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Homeostatic plasticity is important in neurobiology for stabilising neuronal networks in the face of Hebbian forms of synaptic plasticity that are thought to mediate memory storage. Impairment of homeostatic plasticity has also been implicated in neurological diseases such as Rett syndrome and fragile X syndrome. Homeostatic plasticity can be achieved through scaling of the strength of synaptic connections between neurones or by changes in intrinsic excitability. While homeostatic plasticity has been studied mainly using in vitro preparations, it is for the most part not known whether changes of neural activity in vivo induce homeostatic changes. The molecular pathway responsible for homeostatic plasticity still remains unclear. In this thesis, I have used stereotaxic surgery to over express Kir2.1, an inwardly rectifying potassium channel, in vivo in the brains of adult mice. I show that the expression of Kir2.1 through adeno-associated virus (AAV) does not cause any adverse effects in the dentate gyrus nor the CA1 of the mouse hippocampus. I go on to use slice patch clamp methods to measure the change in electrical properties of granule cells in the dentate gyrus and pyramidal cells in CA1 caused by expression of Kir2.1. I show that the excitability of neurones expressing Kir2.1 was reduced compared to control neurones. By 2 weeks after virus injection the neurones showed homeostatic plasticity in response to Kir2.1 over expression. Interestingly, the mechanism of adaptation was different in different types of cells; dentate gyrus granule cells adapted through change in their intrinsic excitability, whereas CA1 pyramidal cells adapted by modifying the strength of their synaptic inputs. To establish whether induction of homeostatic plasticity is associated with changes in gene expression I used fluorescent activated cell sorting (FACs) to isolate pure population of neurones infected with viruses. I then sequenced RNA extracted from neurones expressing Kir2.1 and control neurones. Analysis of the RNAseq data revealed molecular candidates involved in homeostatic plasticity. In summary, I show that Kir2.1 over expression causes change in excitability and subsequent homeostatic plasticity in vivo. The mechanism of adaptation differs between cell types. RNAseq results identify novel candidates for future investigation.

国立情報学研究所で電子化したコンテンツを使用している。

In freshwater fish, such as the rainbow trout (Oncorhynchus mykiss), higher ion concentrations in the body fluids relative to the dilute surrounding environment lead to diffusive ion loss that is countered by active ion uptake. Active ion uptake is achieved via specialised cells in the gill epithelium known as ionocytes, with the species studied to date exhibiting multiple ionocyte subtypes with specific complements of ion transport proteins. To better understand the functions and responses of each ionocyte subtype, methods are needed to isolate specific ionocyte subtypes. This thesis developed a method to use fluorescence-activated cell sorting (FACS) to isolate the peanut lectin agglutinin-positive (PNA+) ionocyte subtype of the trout gill, which is posited to be a base-secreting cell that takes up Cl- ions. A suspension of gill cells dissociated using ethylenediaminetetraacetic acid (EDTA) was labelled with biotinylated PNA that was detected using streptavidin conjugated to a fluorophore, and subjected to FACS to yield a population of PNA+ ionocytes of high viability and purity. To validate the utility of the approach, it was used in a proof-of-principle experiment to evaluate transcript abundance of cytosolic carbonic anhydrase (CAc) in PNA+ ionocytes in trout that were subjected to metabolic alkalosis. This experiment revealed that the relative transcript abundance of CAc was significantly elevated in PNA+ ionocytes of alkalotic trout relative to that of control trout (P = 0.001; N = 7), a response that is consistent with the expected role of PNA+ ionocytes in compensation for systemic alkalosis.

