1
|
Kinebuchi T, Idota N, Tsuboi H, Takaso M, Bando R, Ikegaya H. The genome profiling method can be applied for species identification of biological materials collected at crime scenes. BMC Genet 2019; 20:50. [PMID: 31182029 PMCID: PMC6558897 DOI: 10.1186/s12863-019-0753-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 05/29/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Various biological materials unrelated to humans are found at crime scenes and it is often important to elucidate the origin of these materials. A genetic locus common to several species is conventionally PCR-amplified with universal primers to identify species. However, not all species can be identified using a single locus. In this study, DNA from 13 commonly handled taxa was analyzed to identify species by a genome profiling (GP) method, which involves random PCR and temperature gradient gel electrophoresis. RESULTS In a clustering analysis, we successfully obtained a single cluster for each species. CONCLUSION The GP method is cost-effective and does not require advanced techniques and knowledge in molecular biology. The random sampling of the whole genome using multiple primers provides substantial genomic information. Therefore, the method is effective for classifying a wide range of species, including animals, plants, and insects, and is useful for crime scene investigations.
Collapse
Affiliation(s)
- Takako Kinebuchi
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan
| | - Nozomi Idota
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan
| | - Hajime Tsuboi
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan
| | - Marin Takaso
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan
| | - Risa Bando
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan
| | - Hiroshi Ikegaya
- Department of Forensic Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajiicho, Kamigyo, Kyoto, 602-8566, Japan.
| |
Collapse
|
2
|
Kumari P, Gautam SG, Baba M, Tsukiashi M, Matsuoka K, Yasukawa K, Nishigaki K. DNA-based mutation assay GPMA (genome profiling-based mutation assay): reproducibility, parts-per-billion scale sensitivity, and introduction of a mammalian-cell-based approach. J Biochem 2017; 162:395-401. [PMID: 29186523 DOI: 10.1093/jb/mvx043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 05/28/2017] [Indexed: 11/12/2022] Open
Abstract
Genome profiling-based mutation assay (GPMA) is, to date, the only DNA sequence-based mutation assay that directly measures DNA alterations induced by mutagens. Here, the all-important congruence of mutagen assignment between DNA-based GPMA and the phenotype-based Ames test (the gold standard of mutagen assays) was confirmed qualitatively and semi-quantitatively by means of 94 chemical species (including previously examined 64). The high sensitivity (on the order of 10 ppb) and reproducibility of GPMA were also corroborated by the match between virtually independent experiments conducted in the distant past (10 years ago) and recently. Meanwhile, a standard experimental framework was established: the conditions of 100 parts per billion (ppb) concentration of a chemical and 15-generation culture of Escherichia coli. Moreover, a mammalian cell line (NIH 3T3) was shown to be suitable as a tester organism for the GPMA approach. Preliminary experimental results suggested that this approach can provide a qualitatively equivalent and quantitatively different mutagen assay results relative to the bacteria-based GPMA (renamed as bGPMA). This finding confirmed the effectiveness of the GPMA approach and indicates that mGPMA is a promising way to detect mammalian-cell mutagens.
Collapse
Affiliation(s)
- Parmila Kumari
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Sunita Ghimire Gautam
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Misato Baba
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Motoki Tsukiashi
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Koji Matsuoka
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Kiyoshi Yasukawa
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Koichi Nishigaki
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan.,Center for Single Nanoscale Innovative Devices, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| |
Collapse
|
3
|
Idota N, Tsuboi H, Takaso M, Tojo M, Kinebuchi T, Nakamura M, Ichioka H, Shintani-Ishida K, Ikegaya H. Comparison between Temperature Gradient Gel Electrophoresis of Bacterial 16S rDNA and Diatom Test for Diagnosis of Drowning. J Forensic Sci 2017; 63:752-757. [DOI: 10.1111/1556-4029.13606] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/04/2017] [Accepted: 07/05/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Nozomi Idota
