Showing papers by "Yutaka Suzuki published in 2007"

Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis

Abstract: Mammalian promoters are categorized into TATA and CpG-related groups, and they have complementary roles associated with differentiated transcriptional characteristics. While the TATA box is also found in plant promoters, it is not known if CpG-type promoters exist in plants. Plant promoters contain Y Patches (pyrimidine patches) in the core promoter region, and the ubiquity of these beyond higher plants is not understood as well. Sets of promoter sequences were utilized for the analysis of local distribution of short sequences (LDSS), and approximately one thousand octamer sequences have been identified as promoter constituents from Arabidopsis, rice, human and mouse, respectively. Based on their localization profiles, the identified octamer sequences were classified into several major groups, REG (Regulatory Element Group), TATA box, Inr (Initiator), Kozak, CpG and Y Patch. Comparison of the four species has revealed three categories: (i) shared groups found in both plants and mammals (TATA box), (ii) common groups found in both kingdoms but the utilized sequence is differentiated (REG, Inr and Kozak) and (iii) specific groups found in either plants or mammals (CpG and Y Patch). Our comparative LDSS analysis has identified conservation and differentiation of promoter architectures between higher plants and mammals.

H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational

Abstract: The Human-transcriptome DataBase for Alternative Splicing (H-DBAS) is a specialized database of alternatively spliced human transcripts. In this database, each of the alternative splicing (AS) variants corresponds to a completely sequenced and carefully annotated human full-length cDNA, one of those collected for the H-Invitational human-transcriptome annotation meeting. H-DBAS contains 38 664 representative alternative splicing variants (RASVs) in 11 744 loci, in total. The data is retrievable by various features of AS, which were annotated according to manual annotations, such as by patterns of ASs, consequently invoked alternations in the encoded amino acids and affected protein motifs, GO terms, predicted subcellular localization signals and transmembrane domains. The database also records recently identified very complex patterns of AS, in which two distinct genes seemed to be bridged, nested or degenerated (multiple CDS): in all three cases, completely unrelated proteins are encoded by a single locus. By using AS Viewer, each AS event can be analyzed in the context of full-length cDNAs, enabling the user's empirical understanding of the relation between AS event and the consequent alternations in the encoded amino acid sequences together with various kinds of affected protein motifs. H-DBAS is accessible at http://jbirc.jbic.or.jp/h-dbas/.

Distinct class of putative “non-conserved” promoters in humans: Comparative studies of alternative promoters of human and mouse genes

Abstract: Although recent studies have revealed that the majority of human genes are subject to regulation of alternative promoters, the biological relevance of this phenomenon remains unclear. We have also demonstrated that roughly half of the human RefSeq genes examined contain putative alternative promoters (PAPs). Here we report large-scale comparative studies of PAPs between human and mouse counterpart genes. Detailed sequence comparison of the 17,245 putative promoter regions (PPRs) in 5463 PAP-containing human genes revealed that PPRs in only a minor fraction of genes (807 genes) showed clear evolutionary conservation as one or more pairs. Also, we found that there were substantial qualitative differences between conserved and non-conserved PPRs, with the latter class being AT-rich PPRs of relative minor usage, enriched in repetitive elements and sometimes producing transcripts that encode small or no proteins. Systematic luciferase assays of these PPRs revealed that both classes of PPRs did have promoter activity, but that their strength ranges were significantly different. Furthermore, we demonstrate that these characteristic features of the non-conserved PPRs are shared with the PPRs of previously discovered putative non-protein coding transcripts. Taken together, our data suggest that there are two distinct classes of promoters in humans, with the latter class of promoters emerging frequently during evolution.

Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs

Abstract: Comparasite is a database for comparative studies of transcriptomes of parasites. In this database, each data is defined by the full-length cDNAs from various apicomplexan parasites. It integrates seven individual databases, Full-Parasites, consisting of numerous full-length cDNA clones that we have produced and sequenced: 12 484 cDNA sequences from Plasmodium falciparum, 11 262 from Plasmodium yoelii, 9633 from Plasmodium vivax, 1518 from Plasmodium berghei, 7400 from Toxoplasma gondii, 5921 from Cryptosporidium parvum and 10 966 from the tapeworm Echinococcus multilocularis. Putatively counterpart gene groups are clustered and comparative analysis of any combination of six apicomplexa species is implemented, such as interspecies comparisons regarding protein motifs (InterPro), predicted subcellular localization signals (PSORT), transmembrane regions (SOSUI) or upstream promoter elements. By specifying keywords and other search conditions, Comparasite retrieves putative counterpart gene groups containing a given feature in common or in a species-specific manner. By enabling multi-faceted comparative analyses of genes of apicomplexa protozoa, monophyletic organisms that have evolved to diversify to parasitize various hosts by adopting complex life cycles, Comparasite should help elucidate the mechanism behind parasitism. Our full-length cDNA databases and Comparasite are accessible from http://fullmal.ims.u-tokyo.ac.jp.

