Author: lifewatch

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.

IDENTIFICATION OF HARD BOTTOM INTRODUCED INVERTEBRATE SPECIES IN THE MEDITERRANEAN BASIN AND THEIR ECOLOGICAL RILEVANCE: INFLUENCE ON FOULING SUCCESSIONAL PATTERN

Evaluation of the influence of alien species in environmental monitoring

Organizers: Prof.Adriana Giangrande and Dr Cinzia Gravili – Laboratory of Zoology and Marine Biology, University of Salento, Italy

Where: Lecce, 19/09/2016 – 25/09/2016, BIOforIU Premises (University of Salento)

Deadline for registration: 30/06/2016 – The course is limited to 18 participants. Seats will be reserved in the order of registration (Availability is on first come first served basis)

Preliminary programme: http://medalien.com/preliminary-program/

Registration: http://medalien.com/product/course-alien-species-lecce/

Course Description

The course will take place at the University of Salento (Lecce) for six days (from Monday to Saturday), under the guidance of Prof. Adriana Giangrande (specialist of alien species and polychaete annelids) and Dr. Cinzia Gravili (specialist of alien species and cnidarians, with particularly respect to the group Hydrozoa). The activity will be supported by the staff and the working group of the Laboratory of Systematic in Lecce coordinated by Professor Giangrande.  and will take place in new Laboratories BioForIU

The course aims to analyze the influence of alien species on settlement patterns of fouling communities of the marine ecosystem, but is mainly focused on taxonomy and identification of sessile macroinvertebrate species. During the course tools to identify the major taxonomic phyla of the sessile macrofaunal groups of the fouling (Porifera, Cnidaria, Mollusca, Bryozoa, Polychaeta, Ascidiacea) will be provided considering that the identification of organisms to the species level is one of the major limitations within environmental monitoring of the marine environment. The course will consist of several lectures followed by laboratory practice on both alive and preserved material.

The course will provide teaching aids in the form of guides and other materials with reference (the Zoology and Marine Biology laboratories have reference collections of different phyla characterizing fouling)

It will include a series of seminars about alien species in the Mediterranean basin and their influence on the fouling succession. The practical aspects will be addressed through the material observation (both on material that participants can bring with them and fresh material for alive observation that will be provided by the organizers).

The material will be collected in the Gulf of Taranto which represents one of the most important site in Mediterranean concerning the abundance of alien species, only second to the Venice lagoon. 

Website: http://medalien.com

The 1^st workshop of the EU Horizon 2020 project GLOBIS-B (“GLOBal Infrastructures for Supporting Biodiversity research”) took place in Leipzig from February 29 until March 2. 

GLOBIS-B, coordinated by the University of Amsterdam as part of LifeWatch, supports research infrastructures active in biodiversity and ecosystems research from Australia, Brazil, China, Europe, South Africa and the USA. 

More specifically, the project is focused on potential services supporting research on Essential Biodiversity Variables (EBVs).

An overview of the project and the outcomes of its 1st workshop are summarized at http://www.globis-b.eu/news/7/first_workshop_globis-b_held_in_leipzig.html.

From 22-27 May, MSc and PhD students, as well as early career researchers, are participating to the training course in Taxonomy organised by LifeWatch Italy and DEST in Florence (responsible Dr Bartolozzi).

The course is an opportunity fro young researchers to deepen their knowledge on how to organise and do field research on insects (mainly Coleoptera), how to set and identify the collected material and how to prepare a report on the results of the field study.

2 febbraio 2016

Ore 11:00

Conferenza Stampa di Lancio dell’iniziativa “Ecology 150° Anniversary”

Lecce, Sala della Grottesca, Rettorato, Università del Salento

Prof. Alberto Basset (Presidente Federazione delle Società Europee di Ecologia – EEF), Prof.ssa Emilia Chiancone(Pres. Accademia Nazionale delle Scienze), Giuseppe De Matteis (WWF Oasi), Prof. Michele Carducci (Prof. di Diritto Comparato), Stefano Cristante (Prof. di Sociologia della Comunicazione), Nicola Grasso (Prof. di Diritto Costituzionale).

Ore 12:30

Visita guidata presso la Riserva Naturale delle Cesine

Vernole – gps: 40.350098, 18.336225

Prof. Alberto Basset (Presidente della Federazione delle Società Europee di Ecologia – EEF), Giuseppe De Matteis (WWF Oasi).

Nel 1866, Ernst Haeckel ha formalizzato il concetto di ecologia (dal greco oikos e logos) come “la scienza delle interazioni tra organismi e componenti biotiche e abiotiche del loro ambiente”, caratterizzando l’ecologia in stretta relazione con fisiologia, biogeografia e teoria evoluzionistica.

In questi 150 anni l’ecologia si è evoluta ed è cresciuta come scienza ed è completamente cambiato il contesto socio-economico in cui agiamo. Mai come oggi l’ecologia e società sono strettamente connesse, e mai come oggi diviene fondamentale informare i cittadini e coinvolgerli attivamente nella protezione della biodiversità e dei nostri ecosistemi. Queste le ragioni che ci spingono a riflettere sul concetto di ecologia e le sue implicazioni per la società, celebrando questo 150° anniversario con una serie di attività rivolte al grande pubblico, ed in particolare agli studenti, creando occasioni privilegiate di incontro e condivisione sui temi dell’ecologia. In particolare, vogliamo costruire un percorso che parta dalle origini dell’ecologia, ne discuta l’attuale significato e apra un dibattito sulle direzioni che come scienza dovrebbe o potrebbe prendere.

Le attività pertinenti la celebrazione sono portate avanti insieme a numerose organizzazioni scientifiche e non, dall’Accademia Nazionale delle Scienze, alla Rete di ricerca lungo termine LTER, WWF Oasi, LifeWatch Italia e molte altre; esse assumeranno format diversi, da classiche conferenze e seminari, ad attività di citizen science e per le scuole.