- Department of Forensic Medicine; Graduate School of Medical Science; Kyoto Prefectural University of Medicine; 465 Kajii-cho Kamigyo-ku Kyoto 602-8566 Japan
| | - Hajime Tsuboi
- Department of Forensic Medicine; Graduate School of Medical Science; Kyoto Prefectural University of Medicine; 465 Kajii-cho Kamigyo-ku Kyoto 602-8566 Japan
| | - Marin Takaso
- Department of Forensic Medicine; Graduate School of Medical Science; Kyoto Prefectural University of Medicine; 465 Kajii-cho Kamigyo-ku Kyoto 602-8566 Japan
| | - Misa Tojo
- Department of Forensic Medicine; Graduate School of Medical Science; Kyoto Prefectural University of Medicine; 465 Kajii-cho Kamigyo-ku Kyoto 602-8566 Japan
| | - Takako Kinebuchi
- Department of Forensic Medicine; Graduate School of Medical Science; Kyoto Prefectural University of Medicine; 465 Kajii-cho Kamigyo-ku Kyoto 602-8566 Japan
| | - Mami Nakamura
- Department of Forensic Medicine; Graduate School of Medical Science; Kyoto Prefectural University of Medicine; 465 Kajii-cho Kamigyo-ku Kyoto 602-8566 Japan
| | - Hiroaki Ichioka
- Department of Forensic Medicine; Graduate School of Medical Science; Kyoto Prefectural University of Medicine; 465 Kajii-cho Kamigyo-ku Kyoto 602-8566 Japan
| | - Kaori Shintani-Ishida
- Department of Forensic Medicine; Graduate School of Medical Science; Kyoto Prefectural University of Medicine; 465 Kajii-cho Kamigyo-ku Kyoto 602-8566 Japan
| | - Hiroshi Ikegaya
- Department of Forensic Medicine; Graduate School of Medical Science; Kyoto Prefectural University of Medicine; 465 Kajii-cho Kamigyo-ku Kyoto 602-8566 Japan
| |
Collapse
|
4
|
Diwan D, Masubuchi Y, Furukawa T, Nishigaki K. Ordered genome change of plant and animal body cells revealed by the genome profiling method. FEBS Lett 2016; 590:2119-26. [PMID: 27277546 DOI: 10.1002/1873-3468.12248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/14/2016] [Accepted: 05/20/2016] [Indexed: 01/30/2023]
Abstract
In the past, it was widely thought that, although epigenetically different, the genome sequences of cells are basically the same in a single body. In retrospect, the genome-uniformity idea may have been naïve, considering that DNA polymerases cannot be perfect. Here, a systemic, not sporadic, genome change was demonstrated in a single plant (Arabidopsis) and animal (zebrafish) body using genome DNAs taken in an ordered manner using the genome profiling method. This can be explained because mutations accumulate additively in progeny cells, and these results are critically significant for developmental and oncological research.
Collapse
Affiliation(s)
- Deepti Diwan
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Yuki Masubuchi
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Tatsuya Furukawa
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, Japan
| | - Koichi Nishigaki
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, Japan
| |
Collapse
|
5
|
Tanaka Y, Hirata R, Mashita K, Mclean S, Ikegaya H. Detection of Human Polyomavirus DNA Using the Genome Profiling Method. Open Virol J 2015; 9:29-37. [PMID: 28484580 PMCID: PMC5396359 DOI: 10.2174/1874357901509010029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 10/28/2015] [Accepted: 10/28/2015] [Indexed: 11/25/2022] Open
Abstract
Background In the field of forensic medicine, it is very difficult to know prior to autopsy what kind of virus has infected a body. Objective We assessed the potential of the genome profiling (GP) method, which was developed in the field of bioengineering, to identify viruses belonging to one species. Method Two species in the same family, JC and BK viruses, were used in this study. Using plasmid samples, we compared the findings of molecular phylogenetic analysis using conventional genome sequencing with the results of cluster analysis using the random PCR-based GP method and discussed whether the GP method can be used to determine viral species. Results It was possible to distinguish these two different viral species. In addition to this, in our trial we could also detect the JC virus from a clinical sample. Conclusion This method does not require special reagent sets for each viral species. Though our findings are still in the trial period, the GP method may be a simple, easy, and economical tool to detect viral species in the near future.
