DDBJ update in 2023: the MetaboBank for metabolomics data and associated metadata

The Bioinformation and DNA Data Bank of Japan (DDBJ) Center (https://www.ddbj.nig.ac.jp) provides database archives that cover a wide range of fields in life sciences. As a founding member of the International Nucleotide Sequence Database Collaboration (INSDC), DDBJ accepts and distributes nucleotide sequence data as well as their study and sample information along with the National Center for Biotechnology Information in the United States and the European Bioinformatics Institute (EBI). Besides INSDC databases, the DDBJ Center provides databases for functional genomics (GEA: Genomic Expression Archive), metabolomics (MetaboBank) and human genetic and phenotypic data (JGA: Japanese Genotype-phenotype Archive). These database systems have been built on the National Institute of Genetics (NIG) supercomputer, which is also open for domestic life science researchers to analyze large-scale sequence data. This paper reports recent updates on the archival databases and the services of the DDBJ Center, highlighting the newly redesigned MetaboBank. MetaboBank uses BioProject and BioSample in its metadata description making it suitable for multi-omics large studies. Its collaboration with MetaboLights at EBI brings synergy in locating and reusing public data.

DNA Data Bank of Japan (DDBJ) update report 2022

The Bioinformation and DNA Data Bank of Japan (DDBJ) Center (https://www.ddbj.nig.ac.jp) maintains database archives that cover a wide range of fields in life sciences. As a founding member of the International Nucleotide Sequence Database Collaboration (INSDC), our primary mission is to collect and distribute nucleotide sequence data, as well as their study and sample information, in collaboration with the National Center for Biotechnology Information in the United States and the European Bioinformatics Institute. In addition to INSDC resources, the Center operates databases for functional genomics (GEA: Genomic Expression Archive), metabolomics (MetaboBank), and human genetic and phenotypic data (JGA: Japanese Genotype-Phenotype Archive). These databases are built on the supercomputer of the National Institute of Genetics, whose remaining computational capacity is actively utilized by domestic researchers for large-scale biological data analyses. Here, we report our recent updates and the activities of our services.

DNA Data Bank of Japan (DDBJ) update report 2021

The Bioinformation and DDBJ (DNA Data Bank of Japan) Center (DDBJ Center; https://www.ddbj.nig.ac.jp) operates archival databases that collect nucleotide sequences, study and sample information, and distribute them without access restriction to progress life science research as a member of the International Nucleotide Sequence Database Collaboration (INSDC), in collaboration with the National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute. Besides the INSDC databases, the DDBJ Center also provides the Genomic Expression Archive for functional genomics data and the Japanese Genotype-phenotype Archive for human data requiring controlled access. Additionally, the DDBJ Center started a new public repository, MetaboBank, for experimental raw data and metadata from metabolomics research in October 2020. In response to the COVID-19 pandemic, the DDBJ Center openly shares SARS-CoV-2 genome sequences in collaboration with Shizuoka Prefecture and Keio University. The operation of DDBJ is based on the National Institute of Genetics (NIG) supercomputer, which is open for large-scale sequence data analysis for life science researchers. This paper reports recent updates on the archival databases and the services of DDBJ.

DDBJ update: the Genomic Expression Archive (GEA) for functional genomics data

The Genomic Expression Archive (GEA) for functional genomics data from microarray and high-throughput sequencing experiments has been established at the DNA Data Bank of Japan (DDBJ) Center (https://www.ddbj.nig.ac.jp), which is a member of the International Nucleotide Sequence Database Collaboration (INSDC) with the US National Center for Biotechnology Information and the European Bioinformatics Institute. The DDBJ Center collects nucleotide sequence data and associated biological information from researchers and also services the Japanese Genotype–phenotype Archive (JGA) with the National Bioscience Database Center for collecting human data. To automate the submission process, we have implemented the DDBJ BioSample validator which checks submitted records, auto-corrects their format, and issues error messages and warnings if necessary. The DDBJ Center also operates the NIG supercomputer, prepared for analyzing large-scale genome sequences. We now offer a secure platform specifically to handle personal human genomes. This report describes database activities for INSDC and JGA over the past year, the newly launched GEA, submission, retrieval, and analysis services available in our supercomputer system and their recent developments.

