THE SPATIAL ORGANIZATION OF TRANSCRIPTION IN E. COLI

Transcription, the process of converting genetic information stored in DNA to RNA, lies at the heart of gene expression. Transcription has been studied extensively in vitro to probe its mechanistic detail; however, these conditions differ vastly from the complex environment inside a living cell. Spatial distributions of molecular components have been shown to be an important facet of gene regulation in living systems. First, to gain insight into the regulation of gene expression at the cellular level, we investigated the spatial distributions of various molecular components of transcription in E. coli and their physical correlation with each other using superresolution fluorescence microscopy (Chapter 2). Our results show that while dense RNAP clusters are highly colocalized with rrn operons and nascent rRNA transcripts during fast growth, these RNAP clusters are present independent of rRNA transcription activity, and are likely stably associated with the underlying chromosome structure. Second, we provided the first direct observation of transcription factor mediated DNA looping in live E. coli, and calculated in vivo looping frequencies in the context of different regulatory regimes (Chapter 3). Third, we initiated the development of a reconstituted CRISPR-Cas system to effectively visualize sequence specific genomic sites in live cells in a high-throughput manner. This system would allow for unprecedented insight into eukaryotic genome architecture in intact living cells; Chapter 4 details our efforts in optimizing the reconstituted CRISPR-Cas system first using in vitro assays

The SIK1/CRTC2/CREB1 and TWIST1/PI3K/Akt/GSK3β signaling pathways mediated by microRNA-25-3p are altered in the schizophrenic rat brain

Schizophrenia is a group of severe mental disorders. MiR-25-3p was shown to be involved in various neuropsychiatric diseases and can regulate SIK1 and TWIST1. The CRTC2/CREB1 and PI3K/Akt/GSK3β signaling pathways are downstream pathways of SIK1 and TWIST1, respectively. This study investigated whether miR-25-3p-mediated SIK1/CRTC2/CREB1 and TWIST1/PI3K/Akt/GSK3β signaling pathways are present in an animal model relevant to schizophrenia. A schizophrenic rat model was established by using sub-chronic MK-801 administration. An RNA-seq test was performed to examine the differentially expressed genes (DEGs) in the rat prefrontal cortex (PFC). The mRNA levels of miR-25-3p, SIK1, and TWIST in the PFC and caudate putamen (CPu) were assessed by qRT-PCR. Phosphorylation of the SIK1/CRTC2/CREB1 and TWIST1/PI3K/Akt/GSK3β pathways in the two brain regions was examined by Western blots. The RNA-seq data revealed down-regulated miR-25-3p expression and up-regulated SIK1 and TWIST1 mRNA expression induced by MK-801. Additionally, SIK1 and TWIST1 were shown to be possible downstream responders of miR-25-3p in previous studies. qRT-PCR confirmed the changes of miR-25-3p, SIK1, and TWIST1 induced by MK-801 in both brain regions, which, however, was reversed by risperidone. Furthermore, the phosphorylation of the SIK1/CRTC2/CREB1 pathway was repressed by MK-801, whereas the phosphorylation of the TWIST1/PI3K/Akt/GSK3β pathway was increased by MK-801 in either of the two brain regions. Moreover, the altered phosphorylation of these two signaling pathways induced by MK-801 can be restored by risperidone. In conclusion, this study suggests that altered SIK1/CRTC2/CREB1 and TWIST1/PI3K/Akt/GSK3β signaling pathways mediated by miR-25-3p is very likely to be associated with schizophrenia, revealing potential targets for the treatment and clinical diagnosis of schizophrenia

Unusual Fermi Surface Sheet-Dependent Band Splitting in Sr2RuO4 Revealed by High Resolution Angle-Resolved Photoemission

High resolution angle-resolved photoemission measurements have been carried out on Sr2RuO4. We observe clearly two sets of Fermi surface sheets near the (\pi,0)-(0,\pi) line which are most likely attributed to the surface and bulk Fermi surface splitting of the \beta band. This is in strong contrast to the nearly null surface and bulk Fermi surface splitting of the \alpha band although both have identical orbital components. Extensive band structure calculations are performed by considering various scenarios, including structural distortion, spin-orbit coupling and surface ferromagnetism. However, none of them can explain such a qualitative difference of the surface and bulk Fermi surface splitting between the \alpha and \beta sheets. This unusual behavior points to an unknown order on the surface of Sr2RuO4 that remains to be uncovered. Its revelation will be important for studying and utilizing novel quantum phenomena associated with the surface of Sr2RuO4 as a result of its being a possible p-wave chiral superconductor and a topological superconductor.Comment: 13 pages, 4 figure

Dasatinib vs. imatinib in patients with chronic myeloid leukemia in chronic phase (CML-CP) who have not achieved an optimal response to 3 months of imatinib therapy: the DASCERN randomized study

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Effect of Cleaving Temperature on the Surface and Bulk Fermi Surface of Sr2RuO4 Investigated by High Resolution Angle-Resolved Photoemission

High resolution angle-resolved photoemission measurements are carried out to systematically investigate the effect of cleaving temperature on the electronic structure and Fermi surface of Sr$_2$RuO$_4$. Different from previous reports that high cleaving temperature can suppress surface Fermi surface, we find that the surface Fermi surface remains obvious and strong in Sr$_2$RuO$_4$ cleaved at high temperature, even at room temperature. This indicates that cleaving temperature is not a key effective factor in suppressing the surface bands. On the other hand, in the aged surface of Sr$_2$RuO$_4$ that is cleaved and held for a long time, the bulk bands can be enhanced. We have also carried out laser ARPES measurements on Sr$_2$RuO$_4$ by using vacuum ultra-violet laser (photon energy at 6.994 eV) and found an obvious enhancement of bulk bands even for samples cleaved at low temperature. These information are important in realizing an effective approach in manipulating and detecting the surface and bulk electronic structure of Sr$_2$RuO$_4$. In particular, the enhancement of bulk sensitivity, together with its super-high instrumental resolution of VUV laser ARPES, will be advantageous in investigating fine electronic structure and superconducting properties of Sr$_2$RuO$_4$ in the future