Collapse
Affiliation(s)
- Yuka Tanaka
- Department of Forensic Medicine, Kyoto Prefectural University of Medicine Graduate School of Medical Sciences, 465 Kajii-cho Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Rieko Hirata
- Department of Forensic Medicine, Kyoto Prefectural University of Medicine Graduate School of Medical Sciences, 465 Kajii-cho Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Kyohei Mashita
- Department of Forensic Medicine, Kyoto Prefectural University of Medicine Graduate School of Medical Sciences, 465 Kajii-cho Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Stuart Mclean
- Department of Forensic Medicine, Kyoto Prefectural University of Medicine Graduate School of Medical Sciences, 465 Kajii-cho Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Hiroshi Ikegaya
- Department of Forensic Medicine, Kyoto Prefectural University of Medicine Graduate School of Medical Sciences, 465 Kajii-cho Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto 602-8566, Japan
| |
Collapse
|
6
|
Kumari P, Kamiseki M, Biyani M, Suzuki M, Nemoto N, Aita T, Nishigaki K. Detection of ultra-low levels of DNA changes by drinking water: epidemiologically important finding. J Biochem 2014; 157:113-9. [PMID: 25406322 DOI: 10.1093/jb/mvu072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The safety of drinking water is essential to our health. In this context, the mutagenicity of water needs to be checked strictly. However, from the methodological limit, the lower concentration (less than parts per million) of mutagenicity could not be detected, though there have been of interest in the effect of less concentration mutagens. Here, we describe a highly sensitive mutation assay that detects mutagens at the ppb level, termed genome profiling-based mutation assay (GPMA). This consists of two steps; (i) Escherichia coli culture in the medium with/without mutagens and (ii) Genome profiling (GP) method (an integrated method of random PCR, temperature gradient gel electrophoresis and computer-aided normalization). Owing to high sensitivity of this method, very low concentration of mutagens in tap water could be directly detected without introducing burdensome concentration processes, enabling rapid measurement of low concentration samples. Less expectedly, all of the tap waters tested (22 samples) were shown to be significantly mutagenic while mineral waters were not. Resultantly, this article informs two facts that the GPMA method is competent to measure the mutagenicity of waters directly and the experimental results supported the former reports that the city tap waters contain very low level of mutagenicity reagent trihalomethanes.
Collapse
Affiliation(s)
- Parmila Kumari
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-Ku, Saitama-City, Saitama 338-8570, Japan and Department of Bioengineering, University of Tokyo 2-11-16, Yayoi, Bunkyo-Ku, Tokyo 113-8656, Japan
| | - Meiko Kamiseki
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-Ku, Saitama-City, Saitama 338-8570, Japan and Department of Bioengineering, University of Tokyo 2-11-16, Yayoi, Bunkyo-Ku, Tokyo 113-8656, Japan
| | - Manish Biyani
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-Ku, Saitama-City, Saitama 338-8570, Japan and Department of Bioengineering, University of Tokyo 2-11-16, Yayoi, Bunkyo-Ku, Tokyo 113-8656, Japan
| | - Miho Suzuki
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-Ku, Saitama-City, Saitama 338-8570, Japan and Department of Bioengineering, University of Tokyo 2-11-16, Yayoi, Bunkyo-Ku, Tokyo 113-8656, Japan
| | - Naoto Nemoto
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-Ku, Saitama-City, Saitama 338-8570, Japan and Department of Bioengineering, University of Tokyo 2-11-16, Yayoi, Bunkyo-Ku, Tokyo 113-8656, Japan
| | - Takuyo Aita
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-Ku, Saitama-City, Saitama 338-8570, Japan and Department of Bioengineering, University of Tokyo 2-11-16, Yayoi, Bunkyo-Ku, Tokyo 113-8656, Japan
| | - Koichi Nishigaki
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-Ku, Saitama-City, Saitama 338-8570, Japan and Department of Bioengineering, University of Tokyo 2-11-16, Yayoi, Bunkyo-Ku, Tokyo 113-8656, Japan
| |
Collapse
|
7
|
Sharma H, Kinoshita Y, Fujiu S, Nomura S, Sawada M, Ahmed S, Shibuya M, Shirai K, Takamatsu S, Watanabe T, Yamazaki H, Kamiyama R, Kobayashi T, Arai H, Suzuki M, Nemoto N, Ando K, Uchida H, Kitamura K, Takei O, Nishigaki K. Establishment of a reborn MMV-microarray technology: realization of microbiome analysis and other hitherto inaccessible technologies. BMC Biotechnol 2014; 14:78. [PMID: 25141858 PMCID: PMC4153446 DOI: 10.1186/1472-6750-14-78] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Accepted: 08/15/2014] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND With the accelerating development of bioscience, the problem of research cost has become important. We previously devised and developed a novel concept microarray with manageable volumes (MMV) using a soft gel. It demonstrated the great potential of the MMV technology with the examples of 1024-parallel-cell culture and PCR experiments. However, its full potential failed to be expressed, owing to the nature of the material used for the MMV chip. RESULTS In the present study, by developing plastic-based MMVs and associated technologies, we introduced novel technologies such as C2D2P (in which the cells in each well are converted from DNA to protein in 1024-parallel), NGS-non-dependent microbiome analysis, and other powerful applications. CONCLUSIONS The reborn MMV-microarray technology has proven to be highly efficient and cost-effective (with approximately 100-fold cost reduction) and enables us to realize hitherto unattainable technologies.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Koichi Nishigaki
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama 338-8570, Japan.
