEOM), Faculty Member

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I am PI of the Computational Genomics Lab at SISSA which pertains to the Neuroscience department and associate professor in the PhD program in Functional and Structural Genomics within the department. My scientific interests are centered on the function and the evolution of the non-coding portion of the genome (regulatory regions, noncoding RNAs, repeats), how these features shaped the genomes of living organisms, the way in which they affect transcription and their impact in the establishment of complexity, with a focus on health, disease and the nervous system. I have extensive experience in development and usage of bioinformatics pipelines, data integration and harmonization, tools, methods and databases for large-scale functional genomics data analysis and more than 15 years of teaching experience.

My group has broad experience in:

• Integration and data-mining of publicly available and custom large-scale data.
• Comparative genomics and genome evolution.
• Software, pipeline and bioinformatics databases development.
• Gene expression, promoters, pathways, ontologies and gene sets analysis.
• Genomes, genes and variations annotation.
• Biomarkers discovery.
• Best practices on experimental design.
• Identification of transposable elements activity.
Phone: +39 040 3787705
Address: International School for Advanced Studies (SISSA)
Via Bonomea 265, 34136 Trieste, Italy

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On the genome base composition of teleosts: the effect of environment and lifestyle

BMC Genomics, 2016

The DNA base composition is well known to be highly variable among organisms. Bio-physic studies ... more The DNA base composition is well known to be highly variable among organisms. Bio-physic studies on the effect of the GC increments on the DNA structure have shown that GC-richer DNA sequences are more bendable. The result was the keystone of the hypothesis proposing the metabolic rate as the major force driving the GC content variability, since an increased resistance to the torsion stress is mainly required during the transcription process to avoid DNA breakage. Hence, the aim of the present work is to test if both salinity and migration, suggested to affect the metabolic rate of teleostean fishes, affect the average genomic GC content as well. Moreover, since the gill surface has been reported to be a major morphological expression of metabolic rate, this parameter was also analyzed in the light of the above hypothesis. Teleosts living in different environments (freshwater and seawater) and with different lifestyles (migratory and non-migratory) were analyzed studying three variables: routine metabolic rate, gill area and genomic GC-content, none of them showing a phylogenetic signal among fish species. Routine metabolic rate, specific gill area and average genomic GC were higher in seawater than freshwater species. The same trend was observed comparing migratory versus non-migratory species. Crossing salinity and lifestyle, the active migratory species living in seawater show coincidentally the highest routine metabolic rate, the highest specific gill area and the highest average genomic GC content. The results clearly highlight that environmental factors (salinity) and lifestyle (migration) affect not only the physiology (i.e. the routine metabolic rate), and the morphology (i.e. gill area) of teleosts, but also basic genome feature (i.e. the GC content), thus opening to an interesting liaison among the three variables in the light of the metabolic rate hypothesis.

Cymodocea nodosa response to simulated CO2-driven ocean acidification: a first insight from global transcriptome profiling

by Francesco Musacchia and Remo Sanges

Global climate changes are imposing multiple pressures to marine organisms. The rising atmospheri... more Global climate changes are imposing multiple pressures to marine organisms. The rising atmospheric CO2 concentration is causing substantial changes in ocean physics, chemistry and biology. At least three synergic environmental stressors have been recognized as primary driven by CO2 emissions: ocean warming, oxygen loss and ocean acidification. The effects of CO2-driven ocean acidification on seagrass metabolism remain largely understudied. A few studies have been conducted near submarine volcanic vents, which mimic the future ocean acidification scenarios, allowing researchers to investigate the performance of marine organisms under long-term exposure to high-CO2 levels. Apart from these, some mesocosm-based experiments have investigated growth and physiological responses to high CO2. For this work, we built an outdoor mesocosm facility at the Centre of Marine Sciences’ field station in Algarve, Portugal, to experimentally manipulate CO2 levels and investigate the effects of high-CO...

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