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Article ; Online: Roles of microRNAs in cancers and development.

Takasaki, Shigeru

Methods in molecular biology (Clifton, N.J.)

2015 Volume 1218, Page(s) 375–413

Abstract: MicroRNAs (miRNAs) are small noncoding RNA molecules thought to play an important role in regulating gene expression. Although knowledge of the biological functions of most miRNAs is still limited, miRNAs are thought to regulate the gene expression in ... ...

Abstract	MicroRNAs (miRNAs) are small noncoding RNA molecules thought to play an important role in regulating gene expression. Although knowledge of the biological functions of most miRNAs is still limited, miRNAs are thought to regulate the gene expression in various diseases and embryo development. In this chapter, the roles of miRNAs in human cancers are first examined from the viewpoint of up- and downregulation. Oncogenic miRNAs are involved in the overexpression/upregulation of cancers, whereas suppressive miRNAs are involved in the underexpression/downregulation of cancers. Statistical analysis of the positional nucleotide occurrence features of miRNAs revealed differences between the positional nucleotide occurrences of oncogenic and suppressive miRNAs. A miRNA gene-silencing score was then defined on the basis of the higher and lower levels of the statistical significances of positional nucleotides. Since the miRNA scores were closely related to miRNA frequencies, a method using the scores and nucleotide frequencies to distinguish whether a new miRNA is oncogenic or suppressive is proposed. This chapter also describes the roles of miRNAs in development. As miRNAs can act as cis-regulatory elements in the early embryonic development of Drosophila melanogaster, it is proposed that they mediate signal transduction between genes.
MeSH term(s)	Animals ; Base Composition ; Base Sequence ; Biomarkers, Tumor/chemistry ; Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism ; Cell Transformation, Neoplastic/genetics ; Cell Transformation, Neoplastic/metabolism ; Cell Transformation, Neoplastic/pathology ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster/genetics ; Drosophila melanogaster/growth & development ; Drosophila melanogaster/metabolism ; Embryo, Nonmammalian ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Gene Expression Regulation, Neoplastic ; Gene Silencing ; Humans ; MicroRNAs/chemistry ; MicroRNAs/classification ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Molecular Sequence Data ; Neoplasms/genetics ; Neoplasms/metabolism ; Neoplasms/pathology ; Signal Transduction
Chemical Substances	Biomarkers, Tumor ; Drosophila Proteins ; MicroRNAs
Language	English
Publishing date	2015
Publishing country	United States
Document type	Journal Article ; Review
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-1538-5_24
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Article: Dengue fever.

Tajima, Shigeru / Takasaki, Tomohiko

Nihon rinsho. Japanese journal of clinical medicine

2019 Volume 74, Issue 12, Page(s) 2042–2046

Abstract: Dengue fever is mosquito-transmitted viral diseases. Dengue viruses (DENV) belong to the family Flaviviridae, which includes other clinically important human pathogenic flavivi- ruses. No effective antiviral drugs exist to treat dengue, however, a ... ...

Abstract	Dengue fever is mosquito-transmitted viral diseases. Dengue viruses (DENV) belong to the family Flaviviridae, which includes other clinically important human pathogenic flavivi- ruses. No effective antiviral drugs exist to treat dengue, however, a vaccine for dengue has been licensed in several countries recently. DENV infections are a major cause of morbidity and mortality in most tropical and subtropical areas of the world, but they have also emerged in other regions. In August 2014, an autochthonous case of dengue fever in a patient who had not traveled endemic country was reported in Tokyo after 70 years with no dengue out- breaks.
MeSH term(s)	Dengue/prevention & control ; Humans
Language	Japanese
Publishing date	2019-01-15
Publishing country	Japan
Document type	Journal Article
ZDB-ID	390903-7
ISSN	0047-1852
ISSN	0047-1852
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Article ; Online: Methods for selecting effective siRNA target sequences using a variety of statistical and analytical techniques.

Takasaki, Shigeru

Methods in molecular biology (Clifton, N.J.)

2013 Volume 942, Page(s) 17–55

Abstract: Short interfering RNA (siRNA) has been widely used for studying gene function in mammalian cells but varies markedly in its gene silencing efficacy. Although many design rules/guidelines for effective siRNAs based on various criteria have been reported ... ...

