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Reed J, Mishra B, Pittenger B, Magonov S, Troke J, Teitell MA, Gimzewski JK. Single molecule transcription profiling with AFM. NANOTECHNOLOGY 2007; 18:44032. [PMID: 20721301 PMCID: PMC2922717 DOI: 10.1088/0957-4484/18/4/044032] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. Due to greatly increasing interest in examining minute samples from micro-dissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. Here, we examine the use of single molecule, ordered restriction mapping, combined with AFM, to measure gene transcription levels from very low abundance samples. We frame the problem mathematically, using coding theory, and present an analysis of the critical error sources that may serve as a guide to designing future studies. We follow with experiments detailing the construction of high density, single molecule, ordered restriction maps from plasmids and from cDNA molecules, using two different enzymes, a result not previously reported. We discuss these results in the context of our calculations.
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Affiliation(s)
- Jason Reed
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Bud Mishra
- Department of Computer Science and Mathematics, Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
| | | | | | - Joshua Troke
- Department of Pathology and the Center for Cell Control, an NIH Nanomedicine Development Center, UCLA, Los Angeles, CA 90095, USA
| | - Michael A Teitell
- Department of Pathology and the Center for Cell Control, an NIH Nanomedicine Development Center, UCLA, Los Angeles, CA 90095, USA
- California Nanosystems Institute (CNSI), Los Angeles, CA 90095, USA
| | - James K Gimzewski
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
- California Nanosystems Institute (CNSI), Los Angeles, CA 90095, USA
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Kobashi H, Yaoi T, Oda R, Okajima S, Fujiwara H, Kubo T, Fushiki S. Lysophospholipid receptors are differentially expressed in rat terminal Schwann cells, as revealed by a single cell rt-PCR and in situ hybridization. Acta Histochem Cytochem 2006; 39:55-60. [PMID: 17375210 PMCID: PMC1828080 DOI: 10.1267/ahc.06002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2006] [Accepted: 03/03/2006] [Indexed: 11/22/2022] Open
Abstract
Terminal Schwann cells (TSCs) that cover motor neuron terminals, are known to play an important role in maintaining neuromuscular junctions, as well as in the repair process after nerve injury. However, the molecular characteristics of TSCs remain unknown, because of the difficulties in analyzing them due to their paucity. By using our previously reported method of selectively and efficiently collecting TSCs, we have analyzed the difference in expression patterns of lysophospholipid (LPL) receptor genes (LPA1, LPA2, LPA3, S1P1, S1P2, S1P3, S1P4, and S1P5) between TSCs and myelinating Schwann cells (MSCs). LPL, which includes lysophosphatidic acid (LPA) and sphingosine 1-phosphate (S1P), is the bioactive lipid that induces a myriad of cellular responses through specific members of G-protein coupled receptors for LPA. It turned out that LPA3 was expressed only in TSCs, whereas S1P1 was expressed in TSCs and skeletal muscle, but not in MSCs. Other types of LPL receptor genes, including LPA1, S1P2, S1P3, S1P4, were expressed in both types of Schwann cells. None of the LPL receptor gene family showed MSCs-specific expression.
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Affiliation(s)
- Hiroaki Kobashi
- Department of Pathology and Applied Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine,Kawaramachi-Hirokoji, Kyoto 602–8566, Japan
- Department of Orthopaedics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kyoto 602–8566, Japan
| | - Takeshi Yaoi
- Department of Pathology and Applied Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine,Kawaramachi-Hirokoji, Kyoto 602–8566, Japan
| | - Ryo Oda
- Department of Orthopaedics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kyoto 602–8566, Japan
| | - Seiichiro Okajima
- Department of Orthopaedics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kyoto 602–8566, Japan
| | - Hiroyoshi Fujiwara
- Department of Orthopaedics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kyoto 602–8566, Japan
| | - Toshikazu Kubo
- Department of Orthopaedics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kyoto 602–8566, Japan
| | - Shinji Fushiki
- Department of Pathology and Applied Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine,Kawaramachi-Hirokoji, Kyoto 602–8566, Japan
- Correspondence to: Shinji Fushiki, Department of Pathology and Applied Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kyoto 602–8566, Japan. E-mail:
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Hirota R, Itoh K, Yaoi T, Bamba H, Uno T, Hisa Y, Fushiki S. Molecular Changes in Neurons of Rat Nucleus Ambiguus after Axotomy, As Revealed by a Novel Method of In Vivo Fluorescence Neuronal Labeling Combined with Single-cell RT-PCR. Acta Histochem Cytochem 2005. [DOI: 10.1267/ahc.38.229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Ryuichi Hirota
- Department of Pathology and Applied Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Kyoko Itoh
- Department of Pathology and Applied Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Takeshi Yaoi
- Department of Pathology and Applied Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Hitoshi Bamba
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Toshiyuki Uno
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Yasuo Hisa
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| | - Shinji Fushiki
- Department of Pathology and Applied Neurobiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
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Sakaguchi H, Yaoi T, Suzuki T, Okano H, Hisa Y, Fushiki S. Spatiotemporal patterns of Musashi1 expression during inner ear development. Neuroreport 2004; 15:997-1001. [PMID: 15076722 DOI: 10.1097/00001756-200404290-00013] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Musashi1 (Msi 1) is an RNA binding protein associated with asymmetric cell divisions in neural progenitor cells. To investigate the involvement of Msi1 in the inner ear development, we studied the expression of Msi1 in mouse inner ears with RT-PCR and immunohistochemistry. Immunohistochemistry revealed that Msi1 was expressed in all otocyst cells at embryonic day (E) 10 and 12. Msi1 immunoreactivity became lost in hair cells after E14 in vestibule and after E16 in cochlea, whereas it persisted in supporting cells until adulthood. The subcellular localization of Msi1 changed from "cytoplasmic predominance" to "nuclear predominance" during the first 2 weeks after birth. The present data suggested that Msi may play a role in inner ear development.
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Affiliation(s)
- Hirofumi Sakaguchi
- Department of Pathology and Applied Neurobiology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
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