DDBJ Database updates and computational infrastructure enhancement

The Bioinformation and DDBJ Center (https://www.ddbj.nig.ac.jp) in the National Institute of Genetics (NIG) maintains a primary nucleotide sequence database as a member of the International Nucleotide Sequence Database Collaboration (INSDC) in partnership with the US National Center for Biotechnology Information and the European Bioinformatics Institute. The NIG operates the NIG supercomputer as a computational basis for the construction of DDBJ databases and as a large-scale computational resource for Japanese biologists and medical researchers. In order to accommodate the rapidly growing amount of deoxyribonucleic acid (DNA) nucleotide sequence data, NIG replaced its supercomputer system, which is designed for big data analysis of genome data, in early 2019. The new system is equipped with 30 PB of DNA data archiving storage; large-scale parallel distributed file systems (13.8 PB in total) and 1.1 PFLOPS computation nodes and graphics processing units (GPUs). Moreover, as a starting point of developing multi-cloud infrastructure of bioinformatics, we have also installed an automatic file transfer system that allows users to prevent data lock-in and to achieve cost/performance balance by exploiting the most suitable environment from among the supercomputer and public clouds for different workloads.

DNA Data Bank of Japan: 30th anniversary

The DNA Data Bank of Japan (DDBJ) Center (http://www.ddbj.nig.ac.jp) has been providing public data services for 30 years since 1987. We are collecting nucleotide sequence data and associated biological information from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC), in collaboration with the US National Center for Biotechnology Information and the European Bioinformatics Institute. The DDBJ Center also services the Japanese Genotype-phenotype Archive (JGA) with the National Bioscience Database Center to collect genotype and phenotype data of human individuals. Here, we outline our database activities for INSDC and JGA over the past year, and introduce submission, retrieval and analysis services running on our supercomputer system and their recent developments. Furthermore, we highlight our responses to the amended Japanese rules for the protection of personal information and the launch of the DDBJ Group Cloud service for sharing pre-publication data among research groups.

The Effect of Telephone Advice on Cardiopulmonary Resuscitation (CPR) on the Rate of Bystander CPR in Out-of-Hospital Cardiopulmonary Arrest in a Typical Urban Area

Introduction

The frequency of telephone advice for cardiopulmonary resuscitation (T-CPR) and its effect are unclear. We have few data concerning how many persons who are willing to perform CPR under the setting of the T-CPR system. Most of these data were from action reports in the pre-hospital EMS records. Methods: This study was a population-based observational case series of out-of-hospital cardiopulmonary arrest (OHCPA). The primary outcome was the acceptability of a bystander to perform CPR according to T-CPR. In our emergency department, one medical doctor interviewed the bystanders regarding T-CPR and CPR; this doctor was devoted to obtaining information from the patients.

Results

Of the 803 patients in, T-CPR advice was provided in 47% and CPR was actually performed in 47% independent of T-CPR guidance. Of the 373 cases in which lay persons received T-CPR, 95% provided CPR. Dispatchers could more easily provide T-CPR to family members compared with friends and passengers. Twenty-one percent of callers made emergency calls after consulting with others (indirect call). In non-traumatic victims who underwent bystander CPR, 43% experienced the return of spontaneous circulation, and 5% were discharged with a mild disorder or no neurological abnormality.

Conclusions

We conclude that 95% of bystanders are willing to perform CPR under the T-CPR system, but we cannot conclude that bystander CPR may not affect the survival rate. These findings indicate that bystanders should be guided with T-CPR. (Hong Kong j.emerg. med. 2016;23:220-226)

DNA data bank of Japan (DDBJ) progress report

The DNA Data Bank of Japan Center (DDBJ Center; http://www.ddbj.nig.ac.jp) maintains and provides public archival, retrieval and analytical services for biological information. The contents of the DDBJ databases are shared with the US National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI) within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). Since 2013, the DDBJ Center has been operating the Japanese Genotype-phenotype Archive (JGA) in collaboration with the National Bioscience Database Center (NBDC) in Japan. In addition, the DDBJ Center develops semantic web technologies for data integration and sharing in collaboration with the Database Center for Life Science (DBCLS) in Japan. This paper briefly reports on the activities of the DDBJ Center over the past year including submissions to databases and improvements in our services for data retrieval, analysis, and integration.