Abstract	Short interfering RNA (siRNA) has been widely used for studying gene function in mammalian cells but varies markedly in its gene silencing efficacy. Although many design rules/guidelines for effective siRNAs based on various criteria have been reported recently, there are only a few consistencies among them. This makes it difficult to select effective siRNA sequences in mammalian genes. This chapter first reviews the recently reported siRNA design guidelines and then proposes new methods for selecting effective siRNA sequences from many possible candidates by using decision tree learning, Bayes' theorem, and average silencing probability on the basis of a large number of known effective siRNAs. These methods differ from the previous score-based siRNA design techniques and can predict the probability that a candidate siRNA sequence will be effective. Evaluation of these methods by applying them to recently reported effective and ineffective siRNA sequences for a number of genes indicates that they would be useful for many other genes. They should, therefore, be of general utility for selecting effective siRNA sequences for mammalian genes. The chapter also describes another method using a hidden Markov model to select the optimal functional siRNAs and discusses the frequencies of combinations of two successive nucleotides as an important characteristic of effective siRNA sequences.
MeSH term(s)	Base Sequence ; Bayes Theorem ; Decision Trees ; Gene Silencing ; Genetic Engineering/methods ; Humans ; Markov Chains ; Nucleotides/genetics ; RNA, Small Interfering/genetics ; Statistics as Topic/methods
Chemical Substances	Nucleotides ; RNA, Small Interfering
Language	English
Publishing date	2013
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-62703-119-6_2
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Article ; Online: Japanese Alzheimer's disease and other complex disorders diagnosis based on mitochondrial SNP haplogroups.

Takasaki, Shigeru

International journal of Alzheimer's disease

2012 Volume 2012, Page(s) 245038

Abstract: This paper first explains how the relations between Japanese Alzheimer's disease (AD) patients and their mitochondrial SNP frequencies at individual mtDNA positions examined using the radial basis function (RBF) network and a method based on RBF network ... ...

Abstract	This paper first explains how the relations between Japanese Alzheimer's disease (AD) patients and their mitochondrial SNP frequencies at individual mtDNA positions examined using the radial basis function (RBF) network and a method based on RBF network predictions and that Japanese AD patients are associated with the haplogroups G2a and N9b1. It then describes a method for the initial diagnosis of Alzheimer's disease that is based on the mtSNP haplogroups of the AD patients. The method examines the relations between someone's mtDNA mutations and the mtSNPs of AD patients. As the mtSNP haplogroups thus obtained indicate which nucleotides of mtDNA loci are changed in the Alzheimer's patients, a person's probability of becoming an AD patient can be predicted by comparing those mtDNA mutations with that person's mtDNA mutations. The proposed method can also be used to diagnose diseases such as Parkinson's disease and type 2 diabetes and to identify people likely to become centenarians.
Language	English
Publishing date	2012-07-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	2573333-3
ISSN	2090-0252 ; 2090-8024
ISSN (online)	2090-0252
ISSN	2090-8024
DOI	10.1155/2012/245038
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Article ; Online: Japanese Alzheimer’s Disease and Other Complex Disorders Diagnosis Based on Mitochondrial SNP Haplogroups

Shigeru Takasaki

International Journal of Alzheimer's Disease, Vol

2012 Volume 2012

Keywords	Geriatrics ; RC952-954.6 ; Special situations and conditions ; RC952-1245 ; Internal medicine ; RC31-1245 ; Medicine ; R ; DOAJ:Internal medicine ; DOAJ:Medicine (General) ; DOAJ:Health Sciences ; Neurosciences. Biological psychiatry. Neuropsychiatry ; RC321-571 ; DOAJ:Neurology
Language	English
Publishing date	2012-01-01T00:00:00Z
Publisher	Hindawi Publishing Corporation
Document type	Article ; Online
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Article: Comparative analysis of the susceptibility of Aedes aegypti and Japanese Aedes albopictus to all dengue virus serotypes.

Kobayashi, Daisuke / Kai, Izumi / Faizah, Astri Nur / Moi, Meng Ling / Tajima, Shigeru / Takasaki, Tomohiko / Sasaki, Toshinori / Isawa, Haruhiko

Tropical medicine and health

2023 Volume 51, Issue 1, Page(s) 61

Abstract: Background: Dengue fever, caused by the dengue virus (DENV), is the most common viral infection transmitted by Aedes mosquitoes (mainly Ae. aegypti and Ae. albopictus) worldwide. Aedes aegypti is not currently established in Japan, and Ae. albopictus is ...

