Metagenomics is providing an unprecedented access to the environmental microbial diversity. The amplicon-based metagenomics approach involves the PCR-targeted sequencing of a genetic locus fitting ...different features. Namely, it must be ubiquitous in the taxonomic range of interest, variable enough to discriminate between different species but flanked by highly conserved sequences, and of suitable size to be sequenced through next-generation platforms. The internal transcribed spacers 1 and 2 (ITS1 and ITS2) of the ribosomal DNA operon and one or more hyper-variable regions of 16S ribosomal RNA gene are typically used to identify fungal and bacterial species, respectively. In this context, reliable reference databases and taxonomies are crucial to assign amplicon sequence reads to the correct phylogenetic ranks. Several resources provide consistent phylogenetic classification of publicly available 16S ribosomal DNA sequences, whereas the state of ribosomal internal transcribed spacers reference databases is notably less advanced. In this review, we aim to give an overview of existing reference resources for both types of markers, highlighting strengths and possible shortcomings of their use for metagenomics purposes. Moreover, we present a new database, ITSoneDB, of well annotated and phylogenetically classified ITS1 sequences to be used as a reference collection in metagenomic studies of environmental fungal communities. ITSoneDB is available for download and browsing at http://itsonedb.ba.itb.cnr.it/.
Near UltraViolet High Density (NUV-HD) SiPMs produced by Fondazione Bruno Kessler in collaboration with INFN have been tested and characterized in INFN laboratories. The third generation of these ...devices (HD3) has proven to be suitable to equip the focal plane of the prototype Schwarzschild–Couder Medium Size Telescope (pSCT) proposed for the Cherenkov Telescope Array Observatory. Photosensors have been assembled in 4 16-pixel optical units coupled with TARGET–7 ASIC front-end electronics for amplification and digitization of the signal. At present, 9 modules have been successfully integrated on the pSCT camera and are currently taking data. In this contribution we report on the performances of the HD3 technology as single sensor and as assembled optical units, showing their performance and homogeneity in terms of gain and dark count rate.
Diamond-Like Carbon for the Fast Timing MPGD Colaleo, A.; De Robertis, G.; Licciulli, F. ...
Journal of physics. Conference series,
04/2020, Letnik:
1498, Številka:
1
Journal Article
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The present generation of Micro-Pattern Gaseous Detectors (MPGDs) are radiation hard detectors, capable of detecting effciently particle rates of several MHz/cm2, while exhibiting good spatial ...resolution (≤ 50 µm) and modest time resolution of 5-10 ns, which satisfies the current generation of experiments (High Luminosity LHC upgrades of CMS and ATLAS) but it is not sufficient for bunch crossing identification of fast timing systems at FCC-hh. Thanks to the application of thin resistive films such as Diamond-Like Carbon (DLC) a new detector concept was conceived: Fast Timing MPGD (FTM). In the FTM the drift volume of the detector has been divided in several layers each with their own amplification structure. The use of resistive electrodes makes the entire structure transparent for electrical signals. After some first initial encouraging results, progress has been slowed down due to problems with the wet-etching of DLC-coated polyimide foils. To solve these problems a more in-depth knowledge of the internal stress of the DLC together with the DLC-polyimide adhesion is required. We will report on the production of DLC films produced in Italy with Ion Beam Sputtering and Pulsed Laser Deposition, where we are searching to improve the adhesion of the thin DLC films, combined with a very high uniformity of the resistivity values.
It has already been shown how the shape of the current pulse produced by a SiPM in response to an incident photon is sensibly affected by the characteristics of the front-end electronics (FEE) used ...to read out the detector. When the application requires to approach the best theoretical time performance of the detection system, the influence of all the parasitics associated to the coupling SiPM–FEE can play a relevant role and must be adequately modeled. In particular, it has been reported that the shape of the current pulse is affected by the parasitic inductance of the wiring connection between SiPM and FEE. In this contribution, we extend the validity of a previously presented SiPM model to account for the wiring inductance. Various combinations of the main performance parameters of the FEE (input resistance and bandwidth) have been simulated in order to evaluate their influence on the time accuracy of the detection system, when the time pick-off of each single event is extracted by means of a leading edge discriminator (LED) technique.
Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and proteome diversity, particularly in human and other vertebrates. However, the proportion of ...alternative transcripts and proteins actually endowed with functional activity is currently highly debated. We present here a new release of ASPicDB which now provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256 939 protein variants from 17 191 multi-exon genes have been extensively annotated through state of the art machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPI-anchor propeptides, transmembrane and coiled-coil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user. The retrieval interface also enables the selection of protein variants showing specific differences in the annotated features. ASPicDB is available at http://www.caspur.it/ASPicDB/.
Motivation: Alternative splicing has recently emerged as a key mechanism responsible for the expansion of transcriptome and proteome complexity in human and other organisms. Although several online ...resources devoted to alternative splicing analysis are available they may suffer from limitations related both to the computational methodologies adopted and to the extent of the annotations they provide that prevent the full exploitation of the available data. Furthermore, current resources provide limited query and download facilities. Results: ASPicDB is a database designed to provide access to reliable annotations of the alternative splicing pattern of human genes and to the functional annotation of predicted splicing isoforms. Splice-site detection and full-length transcript modeling have been carried out by a genome-wide application of the ASPic algorithm, based on the multiple alignments of gene-related transcripts (typically a Unigene cluster) to the genomic sequence, a strategy that greatly improves prediction accuracy compared to methods based on independent and progressive alignments. Enhanced query and download facilities for annotations and sequences allow users to select and extract specific sets of data related to genes, transcripts and introns fulfilling a combination of user-defined criteria. Several tabular and graphical views of the results are presented, providing a comprehensive assessment of the functional implication of alternative splicing in the gene set under investigation. ASPicDB, which is regularly updated on a monthly basis, also includes information on tissue-specific splicing patterns of normal and cancer cells, based on available EST sequences and their library source annotation. Availability: www.caspur.it/ASPicDB Contact: graziano.pesole@biologia.uniba.it Supplementary information: Supplementary data are available at Bioinformatics online.
PLANT-PIs is a database developed to facilitate retrieval of information on plant protease inhibitors (PIs) and related genes. For each PI, links to sequence databases are reported together with a ...summary of the functional properties of the molecule (and its mutants) as deduced from literature. PLANT-PIs contains information for 351 plant PIs, plus several isoinhibitors. The database is accessible at http://bighost.area.ba.cnr.it/PLANT-PIs.
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