The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data

The DNA Data Bank of Japan Center (DDBJ Center; http://www.ddbj.nig.ac.jp) maintains and provides public archival, retrieval and analytical services for biological information. Since October 2013, DDBJ Center has operated the Japanese Genotype-phenotype Archive (JGA) in collaboration with our partner institute, the National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency. DDBJ Center provides the JGA database system which securely stores genotype and phenotype data collected from individuals whose consent agreements authorize data release only for specific research use. NBDC has established guidelines and policies for sharing human-derived data and reviews data submission and usage requests from researchers. In addition to the JGA project, DDBJ Center develops Semantic Web technologies for data integration and sharing in collaboration with the Database Center for Life Science. This paper describes the overview of the JGA project, updates to the DDBJ databases, and services for data retrieval, analysis and integration.

Proposal to modify the International Union Against Cancer staging system for perihilar cholangiocarcinomas

BACKGROUND

The International Union Against Cancer (UICC) staging system for perihilar cholangiocarcinoma changed in 2009. The aim of this study was to validate and optimize the UICC system for these tumours.

METHODS

This retrospective study was conducted in eight Japanese hospitals between 2001 and 2010. Perihilar cholangiocarcinoma was defined as a cholangiocarcinoma that involves the hilar bile duct, independent of the presence or absence of a liver mass component. The stratification ability of the UICC tumour node metastasis (TNM) system was compared with that of a modified system.

RESULTS

Of 1352 patients, 35.9, 44.8 and 12.6 per cent had Bismuth type IV tumours, nodal metastasis (N1) and distant metastasis (M1) respectively. T4 tumours (43.2 per cent) and stage IVA (T4 Nany M0; 36.3 per cent) disease were most common. Survival was not significantly different between patients with T3 versus T4 tumours (P = 0.284). Survival for patients with stage IVA disease was comparable to that for patients with stage IIIB tumours (T1-3 N1 M0) (P = 0.426). Vascular invasion, pancreatic invasion, positive margin, N1 and M1 status were identified as independent predictors of survival. When Bismuth type IV tumours were removed from the T4 determinants and N1 tumours grouped together, the modified grouping had a higher linear trend χ2 and likelihood ratio χ2 compared with the original system (245.6 versus 170.3 respectively and 255.8 versus 209.3 respectively).

CONCLUSION

The present data suggest that minimal modification with removal of Bismuth type IV tumours from the T4 determinants and bundling of N1 disease may enhance the prognostic ability of the UICC system. However, this requires validation on an independent data set.

DDBJ progress report: a new submission system for leading to a correct annotation

The DNA Data Bank of Japan (DDBJ; http://www.ddbj.nig.ac.jp) maintains and provides archival, retrieval and analytical resources for biological information. This database content is shared with the US National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI) within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). DDBJ launched a new nucleotide sequence submission system for receiving traditional nucleotide sequence. We expect that the new submission system will be useful for many submitters to input accurate annotation and reduce the time needed for data input. In addition, DDBJ has started a new service, the Japanese Genotype–phenotype Archive (JGA), with our partner institute, the National Bioscience Database Center (NBDC). JGA permanently archives and shares all types of individual human genetic and phenotypic data. We also introduce improvements in the DDBJ services and databases made during the past year.

Gauze packing as damage control for uncontrollable haemorrhage in severe thoracic trauma

Introduction

The usefulness of thoracic damage control (DC) for trauma requiring a thoracotomy is not established. The aim of this study was to clarify the usefulness of thoracic packing as DC surgery.

Methods

This was a retrospective case series study of 12 patients with thoracic trauma suffering uncontrollable intrathoracic haemorrhage and shock who underwent intrathoracic packing. Our thoracic DC technique consisted of ligation and packing over the bleeding point or filling gauze in the bleeding spaces as well as packing for the thoracotomy wound. The success rates of intrathoracic haemostasis, changes in the circulation and the volume of discharge from the thoracic tubes were evaluated.

