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1.  Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures 
Nucleic Acids Research  2016;45(Database issue):D282-D288.
The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described.
doi:10.1093/nar/gkw962
PMCID: PMC5210648  PMID: 27789697
2.  Aldosterone-producing adrenocortical carcinoma with prominent hepatic metastasis diagnosed by liver biopsy: a case report 
Background
Aldosterone-producing adrenocortical carcinoma is a rare malignancy, which is usually diagnosed by histopathological examination of the excised tumor. In inoperable cases, aldosterone-producing ACC diagnosed by immunohistochemical staining of the metastatic tumor for Cytochrome P450 (CYP) 11β has not previously been reported and even in that case staining for adrenocortical-specific adrenal 4 binding protein/steroidogenic factor1 (Ad4BP/SF1) and steroidogenic enzymes has not been reported.
Case presentation
We report the case of a 67-year-old Japanese woman with aldosterone-producing adrenocortical carcinoma. Laboratory findings showed severe hypopotassemia. Endocrinological examination revealed an increased plasma aldosterone concentration and suppressed plasma renin activity. Plasma dehydroepiandrosterone sulfate (DHEA-S) was elevated. Diurnal variation in serum cortisol was lost and administration of 1 mg and 8 mg dexamethasone did not suppress serum cortisol levels. From the 24-h urine collection sample, urine aldosterone and urine cortisol levels were greatly increased. Therefore, autonomous excess production was observed for the three adrenal cortex hormones. Abdominal computed tomography and magnetic resonance imaging showed a right adrenal tumor and a huge liver tumor. Adrenocortical carcinoma with metastatic liver cancer was strongly suggested, however surgery could not be considered due to stage IV disease: the liver tumor was too large and cardiac ultrasonography indicated that her cardiac function was poor. Therefore, a liver biopsy was taken to properly determine the diagnosis. Immunohistochemical stains for Ad4BP/SF1 and steroidogenic enzymes were positive. Ad4BP/SF-1 was originally identified as a steroidogenic, tissue-specific transcription factor implicated in the expression of the steroidogenic CYP gene encoding cytochrome P450s. Hence we could diagnose the patient as having adrenocortical carcinoma with metastatic liver cancer.
Conclusion
This rare case had severe hypopotassemia accompanied with not only increased cortisol and DHEA-S but also aldosterone. We reached the diagnosis of adrenocortical carcinoma with metastatic liver cancer based on positive immunohistochemical staining of Ad4BP/SF1 in the liver biopsy specimen. We have reported the first case of aldosterone-producing adrenocortical carcinoma diagnosed solely by immunohistochemical staining for adrenocortical-specific Ad4BP/SF1 and steroidogenic enzymes in a metastatic liver tumor.
doi:10.1186/s12902-016-0083-0
PMCID: PMC4715337  PMID: 26772981
Adrenocortical carcinoma; Aldosterone; Metastatic liver cancer; Adrenal 4 binding protein/steroidogenic factor 1; Immunohistochemical staining
3.  Effect of One-Week Salt Restriction on Blood Pressure Variability in Hypertensive Patients with Type 2 Diabetes 
PLoS ONE  2016;11(1):e0144921.
Background
Increased short-term blood pressure (BP) variability on 24-hour ambulatory BP monitoring (ABPM) is known to be a risk factor for cardiovascular events. However, very few studies have evaluated the effect of salt restriction on BP variability particularly in hypertensive patients with type 2 diabetes. This study aimed to investigate the effect of salt restriction on systolic BP (SBP) variability.
Methods and Results
10 hypertensive patients with type 2 diabetes and not receiving antihypertensive agents were enrolled in the study. After admission, all patients received a salt-restricted diet and appropriate anti-diabetic treatments and were followed up for 7 consecutive days using ABPM. After the 7-day treatment, the median [interquartile range (IQR)] coefficient of variation (CV) for diurnal SBP variability changed from day 1 to day 7–13.0 [10.8 to 16.8] % to 13.3 [9.1 to 18.9] % (P = 0.959)—and the median [IQR] change between days 1 and 7 was -0.3 [-3.2 to 2.9] %. In addition, CV for BP variability and circadian rhythm of BP varied greatly on a day-by-day basis for 7 days, compared to mean BP values. Interestingly, increased SBP variability was associated with greater day-by-day changes in circadian rhythm of BP.
Conclusions
Salt restriction during 7-day hospitalization led to a -0.3 [-3.2 to 2.9] (median [IQR]) % change from baseline in CV for diurnal SBP variability in 10 hypertensive patients with type 2 diabetes not receiving antihypertensive agents.
