Phylogenetic and biogeographic history of brook lampreys (: Petromyzontidae) in the river basins of the Adriatic Sea based on DNA barcode data.

The Adriatic brook lamprey, zanandreai Vladykov 1955, was described from northeastern Italy. Its distribution is thought to include left tributaries of the River Po and the river basins of the Adriatic Sea from the River Po to the River Isonzo/Soča in Italy, Switzerland and Slovenia. It also shows a geographically isolated distribution in the Potenza River on the Adriatic slope in Central Italy.

The FAIR Cookbook - the essential resource for and by FAIR doers.

The notion that data should be Findable, Accessible, Interoperable and Reusable, according to the FAIR Principles, has become a global norm for good data stewardship and a prerequisite for reproducibility. Nowadays, FAIR guides data policy actions and professional practices in the public and private sectors. Despite such global endorsements, however, the FAIR Principles are aspirational, remaining elusive at best, and intimidating at worst.

Life History Traits of Sperm Whales Linnaeus, 1758 Stranded along Italian Coasts (Cetartiodactyla: Physeteridae).

We investigated the relationship between age and body length, and age at sexual maturity of individuals stranded along the Italian coast. Our molecular analysis shows that all our samples belong to the C.001.

Mediterranean swordfish ( Linnaeus, 1758) population structure revealed by microsatellite DNA: genetic diversity masked by population mixing in shared areas.

Background: The Mediterranean swordfish stock is overfished and considered not correctly managed. Elucidating the patterns of the Mediterranean swordfish population structure constitutes an essential prerequisite for effective management of this fishery resource. To date, few studies have investigated intra-Mediterranean swordfish population structure, and their conclusions are controversial.

Isolation and characterization of two satellite DNAs in Atlantolacerta andreanskyi (Werner, 1929) (Reptilia, Lacertidae).

Two satellite DNAs (satDNAs) have been isolated and characterized from three populations of Atlantolacerta andreanskyi. One satDNA (AAN-TaqI) has been isolated here from the first time. It is characterized by a tendency to AT enrichment (AT = 54.

Implementation and relevance of FAIR data principles in biopharmaceutical R&D.

Biopharmaceutical industry R&D, and indeed other life sciences R&D such as biomedical, environmental, agricultural and food production, is becoming increasingly data-driven and can significantly improve its efficiency and effectiveness by implementing the FAIR (findable, accessible, interoperable, reusable) guiding principles for scientific data management and stewardship. By so doing, the plethora of new and powerful analytical tools such as artificial intelligence and machine learning will be able, automatically and at scale, to access the data from which they learn, and on which they thrive. FAIR is a fundamental enabler for digital transformation.

YummyData: providing high-quality open life science data.

Many life science datasets are now available via Linked Data technologies, meaning that they are represented in a common format (the Resource Description Framework), and are accessible via standard APIs (SPARQL endpoints). While this is an important step toward developing an interoperable bioinformatics data landscape, it also creates a new set of obstacles, as it is often difficult for researchers to find the datasets they need. Different providers frequently offer the same datasets, with different levels of support: as well as having more or less up-to-date data, some providers add metadata to describe the content, structures, and ontologies of the stored datasets while others do not.

Characterization of a satellite DNA in the genera Lacerta and Timon (Reptilia, Lacertidae) and its role in the differentiation of the W chromosome.

In this study, IMO-TaqI satDNA, previously isolated in several species of Lacertidae, was isolated and characterized from four species of the genus Lacerta and three of the genus Timon. The aim was to gain further insights into the evolutionary dynamics of this satDNA, its occurrence among lacertids and to understand if it plays any role in sex chromosome evolution in these seven species. The results here obtained highlighted the presence of this repetitive element in the genome of all the species investigated, thus indicating that IMO-TaqI satDNA is evolutionary conserved among a wide variety of lacertids.

Matching disease and phenotype ontologies in the ontology alignment evaluation initiative.

Background: The disease and phenotype track was designed to evaluate the relative performance of ontology matching systems that generate mappings between source ontologies. Disease and phenotype ontologies are important for applications such as data mining, data integration and knowledge management to support translational science in drug discovery and understanding the genetics of disease.

Results: Eleven systems (out of 21 OAEI participating systems) were able to cope with at least one of the tasks in the Disease and Phenotype track.

Cytogenetic Characterization of a Population of Acanthodactylus lineomaculatus Duméril and Bibron, 1839 (Reptilia, Lacertidae), from Southwestern Morocco and Insights into Sex Chromosome Evolution.

Acanthodactylus lineomaculatus is now regarded as an ecotype of A. erythrurus with which it has been recently synonymized. Despite the wide range of A.

Evolutionary dynamics of Anolis sex chromosomes revealed by sequencing of flow sorting-derived microchromosome-specific DNA.

Squamate reptiles show a striking diversity in modes of sex determination, including both genetic (XY or ZW) and temperature-dependent sex determination systems. The genomes of only a handful of species have been sequenced, analyzed and assembled including the genome of Anolis carolinensis. Despite a high genome coverage, only macrochromosomes of A.

The Effects of Paleoclimatic Events on Mediterranean Trout: Preliminary Evidences from Ancient DNA.