A fixed population of oocytes within primordial follicles, established prior to or just after birth has been firmly believed to support the postnatal mammalian ovary throughout an individual’s reproductive lifespan. However, the identification and isolation of cells from adult mammalian ovaries characterised by the expression of both germ and stem cell markers, suggest the presence of mitotically active cells, termed oogonial stem cells (OSCs) that may have the potential to produce new oocytes in the postnatal mammalian ovary. Putative OSCs have been isolated from adult tissues of several mammalian species, including rodents and humans. Upon reintroduction to the ovarian niche, human and rodent OSCs have generated new oocyte like structures which, at least in rodents, have generated functional oocytes capable of fertilisation and subsequent embryonic development to produce healthy offspring. We hypothesised that OSCs could be isolated from adult bovine ovaries and upon establishment within the appropriate ovarian niche could initiate successful oogenesis. To investigate this hypothesis, we have utilised fluorescently activated cell sorting (FACS) to isolate putative bovine OSCs (bOSCs) and an ovarian aggregate model, in vitro and in vivo to explore the oogenic potential of these cells. Putative bOSCs were successfully isolated by FACS based on the cell surface expression of germ cell marker DDX4 and established in culture. Pluripotency (LIN28 and OCT4) and germ (IFITM3, PRDM1, C-KIT and DAZL) cell associated genes were expressed in putative bOSCs established in culture. However, DDX4 transcripts were not consistently observed throughout bOSC culture. Aggregation of putative bOSCs with neonatal murine ovarian somatic cells to form chimeric ovarian aggregates, cultured in a hanging drop model for 7 days maintained germ cell phenotype, marked by DAZL expression. A subpopulation of putative bOSCs showed a spherical morphology, an increase in cell size and an association with neighbouring cells. Xenotransplantation of chimeric ovarian aggregates to the kidney capsule of immune deficient mice for 21 days generated multi-laminar follicles and structures with morphological similarities to primordial follicles (termed pre-primordial follicle-like structures). RNA Scope was unsuccessful in determining the origin of oocytes within chimeric ovarian aggregates. However, oocytes from pre-antral follicles in chimeric ovarian aggregates (n=6; 60.9± 3.6 μm, mean ± SEM) were significantly (P < 0.0001) larger than murine oocytes (n=38; 34.5± 1 μm, mean ± SEM) aggregated with murine ovarian somatic cells as positive controls, suggesting that these oocytes are undergoing different growth dynamics. This work has shown that putative bOSCs characterised by the expression of pluripotency and germ cell associated genes are present within adult bovine ovarian tissue and can be isolated using FACS and established in culture. These data also suggest that putative bOSCs may have the potential to undergo oogenesis and illustrate the potential use of these cells as a tool to investigate germ cell differentiation.

Philosophiae Doctor - PhD / The estimated 5 × 10³⁰ prokaryotic cells inhabiting our planet sequester some 350–550 Petagrams (1 Pg = 1015 g) of carbon, 85–130 Pg of nitrogen, and 9–14 Pg of phosphorous, making them the largest reservoir of those nutrients on Earth (Whitman et al. 1998). However, reports suggest that only less than 1% of these microscopic organisms are cultivable (Torsvik et al. 1990; Sleator et al. 2008). Until recently with the development of metagenomic techniques, the knowledge of microbial diversity and their metabolic capabilities has been limited to this small fraction of cultivable organisms (Handelsman et al. 1998). While metagenomics has undoubtedly revolutionised the field of microbiology and biotechnology it has been generally acknowledged that the current approaches for metagenomic bio- rospecting / screening have limitations which hinder this approach to fully access the metabolic potentials and genetic variations contained in microbial genomes (Beloqui et al. 2008). In particular, the construction of metagenomic libraries and heterologous expression are amongst the major obstacles. The aim of this study was to develop an ultra-high throughput approach for screening enzyme activities using uncloned metagenomic DNA, thereby eliminating cloning steps, and employing in vitro heterologous expression. To achieve this, three widely used techniques: cell-free transcription-translation, in vitro compartmentalisation (IVC) and Fluorescence Activated Cell Sorting (FACS) were combined to develop this robust technique called metagenomic in vitro compartmentalisation (mIVC-FACS). Moreover, the E. coli commercial cell-free system was used in parallel to a novel, in-house Rhodococcus erythropolis based cell-free system. The versatility of this technique was tested by identifying novel beta-xylosidase encoding genes derived from a thermophilic compost metagenome. In addition, the efficiency of mIVC-FACS was compared to the traditional metagenomic approaches; function-based (clone library screening) and sequence-based (shotgun sequencing and PCR screening). The results obtained here show that the R. erythropolis cell-free system was over thirty-fold more effective than the E. coli based system based on the number of hits obtained per million double emulsions (dE) droplets screened. Six beta-xylosidase encoding genes were isolated and confirmed from twenty-eight positive dE droplets. Most of the droplets that were isolated from the same gate encoded the same enzyme, indicating that this technique is highly selective. A comparison of the hit rate of this screening approach with the traditional E. coli based fosmid library method shows that mIVC-FACS is at least 2.5 times more sensitive. Although only a few hits from the mIVC-FACS screening were selected for confirmation of beta-xylosidase activity, the proposed hit rate suggests that a significant number of positive hits are left un-accessed through the traditional clone library screening system. In addition, these results also suggest that E. coli expression system might be intrinsically sub-optimal for screening for hemicellulases from environmental genomes compared to R. erythropolis system. The workflow required for screening one million clones in a fosmid library was estimated to be about 320 hours compared to 144 hours required via the mIVC-FACS screening platform. Some of the gene products obtained in both screening platforms show multiple substrate activities, suggesting that the microbial consortia of composting material consist of microorganisms that produce enzymes with multiple lignocellulytic activities. While this platform still requires optimisation, we have demonstrated that this technique can be used to isolate genes encoding enzymes from mixed microbial genomes. mIVC-FACS is a promising technology with the potential to take metagenomic studies to the second generation of novel natural products bio-prospecting. The astonishing sensitivity and ultra-high throughput capacity of this technology offer numerous advantages in metagenomic bio-prospecting. / National Research Foundation (NRF)