| |
Collapse
|
8
|
Diwan D, Komazaki S, Suzuki M, Nemoto N, Aita T, Satake A, Nishigaki K. Systematic genome sequence differences among leaf cells within individual trees. BMC Genomics 2014; 15:142. [PMID: 24548431 PMCID: PMC3937000 DOI: 10.1186/1471-2164-15-142] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 02/10/2014] [Indexed: 01/09/2023] Open
Abstract
Background Even in the age of next-generation sequencing (NGS), it has been unclear whether or not cells within a single organism have systematically distinctive genomes. Resolving this question, one of the most basic biological problems associated with DNA mutation rates, can assist efforts to elucidate essential mechanisms of cancer. Results Using genome profiling (GP), we detected considerable systematic variation in genome sequences among cells in individual woody plants. The degree of genome sequence difference (genomic distance) varied systematically from the bottom to the top of the plant, such that the greatest divergence was observed between leaf genomes from uppermost branches and the remainder of the tree. This systematic variation was observed within both Yoshino cherry and Japanese beech trees. Conclusions As measured by GP, the genomic distance between two cells within an individual organism was non-negligible, and was correlated with physical distance (i.e., branch-to-branch distance). This phenomenon was assumed to be the result of accumulation of mutations from each cell division, implying that the degree of divergence is proportional to the number of generations separating the two cells.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Koichi Nishigaki
- Graduate School of Science and Engineering, Department of Functional Materials Science, Saitama University, Saitama 338-8570, Japan.
| |
Collapse
|
9
|
Sharma H, Ohtani F, Kumari P, Diwan D, Ohara N, Kobayashi T, Suzuki M, Nemoto N, Matsushima Y, Nishigaki K. Familial clustering of mice consistent to known pedigrees enabled by the genome profiling (GP) method. Biophysics (Nagoya-shi) 2014; 10:55-62. [PMID: 27493499 PMCID: PMC4629661 DOI: 10.2142/biophysics.10.55] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 08/21/2014] [Indexed: 12/01/2022] Open
Abstract
Familial clustering without any prerequisite knowledge becomes often necessary in Behavioral Science, and forensic studies in case of great disasters like Tsunami and earthquake requiring body-identification without any usable information. However, there has been no well-established method for this purpose although conventional ones such as short tandem repeats (STR) and single nucleotide polymorphism (SNP), which might be applied with toil and moil to some extent. In this situation, we could find that the universal genome distance-measuring method genome profiling (GP), which is made up of three elemental techniques; random PCR, micro-temperature gradient gel electrophoresis (μTGGE), and computer processing for normalization, can do this purpose with ease when applied to mouse families. We also confirmed that the sequencing approach based on the ccgf (commonly conserved genetic fragment appearing in the genome profile) was not completely discriminative in this case. This is the first demonstration that the familial clustering can be attained without a priori sequence information to the level of discriminating strains and sibling relationships. This method can complement the conventional approaches in preliminary familial clustering.