Abstract	Background: Dengue fever, caused by the dengue virus (DENV), is the most common viral infection transmitted by Aedes mosquitoes (mainly Ae. aegypti and Ae. albopictus) worldwide. Aedes aegypti is not currently established in Japan, and Ae. albopictus is the primary vector mosquito for DENV in the country, but knowledge of its viral susceptibility is limited. Therefore, we aimed to clarify the status of DENV susceptibility by comparing the infection and dissemination dynamics of Japanese Ae. albopictus to all known DENV serotypes with those of Ae. aegypti. Methods: After propagation of each DENV serotype in Vero cells, the culture supernatants were mixed with defibrinated rabbit blood and adenosine triphosphate, and the mixture was artificially blood-sucked by two colonies of Ae. albopictus from Japan and one colony of Ae. aegypti from a dengue-endemic country (Vietnam). After 14 days of sucking, the mosquito body was divided into two parts (thorax/abdomen and head/wings/legs) and total RNA was extracted from each sample. DENV RNA was detected in these extracted RNA samples using a quantitative RT-PCR method specific for each DENV serotype, and infection and dissemination rates were analyzed. Results: The Japanese Ae. albopictus colonies were susceptible to all DENV serotypes. Its infection and dissemination rates were significantly lower than those of Ae. aegypti. However, the number of DENV RNA copies in Ae. albopictus was almost not significantly different from that in Ae. aegypti. Furthermore, Japanese Ae. albopictus differed widely in their susceptibility to each DENV serotype. Conclusions: In Japanese Ae. albopictus, once DENV overcame the midgut infection barrier, the efficiency of subsequent propagation and dissemination of the virus in the mosquito body was comparable to that of Ae. aegypti. Based on the results of this study and previous dengue outbreak trends, Ae. albopictus is predicted to be highly compatible with DENV-1, suggesting that this serotype poses a high risk for future epidemics in Japan.
Language	English
Publishing date	2023-11-02
Publishing country	Japan
Document type	Journal Article
ZDB-ID	2209835-5
ISSN	1349-4147 ; 1348-8945
ISSN (online)	1349-4147
ISSN	1348-8945
DOI	10.1186/s41182-023-00553-5
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Article ; Online: Efficient prediction methods for selecting effective siRNA sequences.

Takasaki, Shigeru

Computers in biology and medicine

2010 Volume 40, Issue 2, Page(s) 149–158

Abstract: Although short interfering RNA (siRNA) has been widely used for studying gene functions in mammalian cells, its gene silencing efficacy varies markedly and there are only a few consistencies among the recently reported design rules/guidelines for ... ...

Abstract	Although short interfering RNA (siRNA) has been widely used for studying gene functions in mammalian cells, its gene silencing efficacy varies markedly and there are only a few consistencies among the recently reported design rules/guidelines for selecting siRNA sequences effective for mammalian genes. Another shortcoming of the previously reported methods is that they cannot estimate the probability that a candidate sequence will silence the target gene. This paper first reviewed the recently reported siRNA design guidelines and clarified the problems concerning the guidelines. It then proposed two prediction methods-Radial Basis Function (RBF) network and decision tree learning-and their combined method for selecting effective siRNA target sequences from many possible candidate sequences. They are quite different from the previous score-based siRNA design techniques and can predict the probability that a candidate siRNA sequence will be effective. The methods imply high estimation accuracy for selecting candidate siRNA sequences.
MeSH term(s)	Algorithms ; Animals ; Artificial Intelligence ; Base Sequence ; Computational Biology/methods ; Computer-Aided Design ; Databases, Nucleic Acid ; Decision Trees ; Gene Silencing ; Humans ; Neural Networks (Computer) ; Probability ; RNA Interference ; RNA, Small Interfering/genetics ; RNA, Small Interfering/metabolism ; ROC Curve
Chemical Substances	RNA, Small Interfering
Language	English
Publishing date	2010-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2009.11.011
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Article ; Online: Comparative analysis of the susceptibility of Aedes aegypti and Japanese Aedes albopictus to all dengue virus serotypes

Daisuke Kobayashi / Izumi Kai / Astri Nur Faizah / Meng Ling Moi / Shigeru Tajima / Tomohiko Takasaki / Toshinori Sasaki / Haruhiko Isawa

Tropical Medicine and Health, Vol 51, Iss 1, Pp 1-

2023 Volume 9

Abstract: Abstract Background Dengue fever, caused by the dengue virus (DENV), is the most common viral infection transmitted by Aedes mosquitoes (mainly Ae. aegypti and Ae. albopictus) worldwide. Aedes aegypti is not currently established in Japan, and Ae. ... ...

