1,768 results on '"Base sequence"'
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2. Regulation by gravity of ferulate formation in cell walls of rice seedlings
- Author
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Japan Aerospace Exploration Agency
- Subjects
gravitational effect ,重力効果 ,細胞 ,細胞壁 ,phenylalanine ,rice ,peroxidase ,hydrogen peroxide ,cell ,plant (botany) ,base sequence ,フェニルアラニン ,遺伝子発現 ,ペルオキシダーゼ ,フェルラ酸 ,植物 ,gene expression ,過酸化水素 ,cell wall ,イネ ,塩基配列 ,ferulic acid - Abstract
イネ科植物の細胞壁結合性フェルラ酸とジフェルラ酸の形成には、フェニルアラニンアンモニアリアーゼ(PAL: Phenylalanine Ammonia Lyase)とペルオキシダーゼ(POD: Peroxidase)が重要な役割を担っている。PALとPODには複数の遺伝子が存在し、ファミリーを形成していることから、今年度の研究では、解析対象となる遺伝子の絞り込みと、それら遺伝子の発現解析条件について検討した。また、細胞壁内に存在するシュウ酸酸化酵素(germin)がPOD活性に必須の過酸化水素の生成・供給を介して、ジフェルラ酸の形成に影響する可能性について、活性細胞壁標品を用いて検討した。, Phenylalanine Ammonia-Lyase (PAL) and cell wall Peroxidase (POD) have been shown to be involved in the formation of cell wall-bound ferulic and diferulic acids in graminaceous plants. In rice plants, PAL and POD are encoded by the multi-gene families. In the present study, we chose suitable genes for the analysis of expression level of PAL and POD genes in rice shoots and also determined their analytical conditions. In addition, the contribution of oxalate oxidase (germin) to the formation of diferulic acid in cell walls was examined using isolated active cell wall preparations, because the oxalate oxidase has been shown to produce hydrogen peroxide, a key substance for POD activity., 資料番号: AA0063339001, レポート番号: JAXA-SP-06-033
- Published
- 2007
3. キュウリのオーキシン排出キャリア遺伝子群cDNAの単離と発現解析
- Author
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Kim, Dai-Hee, Kim, Kyung-Min, Fujii, Nobuharu, Hotta, Takuya, Kamada, Motoshi, Miyazawa, Yutaka, and Takahashi, Hideyuki
- Subjects
分子系統樹 ,gravitational effect ,ハイブリダイゼーション ,重力効果 ,fungi ,food and beverages ,リボ核酸 ,peg ,molecular phylogentic tree ,base sequence ,遺伝子発現 ,ペグ ,キュウリ ,gene expression ,塩基配列 ,アミノ酸 ,auxin ,オーキシン ,cucumber ,ribonucleic acid ,hybridization ,amino acid - Abstract
When cucumber (Cucumis sativus L.) seeds germinate in a horizontal position, a protuberance called a peg forms on the lower side of the transition zone. It has been shown that the endogenous levels of IAA that induces peg formation are significantly lower in the upper side of the transition zone than that in the lower side. To understand the mechanism of decrease of auxin in the upper side of the transition zone in response to gravity, cucumber cDNAs similar to PIN auxin efflux carrier gene were isolated and tissue specificity of their mRNA accumulation was investigated. The results indicate that mRNAs of CsPIN1, CsPIN4 and CsPIN6 accumulate in the transition zone of 24-h-old cucumber seedlings that initiate peg formation. CsPIN1 mRNA abundantly accumulates in xylem and endodermis. CsPIN4 mRNA abundantly accumulates in xylem. CsPIN6 mRNA abundantly accumulates in phloem and pith, and also accumulates in endodermis and cortex. Further study of these CsPINs will reveal the auxin transport system regulating peg formation of cucumber., 資料番号: AA0048095068
- Published
- 2005
4. Phylogenetic Position of a Deep-Sea Ascidian, Megalodicopia hians, Inferred from the Molecular Data
- Author
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Akira Takeuchi, Takeshi Naganuma, Yasunori Saito, Mari Ogawa, Atsushi Kurabayashi, Makiko Okuyama, and Zhang Jing
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animal structures ,Molecular Sequence Data ,Biology ,DNA, Mitochondrial ,DNA, Ribosomal ,Deep sea ,Corellidae ,Animals ,Cluster Analysis ,Urochordata ,Mitochondrial protein ,Phylogeny ,Likelihood Functions ,Pacific Ocean ,Base Sequence ,Models, Genetic ,Phylogenetic tree ,Ecology ,fungi ,Cionidae ,Sequence Analysis, DNA ,biology.organism_classification ,Megalodicopia hians ,Evolutionary biology ,Close relationship ,embryonic structures ,ComputingMethodologies_DOCUMENTANDTEXTPROCESSING ,Animal Science and Zoology ,Phylogenetic relationship - Abstract
Ascidians inhabit both shallow water and the deep sea. The phylogenetic position of deep-sea ascidians has not been sufficiently investigated because of their unusual habitats. The family Octacnemidae is one such enigmatic deep-sea ascidian. In this report, we determined the sequences of the 18SrDNA and a mitochondrial protein gene of Megalodicopia hians belonging to the family Octacnemidae, and we analyzed its phylogenetic relationship with other ascidians. A phylogenetic relationship of this family with the families Cionidae and/or Corellidae has been suspected based on a small number of morphological characteristics. However, our results suggested that M. hians has a close relationship to the family Corellidae and might originate from them. This is the first report of the molecular phylogenetic analysis of a deep-sea ascidian.
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- 2003
5. Report of plant physiology research project in ISS Science Project Office: Ferulate & Hydro Tropi research and development
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Japan Aerospace Exploration Agency
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gravitational effect ,重力効果 ,細胞壁 ,微小重力 ,rice ,peroxidase ,aerospace environment ,重力屈性 ,base sequence ,microgravity ,gravitropism ,航空宇宙環境 ,遺伝子発現 ,ペルオキシダーゼ ,hydrotropism ,フェルラ酸 ,gene expression ,cell wall ,イネ ,塩基配列 ,水分屈性 ,ferulic acid - Abstract
本研究開発報告は、第4回国際公募採択テーマ「重力によるイネ芽生え細胞壁のフェルラ酸形成の制御機構(Ferulate)」および第5回国際公募採択テーマ「微小重力下における根の水分屈性とオーキシン制御遺伝子の発現(Hydro Tropi)」に関する2006年度の研究開発成果をまとめたものである。, 資料番号: AA0063339000, レポート番号: JAXA-SP-06-033
- Published
- 2007
6. [Emergence of emaraviruses, the eriophyoid mite-transmitted viruses in plants].
- Author
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Kubota K
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- Animals, Base Sequence, Genome, Viral genetics, Plant Diseases prevention & control, RNA Viruses classification, RNA Viruses genetics, Viral Proteins, Mites virology, Plant Diseases virology, Plants virology, RNA Viruses pathogenicity
- Abstract
Members of the genus Emaravirus are plant viruses transmitted by eriophyoid mites. The emaravirus genome consists of multiple, negative-sense, single-stranded RNA segments, that have been shown to be highly divergent. Recent studies have revealed that emaraviruses are associated with long-recognized diseases of world important crops such as fig mosaic disease or sterility mosaic disease of pigeon pea. Furthermore, along with the popularization of deep sequencing technologies, new putative members of emaraviruses have been reported year by year. This paper presents an overview of agricultural damages caused by emaraviruses worldwide and characteristics of their genomic RNAs and proteins. In addition, our research project to prevent a disease of a herb crop (shiso, Perilla frutescens) caused by Perilla mosaic virus, a putative emaravirus recently identified in Japan, is outlined.