Collapse
Affiliation(s)
- Harshita Sharma
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama 338-8570, Japan
| | - Fumihito Ohtani
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama 338-8570, Japan
| | - Parmila Kumari
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama 338-8570, Japan
| | - Deepti Diwan
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama 338-8570, Japan
| | - Naoko Ohara
- Department of Regulatory Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama 338-8570, Japan
| | - Tetsuya Kobayashi
- Department of Regulatory Biology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama 338-8570, Japan
| | - Miho Suzuki
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama 338-8570, Japan
| | - Naoto Nemoto
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama 338-8570, Japan
| | | | - Koichi Nishigaki
- Department of Functional Materials Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama 338-8570, Japan
| |
Collapse
|
10
|
Hamano K, Ueno-Tsuji S, Tanaka R, Suzuki M, Nishimura K, Nishigaki K. Genome profiling (GP) as an effective tool for monitoring culture collections: a case study with Trichosporon. J Microbiol Methods 2012; 89:119-28. [PMID: 22401825 DOI: 10.1016/j.mimet.2012.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 02/08/2012] [Accepted: 02/10/2012] [Indexed: 11/28/2022]
Abstract
Species identification and classification of a large number of microbes are essential and heavy workloads in culture collections and relevant laboratories. The identification of species usually requires different methods depending on species. Therefore, the development of a method which is simple and applicable to any organisms will lessen the burdens, increase the reliability of databases and thus enhance the science on microbes. The genome profiling (GP) method, developed previously, was found effective in monitoring authenticities of all strains/species tested in culture collections and expectedly various species, which was shown by applying the GP and the conventional sequencing methods to identifying and classifying species/strains belonging to the genus Trichosporon (38 strains; 16 species). Small differences between strains (11 strains of Trichosporon asahii and 4 strains of Trichosporon coremiiforme) can be reliably discriminated by GP, which was unsuccessful in the conventional sequencing approach. Importantly, seven possible false-assignments contained in the database were all pointed out by the GP method with near-perfect correctness, showing the power of the GP method.GP was shown to be a potent tool for rapidly and correctly monitoring species and strains of fungi in culture collections owing to its simple and informative natures.
Collapse
Affiliation(s)
- Keiichi Hamano
- Rational Evolutionary Design of Advanced Biomolecules, Saitama Small Enterprise Promotion Corporation, SKIP city, 3-12-18 Kamiaoki, Kawaguchi, Saitama 333-0844, Japan.
| | | | | | | | | | | |
Collapse
|
11
|
Human blood identification using the genome profiling method. Leg Med (Tokyo) 2012; 14:121-5. [PMID: 22285643 DOI: 10.1016/j.legalmed.2012.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 01/04/2012] [Accepted: 01/05/2012] [Indexed: 11/23/2022]
Abstract
In criminal investigations, usually it is necessary to identify whether blood spots found at crime scenes are from humans or not. Nowadays, immunohistochemical methods and DNA analysis are usually used for this purpose. However, such methods and DNA analysis are labor intensive and expensive, and require highly trained skilled technicians. Recently, the genome profiling method (GP method) was developed. However, its use as a human DNA analysis method has not been reported. In this report, an attempt was made to differentiate human blood samples from animal blood samples using the GP method for forensic purposes. DNA extracted from a rat, squirrel, cat, dog, cow, and antelope along with human blood samples were analyzed. Following cluster analysis the human samples clustered into a single group separate from the animal samples. Therefore, although the number of samples was small the results suggest that the GP method might enable us to differentiate human samples from various animal samples. It may become a powerful tool in the field of forensic science.
Collapse
|
12
|
Ahmed S, Komori M, Tsuji-Ueno S, Suzuki M, Kosaku A, Miyamoto K, Nishigaki K. Genome profiling (GP) method based classification of insects: congruence with that of classical phenotype-based one. PLoS One 2011; 6:e23963. [PMID: 21912611 PMCID: PMC3166070 DOI: 10.1371/journal.pone.0023963] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 08/02/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Ribosomal RNAs have been widely used for identification and classification of species, and have produced data giving new insights into phylogenetic relationships. Recently, multilocus genotyping and even whole genome sequencing-based technologies have been adopted in ambitious comparative biology studies. However, such technologies are still far from routine-use in species classification studies due to their high costs in terms of labor, equipment and consumables. METHODOLOGY/PRINCIPAL FINDINGS Here, we describe a simple and powerful approach for species classification called genome profiling (GP). The GP method composed of random PCR, temperature gradient gel electrophoresis (TGGE) and computer-aided gel image processing is highly informative and less laborious. For demonstration, we classified 26 species of insects using GP and 18S rDNA-sequencing approaches. The GP method was found to give a better correspondence to the classical phenotype-based approach than did 18S rDNA sequencing employing a congruence value. To our surprise, use of a single probe in GP was sufficient to identify the relationships between the insect species, making this approach more straightforward. CONCLUSION/SIGNIFICANCE The data gathered here, together with those of previous studies show that GP is a simple and powerful method that can be applied for actually universally identifying and classifying species. The current success supported our previous proposal that GP-based web database can be constructible and effective for the global identification/classification of species.
