Comparative Genomics: Basic and Applied Research


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A present day student of biology is expected to conceptualize the sequence of genome-gene-molecule-cell with reference to specific tissue, organ and a body system. In other words evolutionary and morbid changes at the genome level could be the basis of normal human variation and disease. During the last decade, rapid progress has been made in new genome-level diagnostic and prognostic laboratory methods.

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Applications of individual genomic information in clinical medicine have led to the prospect of robust evidence-based personalized medicine. Genomics has led to the discovery and development of a number of new drugs with far reaching implications in pharmaco-therapeutics. The existence of Genomic Medicine around us that is inseparable from molecular medicine. Both genomic and molecular medicines are in fact two dimensions of the integrated modern molecular medicine with tremendous implications for the future of clinical medicine.

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Comparative genomics

Publications should be included electronically within the application deadline. Department of Animal and Aquacultural Sciences provides fundamental, innovative research and practical solutions to improve productivity and sustainability across the agriculture and aquaculture sector. The main objective of BIOVIT is to contribute to the development of sustainable agriculture and food production systems through basic and applied research on plants and animals including fish aquaculture.

There are currently bachelor and master students, and 90 PhD students, enrolled in these programmes. The faculty has approximately permanent and temporary scientific employees, including technicians, and 18 administrative positions. The responsibility for the jobs published on this website, including the job description, lies entirely with the publishing institutions.

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Please enable JavaScript in your browser. Higher Education Institute. Biological sciences. First Stage Researcher R1. Coastal waters are subject to relevant changes in temperature, salinity and oxygen availability due to seasonal variations, which can result in significant alterations of the microbial communities, occasionally leading to an increased presence of bacteria and to harmful algal blooms.

In addition, costal marine waters are among the most heavily impacted environments by anthropic activities and pollution by heavy metals, fertilizers, hydrocarbons, etc. Marine filter-feeding bivalve mollusks have developed specific defense strategies to deal with these potential hazards. In particular the mussel Mytilus galloprovincialis , an important seafood in the Mediterranean area, is relatively tolerant to a wide range of pathogens and environmental changes, thus being often selected as a sentinel species in ecotoxicological investigations.

However, even though mortality events caused by infective agents and parasites apparently occur less frequently in mussels than in other bivalves, the molecular bases of such tolerance are unknown. The main aim of this project is to elucidate the molecular players involved in the bivalve immune response, using a combination of classical molecular biology techniques and —omic approaches.

This topic is of particular interest in invertebrates, which are organisms unable to mount long-term responses due to the lack of an adaptive immune system. The application of next generation sequencing technologies to the study of mussel transcriptome has already permitted to evidence that massive events of gene family expansion and the fast diversification rate of immune receptors and effectors are essential for pathogen sensing and targeting in this species.

The main lines of research in this project concern the in depth study of the variability and the regulation of mussel pattern recognition receptors PRRs , antimicrobial peptides AMPs and of the signal transduction pathways involved in the bivalve innate immune response to bacteria, viruses and other parasites. On the other hand, the available genome of the Pacific oyster Crassostrea gigas comparatively offers an opportunity for the study of the same topic in a species which is in turn rather susceptible to pathogen-associated mass mortalities. The increasing accessibility of next generation sequencing technologies now permits the analysis of non-model organisms which have been so far almost completely neglected in genetic and genomic studies due to a series of heterogeneous factors including excessive costs, huge genome sizes and difficult maintenance of specimen in laboratory conditions.

Owing to the demolition of these technical barriers, in the past few years our laboratory moved towards the study of species of high importance in the field of evolutionary biology. In we sequenced and assembled the transcriptome of the Indonsian coelacanth Latimeria menadoensis , a resource which was fundamental in the genome annotation process of its sister species, the African coelacanth Latimeria chalumnae. Not just limited to transcriptomic analysis, this line of research permitted to the study of different aspects of coelacanth biology and evolution, including sex determination, purine metabolism and the activity of transposable elements and atypical RNAs.

At the present time our study is focused on the lungfish Protopterus annectens , which has been clarified as the most likely true ancestor of tetrapods by the coelacanth genome paper.

Nature Genetics

Besides coelacanths, other species of interest in the field of evolutionary and comparative genomics are those adapted to extreme environments, such as Antarctic notothenioid fishes which have developed peculiar strategies to cope with freezing water temperatures, and more common fishes of great commercial importance in aquaculture, such as the seabass Dicentrachus labrax , which we have recently analyzed by RNA-seq to identify T-cell specific transcripts which might play a fundamental role in fish innate and acquired immune responses.

In the frame of the coffee genome initiative we are involved in the transcriptome definition and on the comparative analysis of gene involved in biochemical pathways of peculiar interest like caffeine, chlorogenic acids, monoterpene synthases and aquaporins. Prokaryotic and eukaryotic metabarcoding Researchers involved: Alberto Pallavicini and Fiorella Florian. DNA metabarcoding refers to the automated identification of multiple species from a single bulk sample containing entire organisms or from a single environmental sample containing degraded DNA soil, water, faeces, skin, etc.

Our unit works on the definition of the microbial community of aquacultured bivalves but also, in collaboration with ecologists, on samples of different marine niches for the ecological assessment of microbial and zooplakton communities. Moreover these techniques are applied to explore human-microbes interactions.


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Humans live in constant association with microbes that are present on surfaces and in cavities of the human body, and even within our cells. The number of our microbial companions exceeds by at least ten-fold those of cells of our own body and the number of unique genes they encode is at least fold greater than the number of genes in our own genome.

This complex and dynamic microbiota has a profound influence on physiology, nutrition, immunity and development and disruptions in these human-associated microbial communities are a significant factor in many diseases. Defining the dynamic microbial diversity represents the next frontier of genomics.

In this contest bacterial metabarcoding analysis are ongoing for gut, vaginal and tooth samples linked to different pathologies.

Amemiya, C. The African coelacanth genome provides insights into tetrapod evolution Nature, , pp. Cited times.

Comparative Genomics: Basic and Applied Research Comparative Genomics: Basic and Applied Research
Comparative Genomics: Basic and Applied Research Comparative Genomics: Basic and Applied Research
Comparative Genomics: Basic and Applied Research Comparative Genomics: Basic and Applied Research
Comparative Genomics: Basic and Applied Research Comparative Genomics: Basic and Applied Research
Comparative Genomics: Basic and Applied Research Comparative Genomics: Basic and Applied Research
Comparative Genomics: Basic and Applied Research Comparative Genomics: Basic and Applied Research

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