In this pilot study for the first time, ancient DNA has been extracted from bone remains of Salmo trutta. These samples were from a stratigraphic succession located in a coastal cave of Calabria (southern Italy) inhabited by humans from upper Palaeolithic to historical times. Seven pairs of primers were used to PCR-amplify and sequence from 128 to 410 bp of the mtDNA control region of eleven samples.

Biocomplexity in Populations of European Anchovy in the Adriatic Sea.

The sustained exploitation of marine populations requires an understanding of a species' adaptive seascape so that populations can track environmental changes from short- and long-term climate cycles and from human development. The analysis of the distributions of genetic markers among populations, together with correlates of life-history and environmental variability, can provide insights into the extent of adaptive variation. Here, we examined genetic variability among populations of mature European anchovies (n = 531) in the Adriatic (13 samples) and Tyrrhenian seas (2 samples) with neutral and putative non-neutral microsatellite loci.

Coupling Demographic and Genetic Variability from Archived Collections of European Anchovy (Engraulis encrasicolus).

It is well known that temporal fluctuations in small populations deeply influence evolutionary potential. Less well known is whether fluctuations can influence the evolutionary potentials of species with large census sizes. Here, we estimated genetic population parameters from as survey of polymorphic microsatellite DNA loci in archived otoliths from Adriatic European anchovy (Engraulis encrasicolus), a fish with large census sizes that supports numerous local fisheries.

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data.

Isolation and characterization of two satellite DNAs in some Iberian rock lizards (Squamata, Lacertidae).

Satellite DNAs represent a large portion of all high eukaryotic genomes. They consist of numerous very similar repeated sequences, tandemly arranged in large clusters up to 100 million base pairs in length, usually located in the heterochromatic parts of chromosomes. The biological significance of satDNAs is still under discussion, but most of their proposed functions are related to heterochromatin and/or centromere formation and function.

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

Background: BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research.

Results: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces.

Towards linked open gene mutations data.

Background: With the advent of high-throughput technologies, a great wealth of variation data is being produced. Such information may constitute the basis for correlation analyses between genotypes and phenotypes and, in the future, for personalized medicine. Several databases on gene variation exist, but this kind of information is still scarce in the Semantic Web framework.

Gauging triple stores with actual biological data.

Background: Semantic Web technologies have been developed to overcome the limitations of the current Web and conventional data integration solutions. The Semantic Web is expected to link all the data present on the Internet instead of linking just documents. One of the foundations of the Semantic Web technologies is the knowledge representation language Resource Description Framework (RDF).

Semantic Web applications and tools for the life sciences: SWAT4LS 2010.

As Semantic Web technologies mature and new releases of key elements, such as SPARQL 1.1 and OWL 2.0, become available, the Life Sciences continue to push the boundaries of these technologies with ever more sophisticated tools and applications.

Knowledge sharing and collaboration in translational research, and the DC-THERA Directory.

Biomedical research relies increasingly on large collections of data sets and knowledge whose generation, representation and analysis often require large collaborative and interdisciplinary efforts. This dimension of 'big data' research calls for the development of computational tools to manage such a vast amount of data, as well as tools that can improve communication and access to information from collaborating researchers and from the wider community. Whenever research projects have a defined temporal scope, an additional issue of data management arises, namely how the knowledge generated within the project can be made available beyond its boundaries and life-time.

Chromosomal study of a lamprey (Lampetra zanandreai Vladykov, 1955) (Petromyzonida: Petromyzontiformes): conventional and FISH analysis.

Karyotype and other chromosomal characteristics in the Adriatic brook lamprey Lampetra zanandreai, representative of one of the most ancestral group of vertebrates, were examined using conventional (Ag-staining, C-banding as well as CMA(3) and DAPI fluorescence) and molecular (FISH with 18/28S rDNA and EcoRI satDNA as probes) protocols with metaphase chromosomes derived from whole blood cultures. The chromosome complement had a modal diploid chromosome number of 2n = 164, as in other petromyzontid lamprey species. Ag-staining and CMA(3) fluorescence, as well as FISH with 18/28S rDNA probes, detected nucleolar organizer regions (NORs) close to the centromeres of the biarmed chromosomes of pairs 1 and 2, the largest chromosome pairs of the complement.

Biomedical semantics in the Semantic Web.

The Semantic Web offers an ideal platform for representing and linking biomedical information, which is a prerequisite for the development and application of analytical tools to address problems in data-intensive areas such as systems biology and translational medicine. As for any new paradigm, the adoption of the Semantic Web offers opportunities and poses questions and challenges to the life sciences scientific community: which technologies in the Semantic Web stack will be more beneficial for the life sciences? Is biomedical information too complex to benefit from simple interlinked representations? What are the implications of adopting a new paradigm for knowledge representation? What are the incentives for the adoption of the Semantic Web, and who are the facilitators? Is there going to be a Semantic Web revolution in the life sciences?We report here a few reflections on these questions, following discussions at the SWAT4LS (Semantic Web Applications and Tools for Life Sciences) workshop series, of which this Journal of Biomedical Semantics special issue presents selected papers from the 2009 edition, held in Amsterdam on November 20th.

DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells.

Background: The advent of Systems Biology has been accompanied by the blooming of pathway databases. Currently pathways are defined generically with respect to the organ or cell type where a reaction takes place. The cell type specificity of the reactions is the foundation of immunological research, and capturing this specificity is of paramount importance when using pathway-based analyses to decipher complex immunological datasets.