Results

Packing was undertaken for the thoracic wall in five patients, for the lung in four patients, for the vertebrae in two patients and for the descending thoracic aorta in one patient. Haemostasis was achieved successfully in seven cases. Of these, the volume of discharge from the thoracic tube exceeded 400ml/hr within three hours after packing in three patients, decreased to less than 200ml/hr within seven hours in six patients and decreased to 100ml/hr within eight hours in six patients. Systolic pressure could be maintained over 70mmHg by seven hours after packing.

Conclusions

Intrathoracic packing is useful for some patients, particularly in the space around the vertebrae, at the lung apex, and between the diaphragm and the thoracic wall. After packing, it is advisable to wait for three hours to see whether vital signs can be maintained and then to wait further to see if the discharge from the thoracic tube decreases to less than 200ml/hr within five hours.

Left hepatic trisectionectomy for advanced perihilar cholangiocarcinoma

BACKGROUND

Data on outcomes of left hepatic trisectionectomy (LT) for perihilar cholangiocarcinoma are limited. The aim of this study was to clarify short- and long-term outcomes of LT for perihilar cholangiocarcinoma.

METHODS

Patients with perihilar cholangiocarcinoma who underwent LT between January 2000 and October 2011 were analysed. Surgical variables, mortality, morbidity (Clavien grade I-V), recurrence sites and survival were compared between subjects who underwent LT, right hemihepatectomy or left hemihepatectomy.

RESULTS

A total 214 patients underwent resection for perihilar cholangiocarcinoma, 25 (11·7 per cent) of whom underwent LT, 88 (41·1 per cent) right hemihepatectomy and 94 (43·9 per cent) left hepatectomy. There were no deaths among those who had LT, but 20 patients developed complications. The incidence of grade IIIa complications was significantly higher among patients who underwent LT than in patients who had right or left hemihepatectomy (P = 0·001 and P < 0·001 respectively). Only one patient developed a grade IIIb or IV complication (liver failure) after LT. The overall 5-year survival rate after LT was 39 per cent and median survival was 45 months. There were no significant differences in survival between patients who underwent LT and those who had a right or left hemihepatectomy.

CONCLUSION

LT may provide a good outcome for advanced perihilar cholangiocarcinoma.

Immune cell infiltration as an indicator of the immune microenvironment of pancreatic cancer

Background:

The host immune reaction is represented by immune/inflammatory cell infiltrates. Here we systematically analysed tumour-infiltrating immune/inflammatory cells in pancreatic ductal carcinoma (PDC) and evaluated their clinicopathological impact.

Methods:

Using immunohistochemistry, we examined tumour-infiltrating CD68⁺ pan-macrophages, HLA-DR⁺CD68⁺ M1 macrophages (M1), CD163⁺ or CD204⁺ M2 macrophages (M2), CD66b⁺ neutrophils (Neu), CD4⁺ T cells (CD4⁺T), CD8⁺ T cells (CD8⁺T), and FOXP3⁺CD4⁺ regulatory T cells (Treg) in 212 cases of PDC, and conducted correlation and survival analyses using the Kaplan–Meier method and Cox proportional hazards model.

Results:

Higher levels of tumour-infiltrating pan-macrophages, M2, Neu, or the ratio of Tregs to CD4⁺T (%Treg) were significantly associated with shorter survival, whereas higher levels of tumour-infiltrating CD4⁺T, CD8⁺T, or the ratio of M1 to pan-macrophages (%M1) were significantly associated with longer survival. Survival analysis of pairs of these variables revealed that some of the resulting patient groups had exclusively longer survival. We then connected the apparently related factors, and two significant variables emerged: tumour-infiltrating CD4⁺T^high/CD8⁺T^high/%Treg^low and tumour-infiltrating %M1^high/M2^low. Multivariate survival analysis revealed that these variables were significantly correlated with longer survival and had a higher hazard ratio.

Conclusion:

Tumour-infiltrating CD4⁺T^high/CD8⁺T^high/%Treg^low and %M1^high/M2^low are independent prognosticators useful for evaluating the immune microenvironment of PDC.

Gauze packing as damage control for uncontrollable haemorrhage in severe thoracic trauma

Introduction

The usefulness of thoracic damage control (DC) for trauma requiring a thoracotomy is not established. The aim of this study was to clarify the usefulness of thoracic packing as DC surgery.