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- 2017
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7. PCR-Based Method for the Detection of Toxic Mushrooms Causing Food-Poisoning Incidents.
- Author
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Nomura C, Masayama A, Yamaguchi M, Sakuma D, and Kajimura K
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- Agaricales genetics, Base Sequence, DNA Barcoding, Taxonomic methods, DNA Primers, DNA, Fungal genetics, DNA, Fungal isolation & purification, Gastric Juice, Japan, Time Factors, Agaricales isolation & purification, Foodborne Diseases diagnosis, Foodborne Diseases etiology, Polymerase Chain Reaction methods
- Abstract
In this study, species-specific identification of five toxic mushrooms, Chlorophyllum molybdites, Gymnopilus junonius, Hypholoma fasciculare, Pleurocybella porrigens, and Tricholoma ustale, which have been involved in food-poisoning incidents in Japan, was investigated. Specific primer pairs targeting internal transcribed spacer (ITS) regions were designed for PCR detection. The specific amplicons were obtained from fresh, cooked, and simulated gastric fluid (SGF)-treated samples. No amplicons were detected from other mushrooms with similar morphology. Our method using one-step extraction of mushrooms allows rapid detection within 2.5 hr. It could be utilized for rapid identification or screening of toxic mushrooms.
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- 2017
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8. Case study of a spinal muscular atrophy type 1 patient retaining one allele of the SMN1 gene.
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Yamada H, Nishida Y, Matsumoto T, Maihara T, and Nishio H
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- Alleles, Base Sequence, Exons, Humans, Infant, Male, Spinal Muscular Atrophies of Childhood genetics, Survival of Motor Neuron 1 Protein genetics
- Published
- 2016
9. A female patient with a hot spot mutation of PRRT2 gene suffering from several types of epileptic seizures in infancy.
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Matsushita HB, Okano S, Ishii A, and Hirose S
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- Base Sequence, Child, Preschool, Electroencephalography, Epilepsy physiopathology, Female, Humans, Seizures physiopathology, Epilepsy genetics, Membrane Proteins genetics, Mutation, Nerve Tissue Proteins genetics, Seizures genetics
- Abstract
Benign familial infantile epilepsy (BFIE) is characterized by non-febrile focal seizures, which sometimes evolve to secondarily generalized seizures and are usually resolved in the second year. Proline-rich transmembrane protein 2 (PRRT2) is confirmed as the major cause of BFIE, familial paroxysmal kinesigeneic dystonia (PKD) and infantile convulsions and choreoathetosis (ICCA) syndrome. We examined a female patient with a hot spot mutation of PRRT2 gene. She had recurrent tonic seizures when she was three months old. The seizures were controlled by several kinds of anticonvulsants. Then, she had several times of focal seizures daily at nine months old. However, the seizures were stopped by small amounts of carbamazepine. Later, when she was two years old, she experienced frequent motor seizures characterized by truncal flexion and swaying the body with partially disturbed consciousness. Her father also had the same PRRT2 gene mutation and non-febrile seizures in infancy. The patient had mild to moderate mental retardation, whereas her father was mentally normal. Therefore, the patient revealed a quiet different phenotype from that of her father as a carrier of the same PRRT2 gene mutation. We speculate that the PRRT2 mutation had caused the BFIE-like seizures both in the patient and her father, whereas other unknown genetic factors specific for the patient might be associated with the atypical seizures observed only in her.
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- 2016
10. Design of antisense oligonucleotides.
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Obika S and Kasahara Y
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- Animals, Base Sequence, Humans, Molecular Structure, RNA, Messenger chemistry, Drug Design, Drug Discovery methods, Oligonucleotides, Antisense
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- 2016
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11. Neuraminidase Amino Acid Sequences of Influenza A/H3N2 and B Viruses Isolated from Influenza Patients in the 2014/15 Japanese Influenza Season.
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Ikematsu H, Chong Y, Shirane K, Toh H, Sasaki H, Matsumoto S, Noda N, Hotta T, Uchiumi T, and Kang D
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- Amino Acid Sequence, Base Sequence, Humans, Influenza A Virus, H3N2 Subtype genetics, Influenza, Human virology, Japan, Neuraminidase isolation & purification, Influenza A Virus, H3N2 Subtype enzymology, Neuraminidase genetics
- Abstract
Background: Neuraminidase (NA) is a surface protein essential for influenza virus replication. NA inhibitors are commonly used for the treatment of influenza patients in Japan. Several mutations that reduce the effect of NA inhibitors have been reported. We sequenced the whole NA segment of isolated virus from influenza patients and investigated the relation between the NA amino acid sequence and the 50% inhibitory concentration (IC_50) of four NA inhibitors., Materials and Methods: Forty A/H3N2 and 19 B influenza virus isolated from patients in the 2014/15 influenza season were analyzed. The IC_50 was determined by a neuraminidase inhibition assay using a fluorescent substrate. Viral RNA was amplified by RT-PCR and the genome was sequenced using a next generation sequencer. The deduced amino acid sequences were analyzed., Results: There was no AA change in the NA catalytic site of the A/H3N2 and B viruses isolated in the 2014-15 influenza season. There was no significant relation between the NA amino acids and the IC_50 of the four NA inhibitors for A/H3N2 or B viruses., Conclusion: The catalytic site of NA was highly conserved for these A/H3N2 and B viruses. No emergence of NA amino acid mutations related to the sensitivity of the four currently used NA inhibitors was observed.
- Published
- 2016
12. [A 6-month-old female patient who suffered clustering of afebrile seizures].
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Yamamoto T
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- Base Sequence, Electroencephalography, Female, Humans, Infant, Membrane Proteins genetics, Mutation, Nerve Tissue Proteins genetics, Pedigree, Seizures, Febrile physiopathology, Seizures, Febrile genetics
- Published
- 2016
13. [Dengue Fever Infection Confirmed with an Epidemiological Survey and Genetic Analysis: The Case was Suspected as SFTS Based on the Primary First Information].
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Kaburagi Y, Kaetsu A, Kobori S, Udno H, Kikuchi K, Tomari K, and Miyazaki M
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- Base Sequence, Genetic Association Studies, Humans, Molecular Sequence Data, Dengue epidemiology, Phlebovirus genetics, Surveys and Questionnaires
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- 2016
- Full Text
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14. [A Family Affected by Lynch Syndrome Caused by MSH6 Germline Mutation].
