A5078306757- Chromosomal and Genetic Variations
- RNA Research and Splicing
- Cancer-related molecular mechanisms research
- RNA modifications and cancer
- Diatoms and Algae Research
- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Protist diversity and phylogeny
- RNA and protein synthesis mechanisms
- Genetics, Aging, and Longevity in Model Organisms
- Epigenetics and DNA Methylation
- Marine and coastal ecosystems
- CRISPR and Genetic Engineering
- Genomics and Chromatin Dynamics
- Genetics and Neurodevelopmental Disorders
- MicroRNA in disease regulation
- Molecular Biology Techniques and Applications
- Marine and coastal plant biology
- RNA regulation and disease
- Cephalopods and Marine Biology
- Physiological and biochemical adaptations
- Genetic Neurodegenerative Diseases
- Insect behavior and control techniques
- Diptera species taxonomy and behavior
- Genomic variations and chromosomal abnormalities
Scuola Internazionale Superiore di Studi Avanzati
2018-2025
Italian Institute of Technology
2019-2025
Istituto Nazionale di Fisica Nucleare, Sezione di Genova
2023
International School of Trieste
2023
Stazione Zoologica Anton Dohrn
2013-2022
Biogem
2004-2016
University of Naples Federico II
2015
Telethon Institute Of Genetics And Medicine
2006-2011
Cluster in Biomedicine
2007-2010
AREA Science Park
2007-2010
The genome of the Southern Ocean phytoplankton Fragilariopsis cylindrus differs markedly from genomes its more temperate relatives, with divergent alleles being differentially expressed in environmentally specific conditions such as freezing and darkness. Diatoms are main primary producers Ocean, but how they have adapted to an environment extremes light temperature has remained unknown. Here Thomas Mock et al. report sequence a cold-adapted diatom cylindrus, compare this 'psychrophile'...
Germline CDH1 point or small frameshift mutations can be identified in 30–50% of hereditary diffuse gastric cancer (HDGC) families. We hypothesized that genomic rearrangements would found HDGC and 160 families with either two cancers first-degree relatives at least one (DGC) diagnosed before age 50, three more DGC close any age. Sixty-seven carried germline mutations. screened DNA from the 93 mutation negative probands for large by Multiplex Ligation-Dependent Probe Amplification. Potential...
MicroRNAs (miRNAs) and transcription factors control eukaryotic cell proliferation, differentiation, metabolism through their specific gene regulatory networks. However, differently from factors, our understanding of the processes regulated by miRNAs is currently limited. Here, we introduce network analysis as a new means for gaining insight into miRNA biology. A systematic all human based on Co-expression Meta-analysis Targets (CoMeTa) assigns high-resolution biological functions to...
Summary Microalgae play a major role as primary producers in aquatic ecosystems. Cell signalling regulates their interactions with the environment and other organisms, yet this process phytoplankton is poorly defined. Using marine planktonic diatom Pseudo‐nitzschia multistriata , we investigated cell response to cues released during sexual reproduction, an event that demands strong regulatory mechanisms impacts on population dynamics. We sequenced genome of P. performed phylogenomic...
The eukaryotic transcriptome is composed of thousands coding and long non-coding RNAs (lncRNAs). However, we lack a software platform to identify both RNA classes in given transcriptome. Here introduce Annocript, pipeline that combines the annotation protein transcripts with prediction putative lncRNAs whole transcriptomes. It downloads indexes needed databases, runs analysis produces human readable standard outputs together summary statistics analysis.Annocript distributed under GNU General...
Diatoms are phytoplanktonic organisms that grow successfully in the ocean where light conditions highly variable. Studies of molecular mechanisms acclimation marine diatom Phaeodactylum tricornutum show carotenoid de-epoxidation enzymes and LHCX1, a member light-harvesting protein family, both contribute to dissipate excess energy through non-photochemical quenching (NPQ). In this study, we investigate role other members LHCX family stress responses. Our analysis available genomic data shows...
Abstract Predicting responses of plankton to variations in essential nutrients is hampered by limited situ measurements, a poor understanding community composition, and the lack reference gene catalogs for key taxa. Iron driver dynamics and, therefore, global biogeochemical cycles climate. To assess impact iron availability on communities, we explored comprehensive bio‐oceanographic bio‐omics data sets from Tara Oceans context products two state‐of‐the‐art scale models. We obtained novel...
In anamniote embryos, the major wave of zygotic genome activation starts during mid-blastula transition. However, some genes escape global repression, are activated substantially earlier, and contribute to minor activation. The mechanisms underlying little understood. We explored genomic organization cis-regulatory a transcription body, in which is first detected zebrafish. identified miR-430 cluster as having excessive copy number highest density Pol-II-transcribed promoters genome, this...
The transition from quiescence to proliferation is a key regulatory step that can be induced by serum stimulation in cultured fibroblasts. transcription factor Myc directly mitogens and drives secondary gene expression program remains largely unknown. Using mRNA profiling, we identify close 300 Myc-dependent response (MDSR) genes, which are manner mouse Mapping of genomic Myc-binding sites ChIP-seq technology revealed most MDSR genes were targeted Myc, but represented minor fraction (5.5%)...
