Clinical Usefulness of a Short Version of the Internet Addiction Test to Screen for Probable Internet Addiction in Adolescents with Autism Spectrum Disorder

Internet addiction (IA) is defined as the condition of being addicted to all sorts of activities on the Internet. Individuals with neurodevelopmental disorders, including autism spectrum disorder (ASD), may be susceptible to IA. Early detection and intervention for probable IA are important to prevent severe IA. In this study, we investigated the clinical usefulness of a short version of the Internet Addiction Test (s-IAT) for the screening of IA among autistic adolescents. The subjects were 104 adolescents with a confirmed diagnosis of ASD. They were requested to answer 20 questions from the original Internet Addiction Test (IAT). In the data analysis process, we comparatively calculated the sum of scores to the 12 questions of s-IAT. In total, 14 of the 104 subjects were diagnosed as having IA based on the face-to-face clinical interview that was regarded as the gold standard. Statistical analysis suggested that the optimal cut-off for s-IAT was at 35. When we applied the cut-off of 70 on the IAT, only 2 of 14 subjects (14.3%) with IA were screened positive, whereas 10 (71.4%) of them were screened by using the cut-off point of 35 on s-IAT. The s-IAT might be useful for the screening of IA in adolescents with ASD.

The Efficacy of Early Start Denver Model Intervention in Young Children with Autism Spectrum Disorder Within Japan: A Preliminary Study

Objectives

Among the many intervention programs for children with autism spectrum disorder (ASD), the Early Start Denver Model (ESDM) is one of the few approaches that has succeeded in demonstrating clinical efficacy in randomized control trials. Here, we investigate the clinical efficacy of ESDM intervention in young children with ASD in a community setting within Japan.

Methods

All subjects were children with ASD who received ESDM intervention during the study period. Each ESDM session lasted 75 min and occurred once per week for at least 12 weeks. The outcome measures consisted of the Kyoto Scale of Psychological Development (K-test), Aberrant Behavior Checklist-Japanese version (ABC-J), and the Clinical Global Impression-Severity scale (CGI-S).

Results

Twenty-seven subjects (29.4±6.4 months old) received ESDM intervention that lasted for 8.0±2.6 months on average. The score on Language and Social developmental quotient on the K-test increased significantly after the intervention. The total scores on the ABC-J and CGI-S significantly decreased after completion of the ESDM intervention.

Conclusion

Our results suggest that ESDM intervention could reduce the severity of distinct clinical features of ASD, such as impairments in social interaction and communication assessed by the K-test, and maladaptive behavior rated by the ABC-J and CGI-S. We believe that the ESDM adapted to each institution might become one of the standard options for children with ASD in Japan.

Internet Addiction and Attention-Deficit/Hyperactivity Disorder Traits among Female College Students in Japan

Objectives:

Previous studies have reported that internet addiction (IA) is associated with attention-deficit/hyperactivity disorder (ADHD) consistently. However, in terms of gender, there are controversial findings. We aimed to investigate the relation between IA and self-acknowledged ADHD traits among female college students in Japan.

Methods:

The study questionnaire consisted of questions about demographics, Adult ADHD Self-Report Scale-V1.1 Part A (ADHD screener) and Young’s Internet Addiction Test (IAT). When four or more items are more frequent than the cut-off on ADHD screener, the subject was categorized into students with a positive ADHD screen. We defined students with total IAT score of 70 and higher as IA.

Results:

A total number of respondents was 369 (mean age: 19.0±0.7 years). Seventy-seven subjects were screened positive on ADHD screener (20.9%). Students with a positive ADHD screen scored significantly higher on the IAT (54.2±14.2 vs. 42.5±11.3). The rates of IA in students with and without a positive ADHD screen were 18.2% and 1.0%, respectively.

Conclusion:

Results of this study demonstrated the relation between IA and self-evaluated ADHD traits among female college students in Japan. Appropriate education for students on how to use the internet properly will be necessary to prevent IA.

Deuterium MR in Vivo Imaging of the Rat Eye Using 2H2O

In vivo euterium MR imaging (2H MR) was investigated in rats after intraperitoneal administration of deuterated saline, and a dynamic study of the water movement in rat eyes was performed. Deuterium MR imaging was carried out by means of a gradient-echo (GRE) and a spin-echo (SE) pulse sequence. The rat eye was imaged in 2H MR more selectively by SE than by GRE, but a lower signal-to-noise ratio was obtained in 2H MR imaging using the SE sequence. The MR signal intensity of the rat eye was followed by a 3-compartment model, which enabled determination of the flow rate constant of the water in the eye (0.359/min). Deuterium MR imaging is useful to visualize the dynamic change of water in rat eyes using 2H MR at the same magnetic field (2 T) that can also be used for conventional MR imaging in humans.

Identification of a new adhesin-like protein from Lactobacillus mucosae ME-340 with specific affinity to the human blood group A and B antigens

AIMS

To identify and characterize a new adhesin-like protein of probiotics that show specific adhesion to human blood group A and B antigens.

METHODS AND RESULTS

Using the BIACORE assay, the adhesion of cell surface components obtained from four lactobacilli strains that adhered to blood group A and B antigens was tested. Their components showed a significant adhesion to A and B antigens when compared to the bovine serum albumin (BSA) control. The 1 mol l(-1) GHCl fraction extracted from Lactobacillus mucosae ME-340 contained a 29-kDa band (Lam29) using SDS-PAGE. The N-terminal amino acid sequence and homology analysis showed that Lam29 was 90% similar to the substrate-binding protein of the ATP-binding cassette (ABC) transporter from Lactobacillus fermentum IFO 3956. The complete nucleotide sequence (858 bp) of Lam29 was determined and encoded a protein of 285 amino acid residues. Phylogenetic analysis and multiple sequence alignments indicated this protein may be related to the cysteine-binding transporter.