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Chika N, Kumamoto K, Suzuki O, Fukuchi M, Matsuzawa T, Kumagai Y, Ishibashi K, Eguchi H, Mochiki E, and Ishida H
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- Base Sequence, Colorectal Neoplasms, Hereditary Nonpolyposis complications, Humans, Male, Microsatellite Instability, Middle Aged, Pedigree, Sigmoid Neoplasms pathology, Sigmoid Neoplasms surgery, Colorectal Neoplasms, Hereditary Nonpolyposis genetics, DNA-Binding Proteins genetics, Germ-Line Mutation, Sigmoid Neoplasms genetics
- Abstract
The clinical features of Lynch syndrome caused by MSH6 are not fully understood since very few cases have been described in Japan. We report 2 cases of Lynch syndrome with germline mutation of MSH6 in a family. Case 1: A 47-year-old man was referred to our department due to positive fecal occult blood test. He had family history of endometrial cancer and gastric cancer (mother), and bladder cancer (father). We performed sigmoidectomy for sigmoid cancer. The pathological findings revealed mucosal cancer (pTis, pN0, H0, P0, pStage 0). Since the patient met the revised Bethesda guidelines, we performed microsatellite instability (MSI) testing and immunohistochemistry for mismatch repair genes (MLH1, MSH2, MSH6, and PMS2) as screening for Lynch syndrome. MSI-high and loss of MSH6 were found. Based on these results, genetic testing of MSH6 revealed a frame-shift mutation in codon 604 (c. 1806-1809delAAG/p. Glu604LeufsX5). Case 2: The patient was a younger brother of case 1. The same mutation was detected in the MSH6 gene.
- Published
- 2015
15. [Clinicopathological Study of Pilomyxoid-Spectrum Astrocytomas:An Analysis of the BRAF Gene. Report of Two Cases].
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Ito T, Sato K, Oikawa M, Sugio H, Asanome T, Ozaki Y, Nakamura H, Tanaka S, Tsuda M, and Nagashima K
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- Adult, Astrocytoma diagnosis, Astrocytoma physiopathology, Base Sequence, Brain Neoplasms pathology, Brain Neoplasms physiopathology, Child, Electroencephalography, Humans, Immunohistochemistry, Magnetic Resonance Imaging, Male, Molecular Sequence Data, Astrocytoma genetics, Brain Neoplasms genetics, Proto-Oncogene Proteins B-raf genetics
- Abstract
In contrast to pilocytic astrocytomas(PAs), pilomyxoid astrocytomas(PMAs)demonstrate monophasic piloid cells with angiocentric distribution and a more aggressive clinical course. Recently, several reports have described combined histological features of both subtypes;accordingly, these were termed intermediate pilomyxoid tumors(IPTs). The KIAA1549-BRAF fusion gene has been found in approximately 70% of PAs, but is reportedly rare in PMAs. We describe a clinicopathological study of two patients with pilomyxoid-spectrum astrocytoma(PMSA). Case 1 was of a 29-year-old man who presented with a generalized seizure. Gadolinium-magnetic resonance imaging(Gd-MRI)demonstrated a less enhanced tumor in the left temporal lobe. Case 2 was of a 9-year-old boy who presented with headache. Gd-MRI revealed an irregularly enhanced tumor in the left cerebellum. In Case 1, the tumor showed monomorphous bipolar cells in a myxoid background and angiocentric arrangement;therefore, the diagnosis was PMA. In Case 2, part of the tumor had a myxoid, angiocentric pattern characteristic of PMA;the other part had a biphasic pattern characteristic of PA. PMA and PA were mixed in a 7:3 ratio;therefore, IPT was diagnosed. No BRAF V600E mutations were found by immunohistochemistry and sequencing in either case. Three major KIAA1549-BRAF fusion subtypes were analyzed by quantitative reverse transcription polymerase chain reaction(RT-PCR)and sequencing. No fusions were found in Case 1. However, K16-B9 fusion was identified in Case 2, and this fusion was more prevalent in the PA component than in the PMA component. In summary, no BRAF V600E mutations were found in PMSAs, but KIAA1549-BRAF fusion was identified in IPT, particularly in the PA component.
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- 2015
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16. [Two Cases of Primary Intracranial Solitary Fibrous Tumor:Genetic Examination of NAB2-STAT6 Fusion and Its Association with Hemangiopericytoma].
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Kikuchi A, Fujita T, Takahashi Y, Yokosako S, Yoshimura C, Akagawa H, Fujibayashi M, Kubo O, Onda H, and Kasuya H
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- Adult, Base Sequence, Brain Neoplasms pathology, Brain Neoplasms surgery, Exons, Gene Expression Regulation, Neoplastic, Hemangiopericytoma surgery, Humans, Introns, Male, Recombinant Proteins genetics, Solitary Fibrous Tumors surgery, Brain Neoplasms genetics, Hemangiopericytoma genetics, Repressor Proteins genetics, STAT6 Transcription Factor genetics, Solitary Fibrous Tumors genetics
- Abstract
Using whole exome and transcriptome sequencing, NAB2-STAT6 gene fusions have recently been identified in patients with solitary fibrous tumors (SFT). We report two cases of SFT in which NAB2-STAT6 fusions were identified. The patients were a 32-year-old man with a parasagittal tumor involving the superior sagittal sinus, and a 40-year-old man with a cerebellar convexity tumor partially involving the transverse sinus. Their tumors were gross totally resected and diagnosed to be SFT according to the following pathological findings:the tumors were composed of spindle cells with a patternless architecture, with prominent stromal collagen and staghorn vessels. An immunohistochemical study yielded positive results for CD34, CD99, and Bcl-2 and negative results for EMA, GFAP, and S100. The MIB-1 indexes were 13 and 7%, respectively. NAB2-STAT6 fusions were detected in both cases with a common fusion variant, NAB2ex6-STAT6ex16/17. We also identified NAB2-STAT6 fusions in two hemangiopericytomas diagnosed in the past with a common variant of NAB2ex6-STAT6ex16/17. These findings suggest that solitary fibrous tumor and hemangiopericytoma may be diagnosed based on the presence of NAB2-STAT6 fusion, and not classified separately because of the same genetic background.
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- 2015
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17. [The 42nd Scientific Meeting: Perspectives of Internal Medicine; Considerations to treatment and care of cancer by internists in the era of increasing cancer mortality; 2. Fruits of Basic Research on Cancer; 2) Clinical application of cancer genome analyses].
- Author
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Mano H
- Subjects
- Base Sequence, Humans, Mutation, Neoplasms drug therapy, Oncogene Proteins, Fusion genetics, Risk Factors, Genome, Human, Neoplasms genetics
- Published
- 2015
- Full Text
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18. [A Case of Hereditary Medullary Thyroid Cancer (MEN2A/FMTC) Diagnosed at the Time of Recurrence].
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Enomoto K, Shimizu K, Hirose M, Miyabe H, Morizane N, Takenaka Y, Shimazu K, Fushimi H, and Uno A
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- Adult, Base Sequence, Carcinoma, Medullary genetics, Carcinoma, Medullary pathology, Carcinoma, Medullary surgery, Humans, Magnetic Resonance Imaging, Male, Multimodal Imaging, Multiple Endocrine Neoplasia Type 2a genetics, Multiple Endocrine Neoplasia Type 2a surgery, Mutation, Positron-Emission Tomography, Proto-Oncogene Proteins c-ret genetics, Recurrence, Thyroid Neoplasms genetics, Thyroid Neoplasms surgery, Thyroidectomy, Tomography, X-Ray Computed, Carcinoma, Medullary congenital, Multiple Endocrine Neoplasia Type 2a pathology, Thyroid Neoplasms pathology
- Abstract
We report a 42-year-old man with hereditary medullary thyroid cancer (multiple endocrine neoplasia, MEN2A/familial medullary thyroid carcinoma, FMTC), which was diagnosed at the time of tumor recurrence. He had a past history of a left thyroidectomy with neck dissection 7 years previously. A RET gene analysis revealed a point mutation (codon 618), and we diagnosed him as having hereditary medullary thyroid cancer. We resected the recurrent tumor in the right thyroid lobe together with performing a right lateral and central neck dissection. A RET gene analysis should be performed for patients with medullary thyroid cancer. When a RET gene mutation is present, a total thyroidectomy must be performed for the medullary thyroid cancer.