Methods

This was a retrospective case series study of 12 patients with thoracic trauma suffering uncontrollable intrathoracic haemorrhage and shock who underwent intrathoracic packing. Our thoracic DC technique consisted of ligation and packing over the bleeding point or filling gauze in the bleeding spaces as well as packing for the thoracotomy wound. The success rates of intrathoracic haemostasis, changes in the circulation and the volume of discharge from the thoracic tubes were evaluated.

Results

Packing was undertaken for the thoracic wall in five patients, for the lung in four patients, for the vertebrae in two patients and for the descending thoracic aorta in one patient. Haemostasis was achieved successfully in seven cases. Of these, the volume of discharge from the thoracic tube exceeded 400ml/hr within three hours after packing in three patients, decreased to less than 200ml/hr within seven hours in six patients and decreased to 100ml/hr within eight hours in six patients. Systolic pressure could be maintained over 70mmHg by seven hours after packing.

Conclusions

Intrathoracic packing is useful for some patients, particularly in the space around the vertebrae, at the lung apex, and between the diaphragm and the thoracic wall. After packing, it is advisable to wait for three hours to see whether vital signs can be maintained and then to wait further to see if the discharge from the thoracic tube decreases to less than 200ml/hr within five hours.

Hepatic artery reconstruction following ablative surgery for hepatobiliary and pancreatic malignancies

OBJECTIVE

Hepatic artery (HA) reconstruction is an important part of resective surgery for advanced hepatobiliary and pancreatic malignancies, but few reports have been published. To identify indications for HA reconstruction, we retrospectively analyzed our surgical procedures and outcomes.

METHODS

En-bloc resection of advanced hepatobiliary and pancreatic malignancies followed by HA reconstruction was performed in 35 patients. Patients ranged in age from 27 to 81 years and included 18 men and 17 women. The primary site of cancer included the bile duct in 22 patients, the pancreas in 7, and others in 6. Reconstruction of the HA was necessitated by HA resection due to direct cancer invasion in 29 patients and by accidental arterial injury during surgical procedure in 6 patients.

RESULTS

The HA was reconstructed with end-to-end anastomosis between hepatic arteries in 17 patients. Transposition of an intra-abdominal artery, such as the gastroepiploic artery, was required in 14 patients, and arterial grafting was required in 4 patients. Although the HA patency was achieved in 30 patients, 4 cases of arterial thrombosis and 1 case of arterial rupture developed postoperatively. The overall RFS time was analyzed in all patients, and mean and median RFS times were 18 and 9 months, respectively.

CONCLUSION

Although oncologic outcomes remain poor, HA resection and reconstruction can be performed in selected patients. We believe that the method of first choice for HA reconstruction is end-to-end anastomosis between HAs. A vascular autograft should be used only in selected cases.

DDBJ progress report

The DNA Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) provides a nucleotide sequence archive database and accompanying database tools for sequence submission, entry retrieval and annotation analysis. The DDBJ collected and released 3 637 446 entries/2 272 231 889 bases between July 2009 and June 2010. A highlight of the released data was archive datasets from next-generation sequencing reads of Japanese rice cultivar, Koshihikari submitted by the National Institute of Agrobiological Sciences. In this period, we started a new archive for quantitative genomics data, the DDBJ Omics aRchive (DOR). The DOR stores quantitative data both from the microarray and high-throughput new sequencing platforms. Moreover, we improved the content of the DDBJ patent sequence, released a new submission tool of the DDBJ Sequence Read Archive (DRA) which archives massive raw sequencing reads, and enhanced a cloud computing-based analytical system from sequencing reads, the DDBJ Read Annotation Pipeline. In this article, we describe these new functions of the DDBJ databases and support tools.

Extended right hemihepatectomy for gallbladder carcinoma involving the hepatic hilum

BACKGROUND

Major hemihepatectomy for advanced gallbladder carcinoma remains controversial as it is associated with serious postoperative complications and poor prognosis.

METHODS

All those who underwent extended right hemihepatectomy were identified from a database of patients with gallbladder carcinoma who had surgical resection between 1999 and 2009. The clinicopathological data for these patients were analysed retrospectively.

