Template Categorie Articoli: Gutemberg

The massive participation of researchers in the First Italian Citizen Science Conference (Rome, November 23-25, 2017) confirmed the great interest raised by the topic and by the prospects of developing the new approach to science it proposes in Italy.

Even though Citizen Science finds applications in many scientific areas, it finds its largest success in environmental monitoring in terms of both amount of collected data and number of participants. In addition, Citizen Science showed its efficacy as a powerful instrument of awareness raising and life-long learning precisely in this context.

The event brought together the Italian researchers committed on these Citizen Science themes also in the perspective of consolidating a National Citizen Science Group, as in the case of several other European countries. Indeed, in order to ‘network’, one needs to have a clear picture of the project’s strengths and weaknesses and share experiences and perspectives.

The Conference confirmed that Citizen Science not only may provide a potentially relevant contribution to research activities, but in addition represents an effective means to disseminate research among citizens so as to build a scientifically conscious citizenship and put science in its rightful position in common culture.

In this respect, Citizen Science is also a potent instrument for social inclusion in the light of the responsible research and innovation actions at the basis of Horizon 2020.

Citizen Science puts forward numerous challenges, also in terms of ICT: data aggregation and integration, inclusion and maintenance processes over time, validation protocols for data usage in research activities, to name a few.

The complete book of abstracts is available on the Conference website: http://www.citizensciencerome2017.com/wp-content/uploads/2017/11/Volume-ABSTRACTS_COMPLETO.pdf

As well as the collection of posters presented: http://www.citizensciencerome2017.com/wp-content/uploads/2017/11/POSTER-CON-ELENCO.pdf

LifeWatch Italy (LW-ITA) published a paper in Ecological Informatics (Rosati et al., 2017) on PhytoTraits: a thesaurus on phytoplankton functional traits.

As the other thesauri implemented by LW-ITA, PhytoTraits is the result of the interdisciplinary collaboration of experts both from the functional ecology domain and from information and communication technologies. PhytoTraits is the first initiative to deal with the semantics of phytoplankton functional traits, focusing on morpho-functional traits. It reflects the agreement of a scientific expert community to fix semantic properties of approximately 120 traits.

Following semantic web standard technologies, the thesaurus was implemented in Simple Knowledge Organization System (SKOS), a common data model based on the Resource Description Framework (RDF). Providing harmonised concepts with associated unique and resolvable URIs, PhytoTraits has the potential to significantly reduce the barriers to data discovery, integration, and exchange in the functional ecology domain.

The paper presents the PhytoTraits thesaurus focusing on the methodology used to implement it, the possible use cases of the established semantic resource, and finally discusses the usefulness of the thesaurus and of its future developments.

The paper presents the PhytoTraits thesaurus focusing on the methodology used to implement it, the possible use cases of the established semantic resource, and finally discusses the usefulness of the thesaurus and of its future developments.

From the classic works on Biogeography to the more recent contributions, several authors have been using new terms to describe endemic traits. During the years, these terms have often been proposed with different, and sometimes ambiguous definitions. Since the importance of endemism in terms of e.g. ecology, conservation and evolutionary biology, LifeWatch Italy decided to develop a dedicated structured vocabulary with the aim to create a first reference attempt in this discipline, offering a new free service to the scientific community.

Once a glossary of existing terms with their definitions has been compiled, we made a selection of definitions in order to propose a unique reference. The Endemisms Thesaurus is a vocabulary constituting a public domain, and developed as a service by the LifeWatch Italy – Collections Thematic Centre.

The Thesaurus currently includes 15 terms, 15 definitions, 12 bibliographic notes, and 12 historical notes; implementation of further themes within Biogeography is under evaluation.

LifeWatch Italy has made of alien species and freshwaters one of the key topics of its research activities within the vulnerability of ecosystems to alien species arrival case study proposed at the European level and involving marine, terrestrial and freshwaters ecosystems. In 2014, a first paper was published on the journal Aquatic Conservation: Marine And Freshwater Ecosystems presenting the weak effects of habitat type on the susceptibility to invasive freshwater species. The research work on this topic continues now with a new paper investigating Alien species in Italian freshwater ecosystems: a macroecological assessment of invasion drivers, just published on a Special Issue of Aquatic Invasions.