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- 2015
- Full Text
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19. Migration of plant viruses: Time correlations with the agriculture history and human immigration.
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Ohshima K
- Subjects
- Base Sequence, Genome, Plant genetics, Humans, Sequence Analysis, Time Factors, Agriculture, Brassicaceae virology, Emigration and Immigration, Evolution, Molecular, Mosaic Viruses genetics, Mosaic Viruses pathogenicity, Plants virology
- Abstract
In this review, I made the phylodynamic comparisons of three plant viruses, Turnip mosaic virus (TuMV), Cauliflower mosaic virus (CaMV) and Cucumber mosaic virus (CMV), using the genomic sequences of a large numbers of isolates collected worldwide. We analyzed these genomic nucleotide sequences, in combination with published sequences, to estimate the timescale and rate of evolution of the individual genes of TuMV, CaMV and CMV. The main hosts of the viruses are Brassicaceae crops. We also compared these estimates from complete sequences with those from which non-synonymous and invariate codons had been removed. Our analyses provided a preliminary definition of the present geographical structure of three plant virus populations in the world, and showed that the time of migration of three plant viruses correlate well with agriculture history and human immigration.
- Published
- 2015
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20. [Regulation of metabolism by orphan receptor regulone].
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Morohashi K and Baba T
- Subjects
- Adrenal Cortex Hormones biosynthesis, Animals, Base Sequence, Gonadal Steroid Hormones biosynthesis, Humans, Neoplasms metabolism, Receptors, Cytoplasmic and Nuclear genetics, Energy Metabolism genetics, Gene Expression Regulation genetics, Receptors, Cytoplasmic and Nuclear physiology, Regulon genetics, Regulon physiology
- Published
- 2014
21. [Birt-Hogg-Dubé syndrome with repeated pneumothorax; report of a case].
- Author
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Matsuoka Y, Adachi Y, Metsugi H, Tokushima T, and Adachi Y
- Subjects
- Adult, Base Sequence, Birt-Hogg-Dube Syndrome genetics, Humans, Male, Mutation, Pneumothorax surgery, Proto-Oncogene Proteins genetics, Tomography, X-Ray Computed, Tumor Suppressor Proteins genetics, Birt-Hogg-Dube Syndrome complications, Pneumothorax etiology
- Abstract
A 36-year-old man had been treated by thoracoscopic bullectomy because of left pneumothorax at another hospital. 2 weeks post-surgery, he was transferred to our hospital because of recurrent left pneumothorax. Chest computed tomography (CT) revealed multiple, irregular-shaped pulmonary cysts of various sizes predominating in the apex of both lungs. Thoracoscopy showed diffuse multiple thinwalled small cysts on the visceral pleura. Small cyst with air leakage was sutured and other cysts were cauterized. He was diagnosed as having Birt-Hogg-Dubé (BHD) syndrome by DNA sequence analysis of his FLCN gene.
- Published
- 2014
22. [Genetic analysis reveals misidentification of Mycobacterium lentiflavum as Mycobacterium intracellulare by the COBAS TaqMan MAI test].
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Tomita M, Yoshida S, Tsuyuguchi K, Suzuki K, Okada M, and Hayashi S
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- Base Sequence, Reagent Kits, Diagnostic, Mycobacterium avium Complex genetics, Mycobacterium avium Complex isolation & purification, Nontuberculous Mycobacteria genetics, Nontuberculous Mycobacteria isolation & purification
- Abstract
Objective: To evaluate COBAS TaqMan MAI test misidentification of Mycobacterium lentiflavum as Mycobacterium intracellulare., Materials and Methods: Preliminary comparative analysis identified 13 clinical isolates used in this study as COBAS Amplicor MAV and MIN-negative but COBAS TaqMan MAI-positive. The COBAS TaqMan MAI test limit of detection and reproducibility were evaluated by tenfold dilution series from 3 x 10(8) CFU/mL. Isolate 16S rDNA nucleotide sequences were compared with Mycobacterium avium and M. intracellulare., Results: Discrepancies were observed between isolates identified as M. lentiflavum by 16S rDNA sequencing and as M. intracellulare by the COBAS TaqMan MAI test. The false-positive results were verified by sequence comparison of a randomly sampled clinical isolate and the M. intracellulare reference strain. Sequence analysis of M. lentiflavum and M. intracellulare 16S rDNA amplification products showed at least 3 mismatches between species. The high identity in the sequence was found for M. intracellulare by COBAS TaqMan MAI., Conclusion: In Japan, commercially available nucleic acid probe- and amplification-based tests cannot identify M. lentiflavum. Correct identification, though challenging, is possible using standard cultivation procedures for colony growth. Misleading results using the COBAS TaqMan MAI kit may lead to erroneous diagnoses.
- Published
- 2014
23. [Rapid detection of mutations related to Mycobacterium leprae drug resistance by using Hp-rPCR (hairpin primer- real time PCR) method].
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Kai M
- Subjects
- Base Sequence, Codon genetics, DNA Primers genetics, DNA, Bacterial genetics, Dapsone pharmacology, Double-Blind Method, Genes, Bacterial genetics, Molecular Sequence Data, Quinolones pharmacology, Rifampin pharmacology, Anti-Bacterial Agents pharmacology, Drug Resistance, Bacterial drug effects, Leprostatic Agents pharmacology, Mutation genetics, Mycobacterium leprae drug effects, Mycobacterium leprae genetics, Real-Time Polymerase Chain Reaction methods
- Abstract
Rapid and simple detection method of drug resistance bacteria is required. In the present study, Hp-rPCR (hairpin primer-real time PCR) was applied to Mycobacterium leprae genes to detect mutations. Target sites of the method were as follows: first base and second base on 53rd codon and second base on 55th codon infolP1 gene for dapsone resistance, first base on 441st codon and 451st codon and second base on 456th and 458th codon in rpoB gene for rifampicin resistance, and first base on 89th codon and second base on 91st codon in gyrA gene for quinolone resistance which were common mutation sites in clinical reports. The total number of the target sites was 9. Mycobacterium leprae, Thai-53, Zensho-2 and Zensho-4 were used as reference bacteria in the present study and clear, reliable results were obtained. Double-blind study was conducted using 15 samples. The number of target sites was calculated as 135 in total by 9 sites in 15 samples. There was only one misreading in the blind samples and the sensitivity was more than 99%.
- Published
- 2014
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24. [Genome editing with programmable site-specific nucleases].