CONCLUSIONS

The adhesion of ME-340 strain to blood group A and B antigens was mediated by Lam29 that is a putative component of ABC transporter as an adhesin-like protein.

SIGNIFICANCE AND IMPACT OF THE STUDY

Lactobacillus mucosae ME-340 expressing Lam29 may be useful for competitive exclusion of pathogens via blood group antigen receptors in the human gastrointestinal mucosa and in the development of new probiotic foods.

DDBJ with new system and face

DDBJ (http://www.ddbj.nig.ac.jp) collected and released 1 880 115 entries or 1 134 086 245 bases in the period from July 2006 to June 2007. The released data contains the high-throughput cDNAs of cricket and high-quality draft genome of medaka among others. Our computer system has been upgraded since March 2007. Another new aspect is an efficient data retrieval tool that has recently been equipped and served at DDBJ. It is called All-round Retrieval for Sequence and Annotation, which enables the user to search for keywords also in the Feature/Qualifier of the International Nucleotide Sequence Database Collaboration (http://www.insdc.org/). We will also replace our home page with a more efficient one by the end of 2007.

DDBJ in collaboration with mass-sequencing teams on annotation

In the past year, we at DDBJ (DNA Data Bank of Japan; http://www.ddbj.nig.ac.jp) collected and released 1 066 084 entries or 718 072 425 bases including the whole chromosome 22 of chimpanzee, the whole-genome shotgun sequences of silkworm and various others. On the other hand, we hosted workshops for human full-length cDNA annotation and participated in jamborees of mouse full-length cDNA annotation. The annotated data are made public at DDBJ. We are also in collaboration with a RIKEN team to accept and release the CAGE (Cap Analysis Gene Expression) data under a new category, MGA (Mass Sequences for Genome Annotation). The data will be useful for studying gene expression control in many aspects.

DDBJ in the stream of various biological data

In the past year we at DDBJ (http://www.ddbj.nig. ac.jp) have made a steady increase in the number of data submissions with a 50.6% increment in the number of bases or 46.5% increment in the number of entries. Among them the genome data of man, ascidian and rice hold the top three. Our activity has extended to providing a tool that enables sequence retrieval using regular expressions, and to launching our SOAP server and web services to facilitate the acquisition of proper data and tools from a huge number of biological data resources on websites worldwide. We have also opened our public gene expression database, CIBEX.

DNA Data Bank of Japan (DDBJ) in XML

The DNA Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) has collected and released more entries and bases than last year. This is mainly due to large-scale submissions from Japanese sequencing teams on mouse, rice, chimpanzee, nematoda and other organisms. The contributions of DDBJ over the past year are 17.3% (entries) and 10.3% (bases) of the combined outputs of the International Nucleotide Sequence Databases (INSD). Our complete genome sequence database, Genome Information Broker (GIB), has been improved by incorporating XML. It is now possible to perform a more sophisticated database search against the new GIB than the ordinary BLAST or FASTA search.

DNA Data Bank of Japan (DDBJ) for genome scale research in life science

The DNA Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) has made an effort to collect as much data as possible mainly from Japanese researchers. The increase rates of the data we collected, annotated and released to the public in the past year are 43% for the number of entries and 52% for the number of bases. The increase rates are accelerated even after the human genome was sequenced, because sequencing technology has been remarkably advanced and simplified, and research in life science has been shifted from the gene scale to the genome scale. In addition, we have developed the Genome Information Broker (GIB, http://gib.genes.nig.ac.jp) that now includes more than 50 complete microbial genome and Arabidopsis genome data. We have also developed a database of the human genome, the Human Genomics Studio (HGS, http://studio.nig.ac.jp). HGS provides one with a set of sequences being as continuous as possible in any one of the 24 chromosomes. Both GIB and HGS have been updated incorporating newly available data and retrieval tools.

[Muscle involvement of Stormorken's syndrome]

We described two patients, a mother and daughter, of Stormorken's syndrome. The syndrome is characterized clinically by autosomal dominant inheritance, congenital miosis, thrombocytopenia, asplenia and muscle weakness. Both patients had bleeding tendency, ichthyosis of arms, and muscle weakness. The daughter additionally had short stature (146 cm), low body weight (32 kg) and muscle cramp. Neurological findings of the patients included migraine-like headache, cognitive dysfunction, limitation of upward and lateral gaze, and amydriasis. Femoral muscle MRI of the daughter demonstrated decreased volume with patchy high intensity areas in the hamstrings. A muscle biopsy from the daughter showed myogenic changes with muscle fiber necrosis and regeneration, variation in fiber size, tubular aggregates in approximately 5% of fibers, and fibrous tissue proliferation. Dystrophin, dystrophin-associated proteins and dysferlin were normally expressed. Although both patients had elevated creatine kinase levels and generalized muscle wasting, muscle weakness was mild with slow progression. A certain membrane defect in the platelet and muscle fiber might be responsible for the pathogenesis of this syndrome.

