The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed.
BioHackathon; Bioinformatics; Semantic Web; Web services; Ontology; Visualization; Knowledge representation; Databases; Semantic interoperability; Data models; Data sharing; Data integration
Transdifferentiation is the conversion of cells from one differentiated cell type into another. How functionally differentiated cells already committed to a specific cell lineage can transdifferentiate into other cell types is a key question in cell biology and regenerative medicine. In the present study we show that porcine ovarian follicular GCs (granulosa cells) can transdifferentiate into osteoblasts in vitro and in vivo. Pure GCs isolated and cultured in Dulbecco's modified Eagle's medium supplemented with 20% FBS (fetal bovine serum) proliferated and dedifferentiated into fibroblast-like cells. We referred to these cells as DFOG (dedifferentiated follicular granulosa) cells. Microarray analysis showed that DFOG cells lost expression of GC-specific marker genes, but gained the expression of osteogenic marker genes during dedifferentiation. After osteogenic induction, DFOG cells underwent terminal osteoblast differentiation and matrix mineralization in vitro. Furthermore, when DFOG cells were transplanted subcutaneously into SCID mice, these cells formed ectopic osteoid tissue. These results indicate that DFOG cells derived from GCs can differentiate into osteoblasts in vitro and in vivo. We suggest that GCs provide a useful model for studying the mechanisms of transdifferentiation into other cell lineages in functionally differentiated cells.
dedifferentiated fat cell (DFAT cell); dedifferentiated follicular granulosa (DFOG); differentiation; osteoblast; ovary; transdifferentiation; ACAN, aggrecan; ALP, alkaline phosphatase; ALPL, ALP liver/bone/kidney; BMP, bone morphogenetic protein; BMSC, bone marrow stromal cell; BSP, bone sialoprotein; Cy3, indocarbocyanine; CYP11A1, cytochrome P450 family 11 subfamily A1; CYP19A3, cytochrome P450 family 19 subfamily A3; DAPI, 4′6-diamidino-2-phenylindole; DEX, dexamethasone; DFAT, dedifferentiated fat; DFOG, dedifferentiated follicular granulosa; DLX5, distal-less homeobox 5; DMEM, Dulbecco's modified Eagle's medium; FBS, fetal bovine serum; FSH, follicle-stimulating hormone; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GC, granulosa cell; GEO, Gene Expression Omnibus; IBSP, integrin-binding sialoprotein; INHBB, inhibin β B; LHCGR, luteinizing hormone/choriogonadotropin receptor; LIF, leukaemia-inhibiting factor; NR, nuclear receptor; OM, osteogenic medium; OSX, osterix; POU5F1, POU class 5 homeobox 1; RT, reverse transcription; RUNX2, Runt-related transcription factor 2; Sox9, SRY (sex determining region Y)-box 9; SPP1, secreted phosphoprotein 1; TC, theca cell