Trial Registration
UMIN Clinical Trials Registry UMIN000016243
doi:10.1371/journal.pone.0144921
PMCID: PMC4701465  PMID: 26731185
4.  Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB 
Bioinformatics  2015;32(4):619-620.
Summary: Omokage search is a service to search the global shape similarity of biological macromolecules and their assemblies, in both the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB). The server compares global shapes of assemblies independent of sequence order and number of subunits. As a search query, the user inputs a structure ID (PDB ID or EMDB ID) or uploads an atomic model or 3D density map to the server. The search is performed usually within 1 min, using one-dimensional profiles (incremental distance rank profiles) to characterize the shapes. Using the gmfit (Gaussian mixture model fitting) program, the found structures are fitted onto the query structure and their superimposed structures are displayed on the Web browser. Our service provides new structural perspectives to life science researchers.
Availability and implementation: Omokage search is freely accessible at http://pdbj.org/omokage/.
Contact: hirofumi@protein.osaka-u.ac.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btv614
PMCID: PMC4743628  PMID: 26508754
5.  Diabetic Cardiovascular Disease Induced by Oxidative Stress 
Cardiovascular disease (CVD) is the leading cause of morbidity and mortality among patients with diabetes mellitus (DM). DM can lead to multiple cardiovascular complications, including coronary artery disease (CAD), cardiac hypertrophy, and heart failure (HF). HF represents one of the most common causes of death in patients with DM and results from DM-induced CAD and diabetic cardiomyopathy. Oxidative stress is closely associated with the pathogenesis of DM and results from overproduction of reactive oxygen species (ROS). ROS overproduction is associated with hyperglycemia and metabolic disorders, such as impaired antioxidant function in conjunction with impaired antioxidant activity. Long-term exposure to oxidative stress in DM induces chronic inflammation and fibrosis in a range of tissues, leading to formation and progression of disease states in these tissues. Indeed, markers for oxidative stress are overexpressed in patients with DM, suggesting that increased ROS may be primarily responsible for the development of diabetic complications. Therefore, an understanding of the pathophysiological mechanisms mediated by oxidative stress is crucial to the prevention and treatment of diabetes-induced CVD. The current review focuses on the relationship between diabetes-induced CVD and oxidative stress, while highlighting the latest insights into this relationship from findings on diabetic heart and vascular disease.
doi:10.3390/ijms161025234
PMCID: PMC4632800  PMID: 26512646
diabetes mellitus; oxidative stress; cardiovascular disease; diabetic heart; diabetic vascular disease
6.  Effects of co-administration of candesartan with pioglitazone on inflammatory parameters in hypertensive patients with type 2 diabetes mellitus: a preliminary report 
Background
Angiotensin receptor blockers (ARBs) are reported to provide direct protection to many organs by controlling inflammation and decreasing oxidant stress. Pioglitazone, an anti-diabetic agent that improves insulin resistance, was also reported to decrease inflammation and protect against atherosclerosis. This study aimed to evaluate the utility of combination therapy with both medicines from the viewpoint of anti-inflammatory effects.
Methods
We administered candesartan (12 mg daily) and pioglitazone (15 mg daily) simultaneously for 6 months to hypertensive patients with type 2 diabetes mellitus (T2DM) and evaluated whether there were improvements in the serum inflammatory parameters of high-molecular-weight adiponectin (HMW-ADN), plasminogen activator inhibitor-1 (PAI-1), highly sensitive C-reactive protein (Hs-CRP), vascular cell adhesion molecule-1 (VCAM-1), and urinary-8-hydroxydeoxyguanosine (U-8-OHdG). We then analyzed the relationship between the degree of reductions in blood pressure and HbA1c values and improvements in inflammatory factors. Furthermore, we analyzed the relationship between pulse pressure and the degree of lowering of HbA1c and improvements in inflammatory factors. Finally, we examined predictive factors in patients who received benefits from the co-administration of candesartan with pioglitazone from the viewpoint of inflammatory factors.
Results
After 6 months of treatment, in all patients significant improvements from baseline values were observed in HMW-ADN and PAI-1 but not in VCAM-1, Hs-CRP, and U-8-OHdG. Changes in HbA1c were significantly correlated with changes in HMW-ADN and PAI-1 in all patients, but changes in blood pressure were not correlated with any of the parameters examined. Correlation and multilinear regression analyses were performed to determine which factors could best predict changes in HbA1c. Interestingly, we found a significant positive correlation of pulse pressure values at baseline with changes in HbA1c.
