169,752 research outputs found
LandWorks Sardinia 2013 Punta Rossa/Caprera - La Maddalena
No full textThe operative workshop setting will be the NORTH-EST cost of Sardinian Island, inside the administrative limits of the Parco nazionale dell’arcipelago della Maddalena, unique natural and cultural heritage inside Mediterranean Landscape Area, as a first site, on the north dunescape in Monti d’Arena Area, where is situated an important residual part of quite well kept mediterranean dunescape example; the ex fortress of XIX century defensive landscape in Punta Rossa, on the extreme south part of the little Caprera Island, where is still visible the ruins of the military architecture area; the Sailing Center Park, where are now the main settlement of different size ships, where most of military and civil sailing carrier start from Mediterranean to over the world for decades of important sailing generations champions. Actually those sites represent a fundamental open air museum that tell to the visitors the history of a fundamental period for industry military development (“civilization”) of the Sardinian Island
The Caprera Canyon (north–eastern Sardinia): A hotspot of cetacean diversity in the western Mediterranean Sea
No full textThe Caprera Canyon, a submarine canyon system off Sardinia in the western Mediterranean, was thought to be an important cetacean habitat, though studies on the area remained limited. To address this knowledge gap, 216 boat-based surveys were conducted between 2011 and 2019, covering 8443 km, using both research and whale-watching vessels. The distribution, diversity, relative abundance (Encounter Rate - ER), and habitat use of cetaceans were described, along with relevant behavioural and ecological observations. A total of 8 species were reported across 810 sightings, encompassing 7 out of the 8 cetaceans regularly found in the western Mediterranean Sea. These species, in order of relative abundance, include the striped dolphin (Stenella coeruleoalba), fin whale (Balaenoptera physalus), Cuvier's beaked whale (Ziphius cavirostris), sperm whale (Physeter macrocephalus), Risso's dolphin (Grampus griseus), common dolphin (Delphinus delphis), bottlenose dolphin (Tursiops truncatus), and a single observation of Sowerby's beaked whale Mesoplodon bidens. This results in an overall ER of 10.6 sightings/100 km. ERs indicate that some species are particularly abundant in the study area, with Cuvier's beaked whale registering one of the highest ER values ever documented in the Mediterranean Sea. Calves and behavioural observations suggest that the study area serves as both a breeding and feeding ground for most species. The high cetacean diversity and relative abundance, along with the regular occurrence of endangered and vulnerable species, identify the Caprera Canyon as an important hotspot for cetacean diversity. Habitat suitability models using the maximum entropy (MaxEnt) approach highlight that other smaller canyons surrounding the Caprera Canyon could provide suitable habitats for deep diving species. The results presented here serve as reference data for future studies on the ecology and long-term dynamics of cetaceans in the central-western Tyrrhenian Sea. We highlight that the Caprera Canyon and surrounding areas could benefit from being designated as an Important Marine Mammal Area (IMMA), potentially supporting conservation efforts, guiding marine spatial planning, and informing policy development to mitigate threats in the region
ProCMD: a database and 3D web resource for protein C mutants
Get PDFBackground: Activated Protein C (ProC) is an anticoagulant plasma serine protease which also plays an important role in controlling inflammation and cell proliferation. Several mutations of the gene are associated with phenotypic functional deficiency of protein C, and with the risk of developing venous thrombosis. Structure prediction and computational analysis of the mutants have proven to be a valuable aid in understanding the molecular aspects of clinical thrombophilia. Results: We have built a specialized relational database and a search tool for natural mutants of protein C. It contains 195 entries that include 182 missense and 13 stop mutations. A menu driven search engine allows the user to retrieve stored information for each variant, that include genetic as well as structural data and a multiple alignment highlighting the substituted position. Molecular models of variants can be visualized with interactive tools; PDB coordinates of the models are also available for further analysis. Furthermore, an automatic modelling interface allows the user to generate multiple alignments and 3D models of new variants. Conclusion: ProCMD is an up-to-date interactive mutant database that integrates phenotypical descriptions with functional and structural data obtained by computational approaches. It will be useful in the research and clinical fields to help elucidate the chain of events leading from a molecular defect to the related disease. It is available for academics at the URL http://www.itb.cnr.it/procmd/
Clinical Impact and Prognostic Role of KRAS/BRAF/PIK3CA Mutations in Stage I Colorectal Cancer