京都大学 / 新制・課程博士 / 博士(医学) / 甲第25177号 / 医博第5063号 / 新制||医||1071(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 川口 義弥, 教授 山中 伸弥, 教授 湊谷 謙司 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

The discovery of neural stem cells (NSC) within the adult mammalian brain continues to fuel optimism regarding the ability of potential regenerative medicine applications to provide enhanced functional recovery from brain injuries. The adult NSC population is maintained within a complex microenvironment, referred to as the niche, where a unique cellular and extracellular environment maintains and regulates the NSC population and their progeny, enabling ongoing neurogenesis throughout adulthood. Characterization of how NSC interact with the extracellular environment and other cell subpopulations is an active area of research that will generate fundamental design parameters for biomaterial and tissue engineering strategies for neural tissue repair. A major obstacle to further progress is the lack of access to purified populations of primary NSC, a challenge which became the focus of this thesis. To address this obstacle, experimental methods were developed and optimized for isolating neural stem and progenitor cells (NSPC) from the adult NSC niche with fluorescence activated cell sorting (FACS). These methods were enhanced by the incorporation of a fluorescent reporter mouse driven by the gene Sox2, a neural stem cell associated transcription factor, which allowed NSPC enrichment within the Sox2+ population. The FACS based research approach was further developed to include additional surface antigens allowing isolation of NSPC at over 34% purity. The highly enriched population of NSPC was subjected to vital dye cell cycle analysis leading to the observation that an active and quiescent fraction exists within the NSPC pool that is delineated by β1-integrin expression. Access to enriched primary adult NSPC will lead to more a more accurate understanding of NSC dynamics with implications in fundamental biological research as well as biomaterials and tissue engineering.