Abstract	Abstract Background Dengue fever, caused by the dengue virus (DENV), is the most common viral infection transmitted by Aedes mosquitoes (mainly Ae. aegypti and Ae. albopictus) worldwide. Aedes aegypti is not currently established in Japan, and Ae. albopictus is the primary vector mosquito for DENV in the country, but knowledge of its viral susceptibility is limited. Therefore, we aimed to clarify the status of DENV susceptibility by comparing the infection and dissemination dynamics of Japanese Ae. albopictus to all known DENV serotypes with those of Ae. aegypti. Methods After propagation of each DENV serotype in Vero cells, the culture supernatants were mixed with defibrinated rabbit blood and adenosine triphosphate, and the mixture was artificially blood-sucked by two colonies of Ae. albopictus from Japan and one colony of Ae. aegypti from a dengue-endemic country (Vietnam). After 14 days of sucking, the mosquito body was divided into two parts (thorax/abdomen and head/wings/legs) and total RNA was extracted from each sample. DENV RNA was detected in these extracted RNA samples using a quantitative RT-PCR method specific for each DENV serotype, and infection and dissemination rates were analyzed. Results The Japanese Ae. albopictus colonies were susceptible to all DENV serotypes. Its infection and dissemination rates were significantly lower than those of Ae. aegypti. However, the number of DENV RNA copies in Ae. albopictus was almost not significantly different from that in Ae. aegypti. Furthermore, Japanese Ae. albopictus differed widely in their susceptibility to each DENV serotype. Conclusions In Japanese Ae. albopictus, once DENV overcame the midgut infection barrier, the efficiency of subsequent propagation and dissemination of the virus in the mosquito body was comparable to that of Ae. aegypti. Based on the results of this study and previous dengue outbreak trends, Ae. albopictus is predicted to be highly compatible with DENV-1, suggesting that this serotype poses a high risk for future epidemics in ...
Keywords	Dengue ; DENV ; DENV-1 ; Mosquito ; Aedes ; Aedes albopictus ; Arctic medicine. Tropical medicine ; RC955-962
Subject code	630
Language	English
Publishing date	2023-11-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Selecting effective siRNA target sequences by using Bayes' theorem.

Takasaki, Shigeru

Computational biology and chemistry

2009 Volume 33, Issue 5, Page(s) 368–372

Abstract: Short interfering RNA (siRNA) has been widely used for studying gene functions in mammalian cells but varies markedly in its gene silencing efficacy. Although many design rules/guidelines for effective siRNAs based on various criteria have been reported ... ...

Abstract	Short interfering RNA (siRNA) has been widely used for studying gene functions in mammalian cells but varies markedly in its gene silencing efficacy. Although many design rules/guidelines for effective siRNAs based on various criteria have been reported recently, there are few consistencies among them. This makes it difficult to select effective siRNA sequences in mammalian genes. Another shortcoming of most previously reported methods is that they cannot estimate the probability that a candidate sequence will silence the target gene. The analytical prediction method proposed in the present study uses Bayes' theorem to select effective siRNA target sequences from many possible candidate sequences. It is quite different from the previous score-based siRNA design techniques and can predict the probability that a candidate siRNA sequence will be effective. The results of evaluating it by applying it to recently reported effective and ineffective siRNA sequences for various genes indicate that it would be useful for many other genes. It should therefore be useful for selecting siRNA sequences effective for mammalian genes.
MeSH term(s)	Animals ; Bayes Theorem ; Computational Biology ; Gene Silencing ; Models, Genetic ; RNA, Small Interfering/genetics ; ROC Curve ; Substrate Specificity
Chemical Substances	RNA, Small Interfering
Language	English
Publishing date	2009-10
Publishing country	England
Document type	Journal Article
ISSN	1476-928X
ISSN (online)	1476-928X
DOI	10.1016/j.compbiolchem.2009.07.009
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Article: Methods for selecting effective siRNA sequences by using statistical and clustering techniques.

Takasaki, Shigeru

Methods in molecular biology (Clifton, N.J.)

2009 Volume 487, Page(s) 1–39

Abstract: Short interfering RNAs (siRNAs) have been widely used for studying gene functions in mammalian cells but vary markedly in their gene-silencing efficacy. Although many design rules/guidelines for effective siRNAs based on various criteria have been ... ...

Abstract	Short interfering RNAs (siRNAs) have been widely used for studying gene functions in mammalian cells but vary markedly in their gene-silencing efficacy. Although many design rules/guidelines for effective siRNAs based on various criteria have been reported recently, there are only a few consistencies among them. This makes it difficult to select effective siRNA sequences targeting mammalian genes. This chapter first reviews the reported siRNA design guidelines and clarifies the problems concerning the current guidelines. It then describes the recently reported new scoring methods for selecting effective siRNA sequences by using statistics and clustering techniques such as the self-organizing map (SOM) and the radial basis function (RBF) network. In the proposed three methods, individual scores are defined as a gene degradation measure based on position-specific statistical significances. The effectiveness of the methods was confirmed by evaluating effective and ineffective siRNAs for recently reported genes and comparison with other reported scoring methods. The sizes (values) of these scores are closely correlated with the degree of gene degradation, and the scores can easily be used for selecting high-potential siRNA candidates. The evaluation results indicate that the proposed new methods are useful for selecting siRNA sequences targeting mammalian mRNA sequences.
MeSH term(s)	Animals ; Cluster Analysis ; Computational Biology/methods ; Gene Silencing ; Humans ; RNA, Small Interfering/genetics ; RNA, Small Interfering/isolation & purification
Chemical Substances	RNA, Small Interfering
Language	English
Publishing date	2009
Publishing country	United States
Document type	Journal Article ; Review
ISSN	1064-3745
ISSN	1064-3745
DOI	10.1007/978-1-60327-547-7_1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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