Abstract Cyanobacteria are among the most important primary producers on E arth. However, evolutionary forces driving cyanobacterial species diversity remain largely enigmatic due to both their distinction from macro‐organisms and an undersampling of sequenced genomes. Thus, we present a new genome S ynechococcus ‐like cyanobacterium novel lineage. Further, analyse all existing 16 rRNA sequences genomes cyanobacteria. Chronograms showed extremely polyphyletic relationships in , which has not...
Abstract The common octopus, Octopus vulgaris , is an active marine predator known for the richness and plasticity of its behavioral repertoire, remarkable learning memory capabilities. other coleoid cephalopods, cuttlefish squid, possess largest nervous system among invertebrates, both cell counts body to brain size. O . has been at center a long-tradition research into diverse aspects biology. To leverage in this iconic species, we generated 270 Gb genomic sequencing data, complementing...
Diatoms are among the most diverse eukaryotic microorganisms on Earth, they responsible for a large fraction of primary production in oceans and can be found different habitats. Pseudo-nitzschia marine planktonic diatoms blooms coastal oceanic waters. We analyzed transcriptome three species, arenysensis, delicatissima multistriata, with levels genetic relatedness. These species have worldwide distribution last one produces neurotoxin domoic acid. were able to annotate about 80% sequences...
Long Interspersed Nuclear Elements-1s (L1s) are transposable elements that constitute most of the genome's transcriptional output yet have still largely unknown functions. Here we show L1s required for proper mouse brain corticogenesis operating as regulatory long non-coding RNAs. They contribute to regulation balance between neuronal progenitors and differentiation, migration post-mitotic neurons proportions different cell types. In cortical cultured neurons, L1 RNAs mainly associated...
Abstract Summary: OneChannelGUI is an add-on Bioconductor package providing a new set of functions extending the capability affylmGUI package. This library provides graphical interface (GUI) for libraries to be used quality control, normalization, filtering, statistical validation and data mining single channel microarrays. Affymetrix 3′ expression (IVT) arrays as well whole transcript arrays, i.e. gene/exon 1.0 ST, are actually implemented. oneChannelGUI available most platforms on which R...
Zebrafish transgenesis is increasingly popular owing to the optical transparency and external development of embryos, which provide a scalable vertebrate model for in vivo experimentation. The ability express transgenes tightly controlled spatio-temporal pattern an important prerequisite exploitation zebrafish wide range biomedical applications. However, conventional methods are plagued by position effects: regulatory environment genomic integration sites leads variation expression patterns...
Abstract Background Sexual reproduction is an obligate phase in the life cycle of most eukaryotes. Meiosis varies among organisms, which reflected by variability gene set associated to process. Diatoms are unicellular organisms that belong stramenopile clade and have unique cycles can include a sexual phase. Results The exploration five diatom genomes one transcriptome led identification 42 genes potentially involved meiosis. While these majority known meiosis-related genes, several...
Abstract Diatoms and copepods are main actors in marine food webs. The prey–predator interactions between them affect bloom dynamics, shape ecosystems impact the energy transfer to higher trophic levels. Recently it has been demonstrated that presence of grazers may diatom prey beyond direct effect grazing. Here, we investigated response chain-forming centric Skeletonema marinoi grazer cues, including changes morphology, gene expression metabolic profile. S. cells were incubated with Calanus...
During the development of central nervous system (CNS), combinations transcription factors and signalling molecules orchestrate patterning, specification differentiation neural cell types. In vertebrates, three types melanin-containing pigment cells, exert a variety functional roles including visual perception. Here we analysed mechanisms underlying within CNS simple chordate, ascidian Ciona intestinalis. tadpole larvae exhibit basic chordate body plan characterized by small number cells. We...
ABSTRACT Background The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic mollusc with a circumglobal distribution in the deep ocean, except high Arctic and Antarctic waters. elusiveness of species makes it difficult to study. Thus, having genome assembled for this deep-sea–dwelling will allow several pending evolutionary questions be unlocked. Findings We present draft assembly that includes 200 Gb Illumina reads, 4 Moleculo synthetic long 108 Chicago libraries, final size...
While much experimental data shows that vaccination efficiently inhibits a subsequent challenge by transplantable tumor, its ability to inhibit the progress of autochthonous preneoplastic lesions is virtually unknown. In this article, we show combined DNA and cell vaccine persistently such in murine HER-2/neu mammary carcinogenesis model. At 10 weeks age, all ten gland samples from HER-2/neu–transgenic mice displayed foci hyperplasia progressed invasive tumors. Vaccination with plasmids...
Bacterioplankton are fundamental components of marine ecosystems and influence the entire biosphere by contributing to global biogeochemical cycles key elements. Yet, there is a significant gap in knowledge about their diversity specific activities, as well environmental factors that shape community composition function. Here, distribution surface bacterioplankton along coastline Gulf Naples (GON; Italy) were investigated using flow cytometry coupled with high-throughput sequencing 16S rRNA...