Serotonin 5-HT2 receptors in schizophrenic patients studied by positron emission tomography

Using positron emission tomography (PET) and [11C]N-methylspiperone (NMSP), we examined 5-HT2 receptors in the cortex of schizophrenic patients in whom we previously observed decreased prefrontal D1 receptor binding. The subjects were 10 neuroleptic-naive schizophrenic patients, 7 schizophrenic patients who were drug-free but had previously been treated with neuroleptics, and 12 normal controls. A non-significant trend towards decreased prefrontal [11C]NMSP binding was observed in the neuroleptic-treated patients, suggesting a possible effect of previous neuroleptic treatment on the alteration in cortical 5-HT2 function. However, the neuroleptic-naive patients showed no noticeable difference in cortical [11C]NMSP binding compared to controls. Our results do not rule out the role of 5-HT2 function as a crucial site of therapeutic activity of schizophrenia, but they do suggest that cortical 5-HT2 receptors might not be primarily involved in the pathophysiology of schizophrenia.

DNA data bank of Japan (DDBJ) in collaboration with mass sequencing teams

We at DDBJ (http://www.ddbj.nig.ac.jp) process and publicise the massive amounts of data submitted mainly by Japanese genome projects and sequencing teams. It is emphasised that the collaboration between data producing teams and the data bank is crucial in carrying out these processes smoothly. The amount of data submitted in 1999 is so large that it alone exceeds the total amount submitted in the preceding 10 years. To cope with this situation, we have developed tools not only for processing such massive amounts of data but also for efficiently retrieving data on demand.

Evolutionary pattern of influenza B viruses based on the HA and NS genes during 1940 to 1999: origin of the NS genes after 1997

Phylogenetic analysis was carried out for genes encoding hemagglutinin (HA) (24 new and 25 previously reported sequences) and nonstructural proteins (NS) (22 new and 14 previously reported sequences) of influenza B virus isolates obtained from 1940 to 1999. Two antigenically and genetically distinct HA lineages are presently known to exist. Divergence into these two lineages was estimated to have occurred around 1969. Phylogenetic analysis of NS genes revealed that their phylogenetic relationships were not linked to the two HA lineages but suggested that reassortment of viral genes between the viruses of two HA lineages had occurred. In addition two distinct NS lineages which were not linked to the two HA lineages were observed. Viruses isolated after 1997 formed their own lineage in combination with B/Houston/84 while other virus isolates obtained from 1973 to 1995 comprised the other NS lineage.

Genomic organization around the centromeric end of the HLA class I region: large-scale sequence analysis

We previously sequenced two regions around the centromeric end of HLA class I and the boundary between class I and class III. In this paper we analyze the two regions of about 385 kb and confirm, giving a new line of evidence, that the following two pairs of the genomic segments were duplicated in evolution: (i) a 43-kb genomic segment including the HLA-B gene showing the highest polymorphism among the classical HLA class I loci (class Ia) and a 40-kb segment including the HLA-C locus showing the lowest polymorphism and (ii) a 52-kb segment including the MIC (MHC class I chain related gene) B and a 35-kb segment including MICA. We also found that repetitive elements such as SINEs, LINEs, and LTRs occupy as much as 47% of nucleotides in this 385-kb region. This unusually high content of repetitive elements indicates that repeat-mediated rearrangements have frequently occurred in the evolutionary history of the HLA class Ia region. Analysis of LINE compositions within the two pairs of duplicated segments revealed that (i) LINEs in these regions had been dispersed prior to both the duplication of the HLA-B and -C loci and the duplication of the MICB and MICA loci, and (ii) the divergence of the HLA-B and -C loci occurred prior to the duplication of the MICA and MICB loci. To find novel genes responsible for HLA class I-associated or other diseases, we performed computer analysis applying GenScan and GRAIL to GenBank's dbEST. As a result, at least five as yet uncharacterized genes were newly mapped on the HLA class I centromeric region studied. These novel genes should be analyzed further to determine their relationships to diseases associated with this region.

A phosphonate-induced gene which promotes Penicillium-mediated bioconversion of cis-propenylphosphonic acid to fosfomycin

Penicillium decumbens is able to epoxidize cis-propenylphosphonic acid (cPA) to produce the antibiotic fosfomycin [FOM; also referred to as phosphonomycin and (-)-cis-1,2-epoxypropylphosphonic acid], a bioconversion of considerable commercial significance. We sought to improve the efficiency of the process by overexpression of the genes involved. A conventional approach of isolating the presumed epoxidase and its corresponding gene was not possible since cPA epoxidation could not be achieved with protein extracts. As an alternative approach, proteins induced by cPA were detected by two-dimensional gel electrophoresis. The observation that a 31-kDa protein (EpoA) was both cPA induced and overaccumulated in a strain which more efficiently converted cPA suggested that it might take part in the bioconversion. EpoA was purified, its amino acid sequence was partially determined, and the corresponding gene was isolated from cosmid and cDNA libraries with oligonucleotide probes. The DNA sequence for this gene (epoA) contained two introns and an open reading frame encoding a peptide of 277 amino acids having some similarity to oxygenases. When the gene was subcloned into P. decumbens, a fourfold increase in epoxidation activity was achieved. epoA-disruption mutants which were obtained by homologous recombination could not convert cPA to FOM. To investigate the regulation of the epoA promoter, the bialaphos resistance gene (bar, encoding phosphinothricin acetyltransferase) was used to replace the epoA-coding region. In P. decumbens, expression of the bar reporter gene was induced by cPA, FOM, and phosphorous acid but not by phosphoric acid.