- Author
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Yamamoto T, Sakamoto N, and Sakuma T
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- Animals, Base Sequence, DNA Breaks, Double-Stranded, Disease Models, Animal, Gene Knock-In Techniques methods, Gene Knockdown Techniques methods, Molecular Sequence Data, Virus Replication genetics, CRISPR-Cas Systems genetics, Gene Targeting methods, Genome genetics
- Abstract
Genome editing is a cutting-edge technology that enables to modify the target gene using programmable site-specific nucleases, such as TALENs and CRISPR/Cas9. Currently, cell and animal models of human diseases have been competitively created throughout the world, because genome editing technology paved the way for genetic modifications even in cells and organisms that had been difficult to manipulate the genome. In this review, we introduce the basic principles and current situations of genome editing with programmable nucleases.
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- 2014
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25. [Bioinformatics on new human adenoviruses causing nosocomial infection].
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Aoki K, Kaneko H, Kitaichi N, Watanabe H, Ishida S, and Ohno S
- Subjects
- Adenoviruses, Human chemistry, Animals, Base Sequence, Haplorhini, Humans, Keratoconjunctivitis, Infectious virology, Adenoviruses, Human genetics, Computational Biology, Cross Infection virology
- Abstract
Human adenovirus (HAdV) causing epidemic keratoconjunctivitis is limited to D and E species. Recent progress in bioinformatics revealed that these viruses attach to the host with fibers, infiltrate the host cells via RGD (Arg-Gly-Asp) motif of penton base, and reveal their serological reaction by hexons. Loops 1 and 2 are the variable regions of each hexon. The possibility that a novel adenovirus later named HAdV-52 was transmitted over the wall of species' from monkeys to humans was reported. The recombination of the above three hot spots introduces novel types such as HAdV-53, -54, and -56. Boinformatics may provide rapid genotyping in nosocomial infection, predicting future epidemics, and an estimate of the therapeutic target molecules in the near future.
- Published
- 2013
26. [Transcriptional regulation of RAAS genes--in vivo analysis by artificial chromosome transgenic mouse].
- Author
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Tanimoto K and Fukamizu A
- Subjects
- Animals, Base Sequence, Humans, Mice, Mice, Transgenic, Chromosomes, Artificial genetics, Gene Expression Regulation genetics, Renin-Angiotensin System genetics, Transcription, Genetic genetics
- Published
- 2012
27. [Botulism: structure and function of botulinum toxin and its clinical application].
- Author
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Oguma K, Yamamoto Y, Suzuki T, Fatmawati NN, and Fujita K
- Subjects
- Amino Acid Sequence, Animals, Base Sequence, Botulinum Toxins genetics, Botulinum Toxins physiology, Botulism microbiology, Clostridium botulinum, Dystonia drug therapy, Humans, Trigeminal Neuralgia drug therapy, Botulinum Toxins chemistry, Botulinum Toxins therapeutic use
- Abstract
Clostridium botulinum produces seven immunological distinct poisonous neurotoxins, A to G, with molecular masses of approximately 150kDa. In acidic foods and culture fluid, the neurotoxins associate with non-toxic components, and form large complexes designated progenitor toxins. The progenitor toxins are found in three forms named LL, L, and M. These neurotoxins and progenitor toxins were purified, and whole nucleotide sequences of their structure genes were determined. In this manuscript, the structure and function of these toxins, and the application of these toxins to clinical usage have been described.
- Published
- 2012
28. [Analysis of the complete hepatitis B virus genomes in a patient for repeated seroconversion to anti-HBe antibody due to co-infection with two virus clones].
- Author
-
Yukimasa N, Uzawa R, and Fukuchi K
- Subjects
- Base Sequence, Clone Cells, Coinfection, Genome, Viral, Hepatitis B virus immunology, Humans, Mutation, Polymerase Chain Reaction, Hepatitis B Antibodies analysis, Hepatitis B virus genetics, Hepatitis B, Chronic immunology
- Abstract
We report a case of repeated seroconversion to anti-HBe antibody in a patient with chronic hepatitis B. We amplified and cloned sections of the hepatitis B virus (HBV) genes by polymerase chain reaction (PCR), and sequenced the PCR products. The results were analyzed by connecting all of the sequences to generate complete genomes. As a result, we confirmed the coexistence of two different HBV clones, both of which had the same subtype (adr) and genotype (C2). Neither clone had mutations in the S gene region in sequences involved in gene expression or in sequences involved in drug resistance. However, both clones had mutations in the core promoter(A1762T, G1764A). In one HBe antibody-positive clone, a pre-core mutation associated with HBe antigen negativity (G1896A) was found. In addition, pre-S2 deletion and 6 amino acid substitutions in the core protein gene were detected in this clone. The other HBe antigen-positive clone was essentially wild-type. Interestingly, this clone had accumulated mutations, which participated in DNA polymerase inactivation in the P gene region. Therefore, it is expected that this clone cannot replicate its own DNA polymerase. Consequently, this repeated seroconversion phenomenon was suggested to be responsible for the observed findings. In conclusion, analysis of the complete HBV genome has greatly expanded the number of mutations identified, and this method is useful for understanding the causes of rare cases of hepatitis B.
- Published
- 2012
29. [Chemical and genetic diversity of Ligularia plants collected in the Hengduan Mountains, China].
- Author
-
Saito Y
- Subjects
- Asteraceae classification, Base Sequence, China, Chromatography, Thin Layer, Evolution, Molecular, Molecular Conformation, Phylogeny, Plant Roots chemistry, Sesquiterpenes chemistry, Sesquiterpenes isolation & purification, Asteraceae chemistry, Asteraceae genetics, Biodiversity, Genetic Variation
- Abstract
The Hengduan Mountains area of China is rich in plant resources. The Ligularia species, which belong to Senecioneae and Asteraceae, distributed in this area are highly diversified and contain 6 sections and over 100 species, and are considered to be in on-going evolution and diversification. To understand the inter- and intra-specific diversity of these plants and to elucidate the mechanism of diversification, we analyzed Ligularia plants by chemical, genetic, geographical, ecological, and morphological approaches. We investigated 4 species, and isolated 26 novel compounds. Based on the chemical composition of root extract as well as nucleotide sequence variations in internal transcribed spacers (ITS), we obtained 3 findings. (i) L. virgaurea is classified into two groups, ligularol type and virgaurenone type from the view point of chemical constituents, which are phylogenetically distinguished from each other, (ii) L. subspicata and L. lamarum have an overlapped chemical spectrum, but showed no clear genetic correlation, and (iii) L. cyathiceps showed no significant variations in either chemical constituents or nucleotide sequences.
- Published
- 2012
- Full Text
- View/download PDF
30. [Overview for personal genome analysis].
- Author
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Toda T and Tsuji S
- Subjects
- Base Sequence, Genetic Diseases, Inborn genetics, Humans, Genome, Human
- Published
- 2011
- Full Text
- View/download PDF
31. [Sequence analysis subtyping of the 56-kDa protein-encoding gene of Karp-type Orientia tsutsugamushi isolated in scrub typhus cases].