RESULTS

A total of 126 patients underwent surgical resection, 35 of whom had extended right hemihepatectomy. There were no deaths, but 16 patients had complications. The mean(s.d.) duration of operation and blood loss were 564(206) min and 1472(1268) ml respectively. No blood transfusions were needed in 28 patients. Tumour stage (International Union Against Cancer, sixth edition) was IIA in four, IIB in four, III in 15 and IV in 12 patients. The overall 5-year survival rate was 17 per cent with a median survival of 2·2 years. Three patients survived more than 5 years. The presence of hepatic metastases and gallbladder carcinoma originating from the cystic duct were indicators of poor prognosis.

CONCLUSION

Extended right hemihepatectomy for gallbladder cancer is safe and may contribute to long-term survival in selected patients.

Insertion sequence elements of Pseudomonas savastanoi: Nucleotide sequence and homology with Agrobacterium tumefaciens transfer DNA

Two types of transposable elements, IS51 and IS52 (IS, insertion sequence), were found in Pseudomonas syringae subsp. savastanoi (P. savastanoi) that spontaneously insert into and inactivate iaaM; the insertion results in the loss of indoleacetic acid production and attenuation of virulence. The nucleotide sequences of both IS elements have sizes and structural features common to other prokaryotic IS elements; IS51 is 1311 base pairs (bp) long and has terminal inverted repeats of 26 bp; IS52 is 1209 bp long and has terminal inverted repeats of 10 bp with a 1 bp mismatch. In the insertion involving IS51, the trinucleotide sequence CAG is duplicated within iaaM sequences at the recombination junction; in those involving IS52 the tetranucleotide sequences TTAG or CTAG are duplicated within iaaM sequences at the recombination junction. A copy of IS51 occurs 2.5 kilobases downstream from IaaH. In contrast to the high copy number of IS51 in the genome of the bacterium, only a few copies of IS52 are present. No nucleotide sequence homology was found between IS51 and IS52. However, a striking nucleotide sequence homology was found between a 531-bp region of IS51 and a portion of the central region of transfer DNA (T-DNA) in the octopine plasmid pTi15955 from Agrobacterium tumefaciens. These observations, together with our earlier finding on the homology between iaaM and iaaH and between gene 1 and gene 2 of transfer DNA, further suggest that genes for indoleacetic acid production in the two systems have a common origin.

Nucleotide sequences of the Pseudomonas savastanoi indoleacetic acid genes show homology with Agrobacterium tumefaciens T-DNA

We report the nucleotide sequences of iaaM and iaaH, the genetic determinants for, respectively, tryptophan 2-monooxygenase and indoleacetamide hydrolase, the enzymes that catalyze the conversion of L-tryptophan to indoleacetic acid in the tumor-forming bacterium Pseudomonas syringae pv. savastanoi. The sequence analysis indicates that the iaaM locus contains an open reading frame encoding 557 amino acids that would comprise a protein with a molecular weight of 61,783; the iaaH locus contains an open reading frame of 455 amino acids that would comprise a protein with a molecular weight of 48,515. Significant amino acid sequence homology was found between the predicted sequence of the tryptophan monooxygenase of P. savastanoi and the deduced product of the T-DNA tms-1 gene of the octopine-type plasmid pTiA6NC from Agrobacterium tumefaciens. Strong homology was found in the 25 amino acid sequence in the putative FAD-binding region of tryptophan monooxygenase. Homology was also found in the amino acid sequences representing the central regions of the putative products of iaaH and tms-2 T-DNA. The results suggest a strong similarity in the pathways for indoleacetic acid synthesis encoded by genes in P. savastanoi and in A. tumefaciens T-DNA.