Domain dislocation: a change of core structure in periplasmic binding proteins in their evolutionary history

Periplasmic binding proteins (PBPs) serve as receptors for various water-soluble ligands in ATP-binding cassette (ABC) transport systems, and form one of the largest protein families in eubacterial and archaebacterial genomes. They are considered to be derived from a common ancestor, judging from their similarities of three-dimensional structure, their mechanism of ligand binding and the operon structure of their genes. Nevertheless, there are two types of topological arrangements of the central beta-sheets in their core structures. It follows that there must have been differentiation in the core structure, which we call "domain dislocation", in the course of evolution of the PBP family. To find a clue as to when the domain dislocation occurred, we constructed phylogenetic trees for PBPs based on their amino acid sequences and three-dimensional structures, respectively. The trees show that the proteins of each type clearly cluster together, strongly indicating that the change in the core structure occurred only once in the evolution of PBPs. We also constructed a phylogenetic tree for the ABC proteins that are encoded by the same operon of their partner PBP, and obtained the same result. Based on the phylogenetic relationship and comparison of the topological arrangements of PBPs, we obtained a reasonable genealogical chart of structural changes in the PBP family. The present analysis shows that the unidirectional change of protein evolution is clearly deduced at the level of protein three-dimensional structure rather than the level of amino acid sequence.

DNA Data Bank of Japan dealing with large-scale data submission

The DNA Data Bank of Japan (DDBJ) (http//:www.ddbj.nig.ac.jp) has developed a software system for mass submissions to cope with a recent expansion of EST and genome data submissions. The system is composed of four parts, the WWW data submission, large-scale submission, submission management and storing. Using this system one can submit data on a large number of sequences or a very long sequence while checking the consistency between the annotation and sequence without much effort. DDBJ has received large scale data of Homo sapiens, Arabidopsis and Pyrococcus from Japanese researchers who made full use of the new submission system.

Formal design and implementation of an improved DDBJ DNA database with a new schema and object-oriented library

MOTIVATION

The DNA Data Bank of Japan (DDBJ) has developed a new DNA database system with a new schema design to accommodate rapid change and growth of requirements on the system.

RESULTS

The new schema and systems were created using an object-oriented design approach. The design was accomplished in accordance with ANSI/SPARC three-level schema architecture. First, the conceptual schema was designed using a functional model named AIS (associative information structure) and was visualized in extended diagram format. The model is a natural extension of an ER (entity relationship) model and describes real-world objects in binary associations between entities with the concept of order. Second, the schema was mapped on a relational database as a physical schema. All details are concentrated in this schema and the layer lying above enjoys physical independence. Finally, as another layer, external modeling was introduced for the database applications interface. It provides set-at-a-time basis operations and was implemented as a C++ object-oriented library. On this common framework of a new schema, a new annotator's workbench named Yamato II and a World Wide Web (WWW) submission system named Sakura have been successfully developed to improve drastically daily transactions in the DDBJ.

AVAILABILITY

Sakura is available at the following address: http://sakura.ddbj.nig.ac.jp.

CONTACT

hsugawar@genes.nig.ac.jp

Virtualized angioscopy of the thoracic aorta in a rabbit model of atherosclerosis

The purpose of this study was to apply virtual reality technology to spiral computed tomographic (CT) angiogram images in a rabbit model of atherosclerosis and to correlate the images with histopathologic evaluation of the aorta. Image data were transferred to the virtual endoscope system in a graphics workstation. "Virtualized angioscopy" includes an interactive graphic user interface, which controls the viewpoint, the direction of the observation, and rendering and navigation functions. The virtual angioscopy system demonstrated irregularities of the luminal surface of the ascending aorta and a smooth luminal surface in the descending aorta. These observations were correlated with histopathologic findings. The results of this study indicate that the potential and real benefits of virtualized angioscopy far outweigh several technical limitations.

DNA Data Bank of Japan at work on genome sequence data

We at the DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) have recently begun receiving, processing and releasing EST and genome sequence data submitted by various Japanese genome projects. The data include those for human, Arabidopsis thaliana, rice, nematode, Synechocystis sp. and Escherichia coli. Since the quantity of data is very large, we organized teams to conduct preliminary discussions with project teams about data submission and handling for release to the public. We also developed a mass submission tool to cope with a large quantity of data. In addition, to provide genome data on WWW, we developed a genome information system using Java. This system (http://mol.genes.nig.ac.jp/ecoli/) can in theory be used for any genome sequence data. These activities will facilitate processing of large quantities of EST and genome data.

Development of a 3D CT-scanner using a cone beam and video-fluoroscopic system

We describe the design and implementation of a system that acquires three-dimensional (3D) data of high-contrast objects such as bone, lung, and blood vessels (enhanced by contrast agent). This 3D computed tomography (CT) system is based on a cone beam and video-fluoroscopic system and yields data that is amenable to 3D image processing. An X-ray tube and a large area two-dimensional detector were mounted on a single frame and rotated around objects in 12 seconds. The large area detector consisted of a fluorescent plate and a charge coupled device (CCD) video camera. While the X-ray tube was rotated around the object, a pulsed X-ray was generated (30 pulses per second) and 360 projected images were collected in a 12-second scan. A 256 x 256 x 256 matrix image was reconstructed using a high-speed parallel processor. Reconstruction required approximately 6 minutes. Two volunteers underwent scans of the head or chest. High-contrast objects such as bronchial, vascular, and mediastinal structures in the thorax, or bones and air cavities in the head were delineated in a "real" 3D format. Our 3D CT-scanner appears to produce data useful for clinical imaging and 3D image processing.