Neben chemotherapeutischen und chirurgischen Maßnahmen ist die Bestrahlung integraler Bestandteil multimodaler Therapiekonzepte bei malignen Tumorerkrankungen. In diesem Zusammenhang spielt der Einblick in physiologische und pathophysiologische Abläufe in menschlichen Zellen und auf molekularer Ebene  eine zunehmende Rolle. Auf diese Weise werden komplexe Stoffwechselwege mit ihren unterschiedlichen Funktionen und ihren aus einzelnen Proteinen bestehenden Komponenten immer besser verstanden. Allerdings entstehen durch die Kenntnis dieser Stoffwechselwege neue Fragen, die Gegenstand medizinischer Forschung sind.  Der TGFβ-Signalweg ist ein wesentlicher intrazellulärer Signalweg, der neben zahlreichen anderen Funktionen einen Einfluss auf die Entstehung bestimmter Tumorerkrankungen hat. Eine Vielzahl an Einzelnukleotid-Polymorphismen (single nucleotide polymorphisms, SNP) ist bekannt sowie die Erkenntnis darüber, dass die Anwesenheit von verschiedenen Varianten eines SNP einen Einfluss auf die Zellvitalität hat je nach Behandlungsbedingung. Ziel dieser Arbeit war es den Einfluss von Keimbahn-Polymorphismen in Genen des TGFβ-Signalwegs und der DNA-Reparatur auf die Strahlenempfindlichkeit lymphoblastoider Zellen zu untersuchen. Hierzu wurden 54 käuflich erworbene lymphoblastoide Zellen angezüchtet. Jede dieser Zelllinien wurde sechs parallelen Behandlungsbedingungen unterworfen. Neben der unbehandelten Kontrolle und einer mit anti-TGFβ behandelten Kontrolle wurden Zellen einer alleinigen Bestrahlung mit 3 Gy ausgesetzt. Darüber hinaus wurden Zellen 16 Stunden vor der Bestrahlung mit TGFβ1 oder anti-TGFβ vorinkubiert oder unmittelbar nach der Bestrahlung mit TGFβ1 behandelt.  Nach Ablauf einer 24-stündigen Inkubationszeit erfolgte die Zellvitalitätsmessung mittels FACS (fluorescence activated cell sorting)–Analyse. Die Ergebnisse wurden mit Daten von insgesamt 1656 polymorphen Positionen (aus HapMap Datenbank) aus 21 Kandidatengenen korreliert. Auf diese Weise sollte der Einfluss dieser Polymorphismen auf die Zellvitalität ermittelt werden. Sowohl bei SMAD3 als auch bei SMAD7 fanden sich jeweils 2 SNP, die ein perfektes bzw hohes Kopplungsungleichgewicht (linkage disequilibrium) aufwiesen. Insgesamt waren zwölf Polymorphismen aus acht Genen (TGFBR1, SMAD2, SMAD3, SMAD7, BRCA2, MSH2, MSH6 und XRCC1) mit signifikanten Veränderungen der Zellvitalität assoziiert. Das Variantenallel scheint bis auf wenige Ausnahmen einen zytoprotektiven Effekt zu haben. Ausnahmen sind 3 SNP der Gene BRCA2, SMAD3 und SMAD 7, bei denen der Wildtyp mit höherer Zellvitalität einhergeht. Bei alleiniger Bestrahlung wirkten sich SNP aus SMAD3, SMAD7, MSH2 und MSH6 modulierend auf die Zytotoxizität aus, wenn auch statistisch nicht signifikant. Interessanterweise zeigten sich bei Betrachtung der Auswirkung einer Stimulation mit TGFβ1 vor und nach Bestrahlung mit 3 Gy dieselben SNP als statistisch signifikante Modellprädiktoren wie auch bei alleiniger Bestrahlung mit Ausnahme eines SNP aus SMAD3.  Bei Vorinkubation mit TGFβ1 wirkte sich die MSH2-Variante stärker aus. Hier entstand beim Wildtyp ein zusätzlich zytotoxischer Einfluss im Vergleich zur Stimulation nach Bestrahlung. Bei Inhibition durch anti-TGFβ vor der Bestrahlung zeigte noch ein SNP aus MSH6 und ein SNP aus SMAD7 einen zytoprotektiven Effekt.  Einige Ergebnisse dieser Arbeit könnten, sofern sie im Verlauf durch nachfolgende Studien bestätigt bzw. erweitert werden helfen Therapiekonzepte maligner Tumoren zu optimieren und eine individuelle Radiotherapie zu ermöglichen.

The Diploma Thesis deals with an implementation of the new method for an assessment of a cloning efficiency of the cancer stem cells separated by a high speed cell sorter. The cell-sowing on the microtitration plates was performed by the flow cytometry method in a combination with the high speed cell sorter. In the first part of the Diploma Thesis the new method was introduced and tested on the selected cell lines. The obtained results were compared with the results of the limiting dilution assay within four cell lines. As for the second part of my Diploma Thesis, the method was practically applied to analysis of the cloning capacity of two subpopulations of cE2 cells based on the expressions of characteristic markers of stem and cancer stem cells - CD44 and CD 133. Based on the findings, the new method can be introduced as an approved proceeding for the cloning capacity assessment of cancer stem cells in other workplaces that possess analogical device equipment.