Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA).

Alicyclobacillus acidocaldarius (Darland and Brock 1971) is the type species of the larger of the two genera in the bacillal family 'Alicyclobacillaceae'. A. acidocaldarius is a free-living and non-pathogenic organism, but may also be associated with food and fruit spoilage. Due to its acidophilic nature, several enzymes from this species have since long been subjected to detailed molecular and biochemical studies. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family 'Alicyclobacillaceae'. The 3,205,686 bp long genome (chromosome and three plasmids) with its 3,153 protein-coding and 82 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project

Complete genome sequence of Thermaerobacter marianensis type strain (7p75a).

Thermaerobacter marianensis Takai et al. 1999 is the type species of the genus Thermaerobacter, which belongs to the Clostridiales family Incertae Sedis XVII. The species is of special interest because T. marianensis is an aerobic, thermophilic marine bacterium, originally isolated from the deepest part in the western Pacific Ocean (Mariana Trench) at the depth of 10.897m. Interestingly, the taxonomic status of the genus has not been clarified until now. The genus Thermaerobacter may represent a very deep group within the Firmicutes or potentially a novel phylum. The 2,844,696 bp long genome with its 2,375 protein-coding and 60 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project

Transcriptional landscape of neuronal and cancer stem cells

Tumor mass is composed by heterogeneous cell population including a subset of “cancer stem cells” (CSC). Oncogenic signals foster CSC by transforming tissue stem cells or by reprogramming progenitor/differentiated cells towards stemness. Thus, CSC share features with cancer and stem cells (e.g. self-renewal, hierarchical developmental program leading to differentiated cells, epithelial/mesenchimal transition) and these latter are maintained by the constitutive activation of stemness-promoting signals. CSC could trigger tumor formation, drive to resistance to conventional therapeutics and underlie patients’ relapse. Indeed, stem cell signatures have been associated with poor prognosis in various. This background makes the identification of CSC molecular features mandatory to highlight the survival inner working and to design novel CSC specific therapeutic strategies. Medulloblastoma (MB) is the most common childhood malignant brain tumor and a leading cause of cancerrelated morbidity and mortality. Current multimodal therapies are effective in about 50% of patients but often cause long-term side effects, i.e. developmental, neurological, neuroendocrine and psychosocial deficits (Northcott PA Nature Rev cancer 2012). For many years, MB treated as a single tumor entity despite the divergent tumor histology, patients’ outcome and drug sensitivity, and also by the diversity of the stem cell of origin. Very recently the scenario of human MB has dramatically changed since its heterogeneous biology has been addressed by high-throughput gene expression analysis (oligonucleotide microarrays) or by the powerful genomic next-generation sequencing. These led to the identification of four tumor subgroups (WNT, SHH, Group 3 and Group 4) uncovering the existence of a highly diverse mutational spectra and gene expression. However a quantitative approach has not yet been applied to the transcriptional landscape of Medulloblastoma stem cells (MbSC) through RNA Next Generation Sequencing (RNA-Seq) technology. This is a relevant issue, since RNA-Seq is able to interrogate the genome wide global transcriptome including new transcripts, alternative spliced isoforms and non-coding RNAs. Lower rhombic lip progenitors of the dorsal brainstem are considered the trigger cells in WNT tumors; in SHH subgroup initiation cells are Prominin1+ CD15+ stem cells from the subventricular zone requiring the commitment to Math1+ granule cell progenitors [GCP] of the external granule cell layer [EGL]; while Math1+ or Math1- EGL-GCP or Prominin1+/lineage-negative stem cells sustain the MYC driven Group 3. MbSC derived from SHH tumors and postnatal normal cerebellar stem cells (NcSC) have been reported to share several features. A key signal for both of them is Hedgehog. Furthermore, both NcSC and MbSC display up-regulation of stemness genes (e.g Sox2, Nestin, Nanog, Prom1). Finally, constitutive activation of the Shh pathway by conditional deletion of Ptch1 inhibitory receptor in NcSC, promote medulloblastoma in vivo, producing a mouse model of the human SHH tumor. Acquisition of stemness features may therefore represent the first step of oncogenic conversion. Cooperation with additional oncogenic signals is however needed to enhance MbSC tumorigenicity. In order to understand the MbSCs transcriptional programs, we analyze by RNA-Seq, MbSC derived from Ptch1+/- tumors (Ptch1+/- MbSC). This choice, of a genetically determined model of MB, has allowed us to work with Ptch1+/- MbSC together with appropriate NcSC counterpart, and to analyze biological replicates doing statistical analysis. We identify a number of transcripts, annotated ones, novel isoforms, and long non-coding RNAs, characterizing MbSC and/or NcSC. Some of these genes control stemness or are cancer related and conserved in human medulloblastomas. Interestingly a subset of them, belonging to cell stress response, are of prognostic relevance being significantly related to clinical outcome. Correlation of genes expression characterizing MbSC with survival information from our human medulloblastomas database further demonstrates the significance of these findings. Our data suggest that the modulation of normal and cancer stem cell functions observed in vitro is effective in dissecting the transcriptional programs underlying the in vivo behavior of human medulloblastomas