A clearer distinction between HIV-1 paired isolates from peripheral blood mononuclear cells of asymptomatic carriers with and without CD8+ T-cells at nef rather than env V3 loci

In asymptomatic carriers, the vast majority of human immunodeficiency virus type 1 (HIV-1) infection is non-productive whilst the clinical stage of disease is associated with significant virus expression. Virus-specific CD8+ T-cell functions are believed to play a major role in the generation of heterogeneous virus populations and in subsequent disease progression. Here, we prepared two types of HIV-1 isolate by culturing whole and CD8+ T cell-depleted peripheral blood mononuclear cells (PBMCs) from five asymptomatic carriers. The former is expected to be escape variant populations, whereas the latter would be mixed populations including the former viruses. The analyses of Nef and Env V3 sequence variations of viruses in a total of 77 and 44 DNA clones, respectively, allowed a direct comparison to be made of the differences between the paired isolates. Comparison of Nef sequences between the paired isolates showed them to be more distinct in two carriers with a relatively stable CD4/CD8 ratio (Nos 68 and 69), than in two other carriers with similar CD4/CD8 ratios (Nos 53 and 57), or in carrier No. 67, which had an extremely lower CD4/CD8 ratio. By contrast, a distinction between the paired isolates by use of the Env V3 sequences was only apparent in the latter three carriers. These results indicate that the predominant populations of HIV-1 in Nos 68 and 69 were sensitive to selective pressure from Nef-specific CD8+ T-cells, while those in Nos 53, 57, and 67 were sensitive to pressure from V3-specific CD8+ T-cells. It is noteworthy that Nos 53 and 57 progressed to an AIDS-related complex shortly and several years after this examination. These data suggest that HIV-1-induced pathogenesis is more strongly associated with the generation of variant nef alleles than with env V3 variants, and that these arise by CD8+ T-cell pressure.

Decreased prefrontal dopamine D1 receptors in schizophrenia revealed by PET

Schizophrenia is believed to involve altered activation of dopamine receptors, and support for this hypothesis comes from the antipsychotic effect of antagonists of the dopamine D2 receptor (D2R). D2R is expressed most highly in the striatum, but most of the recent positron emission tomography (PET) studies have failed to show any change in D2R densities in the striatum of schizophrenics, raising the possibility that other receptors may also be involved. In particular, the dopamine D1 receptor (D1R), which is highly expressed in the prefrontal cortex, has been implicated in the control of working memory, and working memory dysfunction is a prominent feature of schizophrenia. We have therefore used PET to examine the distribution of D1R and D2R in brains of drug-naive or drug-free schizophrenic patients. Although no differences were observed in the striatum relative to control subjects, binding of radioligand to D1R was reduced in the prefrontal cortex of schizophrenics. This reduction was related to the severity of the negative symptoms (for instance, emotional withdrawal) and to poor performance in the Wisconsin Card Sorting Test. We propose that dysfunction of D1R signalling in the prefrontal cortex may contribute to the negative symptoms and cognitive deficits seen in schizophrenia.

Evolutionary motif and its biological and structural significance

We developed a method for multiple alignment of protein sequences. The main feature of this method is that it takes the evolutionary relationships of the proteins in question into account repeatedly for execution, until the relationships and alignment results are in agreement. We then applied this method to the data of the international DNA sequence databases, which are the most comprehensive and updated DNA databases in the world, in order to estimate the "evolutionary motif" by extensive use of a supercomputer. Though a few problems needed to be solved, we could estimate the length of the motifs in the range of 20 to 200 amino acids, with about 60 the most frequent length. We then discussed their biological and structural significance. We believe that we are now in a position to analyze DNA and protein not only in vivo and in vitro but also in silico.

DNA Data Bank of Japan in the age of information biology

DNA Data Bank of Japan (DDBJ) began its activities in 1986 in collaboration with EMBL in Europe and GenBank in the United States. DDBJ developed a data submission tool called Sakura, by which researchers can submit their newly sequenced data on WWW from every corner of the world. The data bank also built a database management system (Yamato II), incorporating the techniques and functions of the object-oriented database, in order to efficiently process the data it has collected. A number of research activities in information biology are also going on at DDBJ. Two such activities are also briefly introduced in this report.

Evaluation of blood flow patterns of true and false lumens in dissecting aneurysms using MR phase-contrast techniques

The magnetic resonance phase-contrast technique for the measurement of flow velocity and volume in true and false lumens was studied in six patients with chronic dissecting aneurysms. Phase-contrast images were obtained at a level perpendicular to the dissecting aneurysms of the descending aorta. As the maximum diameter of aneurysms increased, the ratio of the cross-sectional area of the false to the true lumen increased and the peak average velocity in the true lumen during systole was decreased. This technique proved invaluable for determining prognosis and operability for this condition.

Contrast-enhanced MRI with gadodiamide injection in rabbit carcinoma models

This study was designed to demonstrate the broad utility of contrast-enhanced magnetic resonance imaging (MRI) for diagnosis of carcinoma. Twenty-six New Zealand White rabbits of either sex (1.7-3.4 kg) were used for the investigation. VX2 carcinoma (squamous cell carcinoma) was implanted in either the brain, lung, ovary, bone or muscle of rabbits. Contrast agent, Gadodiamide Injection, was administered intravenously at a dose of 0.1 mmol/kg. MR images were obtained by a 1.5 T, or a 2.0 T magnetic field strength super-conductive MRI unit. The intensity of the signal for the carcinoma was increased after administration of contrast agent, and the detectability or diagnostic information of post-contrast images was superior to that of pre-contrast images in all models. In addition, no significant side effects were observed during the MRI examination. After diagnosis using MRI, morphological damage in each model was assessed by gross and histopathological examinations. In contrast-enhanced MRI, though there were variations between the models employed, contrast effects in brain and muscle carcinoma models were generally related to differences in capillary permeability, while imaging in lung, ovary and bone carcinoma models was dependent on differences in blood flow rate and the size of interstitial spaces. Overall, our results demonstrate that contrast-enhanced MRI is a useful and safe method for diagnosing tumors.

