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Alberti, C.

Publications and source records attributed to Alberti, C..

2 recordsLinked to original sources

An early Sox2-dependent gene expression program required for hippocampal dentate gyrus development

The hippocampus is a brain area central for cognition. Mutations in the human SOX2 transcription factor cause neurodevelopmental defects, leading to intellectual disability and seizures, together with hippocampal dysplasia. We generated an allelic series of Sox2 conditional mutations in mouse, deleting Sox2 at different developmental stages. Late Sox2 deletion (from E11.5, via Nestin-Cre) affects only postnatal hippocampal development; earlier deletion (from E10.5, Emx1-Cre) significantly reduces the dentate gyrus, and the earliest deletion (from E9.5, FoxG1-Cre) causes drastic abnormalities, with almost complete absence of the dentate gyrus. We identify a set of functionally interconnected genes (Gli3, Wnt3a, Cxcr4, p73 and Tbr2), known to play essential roles in hippocampal embryogenesis, which are downregulated in early Sox2 mutants, and (Gli3 and Cxcr4) directly controlled by SOX2; their downregulation provides plausible molecular mechanisms contributing to the defect. Electrophysiological studies of the Emx1Cre mouse model reveal altered excitatory transmission in CA1 and CA3 regions.

developmental biology↗

An introduction to MPEG-G, the new ISO standard for genomic information representation

The MPEG-G standardization initiative is a coordinated international effort to specify a compressed data format that enables large scale genomic data to be processed, transported and shared. The standard consists of a set of specifications (i.e., a book) describing: i) a nor-mative format syntax, and ii) a normative decoding process to retrieve the information coded in a compliant file or bitstream. Such decoding process enables the use of leading-edge com-pression technologies that have exhibited significant compression gains over currently used formats for storage of unaligned and aligned sequencing reads. Additionally, the standard provides a wealth of much needed functionality, such as selective access, data aggregation, ap-plication programming interfaces to the compressed data, standard interfaces to support data protection mechanisms, support for streaming and a procedure to assess the conformance of implementations. ISO/IEC is engaged in supporting the maintenance and availability of the standard specification, which guarantees the perenniality of applications using MPEG-G. Fi-nally, the standard ensures interoperability and integration with existing genomic information processing pipelines by providing support for conversion from the FASTQ/SAM/BAM file formats.\n\nIn this paper we provide an overview of the MPEG-G specification, with particular focus on the main advantages and novel functionality it offers. As the standard only specifies the decoding process, encoding performance, both in terms of speed and compression ratio, can vary depending on specific encoder implementations, and will likely improve during the lifetime of MPEG-G. Hence, the performance statistics provided here are only indicative baseline examples of the technologies included in the standard.

bioinformatics↗