Cytokinin/auxin balance in crown gall tumors is regulated by specific loci in the T-DNA

Insertion of the transposon Tn5 into the T-region of the octopine Ti plasmid of Agrobacterium tumefaciens gives rise to crown gall tumors having altered morphology. Three loci within the T-DNA that control tumor morphology have been detected [Garfinkel, D. J., Simpson, R. B., Ream, L. W., White, F. F., Gordon, M. P. & Nester, E. W. (1981) Cell 27, 143-153]. They influence tumor size (tml), production of roots (tmr), or production of shoots (tms). Cytokinin and auxin levels in such mutant tumors were examined by HPLC/radioimmunoassay and HPLC/fluorescence assay, respectively. Free indoleacetic acid levels (in pmol/g) were: uninfected tobacco stem tissues, 128; wild-type A348 tumors, 295; tml mutant tumors, 307; tmr mutant tumors, 129; and tms mutant tumors, 70. Average trans-ribosylzeatin levels were correspondingly: 0.97, 48, 40, 0.54, and 1,400 pmol/g. trans-Ribosylzeatin/indoleacetic acid ratios were as high as 24 in shoot-producing tumors and as low as 0.003 in root-producing tumors. The evidence strongly suggests that tumor phytohormone levels are determined by genes in the T-DNA.

A randomised phase III trial comparing gemcitabine with surgery-only in patients with resected pancreatic cancer: Japanese Study Group of Adjuvant Therapy for Pancreatic Cancer

BACKGROUND

This multicentre randomised phase III trial was designed to determine whether adjuvant chemotherapy with gemcitabine improves the outcomes of patients with resected pancreatic cancer.

METHODS

Eligibility criteria included macroscopically curative resection of invasive ductal carcinoma of the pancreas and no earlier radiation or chemotherapy. Patients were randomly assigned at a 1 : 1 ratio to either the gemcitabine group or the surgery-only group. Patients assigned to the gemcitabine group received gemcitabine at a dose of 1000 mg m(-2) over 30 min on days 1, 8 and 15, every 4 weeks for 3 cycles.

RESULTS

Between April 2002 and March 2005, 119 patients were enrolled in this study. Among them, 118 were eligible and analysable (58 in the gemcitabine group and 60 in the surgery-only group). Both groups were well balanced in terms of baseline characteristics. Although heamatological toxicity was frequently observed in the gemcitabine group, most toxicities were transient, and grade 3 or 4 non-heamatological toxicity was rare. Patients in the gemcitabine group showed significantly longer disease-free survival (DFS) than those in the surgery-only group (median DFS, 11.4 versus 5.0 months; hazard ratio=0.60 (95% confidence interval (CI): 0.40-0.89); P=0.01), although overall survival did not differ significantly between the gemcitabine and surgery-only groups (median overall survival, 22.3 versus 18.4 months; hazard ratio=0.77 (95% CI: 0.51-1.14); P=0.19).

CONCLUSION

The current results suggest that adjuvant gemcitabine contributes to prolonged DFS in patients undergoing macroscopically curative resection of pancreatic cancer.

Exploration and grading of possible genes from 183 bacterial strains by a common protocol to identification of new genes: Gene Trek in Prokaryote Space (GTPS)

A large number of complete microorganism genomes has been sequenced and submitted to the public database and then incorporated into our complete genome database, Genome Information Broker (GIB, http://gib.genes.nig.ac.jp/). However, when comparative genomics is carried out, researchers must be aware that there are protein-coding genes not confirmed by homology or motif search and that reliable protein-coding genes are missing. Therefore, we developed a protocol (Gene Trek in Prokaryote Space, GTPS) for finding possible protein-coding genes in bacterial genomes. GTPS assigns a degree of reliability to predicted protein-coding genes. We first systematically applied the protocol to the complete genomes of all 123 bacterial species and strains that were publicly available as of July 2003, and then to those of 183 species and strains available as of September 2004. We found a number of incorrect genes and several new ones in the genome data in question. We also found a way to estimate the total number of orthologous genes in the bacterial world.

Randomized clinical trial of hepatectomy using intermittent pedicle occlusion with ischaemic intervals of 15 versus 30 minutes

Background

The optimal ischaemic interval during hepatectomy with intermittent pedicle occlusion (IPO) remains to be established. The aim of the present randomized clinical trial was to compare the short-term outcome of hepatectomy using IPO with an ischaemic interval of 15 versus 30 min.

Methods

Between October 2002 and September 2004, 108 consecutive patients scheduled to undergo hepatectomy without bilioenterostomy were enrolled. During liver transection, IPO was performed with an ischaemic interval of either 15 min with 5 min of reperfusion (standard group, SG) or 30 min with 5 min of reperfusion (prolonged group, PG). After randomization and subsequent exclusion of certain patients, 44 patients in the SG and 48 in the PG were analysed.