Contrast-enhanced MRI with gadodiamide injection in rat disease models

The present study was designed to confirm the usefulness of contrast-enhanced magnetic resonance imaging (MRI) in diagnosing strokes of stroke-prone spontaneously hypertensive rats (SHRSP) and middle cerebral artery (MCA) occlusion, hepatocellular carcinoma and hydronephrosis of each experimental rat model. Male Sprague-Dawley rats (250-500 g), male SHRSP (ca. 250 g) and male F344 rats (ca. 300 g) were used for the investigation. Gadodiamide injection (Omniscan, Daiichi Pharmaceutical Co., Ltd. and Nycomed AS, Norway) was administered intravenously as the contrast agent at a dose of 0.1 mmol/kg except in hydronephrosis, where a dose of 0.05 mmol/kg was used. Magnetic resonance (MR) images were obtained with a 1.5T or a 2.0T magnetic field strength MRI unit. The signal intensity of the stroke lesions was increased after administration of gadodiamide injection in SHRSP and MCA-occluded rats. Hepatocellular carcinoma was undetectable without the use of the contrast agent, but the signal intensity of the tumor increased after administration of the gadodiamide injection, allowing the lesions to be detected. The signal intensity of the renal medulla increased in the non-ligated kidney, but not in the hydronephrotic kidney. The information given by the post-contrast images were superior to those obtained from the pre-contrast images in all the models. Contrast effects in SHRSP and MCA-occluded rats were related to differences in capillary permeability, those in rats with hepatocellular carcinoma depended on differences in vascularity, and those in hydronephrotic rats depended on blood flow and permeability.

Differences in metabolic and morphological reactions after radiation therapy: proton NMR spectroscopy and imaging of patients with intracranial tumors

PURPOSE

The purpose of the present study was to detect tumor cell viability, the diagnosis of which is the most important point in clinical therapy for malignant tumors. The advent of localized proton spectroscopy has made this detection possible. The spectral peak intensities were found to be very different depending on tumor tissue pathology.

METHODS

The tumor cell reaction after radiation therapy was examined with proton localized spectroscopy in addition to enhanced MR imaging using a 1.5 Tesla MR system (Philips, Gyroscan S15-HP). Plain MR images (short spin echo) were used for localization pilot images, and after the MRS study, contrast enhanced MRI was carried out. Studies were performed pre-radiation, mid-radiation, and post-radiation if possible.

MATERIALS

Sixteen patients (total 27 examinations) with intracranial tumors and three normal volunteers underwent proton NMR localized spectroscopy. The brain tumors were diagnosed before the MR study, and nine patients had metastatic brain tumors, such as adenocarcinoma, squamous cell carcinoma, and small cell carcinoma, and seven other patients were diagnosed with glioma-type tumors.

RESULTS

The reaction patterns of proton NMR spectroscopy of brain tumors after radiation therapy were very different and depended on tumor histology.

CONCLUSION

Proton NMR spectroscopy is an excellent means of determining tumor cell viability.

Deuterium MR in vivo imaging of the rat eye using 2H2O

In vivo deuterium MR imaging (2H MR) was investigated in rats after intraperitoneal administration of deuterated saline, and a dynamic study of the water movement in rat eyes was performed. Deuterium MR imaging was carried out by means of a gradient-echo (GRE) and a spin-echo (SE) pulse sequence. The rat eye was imaged in 2H MR more selectively by SE than by GRE, but a lower signal-to-noise ratio was obtained in 2H MR imaging using the SE sequence. The MR signal intensity of the rat eye was followed by a 3-compartment model, which enabled determination of the flow rate constant of the water in the eye (0.359/min). Deuterium MR imaging is useful to visualize the dynamic change of water in rat eyes using 2H MR at the same magnetic field (2 T) that can also be used for conventional MR imaging in humans.

Hypersensitivity of cortical muscarinic receptors in Parkinson's disease demonstrated by PET

The status of muscarinic receptors (mAChRs) is not clear in Parkinson's disease (PD). We measured mAChR binding in the brain of eight patients with PD and eight, age-matched, healthy controls by positron emission tomography (PET) and [11C]N-methyl-4-piperidyl benzilate ([11C]NMPB). PD patients were not demented according to DSM III criteria but showed significant frontal lobe dysfunction in the Modified Wisconsin Card Sorting Test. A mean K3 value, which is an index of mAChR binding calculated by a graphical method, was 20% higher in the frontal cortex of PD patients than controls (p < 0.05). Hypersensitivity of mAChRs in the frontal cortex of PD patients may be a response to a loss of ascending cholinergic input to that region, and may relate to frontal lobe dysfunction in PD.

Deuterium magnetic resonance imaging of rabbit eye in vivo

We used deuterium magnetic resonance imaging (2H MRI) to visualize water movement in the rabbit eye. Dynamic 2H MRI was obtained every 3.5 min at 2 tesla by FLASH pulse sequence (TR, 300 ms; TE, 10 ms; alpha = 90 degrees) with a slice thickness of 10 mm using a surface coil (4 cm in diameter). After topical administration (0.2 ml D2O), only the aqueous chamber was imaged, and the signals decreased mono-exponentially. The flow rate was 0.113/min, in agreement with that already reported. After intravenous administration of deuterated saline (3 ml/kg), the aqueous chamber became visible first during imaging, then by the vitreous body. The signals around the lens were only faintly detected. Thus, deuterium MRI was determined to be useful for visualizing water movement in the eye.