- Author
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Kaneko A, Seto J, Aoki T, and Otani K
- Subjects
- Adult, Aged, Aged, 80 and over, Amino Acid Sequence, Base Sequence, Female, Humans, Japan, Male, Middle Aged, Orientia tsutsugamushi genetics, Antigens, Bacterial genetics, Bacterial Proteins genetics, Orientia tsutsugamushi classification, Scrub Typhus microbiology
- Abstract
To determine the Karp-type Orientia tsutsugamushi subtype in northern Japan, i.e., Yamagata, Niigata, and Akita Prefectures, we analyzed the partial nucleotide sequence of the 56-kDa protein-encoding gene of 30 isolates from scrub typhus cases. Based on sequencing results, we classified isolates into two groups of 27 and 3 isolates. Nucleotide sequences of 27 isolates were homologous to the yeo-joo strain, classified as a JP-1 subtype. The three isolates were each homologous to a stain of CMM1, KNP1, or KNP2, classified as JP-2 subtypes. Phylogenetic tree analysis showed the 27 isolates forming a cluster with the yeo-joo strain and the three isolates with the CMM, KNP1, and KNP2 strains and therefore belonging to these subtypes. The Karp-type O. tsutsugamushi JP-2 subtype predominates in Japan, the JP-1 subtype probably the predominates in the area investigated. O. tsutsugamushi JP-1 subtype strains must therefore be isolated from subjects in this area and comprehensively studied.
- Published
- 2011
- Full Text
- View/download PDF
32. [Bioinformatics technologies for the analysis of antigenic evolution of influenza viruses].
- Author
-
Ito K
- Subjects
- Animals, Base Sequence, Humans, Influenza, Human prevention & control, Influenza, Human virology, Orthomyxoviridae Infections virology, Antigens, Viral genetics, Computational Biology methods, Computational Biology trends, Evolution, Molecular, Influenza A virus genetics, Influenza A virus immunology, Influenza Vaccines immunology, Mutation
- Abstract
Human influenza viruses mutate from time to time, causing annual epidemics worldwide. The strong immune pressure in the human population selects a new variant every year, and the antigenic change is one of the primary reasons why vaccination is not a perfect measure to control seasonal influenza. Thus prediction of antigenic change of influenza A virus has been one of the major public health goals. In this review bioinformatics technologies that have been developed to achieve this goal were summarized.
- Published
- 2011
- Full Text
- View/download PDF
33. [Chromoblastomycosis caused by Fonsecaea monophora].
- Author
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Sugiyama Y, Suzuki Y, Sugaya K, Tokura Y, Yaguchi T, Kamei K, and Nishimura K
- Subjects
- Administration, Oral, Antifungal Agents administration & dosage, Ascomycota genetics, Base Sequence, Chromoblastomycosis pathology, Chromoblastomycosis therapy, Humans, Hyperthermia, Induced methods, Japan, Male, Middle Aged, Philippines ethnology, Pyrimidines administration & dosage, RNA, Fungal genetics, RNA, Ribosomal genetics, Treatment Outcome, Triazoles administration & dosage, Voriconazole, Ascomycota isolation & purification, Chromoblastomycosis microbiology
- Abstract
Fonsecaea species are major etiologic agents of Chromoblastomycosis (CBM). By genetic analysis, the genus Fonsecaea has recently been revised and classified into F. pedorosoi, F. monophora and F. nubica. Here we report a severe chronic case of CBM caused by F. monophora. A 55-year-old Filipino male developed progressive skin lesions on the left lateral ankle in 1973, when he worked at a coconut plantation in the Philippines. In 1999, he received medical treatments for enlarged, multiple lesions on the left lower limb. When he moved to Japan in 2005, the lesions were remarkably improved and he discontinued taking the medicine. On our first examination in October 2008, a large, reddish, cicatricial plaque was observed on the left lower aspect of his leg. Several tumorous lesions surrounded the plaque, indicating that the therapies performed before had been insufficient. In addition, there were many patchy scars scattered on the thigh and the upper part of the lower leg. The diagnosis of CBM was made by the presence of muriform cells. Black, pulverulent colonies were yielded in culture of skin scrapings and tissues. Although the fungus could not be identified by microscopic morphology, r-RNA ITS sequence analysis enabled identification of Fonsecaea monophora. The patient responded well to oral voriconazole combined with local thermotherapy using pocket warmers. The tumoral masses subsided in 6 months, leaving pink scars with negative fungal culture. Voriconazole treatment was continued for 18 months. It seems that drugs are insufficiently delivered in the cicatricial lesions because of the paucity of blood flow, suggesting that a long-term follow-up is necessary for such a case., (Copyright © 2011 The Japanese Society for Medical Mycology)
- Published
- 2011
- Full Text
- View/download PDF
34. [Endogenous bornavirus elements in mammalian genome].
- Author
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Horie M and Tomonaga K
- Subjects
- Animals, Base Sequence, DNA genetics, Humans, Molecular Sequence Data, Retroelements, Reverse Transcription, Virus Integration, Bornaviridae genetics, Genome, Mammals genetics, Mammals virology
- Abstract
Approximately 8% of our genome is made up of endogenous retroviral elements. Endogenous retrovirus is a fossil record of ancient retrovirus infection and, therefore, gives important insights into the evolutional relationship between retroviruses and their hosts. On the other hand, until recently, it has been believed that no endogenous non-retroviral viruses exist in animal genomes. We lately discovered endogenous elements homologous to the nucleoprotein of bornaviruses, a negative-strand RNA virus, in the genomes of many mammalian species, including humans. We also demonstrated that mRNA of extant mammalian bornavirus, Borna disease virus, is reverse-transcribed and integrated into the host genome DNA. These findings provided novel insights not only into the interaction between RNA viruses and their hosts, but also into the mechanism underlying the gain of novelty in mammalian genomes. In this review, we will briefly summarize our recent knowledge about endogenous bornavirus elements and also introduce some recent discoveries regarding endogenous elements of non-retroviral viruses in vertebrate genomes.
- Published
- 2010
- Full Text
- View/download PDF
35. [Genetic diagnostics of pathogenic splicing abnormalities in the clinical laboratory--pitfalls and screening approaches].
- Author
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Niimi H, Ogawa T, Note R, Hayashi S, Ueno T, Harada K, Uji Y, and Kitajima I
- Subjects
- Adolescent, Adult, Base Sequence, DNA, Complementary genetics, Humans, Male, Molecular Sequence Data, Antithrombin III Deficiency diagnosis, Antithrombin III Deficiency genetics, Clinical Laboratory Techniques, Molecular Diagnostic Techniques methods, Mutation, Protein S Deficiency diagnosis, Protein S Deficiency genetics, RNA Splicing genetics, RNA, Messenger genetics
- Abstract
In recent years, genetic diagnostics of pathogenic splicing abnormalities are increasingly recognized as critically important in the clinical genetic diagnostics. It is reported that approximately 10% of pathogenic mutations causing human inherited diseases are splicing mutations. Nonetheless, it is still difficult to identify splicing abnormalities in routine genetic diagnostic settings. Here, we studied two different kinds of cases with splicing abnormalities. The first case is a protein S deficiency. Nucleotide analyses revealed that the proband had a previously reported G to C substitution in the invariant AG dinucleotide at the splicing acceptor site of intronl/exon2, which produces multiple splicing abnormalities resulting in protein S deficiency. The second case is an antithrombin (AT) deficiency. This proband had a previously reported G to A substitution, at nucleotide position 9788 in intron 4, 14 bp in front of exon 5, which created a de novo exon 5 splice site and resulted in AT deficiency. From a practical standpoint, we discussed the pitfalls, attentions, and screening approaches in genetic diagnostics of pathogenic splicing abnormalities. Due to the difficulty with full-length sequence analysis of introns, and the lack of RNA samples, splicing mutations may escape identification. Although current genetic testing remains to be improved, to screen for splicing abnormalities more efficiently, it is significant to use an appropriate combination of various approaches such as DNA and/or RNA samples, splicing mutation databases, bioinformatic tools to detect splice sites and cis-regulatory elements, and in vitro and/or in vivo experimentally methods as needed.
