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Sviluppo e validazione di un cDNA microarray a scala genomica in Mytilus galloprovincialis
Get PDFMarine bivalves of the genus Mytilus are intertidal filter-feeders commonly used as biosensors of coastal pollution. Indeed, mussels readily bioaccumulate both organic and metal pollutants, and react to changes with physiological and genetic mechanisms. However, one main problem in using mussels as bio-sensors is the poor characterization of their functional and defence reactions. The currently used biomarkers provide insufficient understanding of mussel physiology status or stressor-induced effects, and knowledge of mussel genome structure, function and evolution are still lacking. Therefore, genomic approaches are needed to increase our knowledge of physiological processes and to better understanding molecular
and cellular mechanisms involved in the stress responses.
Based on the production and massive sequencing of 3'ESTs library from main mussel tissues, we arrayed, in collaboration of C.R.I.B.I., University of Padova, the first collection of selected transcript 1714 tags on glass slides as MytArray 1.0.
In order to use this molecular platform defined in 2003, it has been necessary to refresh the physical collection of the bacterial clones bearing cDNA inserts in recombinant plasmids. Then, microarrays have been spotted and hybridisation experiments realized.
The potential use of this novel tool was evaluated by analyzing gene expression changes in mussels exposed to mixture of toxic and genotoxic metals in laboratory and in their natural environment (Venice lagoon, Italy).
Among the potential toxic contaminants, heavy metals can damage cell components, disturb cell signalling and are expected to modulate the expression of many genes. After competitive ibridisation experiments on MytArry 1.0, we found gene expression changes in gill and digestive gland in mussels treated with increasing micromolar doses of a metal mixture (Cd, Cu, Hg). Results appear instructive and consistent with the enhance of chromosomal damage in gill cells of same mussels (evaluated as increases of micronuclei and other nuclear
abnormalities). The transcriptional changes raised in dose-dependent manner and transcripts showing consistent expression trends revealed the complexity of the induced cellular response, with the most evident changes referring to: ion homeostasis (i.e metallothionein 10IV isoform, ferritin), protein turnover (sequestosome 1 and proteasome subunits) and chaperones (hsp70, hsp90, shsp24), regulation of apoptosis and DNA damage-inducible transcripts (gadd45, apoptosis inhibitor 2), cell motility and adhesion. The subsequent real-time PCR performed supports further these results.
To assess the potential use of the mussel microarray in environment, I evaluated the transcriptional digestive gland profiles of mussels living in the Venice lagoon.
Venice lagoon is a unique case and significant concentrations of cadmium, mercury, PAHs, PCBs and dioxin-like compounds are recurrently detected in theindustrial area near the town. Native mussels were sampled in the early summer in 2005, 2006, 2007, from zones affected differently by chemical pollution: from industrial district channels and from Lido lagoon inlet relatively uncontaminated. Offshore mussel farm, was chosen as a source of reference. I performed the competitive hybridisation experiments on DG samples and detected differentially expressed genes are grouped into different functional categories.
In mussels of the industrial canals (Marghera, Venice) microarray analysis performed on individual mussels indicated a general profile similarity which make them distinguishable from mussels living in less polluted sites. Chemical data support this work hypothesis.
The number of biological replicates influence the study size but, how much the individual variability can influence our studies? To try to answer to this question, I performed new hybridisation experiments by using the pool from the same samples. The overall clustering of transcriptional profiles can be compared with data already obtained from individual mussel tissues even though only transcripts with significant expression values are found.
In all three years, the suggestive presence of gene markers, tracing organic contaminants and heavy metals in mussels from the industrial district is consistent with reported trends of chemical contamination.
Finally, I contributed to the preparation of samples generating new primary cDNA libraries and a unique normalized library from mussels treated with with chemical and biological contaminants in order to enlarge the transcript collection and better understanding transcriptional mussel responses (work in collaboration with C.R.I.B.I and UniTrieste). Massive sequencing of the primary and normalized libraries yielded positive results and information obtained are going to be organized in the first intergrated Mytilus databatase
Gene expression profiles of the mussel Myticin C, an antimicrobial peptide displaying high sequence variability
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Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Expression and diversity of AMP and other immune-related molecules in M. galloprovincialis
No full textAnthropogenic activities, accidental events and global climate trends currently threaten the marine biological resources as they impose functional adjustments to the biota, change the ecological niches and lead to significant ecosystem changes. In the water column or sediments, bivalves interact with a variety of microorganisms which include commensal, opportunistic species and potential pathogens. Ofter acting together with other detrimental factors, microscopic agents can divert energy from growth and reproduction to the defence reactions, and finally overwhelm the host defenses with onset of diseases and mortality outbreaks in the natural and farmed stocks. Mussels of the genus Mytilus commonly appear more resilient than other bivalves to the environmental variation, and more likely act as pathogen reservoir for the animal species sharing the same habitat. In the frame of the European Integrated project IMAQUANIM, standard and advanced sequencing is confirming abundance and molecular diversity of the antimicrobial peptide precursors expressed in farmed, wild and immunostimulated mussels. Transcripts denoting pathogen recognition receptors also showed significant molecular diversity, namely sequences containing C1q, C-type-lectin or fibrinogen-like domains. Overall, gene expression profiling and massive sequencing progressively unveil the complexity of the innate defences of the Mediterranean mussel
Expressed sequences denoting receptors and other proteins progressively reveal the molecular basis of the mussel immunity
No full textDispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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