Detection of gene expression in synovium of patients with osteoarthritis using a random sequencing method

Abstract: Background The etiology of osteoarthritis (OA) is multifactorial and current research attributes it to a complex network of biochemical factors. We attempted to identify important molecules in OA joint destruction.Patients and methods Synovium was collected from 2 women with hip OA. Total RNA was extracted from the combined synovium. Messenger RNAs (mRNAs) were randomly sequenced for identification with the oligo-capping method. mRNA expression of 9 genes that were found to be frequently expressed was compared in synovium from 7 OA patients and 2 control patients with no signs of arthritis.Results We sequenced 7,339 mRNAs in total and identified 4,247 different kinds, which were ranked in order of frequency. Fibronectin was the protein most frequently expressed (230/7,339), followed by matrix metalloproteinases (MMPs) 1 and 3. The 9 genes selected were those encoding fibronectin 1, MMP1, MMP3, tissue inhibitor of metalloproteinase 3, apolipoprotein L-I (APOL1), syndecan binding protein, insulin-like growt...

Guide body, manufacturing method thereof, and electromagnetic valve device

Abstract: A guide body for an electromagnetic valve device is provided. The device includes a coil assembly surrounding the guide body, a plunger driven by magnetic force and slidably disposed inside the guide body. The guide body slidably guides the plunger in an open/close direction of the valve body along a guide face thereof. The guide body includes a first nonmagnetic section that supports a pole body and a part of the plunger at which the pole body and the plunger oppose each other, a second nonmagnetic section that supports the valve body, and extends at least throughout a sliding range of the valve body, and a magnetic section intermediate the first and second sections so that a portion of the lines of magnetic force passes therethrough. The guide face is formed so as to coaxially support the plunger and the valve body displaceable in the open/close direction.

Intrinsic promoter activities of primary DNA sequences in the human genome.

Abstract: In order to understand an overview of promoter activities intrinsic to primary DNA sequences in the human genome within a particular cell type, we carried out systematic quantitative luciferase assays of DNA fragments corresponding to putative promoters for 472 human genes which are expressed in HEK (human embryonic kidney epithelial) 293 cells. We observed the promoter activities of them were distributed in a bimodal manner; putative promoters belonging to the first group (with strong promoter activities) were designated as P1 and the latter (with weak promoter activities) as P2. The frequencies of the TATA-boxes, the CpG islands, and the overall G þ C-contents were significantly different between these two populations, indicating there are two separate groups of promoters. Interestingly, similar analysis using 251 randomly isolated genomic DNA fragments showed that P2-type promoter occasionally occurs within the human genome. Furthermore, 35 DNA fragments corresponding to putative promoters of non-protein-coding transcripts (ncRNAs) shared similar features with the P2 in both promoter activities and sequence compositions. At least, a part of ncRNAs, which have been massively identified by full-length cDNA projects with no functional relevance inferred, may have originated from those sporadic promoter activities of primary DNA sequences inherent to the human genome.

[Left ventricular-right atrial communication resulting from infective endocarditis].

Abstract: We report a rare case of acquired left ventricular-right atrial communication resulting from infective endocarditis. A 57-year-old male with aortic regurgitation due to infective endocarditis was referred to our hospital because of severe congestive heart failure. Preoperative transthoracic echocardiography showed aortic, mitral and tricuspid severe regurgitations. Intraoperative transesophageal echocardiography revealed left ventricular-right atrial shunt. The fistula was located at the atrioventricular membranous septum. The communication site from the left view was below the commissure between the right coronary cusp and non-coronary cusp, and from the right view was just above the tricuspid annulus of the septal leaflet. The fistula was closed directly with mattress suture and aortic valve replacement and both mitral and tricuspid ring annuloplasty were carried out simultaneously. The postoperative course was uneventful. It is important to inspect shunts carefully in echocardiography of infective endocarditis with massive regurgitations.

[Cancer screening with PET: advantages and limitations].

Abstract: Warburg first reported that tumours are characterized by abnormally increased glucose metabolism accompanied by increase production of lactate. This is a basic principle underlying cancer detection by the glucose analogue 18-F-fluoro-2-deoxy-D-glucose (FDG). FDG positron emission tomography (PET) is currently used widely to examine virtually any part of the body in order to detect tumours, e.g., lung, breast, colorectal, pancreatic and head and neck cancers, malignant lymphoma and malignant melanoma. The advantage of whole-body FDG-PET in comparison with the other imaging modalities is that it allows the entire body to be surveyed seamlessly within a reasonably short period. Furthermore, the staging of most cancers can be determined. The characteristics of whole-body FDG-PET seem to satisfy the requirements for cancer screening. PET used simultaneously with conventional tests can prevent the overlooking of cancer, reduce false-positive results and assist in the interpretation of CT and MRI images. Thus, PET can play a supportive role when used with conventional screening tests. In 1994, PET was applied to cancer screening for the first time at our Imaging Center at Lake Yamanaka in Japan. Within 12 years after starting, a total of 10,292 asymptomatic individuals (6,227 men and 4,065 women; mean age, 52.2 and 52.9 years) participated in 29,090 screening sessions. As a result, malignant tumours were demonstrated in 355 of the 10,292 participants (2.61%). PET findings were true-positive in 175 of the 355 cancers (49.3%).