Get PDFStage I colorectal carcinoma has excellent prognosis, with 5-year survival rate up to 95%. The occurrence of lymphovascular invasion, tumor budding, high number of PDC, or lymph node micrometastases is associated with tumor progression. The aim of this study was to evaluate the mutational status of 62 stage I colorectal carcinomas (CRC) (taken from 37 patients surviving more than five years since the initial diagnosis and from 25 patients who died of disease) and to correlate it with histopathological features and the clinical outcome. Mutations of KRAS, NRAS, BRAF, and PIK3CA genes were analyzed through Myriapod Colon Status Kit, using the high-throughput genotyping platform Sequenom MassARRAY System. Mutations in those genes were found in 31 cases (50%) and mainly in those with poor prognosis. The most frequent mutations occurred at codons 12 and 13 of the KRAS gene (40% of cases). We found concomitant PIK3CA mutations in 5 cases (8%). The presence of PIK3CA mutations was mainly observed in tumors with poor prognosis and with unfavorable histopathological prognostic features. High PDC grade (P = 0.0112), the presence of tumor budding (P = 0.0334), LVI (P < 0.0001), KRAS mutations (P = 0.0228), PIK3CA mutations (P = 0.0214), multiple genetic mutations in KRAS and PIK3CA genes (P = 0.039), and nodal micrometastases (P < 0.0001) were significant prognostic variables for CSS. The presence of LVI was the only independent and statistically significant prognostic variable for CSS in our cohort of pTNM stage I CRCs. The analysis of KRAS/PIK3CA mutational status may be used to identify patients with stage I CRC at high risk of bad outcome and who may need additional treatments, including biological therapies
Comparative analysis of expressed sequence tags from tissues in ripening stages of peach (Prunus persica L. Batsch)
No full textExpressed sequence tag (EST) represents a resource for gene discovery, genome annotation and comparative genomics in plants. ESTs were derived by sequencing clones from five libraries created from two different fruit tissues (skin and mesocarp), at four ripening stages (from post-allegation to post-climacteric) in three different genotypes of peach (OroA, Bolero and Suncrest). A total of 10,847 EST sequences were produced (dataset A); in addition, 21,857 peach ESTs (dataset B) were obtained from public databases. Clustering and assembly of both datasets gave 17,858 unigenes. Analysis of the sequences allowed the assignment of a putative function to 70.8% of the ESTs. In order to define the relationship among fruit tissues transcriptome, a gene ontology analysis was performed. Differences among organs and among different maturation stages of the same organs were identified in organelle, signal transducer and antioxidant activity. A distance matrix of pairwise correlation coefficients analysis was applied between the libraries. Shoot appeared to outgroup and our analysis proved to be an efficient tool to parallel and complement gene expression studies (for example, based on microarray analysis). We conducted an analysis of the frequency of genes putatively involved in the metabolism of some volatiles, which pointed to a predominant presence of those transcripts in the skin. The metabolic pathways of esters and lactones were selected for further isolation and cloning of key genes. The EST database is available at the web site www.itb.cnr.it/estree
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
Molecular Profile, as detected with Mass-Array Spectrometry (Sequenom platform), in primary and metastatic breast carcinoma treated with Exemestane + Everolimus
No full textBackground. PI3K/Akt/mTOR is one of the most important
pathways for the regulation of cell survival, proliferation and
apoptosis. Mutational events occurring in this pathway could lead to malignant transformation and endocrine resistance in
breast cancer. The mTOR inhibitor Everolimus (EVE) interferes
with cellular proliferation by binding FKB12 protein.
EVE has been definitely approved thanks to BOLERO-2
phase III study, which showed a significant prolongation of
Progression Free Survival (PFS) due to the addiction of EVE
to Exemestane therapy, compared to Exemestane alone, in
Hormonal Receptors-positive (RO+) and HER2-negative
(HER2-) metastatic breast cancer patients. Hortobagyi et al.
performed Next Generation Sequencing on 227 BOLERO-2
samples of primary breast carcinoma, to study the potential
correlation between genetic alterations and EVE efficacy. A
greater incidence of mutations in PIK3CA, PTEN, CCND1
and FGFR1/2 genes was detected and it was observed that
patients with no or only one genetic alteration in these genes
derive the most benefit from EVE therapy. To our knowledge,
no previous research has evaluated the mutational status both
in primary and metastatic breast cancers.
Materials and methods. Aim of this study was to evaluate the
molecular profile in primitive breast cancers (21 ductal carcinomas,
3 lobular carcinomas and 1 colloid carcinoma) and
visceral metastases (hepatic and pulmonary), in 25 patients
with advanced breast cancer (RO+ HER2-) treated with EVE
in combination with Exemestane. Thirty-three DNA samples
from 25 patients were examined, 13 from primary0 breast cancers
and 20 from metastatic lesions. In 8 patients, both the primary
tumor and the corresponding metachronous metastasis
were evaluated. Genomic DNA samples from FFPE tumoral
tissue were analized by using OncoCarta v2.0 panel on Mass
Array Sequenom platform. A preliminar Multiplex-PCR, followed
by SAP-dephosphorylating reaction and iPLEX-primer
specific extension, was performed to detect more than 150
single nucleotide variations in mutational hotspots from 18
implicated genes (AKT1, BRAF, CTNNB1, FBX4, FBXW7,
FGFR2, FGFR3, GNAQ, KIT, KRAS, MAP2K1, MAP2K2,
NRAS, PDGFRa, PIK3CA, PTPN11, SOS1, TP53). Differences
were evaluated using Chi-Square and Fisher Tests.
Survival analysis was conducted using Kaplan-Meyer curves.