Results

The mean(s.d.) bilirubin ratio (serum total bilirubin level on day 2 after operation divided by the preoperative level) was 1·6(0·8) in the SG and 1·7(0·8) in the PG (P = 0·874). The transection area per unit transection time was significantly greater in the latter group (median (range) 1·0 (0·4–2·1) versus 0·8 (0·0–1·5) cm2/min; P = 0·046).

Conclusion

There was no difference in the bilirubin ratio when IPO was carried out for 30 or 15 min. By extension of IPO to 30 min, a greater resection area per unit time was possible with preservation of remnant liver function.

Evidence Standards in Experimental and Inferential INSDC Third Party Annotation Data

The Third Party Annotation (TPA) project collects and presents high-quality annotation of nucleotide sequence. Annotation is submitted by researchers who have not themselves generated novel nucleotide sequence. In its first few years, the resource has proven to be popular with submitters from a range of biological research areas. Central to the project is the requirement for high-quality data, resulting from experimental and inferred analysis discussed in peer-reviewed publications. The data are divided into two tiers: those with experimental evidence and those with inferential evidence. Standards for TPA are detailed and illustrated with the aid of case studies.

Escherichia coli K-12: a cooperatively developed annotation snapshot--2005

The goal of this group project has been to coordinate and bring up-to-date information on all genes of Escherichia coli K-12. Annotation of the genome of an organism entails identification of genes, the boundaries of genes in terms of precise start and end sites, and description of the gene products. Known and predicted functions were assigned to each gene product on the basis of experimental evidence or sequence analysis. Since both kinds of evidence are constantly expanding, no annotation is complete at any moment in time. This is a snapshot analysis based on the most recent genome sequences of two E.coli K-12 bacteria. An accurate and up-to-date description of E.coli K-12 genes is of particular importance to the scientific community because experimentally determined properties of its gene products provide fundamental information for annotation of innumerable genes of other organisms. Availability of the complete genome sequence of two K-12 strains allows comparison of their genotypes and mutant status of alleles.

The alpha-aminoadipate pathway for lysine biosynthesis is widely distributed among Thermus strains

We previously reported that lysine is synthesized through the alpha-aminoadipate pathway in Thermus thermophilus HB27 (T. Kosuge and T. Hoshino, FEMS Microbiol. Lett., 169, 361-367, 1998), which was the first report demonstrating the synthesis of lysine through the alpha-aminoadipate pathway in Bacteria. LYS20 and LYS4, which respectively encode homocitrate synthase and homoaconitate hydratase have already been identified as the lysine biosynthetic genes in T. thermophilus HB27. In the present work, we examined eight other Thermus strains for the existence of genes belonging to the alpha-aminoadipate pathway. BamHI- or BglII-digested total DNAs from the eight strains were analyzed by Southern hybridization using LYS20 or LYS4 as a DNA probe. DNA fragments that hybridized with one or both of the genes were detected in seven of the Thermus strains but not in T. ruber. The sizes of the fragments that hybridized with the LYS20 and LYS4 probes were the same among T. thermophilus HB27, T. thermophilus HB8, "T. caldophilus" GK24, and four "T. flavus" strains. For example, a similar 4.3-kb fragment was detected in each of the above seven strains. In this fragment, four open reading frames were found downstream of the LYS4 gene in T. thermophilus HB27. Gene disruption experiments revealed that three open reading frames are involved in lysine biosynthesis in T. thermophilus HB27. These results strongly suggest that the lysine biosynthetic gene cluster for the alpha-aminoadipate pathway is widely distributed in the genus Thermus.

Spontaneous regression of hepatocellular carcinoma with complete necrosis: case report

Spontaneous regression of hepatocellular carcinoma is rare phenomenon. A 74-year-old man was found to have a hepatocellular carcinoma with intrahepatic metastases in the lateral segment of the liver. Before surgery, he developed severe cholangitis due to choledocholithiasis and was treated endoscopically. The tumor marker level decreased markedly, and hepatectomy was performed. The resected tumor demonstrated complete necrosis.