- Published
- 2010
36. [Genetic basis of sponadic Parkinson disease: common disease-multiple rare variants].
- Author
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Mitsui J
- Subjects
- Base Sequence, Exons genetics, Gaucher Disease genetics, Humans, Mutation, Sequence Analysis, DNA, Genetic Variation genetics, Parkinson Disease genetics, beta-Glucosidase genetics
- Published
- 2010
- Full Text
- View/download PDF
37. [Molecular identification of human Diphyllobothrium nihonkaiense using mitochondrial cytochrome c oxidase subunit 1 (cox1) gene sequence].
- Author
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Ono S, Morimoto N, Korenaga M, Kumazawa H, Komatsu Y, Kuge I, Higashidani Y, Ogura K, and Sugiura T
- Subjects
- Adult, Animals, Base Sequence, DNA, Helminth, DNA, Mitochondrial, Diatrizoate Meglumine administration & dosage, Diphyllobothriasis diagnosis, Diphyllobothriasis drug therapy, Diphyllobothrium enzymology, Diphyllobothrium genetics, Diphyllobothrium ultrastructure, Humans, Male, Microscopy, Electron, Molecular Sequence Data, Polymerase Chain Reaction methods, Sequence Analysis, DNA, Treatment Outcome, Young Adult, Diphyllobothriasis parasitology, Diphyllobothrium isolation & purification, Electron Transport Complex IV genetics
- Abstract
Identification of Diphyllobothrium species has been carried out based on their morphology, especially sexual organs. In addition to these criteria, PCR-based identification methods have been developed recently. A 20 year-old Japanese living in Kochi Prefecture passed tapeworm. He was successfully treated with single dose of gastrografin. We examined the morphologic features of the proglottids and eggs using histology and scanning electron microscope. We also analyzed mitochondrial cytochrome c oxidase subunit 1 (cox1) gene of the proglottids. The causative tapeworm species was identified as D. nihonkaiense based on the results of morphologic features and genetic analysis. We discussed the advantage of PCR-based identification methods of Diphyllobothrium species using cox1 sequence in the clinical laboratory.
- Published
- 2010
38. [Molecular identification of fungi].
- Author
-
Gonoi T
- Subjects
- Gene Amplification, Humans, Mycoses microbiology, Base Sequence, Fungi genetics, Polymerase Chain Reaction
- Published
- 2010
39. [New directions in genome science brought by second generation sequencers].
- Author
-
Sugano S and Mizushima-Sugano J
- Subjects
- Humans, Base Sequence, Genome, Human genetics, Genomics trends
- Published
- 2010
40. [MNSs blood group system and antibodies(anti-M, -N, -S and -S antibodies)].
- Author
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Murakami J
- Subjects
- Base Sequence, Blood Grouping and Crossmatching methods, Coombs Test methods, Erythroblastosis, Fetal blood, Erythroblastosis, Fetal diagnosis, Erythroblastosis, Fetal prevention & control, Glycophorins genetics, Hemolysis, Humans, MNSs Blood-Group System genetics, Antibodies blood, Glycophorins immunology, MNSs Blood-Group System immunology, Transfusion Reaction
- Published
- 2010
41. [Mechanism of chromosome protection by telomere and telomerase].
- Author
-
Hiraoka Y and Haraguchi T
- Subjects
- Animals, Base Sequence, Cell Division, DNA Replication genetics, Humans, RNA, Tandem Repeat Sequences, Telomerase genetics, Telomere genetics, Telomere metabolism, Chromosomes, Nobel Prize, Telomerase physiology, Telomere physiology
- Published
- 2010
42. [Bacterial genome analysis and its applications for infectious diseases].
- Author
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Nakagawa I
- Subjects
- Antibodies, Monoclonal, Bacterial Vaccines, Base Sequence, Genotype, Humans, Oligonucleotide Array Sequence Analysis, Bacterial Infections diagnosis, Genome, Bacterial
- Abstract
The availability of genome sequence is revolutionizing the fields of bacteriology and infectious diseases. By the end of 2008, 785 complete genomes including representatives of all notable human pathogens have been sequenced, and over thirty hundreds of bacterial genome projects are going. These huge amount of genomic data has led to unprecedented advances not only in biological interests, but also in pathogen diagnosis, genotyping, detection of virulence, and detection of resistance to antibiotics. In addition, the metagenomic strategy of exploring the complex microbial flora provides a unique access to the understanding of bacterial community interdependence. This genomic information will impact on the research for microbial diseases related on human health.
- Published
- 2009
43. [Second generation sequencer and personal genomics].
- Author
-
Sugano S
- Subjects
- Genome, Human, Human Genome Project, Humans, Sequence Analysis, DNA, Base Sequence, Genomics
- Abstract
Second generation sequencers enabled us to sequence human genome with the speed and the cost 200 to 300 times less than the previous sequencers. Although the short read length is still the problem for reconstitution of copy number variations and genome rearrangements, it is rapidly changing by the development of software and by the improvement of machines. The new sequencers are not only useful for the genome re-sequencing but also for other needs, such as CHIP -seq, DNA modification analysis and transcriptome. We are in the time revolution in the genomics.
- Published
- 2009
44. [Microbiological properties of M. porcinum isolated from a patient with impairments in IL-12/IFN-gamma pathway].
- Author
-
Kazumi Y, Maeda S, Udagawa T, Sugawara I, and Kamiya H
- Subjects
- Animals, Anti-Bacterial Agents pharmacology, Base Sequence, Drug Resistance, Bacterial, Genes, Bacterial genetics, Genetic Predisposition to Disease genetics, Guinea Pigs, Humans, Male, Mycobacterium fortuitum drug effects, Mycobacterium fortuitum genetics, Mycobacterium fortuitum pathogenicity, Signal Transduction physiology, Young Adult, Interferon gamma Receptor, Interferon-gamma, Interleukin-12, Mutation, Mycobacterium fortuitum isolation & purification, Receptors, Interferon genetics, Signal Transduction genetics
- Abstract
Purpose: Mycobacterium porcinum has been successfully isolated from the patient with abnormal signal transduction pathway of IL12/IFN-gamma. The properties of each bacterium were determined by conventional identification methods, DNA sequencing analysis and MIC assay., Materials and Methods: M. porcinum was isolated 7 times from 1996 to 2007 from cervical lymph node, axillary lymph nodes, inguinal lymph node, brachial lymph node and site of a tumor of the patient. In another occasion, mycobacteria were isolated from lavage fluid of the endoscope in routine inspection. Using these mycobacteria, M. porcinum (ATCC33776) and M. fortuitum (ATCC6841), the conventional identification method and MIC assay were carried out. For analyses of the DNA sequencing (rpoB, dnaJ and hsp65), the ATCC type strain of mycobacteria (11 strains) which are closely related to M. porcinum were also used., Results and Discussion: DNA sequencing analyses of the 7 samples isolated from the patient, were concurrently identical in 3 different genes. Drug susceptibility test showed that 7 isolates had no marked change. In conventional identification analyses, M. porcinum (ATCC33776), M. fortuitum (ATCC6841), and M. porcinum that were isolated in 1996, were able to grow at 42 degrees C. However, 6 isolates that were isolated after 1999, did not grow at 42 degrees C. The colony detectable days of these 7 strains changed from 3 to 7. Over the time, the morphology of each colony changed from smooth to rough. Though the initial isolate had the ability to utilize mannitol, the later 4 isolates had no such ability.