Collapse
Affiliation(s)
- Shamim Ahmed
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Manabu Komori
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Sachika Tsuji-Ueno
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Miho Suzuki
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Akinori Kosaku
- Laboratory of Clinical Sciences, Dokkyo Medical University, Tochigi, Japan
| | - Kiyoshi Miyamoto
- Laboratory of Medical Sciences, Dokkyo Medical University, Tochigi, Japan
| | - Koichi Nishigaki
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| |
Collapse
|
13
|
Tominaga T. Rapid determination of multi-locus sequence types of Listeria monocytogenes by microtemperature-gradient gel electrophoresis. J Microbiol Methods 2007; 70:471-8. [PMID: 17628727 DOI: 10.1016/j.mimet.2007.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2007] [Revised: 05/21/2007] [Accepted: 06/04/2007] [Indexed: 11/25/2022]
Abstract
This report presents a new method for identifying multi-locus sequence types of Listeria monocytogenes by microtemperature-gradient gel electrophoresis (mu-TGGE). Genomic comparison of L. monocytogenes serovar 1/2a strains EGD-e and F6854 allowed selection of novel polymorphic sequences lmo0386 and lmo0428 as optimum regions for mu-TGGE analysis, in addition to the previously identified lmo0297 gene. Sequence analysis of a total of 48 standard strains revealed that the strains could be grouped into 7 (lmo0386), 8 (lmo0428) and 12 (lmo0297) sequence types. The PCR products from 2, 4 and 4 sequence types of the lmo0386, lmo0428 and lmo0297 genes were selected as marker alleles, and mu-TGGE analysis of the mixture revealed adequate band separation on a single gel. Furthermore, the primer sets could be successfully mixed in a single tube for multiplex PCR, yielding a rapid and easy strategy for sequence type identification. For practical application, multiplex PCR was performed with Cy3-labeled primers against a sequence type-unknown sample isolated from meat. The resulting products were mixed with Cy5-labeled products of marker alleles whose sequence types were known, and mu-TGGE analysis was performed. Overlapping Cy3 and Cy5 patterns allowed identification of the sequence types at all 3 loci on a single gel. Moreover, the mu-TGGE analysis step took only 9 min. Thus, this novel method of multiplex PCR followed by mu-TGGE analysis could prove useful as a rapid and discriminative tool for tracing the strain types, contamination routes and sources of L. monocytogenes.
Collapse
Affiliation(s)
- Tatsuya Tominaga
- Saitama Industrial Technology Center North Institute, 2-133, Suehiro, Kumagaya, Saitama 360-0031, Japan.
| |
Collapse
|
14
|
Futakami M, Salimullah M, Miura T, Tokita S, Nishigaki K. Novel Mutation Assay with High Sensitivity based on Direct Measurement of Genomic DNA Alterations: Comparable Results to the Ames Test. ACTA ACUST UNITED AC 2007; 141:675-86. [PMID: 17383979 DOI: 10.1093/jb/mvm074] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Almost all of the methodologies developed to date to assay the potential mutagenicity of chemical substances are based on detection of altered phenotypic traits. The alternative approach of directly screening the whole genome for mutations is not feasible because of the logistics of carrying out mass sequencing of genes. Here we describe a novel and highly sensitive mutation assay, which we term the 'genome profiling-based mutation assay' (GPMA) that directly detects mutations generated in genomic DNA. We used GPMA to detect mutations caused by known mutagens such as AF2 and ethidium bromide even at concentrations of 30 ppb. The number of mutations detected was dependent on the number of generations in culture and the concentrations of the mutagens. Almost complete agreement was observed between GPMA and the Ames test in the discrimination of mutagens (63 out of 64). Owing to the high sensitivity of GPMA, the effects of long-term and low-dose exposures and the influence of chemicals of low solubility can also be screened. Thus, genotype-based GPMA can complement the Ames test, which is the standard technology in this field and is based on phenotypic traits.