In this second work, a macroecological approach was proposed to assess the drivers of occurrence of alien species within the whole biota (microorganisms, plants and animals) across several natural freshwater ecosystems and to produce a broad and general assessment of invasion pattern. Alien species were defined accordingly to the related thesaurus developed by LifeWatch Italy, where alien species were identified as those species deliberately, or inadvertently, introduced in Italy by human activities, after the discovery of the New World by Columbus in 1492.

Moreover, in this study, researchers took advantage of the biodiversity dataset of Italian water bodies recently collated by LifeWatch Italy to simultaneously test three groups of variables (propagule pressure, abiotic and biotic characteristics), selected as putative predictors of invasibility of a site.

Results showed that propagule pressure, expressed as proximity to larger inhabited areas, and differences in the native species richness of the receiving community, had a significant role in determining the number of alien species occurrence. Furthermore, body size influenced the occurrence and the colonisation processes of alien species. Finally, climatic characteristics were relevant in determining the chances of a site to be invaded confirming the role of these abiotic filters in the invasion process.

The present paper allowed researchers to provide useful insights in the invasibility pattern highlighted in different areas of the Italian peninsula, so that the results can be useful to identify areas deserving a more intensive monitoring effort to prevent or mitigate alien species arrival.

Multiple sequence alignment (MSA) is one of the critical challenges of bioinformatics as it represents a key step in sequence analysis applications such as phylogeny inference, population genetics and comparative genomics. These applications are considered of paramount importance in molecular biodiversity studies, mainly because their results are directly linked to ecosystems analyses and monitoring. Understanding the population structures based on genetic markers would lead to establish clear correlations between these populations and their surrounding environment or habitat. In addition, the phylogenetic relationship among individuals of the same population, or between different populations, draws a relevant indication on species interactions within a given environment and their history and ability to adaptation.

In this context, in order to reach appropriate conclusions from the above-mentioned applications, it is important to generate a highly accurate multiple sequence alignment. This can be achieved exploiting the protein domains information embedded in their respective DNA coding sequences. MSA-PAD uses either public protein resource (PFAM) or user-defined protein domain/s to guide the construction of DNA multiple sequence alignment. Moreover, MSA-PAD has two alignment strategies: (i) Gene and (ii) Genome. Gene mode alignment respects domains order organization from 5′ to 3′, and resolves the alignment of repetitive domains even when they are in tandem. Genome mode provides a supergene-like alignment ignoring domains order constraint accounting for genomic rearrangements (i.e. mitochondrial or viral genomes). MSA-PAD is freely available as a web application running in a cloud environment at ReCaS data center (https://recasgateway.cloud.ba.infn.it) and available on LifeWatch Catalogue of Services.

Citation: Balech, B., et al. (2015) MSA-PAD: DNA multiple sequence alignment framework based on PFAM accessed domain information, Bioinformatics, 31, 2571-2573

In 2014, LifeWatch Italy launched a call for projects that includes the production of molecular data through High Throughput Sequencing (HTS) technologies and their analysis in order to promote the research in the field of Molecular Biodiversity as well as the multidisciplinary integration of the Italian groups interested in Biodiversity at different levels.

The call focus was “Alien or invasive species and/or their impact on indigenous communities and interactions among species” and all Italian Institutions participating in LifeWatch Italy were eligible.

The call was very successful for the number and outstanding quality of submitted project proposals and for the number of Research Institutions involved. All submitted project were peer reviewed by high-profile international scientists and 12 projects have been approved for an estimated total cost of about 100,000 euros (see here).

Starting from September 2014, all proposed projects have been activated by establishing a close collaboration with the project’s Principal Investigators, integrating their activities and experimental needs with MoBiLab’s consolidated know-how in sequencing technologies through the Illumina platforms and bioinformatics analysis.

Embracing several Meta-Barcoding and Genomic application fields, more than two hundred samples have been sequenced, using the MiSeq and NextSeq500 Illumina platforms available at MoBiLab, for the production of over one billion of sequences and the development of new workflows for the analysis of environments to date not yet explored.

Thanks to the LifeWatch Italy Sequencing Call 2014, interesting results have been produced on new alien species and the impact of invasive species on the indigenous communities of ecosystems under investigation and several papers on high-profile journals have been or are being published. 