The functional staging of Duchenne muscular dystrophy using in vivo 31P MR spectroscopy

We applied 31P magnetic resonance spectroscopy (MRS) for the diagnosis of Duchenne muscular dystrophy (DMD), and evaluated its suitability for early-state DMD diagnosis. The spectral patterns showed typical differences between normal and diseased calf muscle. The signal intensity from each spectrum became weaker with advancing disease stage. We could detect abnormality even at the before imaging modalities.

Measurement of arterial tracer concentrations from cardiac PET images

OBJECTIVE

Cardiac PET imaging offers the potential capability for the noninvasive measurement of arterial input function. This capability is somewhat limited, however, because of partial volume and spillover effects. The purpose of this study was to validate arterial tracer concentration measurements using PET images by assigning a region of interest (ROI) to the left ventricle, left atrium (LA), and ascending aorta.

MATERIALS AND METHODS

We selected [11C]CO and [13N]ammonia as tracers, because the activity of [11C]CO is primarily in the blood pool and that of [13N]ammonia primarily in myocardial tissue. Six [11C]CO and 11 [13N]ammonia PET scans were obtained in 17 subjects. Arterial tracer concentrations determined by PET were compared with those measured by well counting of arterial blood sampling obtained at the midpoint of each image acquisition.

RESULTS

Arterial tracer concentrations as determined by LA-PET imaging correlated closely with those measured by blood sampling (r = 0.996, slope = 1.00 for [11C]CO; r = 0.841, slope = 0.974 for [13N]ammonia). Partial volume and spillover effects were minimized by assigning an ROI to the LA.

CONCLUSION

Arterial tracer concentrations can be measured noninvasively with cardiac PET.

[A pilot study with lung-cancer screening CT (LSCT) at the secondary screening for lung cancer detection]

We have developed computed tomography (CT) equipment for lung-cancer screening (named LSCT) that can be used exclusively for lung-cancer screening with spiral volumetric CT and is available on a screening car. A pilot study with LSCT was performed from November 1992 to January 1993 on 118 screenees at the secondary examination of lung-cancer screening. Scan parameters were as follows: 120 kVp, 50 mA, slice thickness 10 mm, table feed 10 mm/sec, scan time 2 sec/rotation. All the screenees were scanned under quiet respiration instead of the breath-hold technique. Under these scan parameters, LSCT images were almost free from respiratory motion artifacts even at the lung base. Continuity of the bronchial tree and vessels was well maintained in consecutive slices. Pulmonary nodules approximately 5 mm in diameter were clearly depicted. By LSCT, 43 of 118 screenees were diagnosed to need further examinations. And 33 out of 43 screenees underwent detailed examinations. Finally, 16 lung cancers were confirmed. Ten of 16 patients with lung cancer underwent surgery; nine were in stage I and one in stage IIIA. LSCT was considered to be useful in lung-cancer screening.

Serial water changes in human skeletal muscles on exercise studied with proton magnetic resonance spectroscopy and imaging

In vivo 1H-magnetic resonance imaging (MRI) enabled us to study the distribution of water in living tissues and to document changes in human skeletal muscles during physical exercise. The purpose of the present study was to determine the total muscle water changes after exercise using water in 1H-MR spectroscopy and to compare these changes to the signal intensity change on T2*-weighted images and/or to the T2 value change. Seven young male volunteers were positioned in a 1.5 T Philips MR imaging system. They were then asked to dorsiflex their ankle joint against a 2 kg weight once every 2 seconds for 2 minutes. The peak height of water declined according to the clearance curve after exercise in all seven cases with the 1H-MRS similar to the signal intensity. The increasing rate at peak height of total muscle water exceeded both the signal intensity and the T2 value because the water peak height on the 1H-MRS included the extracellular water. In addition, we measured the changes in signal intensity in both calf muscles after walking race exercise. The time intensity curves were used to draw a clearance curve for each muscle group after exercise. It was possible to discern which muscle was used most from the T2*-weighted image that was obtained once after exercise.

Evolution of glutamine synthetase genes is in accordance with the neutral theory of molecular evolution

Evolution of glutamine synthetase gene is discussed on the results of DNA sequence analysis of the gene. Thirty DNA sequences of various organisms spanning from prokaryotes to eukaryotes were collected from the DNA data banks and translated first, they were aligned next, then evolutionary distances were computed, and molecular phylogeny was finally estimated. The results of the alignment reveal that functionally important regions of glutamine synthetase have been evolutionarily more conserved than the remaining regions. The evolutionary distances computed also show that the rate of synonymous substitution is higher than that of nonsynonymous substitution. These are well in accordance with the neutral theory of molecular evolution. Besides, the molecular phylogeny obtained shows that the origin of glutamine synthetase gene is much earlier than the divergence between eukaryotes and prokaryotes, suggesting that the gene is one of the oldest genes functioning now.