Collapse
Affiliation(s)
- Masae Futakami
- Department of Functional Materials Science, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | | | | | | | | |
Collapse
|
15
|
Futakami M, Nishigaki K. Measurement of DNA Mutations Caused by Seconds-period UV-irradiation. CHEM LETT 2007. [DOI: 10.1246/cl.2007.358] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
16
|
Kouduka M, Sato D, Komori M, Kikuchi M, Miyamoto K, Kosaku A, Naimuddin M, Matsuoka A, Nishigaki K. A solution for universal classification of species based on genomic DNA. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2007; 2007:27894. [PMID: 18253463 PMCID: PMC1893011 DOI: 10.1155/2007/27894] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2006] [Revised: 10/08/2006] [Accepted: 10/08/2006] [Indexed: 05/25/2023]
Abstract
Traditionally, organisms have been classified on the basis of their phenotype. Recently, genotype-based classification has become possible through the development of sequencing technology. However, it is still difficult to apply sequencing approaches to the analysis of a large number of species due to the cost and labor. In most biological fields, the analysis of complex systems comprising various species has become an important theme, demanding an effective method for handling a vast number of species. In this paper, we have demonstrated, using plants, fish, and insects, that genome profiling, a compact technology for genome analysis, can classify organisms universally. Surprisingly, in all three of the domains of organisms tested, the phylogenetic trees generated from the phenotype topologically matched completely those generated from the genotype. Furthermore, a single probe was sufficient for the genome profiling, thereby demonstrating that this methodology is universal and compact.
Collapse
Affiliation(s)
- Mariko Kouduka
- Department of Functional Materials Science, Saitama University, Saitama, Japan
| | - Daisuke Sato
- Department of Functional Materials Science, Saitama University, Saitama, Japan
| | - Manabu Komori
- Department of Functional Materials Science, Saitama University, Saitama, Japan
| | - Motohiro Kikuchi
- Chitose Salmon Aquarium Chitose, Youth Educational Foundation, Chitose, Hokkaido, Japan
| | - Kiyoshi Miyamoto
- Institute of Medical Science, Dokkyo Medical University, Tochigi, Japan
| | - Akinori Kosaku
- Institute of Medical Science, Dokkyo Medical University, Tochigi, Japan
| | - Mohammed Naimuddin
- Department of Functional Materials Science, Saitama University, Saitama, Japan
- Biol. Res. and Functions, National Inst. AIST, Tsukuba, Ibaraki, Japan
| | | | - Koichi Nishigaki
- Department of Functional Materials Science, Saitama University, Saitama, Japan
- Rational Evolutionary Design of Advanced Biomolecules, Saitama Small Enterprise Promotion Corporation, SKIP City, Saitama, Japan
| |
Collapse
|
17
|
Tominaga T. Rapid discrimination of Listeria monocytogenes strains by microtemperature gradient gel electrophoresis. J Clin Microbiol 2006; 44:2199-206. [PMID: 16757621 PMCID: PMC1489441 DOI: 10.1128/jcm.00344-06] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microtemperature gradient gel electrophoresis (mu-TGGE) was examined for use for the rapid subtyping of Listeria monocytogenes strains. Comparison of genomes between L. monocytogenes strains F2365 and H7858 identified a sequence encoding a portion of the PRT/PTS system IIA 2 protein domain as appropriate for mu-TGGE analysis. Thirty-one strains belonging to 10 different serovar types were tested by PCR, and sequence analysis of the amplified products revealed that the strains comprise 11 groups. All 55 possible pairs within the 11 groups were examined by mu-TGGE analysis. Of these, 47 pairs could be successfully discriminated, with a total electrophoresis time of only 7 min. Moreover, Cy3/Cy5 labeling allowed rapid identification of the sequence type in unknown strains of L. monocytogenes isolated from meat. These findings collectively indicate that mu-TGGE can be used for the rapid analysis of L. monocytogenes strains, facilitating determination of routes of contamination when these bacteria are found in food products.
Collapse
Affiliation(s)
- Tatsuya Tominaga
- Saitama Industrial Technology Center North Institute, 2-133, Suehiro, Kumagaya, Saitama 360-0031, Japan.
| |
Collapse
|
18
|
Kouduka M, Matuoka A, Nishigaki K. Acquisition of genome information from single-celled unculturable organisms (radiolaria) by exploiting genome profiling (GP). BMC Genomics 2006; 7:135. [PMID: 16740170 PMCID: PMC1523345 DOI: 10.1186/1471-2164-7-135] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Accepted: 06/02/2006] [Indexed: 11/21/2022] Open
Abstract
Background There is no effective method to obtain genome information from single-celled unculturable organisms such as radiolarians. Even worse, such organisms are often very difficult to collect. Sequence analysis of 18S rDNA has been carried out, but obtaining the data has been difficult and it has provided a rather limited amount of genome information. In this paper, we have developed a method which provides a sufficient amount of data from an unculturable organism. The effectiveness of this method was demonstrated by applying it to the provisional classification of a set of unculturable organisms (radiolarians). Results Dendrogram was drawn regarding the single-celled unculturable species based on the similarity score termed PaSS, offering a consistent result with the conventional taxonomy of them built up based on phenotypes. This fact has shown that genome profiling-based technology developed here can obtain genome information being sufficient for identifying and classifying species from a single-celled organism. Conclusion Since this method is so simple, general, and yet powerful, it can be applied to various organisms and cells, especially single-celled, uncluturable ones, for their genome analysis.