- Published
- 2008
45. [Regulation of tissue specific expression of glycan chains].
- Author
-
Suzuki A, Sekine M, and Yonekawa H
- Subjects
- Animals, Base Sequence, Carbohydrate Conformation, Epithelial Cells metabolism, Kidney Tubules, Proximal cytology, Mice, Molecular Sequence Data, N-Acetylglucosaminyltransferases genetics, N-Acetylglucosaminyltransferases physiology, Polysaccharides chemistry, Repetitive Sequences, Nucleic Acid, Transcription Factors genetics, Transcription, Genetic, Kidney Tubules, Proximal metabolism, Organ Specificity, Polysaccharides metabolism, Transcription Factors physiology
- Published
- 2008
46. [Maize domestication and breeding based on genomic variation].
- Author
-
Yamasaki M
- Subjects
- Alleles, Base Sequence, DNA, Plant genetics, Linkage Disequilibrium, Phenotype, Plant Proteins genetics, Quantitative Trait Loci, Genetic Variation genetics, Genome, Plant genetics, Selection, Genetic, Zea mays genetics
- Published
- 2007
47. [Mycobacterium shinshuense and Mycobacterium leprae infections: usefulness of genetical examinations].
- Author
-
Nakanaga K, Suzuki K, Tanigawa K, Iwamoto T, Goto M, Saito H, and Ishii N
- Subjects
- Base Sequence, DNA, Bacterial genetics, Databases, Nucleic Acid, Humans, Mycobacterium isolation & purification, Mycobacterium leprae isolation & purification, Phylogeny, Polymerase Chain Reaction, RNA, Bacterial genetics, RNA, Ribosomal, 16S genetics, Leprosy diagnosis, Leprosy microbiology, Molecular Diagnostic Techniques, Mycobacterium genetics, Mycobacterium Infections diagnosis, Mycobacterium Infections microbiology, Mycobacterium leprae genetics, Skin Ulcer microbiology
- Abstract
Although Mycobacterium shinshuense and M. leprae infections are relatively rare in the fields of dermatology, an early diagnosis is one of the important prognostic factors of these infections. Applications of the genetical examinations such as PCR and 16S rDNA sequencing are helpful in early diagnosis with culture nagative cases. Short target PCR tests are available to detect DNA of M. shinshuense or M. leprae from clinical specimens including formalin fixed-paraffin embedded samples. A partial 16s rDNA sequencing is functional with enough intact bacterial DNA. A similarity search based on the partial 16S rDNA sequences using RIDOM database is an easy and powerful tool to estimate the species of mycobacteria, however, it is not enough for the identification in some cases. For instance, a clinical isolate of M. shinshuense is clearly discriminated from M. leprae (92.75% sequence identity), however, difficult to be identified from M. marinum and M. ulcerans (99.77% sequence identity). The phylogenetic tree based on 16S rDNA sequences is illustrating that both M. leprae (closely related to M. haemophilum) and M. shinshuense (closely related to M. marinum and M. ulcerans, and also M. tuberculosis) are relatively related species and distantly related to rapidly growing species among 30 species of pathogenic mycobacteria which have been isolated in Japan.
- Published
- 2007
- Full Text
- View/download PDF
48. [Molecular dynamics of CCA-addition by CCA-adding enzyme].
- Author
-
Tomita K and Nureki O
- Subjects
- Archaea enzymology, Base Sequence, Nucleotides metabolism, RNA, Transfer genetics, RNA, Transfer metabolism, RNA Nucleotidyltransferases physiology, RNA, Transfer biosynthesis
- Published
- 2007
49. [Target sequences of retrovirus integration].
- Author
-
Tsuruyama T
- Subjects
- Animals, Leukemia Virus, Murine genetics, Mice, Base Sequence, Retroviridae genetics, Virus Integration physiology
- Published
- 2007
50. [Identification of mycobacteria by sequencing of rpoB gene and 16S rRNA].
- Author
-
Kazumi Y, Maeda S, and Sugawara I
- Subjects
- DNA-Directed RNA Polymerases, Molecular Sequence Data, Mycobacterium genetics, Bacterial Proteins genetics, Base Sequence, Mycobacterium isolation & purification, RNA, Ribosomal, 16S analysis, Sequence Analysis, DNA
- Abstract
Purpose: To classify a specific Mycobacterium among various mycobacteria utilizing sequencing of rpoB gene. To classify mycobacteria not identified by DNA-DNA hybridization (DDH) using sequencing of rpoB and 16S rRNA gene., Objects and Methods: Classification of 106 Mycobacteria strains, one Nocardia strain, one Rhodococcus strain, four Gordona strains was made by using partial sequencing of rpoB and 16S rRNA (RIDOM). Thereafter, 38 mycobacteria clinical strains not identified by DDH were classified utilizing the DNA sequencing data., Results: Pairs of M. kansasii and M. gastri, M. abscessus and M. chelonae, M.fortuitum (ATCC49404) and M. polcinum, M. peregrinum and M. septicum, M. farucinogense and M. senegalense and M. fortuitum (ATCC49403), Rhodococcus, Nocardia and Gordona strains were classified using sequencing of rpoB gene. Even though sequencing of rpoB and 16S rRNA gene was utilized, it was impossible to classify M. tuberculosis complex, M. avium family, M. marinum and M. ulcerans, and M. fortitum subsp. fortuitum and M. fortuitum subsp. acetamidolyticus. The 38 mycobacteria clinical strains not identified by DDH were successfully classified using sequencing of both rpoB and 16S rRNA. These sequencing analyses showed that M. heckeshornense, M. branderi, M. intermedium, M. shimoidei, M. wolinskyi, M. malmoense and M. lentiflavum could be identified. Thirty six clinical isolates (94.7%) and 32 clinical isolates (84.2%) were identified by rpoB sequencing and 16S rRNA sequencing (RIDOM), respectively., Conclusion: The classification ratio of mycobacteria including Nocardia, Rhodococcus and Gordona is 69.6% for sequencing of 16S rRNA and 89.3% for sequencing of rpoB gene. Sequencing of rpoB is useful for classification of mycobacteria due to its genetic diversity, but has some limitation in its application. In order to classify mycobacteria more accurately, it is important to combine sequencing of rpoB and 16S rRNA and biochemical/biological tests.
- Published
- 2006
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