[Comparison of two types of mass screening for lung cancer in terms of cost-effectiveness: indirect chest X-ray vs LSCT]

Mass screening for lung cancer is widely performed in Japan, with the photofluoroscopic examination and sputum cytology used as the screening methods. However the clinical efficacy of these screening methods is considered to be inadequate in terms of the survival rate of the screened population. In the previous report we proposed that a specially designed CT technique, called lung cancer screening CT (LSCT), may be useful in screening for lung cancer. In this paper a preliminary comparison is made between the present and future methods of lung cancer screening in terms of cost-effectiveness. A model for cost-effectiveness analysis estimates the net life-years saved by screening and then determines the direct cost of screening including cost of therapy. Various factors are taken into account such as sensitivity of the screening methods, rate of participation in detailed examination, 5-year survival rate of the screened population, cost of the screening method, and average cost of therapy for screen-detected patients and outpatients. An example of the results is as follows: for a population with a lung cancer incidence of 200 x 10(-5) person/year and life expectancy of 30 years, the net person years saved are 672 x 10(-5) for the present screening method and 2376 x 10(-5) for LSCT screening. The cost required to save one person year are 1.46 x 10(5) yen for the present screening method and 2.03 x 10(5) yen for LSCT screening.(ABSTRACT TRUNCATED AT 250 WORDS)

[The effect of CD8+ cells on isolation and replication of HIV-1]

Human immunodeficiency virus type 1 (HIV-1) seropositive individuals are known to have a population of CD8+T lymphocytes which can suppress the replication of the virus. Two hundred and twelve peripheral blood mononuclear cells (PBMC) samples obtained from 42 seropositive individuals were examined for HIV-1 isolation. HIV-1 recovery rate reached almost 90% by coculture of CD8+ cell-depleted PBMC with uninfected normal PBMC. These results indicated the usefulness of panning method of CD8+ cell for isolation of HIV-1 from asymptomatic carriers (AC). To investigate the suppressive effect of CD8+ cells on HIV-1 replication, we characterized HIV-1 isolates from the same blood samples obtained from five AC individuals before and after the removal of CD8+ cells. Comparative studies of paired isolates revealed significant differences in their replication kinetics in the presence of autologous or allogeneic CD8+ cells. The paired isolates from four out of 5 AC individuals revealed significant differences in their genetic structures, although their biological properties, such as replication rate of cell tropism, were almost the same between the paired isolates. One exception, that of paired isolates from one AC with clinical data of near AIDS-related complex showed a similar genetic structure and similar biological properties. Thus, we showed that many AC individuals during the early clinical stages simultaneously carried two or more replication-competent HIV-ls in vivo which have different genomic backgrounds and sensitivity to the antiviral effects of CD8+ cells.

Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site

The relative efficiencies of the maximum-likelihood (ML), neighbor-joining (NJ), and maximum-parsimony (MP) methods in obtaining the correct topology and in estimating the branch lengths for the case of four DNA sequences were studied by computer simulation, under the assumption either that there is variation in substitution rate among different nucleotide sites or that there is no variation. For the NJ method, several different distance measures (Jukes-Cantor, Kimura two-parameter, and gamma distances) were used, whereas for the ML method three different transition/transversion ratios (R) were used. For the MP method, both the standard unweighted parsimony and the dynamically weighted parsimony methods were used. The results obtained are as follows: (1) When the R value is high, dynamically weighted parsimony is more efficient than unweighted parsimony in obtaining the correct topology. (2) However, both weighted and unweighted parsimony methods are generally less efficient than the NJ and ML methods even in the case where the MP method gives a consistent tree. (3) When all the assumptions of the ML method are satisfied, this method is slightly more efficient than the NJ method. However, when the assumptions are not satisfied, the NJ method with gamma distances is slightly better in obtaining the correct topology than is the ML method. In general, the two methods show more or less the same performance. The NJ method may give a correct topology even when the distance measures used are not unbiased estimators of nucleotide substitutions. (4) Branch length estimates of a tree with the correct topology are affected more easily than topology by violation of the assumptions of the mathematical model used, for both the ML and the NJ methods. Under certain conditions, branch lengths are seriously overestimated or underestimated. The MP method often gives serious underestimates for certain branches. (5) Distance measures that generate the correct topology, with high probability, do not necessarily give good estimates of branch lengths. (6) The likelihood-ratio test and the confidence-limit test, in Felsenstein's DNAML, for examining the statistical of branch length estimates are quite sensitive to violation of the assumptions and are generally too liberal to be used for actual data. Rzhetsky and Nei's branch length test is less sensitive to violation of the assumptions than is Felsenstein's test. (7) When the extent of sequence divergence is < or = 5% and when > or = 1,000 nucleotides are used, all three methods show essentially the same efficiency in obtaining the correct topology and in estimating branch lengths.(ABSTRACT TRUNCATED AT 400 WORDS)

Effects of trihexyphenidyl and L-dopa on brain muscarinic cholinergic receptor binding measured by positron emission tomography

The effects of pharmacological intervention on brain muscarinic cholinergic receptor (mAChR) binding were assessed in seven patients with Parkinson's disease by positron emission tomography and carbon-11 labelled N-methyl-4-piperidyl benzilate ([11C]NMPB). [11C]NMPB was injected twice, approximately 2 hours apart, in each patient, to assess the effect of single doses of 4 mg of trihexyphenidyl (n = 5) or 400 mg of L-dopa with 57 mg of benserazide (n = 2) on the binding parameter of mAChRs (K3). There was a mean 28% inhibition of K3 values in the brain in the presence of trihexyphenidyl, which was assumed to reflect mAChR occupancy. No significant change in K3 was observed in the presence of L-dopa. This study demonstrates the feasibility of measuring mAChR occupancy by an anticholinergic medication with PET.