Collapse
Affiliation(s)
- Mariko Kouduka
- Department of Functional Materials Science, Saitama University, Saitama, Japan
| | - Atsushi Matuoka
- Department of Geology Historical Geology, Niigata University, Niigata, Japan
| | - Koichi Nishigaki
- Department of Functional Materials Science, Saitama University, Saitama, Japan
| |
Collapse
|
19
|
Tominaga T. Rapid identification of pickle yeasts by fluorescent PCR and microtemperature-gradient gel electrophoresis. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09735.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
20
|
Naimuddin M, Kurazono T, Nishigaki K. Commonly conserved genetic fragments revealed by genome profiling can serve as tracers of evolution. Nucleic Acids Res 2002; 30:e42. [PMID: 12000847 PMCID: PMC115296 DOI: 10.1093/nar/30.10.e42] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We developed a method to produce, identify and analyze DNA fragments for the purpose of taxonomic classification. Genome profiling (GP) is a strategy that identifies genomic DNA fragments common to closely related species without prior knowledge of the DNA sequence. Random PCR, one of the key technologies of GP, is used to produce fragments and may be used even when there are mutations at the priming site. These fragments can then be distinguished based on the information of mobility and melting pattern when subjected to temperature gradient gel electrophoresis (TGGE). Corresponding fragments among several species, designated as commonly conserved genetic fragments (CCGFs), likely have the same genetic origin or correspond to the same gene. The criteria for identification of CCGFs has been defined and presented here. To assess this prediction, some of the fragments were sequenced and were confirmed to be CCGFs. We show that genome profiles bearing evolutionarily conserved CCGFs can be used to classify organisms and trace evolutionary pathways, among other profound applications.
Collapse
Affiliation(s)
- Mohammed Naimuddin
- Department of Functional Materials Science, Faculty of Engineering, Saitama University, 255 Shimo-Okubo, Saitama, Saitama 338-8570, Japan
| | | | | |
Collapse
|
21
|
Watanabe T, Saito A, Takeuchi Y, Naimuddin M, Nishigaki K. A database for the provisional identification of species using only genotypes: web-based genome profiling. Genome Biol 2002; 3:RESEARCH0010. [PMID: 11864372 PMCID: PMC65688 DOI: 10.1186/gb-2002-3-2-research0010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2001] [Revised: 10/22/2001] [Accepted: 12/05/2001] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND For a long time one could not imagine being able to identify species on the basis of genotype only as there were no technological means to do so. But conventional phenotype-based identification requires much effort and a high level of skill, making it almost impossible to analyze a huge number of organisms, as, for example, in microbe-related biological disciplines. Comparative analysis of 16S rRNA has been changing the situation, however. We report here an approach that will allow rapid and accurate phylogenetic comparison of any unknown strain to all known type strains, enabling tentative assignments of strains to species. The approach is based on two main technologies: genome profiling and Internet-based databases. RESULTS A complete procedure for provisional identification of species using only their genomes is presented, using random polymerase chain reaction, temperature-gradient gel electrophoresis, image processing to generate 'species-identification dots' (spiddos) and data processing. A database website for this purpose was also constructed and operated successfully. The protocol was standardized to make the system reproducible and reliable. The overall methodology thus established has remarkable aspects in that it enables non-experts to obtain an initial species identification without a lot of effort and is self-developing; that is, species can be determined more definitively as the database is used more and accumulates more genome profiles. CONCLUSIONS We have devised a methodology that enables provisional identification of species on the basis of their genotypes only. It is most useful for microbe-related disciplines as they face the most serious difficulties in species identification.
Collapse
Affiliation(s)
- Takehiro Watanabe
- Department of Functional Materials Science, Saitama University, 255 Shimo-Okubo, Saitama, Saitama 338-8570, Japan.
| | | | | | | | | |
Collapse
|
22
|
Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2001. [PMCID: PMC2448396 DOI: 10.1002/cfg.59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|