Travelling through ecosystems and biodiversity: Long-term ecological research for citizens

The third edition of the initiative of informal science communication “Cammini LTER” will take place from July to October 2017: Italian ecologists, active in the Italian long-term ecosystem research network (LTER-Italy) and in the study and analysis of biodiversity (Lifewatch-Italy) will walk and cycle together with citizens along two trails, intended as events of scientific communication and public engagement on ecosystems, biodiversity and environmental sustainability.

The two trails will involve four LTER-Italy sites and they aim at arising people awareness about different ecological and biodiversity issues:

• Biodiversity in action on Apennines, walking through high elevation ecosystems of Gran Sasso and Majella. July 20^th – 23^rd July 2017
• Antropica – Man and pollution of natural resource and ecosystems, a bike tour from the Gulf of Naples to Mar Piccolo in Taranto. September 30^th – October 7^th 2017

The Cammini LTER, going on since 2015, represent a sort of “Via Francigena” of ecological research and offer citizens and students an opportunity to cooperate with researchers and to familiarize with the components and conditions of Italian ecosystems and biodiversity. Through this initiative, a real movement of researchers towards and with citizens is created, in order to promote LTER and LifeWatch activities to a not-expert audience and to increase their ecological awareness and literacy, moving beyond communication deficit to dialogue, sharing scientific views as well as experiences and emotions.

At the LTER-Italy sites and along the trails that connect them, researchers will help citizens to identify fauna and flora, evaluate biodiversity and the effects of climate change, and assess the water quality of lakes and marine areas. Citizens will meet researchers at work, on selected LTER-sites, join them in the fieldwork, understand the importance of long-term ecological studies and take part in citizen science initiatives: these will be realized in close connection with the ICT component of LifeWatch, in particular for the selection of Apps and the management of the data that will be gathered.

Since October 2016, Cammini LTER has crossed the national boundaries, becoming the International initiative “TRAIL”, selected and launched by the International Long-Term Ecological Research Network (ILTER).

Follow updates on the LTER-Italy website and on social networks.

LTER-Italia

International LTER Network

The Alien Species Thesaurus is a structured vocabulary constituting a public domain and distributed as a service by LifeWatch Italy. It is based on a glossary developed by the Mediterranean Thematic Centre in cooperation with the Collection Thematic Centre, and it provides the terminological resources that play a key role in developing the information architecture for the online LifeWatch portal and search platform about alien and invasive species. The Alien Species Thesaurus is deep and complex respect to other thesauri, implementing rich semantic interrelationships among core nodes like: control, impact, pathway of arrival, surveillance of alien species, and presents a cross-cutting nature across different ecosystems.

It is developed on the basis of already existing glossaries created within the framework of international initiatives aimed at the study of alien and invasive species. The terms (or concepts) are shared very broadly by the scientific community, and their definitions derive from guidelines prepared by relevant international organizations, and only in few occasions by peer reviewed papers. Certain terms (like the very broad alien species) have been repeatedly defined by different organisations, research centres, individual researchers, and the present thesaurus provides concept history tables to record changes in the vocabulary over time as the opinion changes.

The Thesaurus currently stores 319 terms with definitions limiting semantic ambiguity, and improving precision and recall due to uniformity of language, and 62 relationships. The idea is to guide all the searchers to use the same term for the same concept, so that search results will be as complete as possible.

The first issue of LifeWatch Italy’s newsletter has just been sent out and is waiting for you in your mailbox! LifeWatch Italy Bulletin has been thought as a quarterly online publication telling our community about LifeWatch activities. Next number will be issued in September 2017.

You can receive the newsletter by subscribing on our home page or having a look at the web browser version.

This first number focuses on:

• Welcome LifeWatch-ERIC

• Ontology & Semantic Web for Biodiversity & Ecosystem Research – Workshop, Lecce, 11-14 July 2017
• A thesaurus on alien species for a faceted search

• LifeWatch Italy Thesauri on functional traits

• Investigating alien and invasive species through NGS at MoBiLaB

• Third edition of Cammini LTER

Stay tuned for the next issue!

GOFC-GOLD LC Office and the GEO BON have just released a new sourcebook for biodiversity monitoring in tropical forests with remote sensing. 

This sourcebook is the result of a joint effort counting the participation of more than 70 authors. The sourcebook is freely accessible from here.