Results. Overall, 11 DNA samples, out of the 33 examined,
were mutated (33%). Mutations were found in 10 ductal carcinomas
and in the colloid carcinoma. Five mutations were
detected in primary breast lesions and 6 in metastatic ones.
All mutations consisted of a single-nucleotide variation resulting
in aminoacidic substitution. Among primary lesions,
mutations were detected in the following genes: PIK3CA
(E545K), FBX4 (G30N), KIT (S709F), MAP2K1 (D67N),
FBXW7 (R465C). They occurred with a frequency of 3%,
respectively, namely in 1 out of 33 samples each. Only in
the AKT1 gene the same mutation (E17K) was found in 2
DNA primary lesion samples. In metastatic lesions, BRAF
(R444W), KIT (G565R), TP53 (R273H), FBXW7 (R479Q),
CTNNB1 (S45F), PIK3CA (E545K), AKT (E17K) were
mutated. Notably, mutations were found exclusively in primary
lesions or in metastatic ones, while only in one patient
both primary and secondary lesions were mutated; however,
these mutations occurred in two different genes: MAP2K1
(D67N) in breast, FBXW7 (R479Q) in metastasis. Of notice,
a reduction in PFS was observed in one patient which carried
3 different mutations (FBX4, PIK3CA, KIT) in the primary
tumor (3.4 month versus an average of 5 month) whereas a
significantly increased PFS (15.9 month) was detected in a
case with 2 mutations (PIK3CA, AKT1) in metastatic lesion.
Conclusion. Although the number of patients and samples is
quite limited, our findings in mutational status support literature
evidence, as genes most frequently mutated were PIK3CA, AKT1 and FBXW7, even if the percentage of PIK3CA and
AKT1 mutations was less than expected. No correlations between
primary and metastatic mutational status were detected
ESTree db: a Tool for Peach Functional Genomics
Get PDFAbstract Background The ESTree db http://www.itb.cnr.it/estree/ represents a collection of Prunus persica expressed sequenced tags (ESTs) and is intended as a resource for peach functional genomics. A total of 6,155 successful EST sequences were obtained from four in-house prepared cDNA libraries from Prunus persica mesocarps at different developmental stages. Another 12,475 peach EST sequences were downloaded from public databases and added to the ESTree db. An automated pipeline was prepared to process EST sequences using public software integrated by in-house developed Perl scripts and data were collected in a MySQL database. A php-based web interface was developed to query the database. Results The ESTree db version as of April 2005 encompasses 18,630 sequences representing eight libraries. Contig assembly was performed with CAP3. Putative single nucleotide polymorphism (SNP) detection was performed with the AutoSNP program and a search engine was implemented to retrieve results. All the sequences and all the contig consensus sequences were annotated both with blastx against the GenBank nr db and with GOblet against the viridiplantae section of the Gene Ontology db. Links to NiceZyme (Expasy) and to the KEGG metabolic pathways were provided. A local BLAST utility is available. A text search utility allows querying and browsing the database. Statistics were provided on Gene Ontology occurrences to assign sequences to Gene Ontology categories. Conclusion The resulting database is a comprehensive resource of data and links related to peach EST sequences. The Sequence Report and Contig Report pages work as the web interface core structures, giving quick access to data related to each sequence/contig.</p
Version VI of the ESTree db: An improved tool for peach transcriptome analysis
Get PDFBackground: The ESTree database (db) is a collection of Prunus persica and Prunus dulcis EST sequences that in its current version encompasses 75,404 sequences from 3 almond and 19 peach libraries. Nine peach genotypes and four peach tissues are represented, from four fruit developmental stages. The aim of this work was to implement the already existing ESTree db by adding new sequences and analysis programs. Particular care was given to the implementation of the web interface, that allows querying each of the database features. Results: A Perl modular pipeline is the backbone of sequence analysis in the ESTree db project. Outputs obtained during the pipeline steps are automatically arrayed into the fields of a MySQL database. Apart from standard clustering and annotation analyses, version VI of the ESTree db encompasses new tools for tandem repeat identification, annotation against genomic Rosaceae sequences, and positioning on the database of oligomer sequences that were used in a peach microarray study. Furthermore, known protein patterns and motifs were identified by comparison to PROSITE. Based on data retrieved from sequence annotation against the UniProtKB database, a script was prepared to track positions of homologous hits on the GO tree and build statistics on the ontologies distribution in GO functional categories. EST mapping data were also integrated in the database. The PHP-based web interface was upgraded and extended. The aim of the authors was to enable querying the database according to all the biological aspects that can be investigated from the analysis of data available in the ESTree db. This is achieved by allowing multiple searches on logical subsets of sequences that represent different biological situations or features. Conclusions: The version VI of ESTree db offers a broad overview on peach gene expression. Sequence analyses results contained in the database, extensively linked to external related resources, represent a large amount of information that can be queried via the tools offered in the web interface. Flexibility and modularity of the ESTree analysis pipeline and of the web interface allowed the authors to set up similar structures for different datasets, with limited manual intervention
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