Conclusions
Our data suggest that the pulse pressure value at baseline is a key predictive factor of changes in HbA1c. Co-administration of candesartan with pioglitazone, which have anti-inflammatory (changes in HMW-ADN and PAI-1) effects and protective effects on organs, could be an effective therapeutic strategy for treating hypertensive patients with type 2 diabetes mellitus.
Trial registration
UMIN-CTR: UMIN000010142
doi:10.1186/1475-2840-12-71
PMCID: PMC3663745  PMID: 23635096
Candesartan; Angiotensin receptor blockers; Type 2 diabetes mellitus; Inflammatory parameters; Pulse pressure
7.  Effects of candesartan in hypertensive patients with type 2 diabetes mellitus on inflammatory parameters and their relationship to pulse pressure 
Background
Angiotensin receptor blockers (ARBs) are reported to provide direct protection to many organs by controlling inflammation and decreasing oxidant stress in patients without arteriosclerosis. This study aimed to evaluate (1) whether an ARB (candesartan) decreases values for inflammatory parameters in hypertensive patients with type 2 diabetes mellitus of long duration accompanied by arteriosclerosis and (2) whether there any predictors of which patients would receive the benefits of organ protection by candesartan.
Methods
We administered candesartan therapy (12 mg daily) for 6 months and evaluated whether there was improvement in serum inflammatory parameters high molecular weight adiponectin (HMW-ADN), plasminogen activator inhibitor-1 (PAI-1), highly sensitive C-reactive protein (Hs-CRP), vascular cell adhesion molecule-1 (VCAM-1) in serum and urinary-8-hydroxydeoxyguanosine (U-8-OHdG). We then analyzed the relationship between the degree of lowering of blood pressure and inflammatory factors and the relationship between pulse pressure and inflammatory factors. Finally, we analyzed predictive factors in patients who received the protective benefit of candesartan.
Results
After 6 months of treatment, significant improvements from baseline values were observed in all patients in HMW-ADN and PAI-1 but not in Hs-CRP, VCAM-1 and U-8-OHdG. Multilinear regression analysis was performed to determine which factors could best predict changes in HMW-ADN and PAI-1. Changes in blood pressure were not significant predictors of changes in metabolic factors in all patients. We found that the group with baseline pulse pressure <60 mmHg had improved HMW-ADN and PAI-1 values compared with the group with baseline pulse pressure ≥ 60 mmHg. These results suggest that pulse pressure at baseline could be predictive of changes in HMW-ADN and PAI-1.
Conclusions
Candesartan improved inflammatory parameters (HMW-ADN and PAI-1) in hypertensive patients with type 2 diabetes mellitus of long duration independent of blood pressure changes. Patients with pulse pressure <60 mmHg might receive protective benefits by candesartan.
Trial registration
UMIN000007921
doi:10.1186/1475-2840-11-118
PMCID: PMC3489584  PMID: 23034088
Candesartan; Angiotensin receptor blockers; Type 2 diabetes mellitus; Inflammatory parameters; Pulse pressure
8.  Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format 
Nucleic Acids Research  2011;40(Database issue):D453-D460.
The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB) and accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized in this article. To enhance the interoperability of the PDB data, we have recently developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, along with its ontology in the Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary. Being in the standard format for the Semantic Web, the PDB/RDF data provide a means to integrate the PDB with other biological information resources.
doi:10.1093/nar/gkr811
PMCID: PMC3245181  PMID: 21976737
9.  Inducible nitric oxide has protective effect on fumonisin B1 hepatotoxicity in mice via modulation of sphingosine kinase 
Toxicology  2006;229(1-2):42-53.
Fumonisin B1, a natural mycotoxin, is an inhibitor of ceramide synthase causing marked dysregulation of sphingolipid metabolism in cells. This mycotoxin causes accumulation of free sphingoid bases (sphingosine and dihydrosphingosine or sphinganine) and their metabolites, important messengers involved in signal transduction leading to either cell survival or death. Free sphingoid bases are known apoptotic molecules whereas their respective 1-phosphates are protective. We previously reported that fumonisin B1 caused sphingosine kinase (SPHK) induction along with the increase of serine palmitoyltransferase (SPT). Fumonisin B1 also increased inducible nitric oxide synthase (iNOS) expression. In the current study we employed mice strain with the targeted deletion of iNOS gene (Nos-KO) to evaluate the role of nitric oxide (NO) on fumonisin B1-induced hepatotoxicity. The Nos-KO mice exhibited increased hepatotoxicity after subacute fumonisin B1 exposure compared to their wild type counterparts, the liver regeneration was lower in Nos-KO compared to that in the WT mice. Increased hepatotoxicity in Nos-KO was not related to the extent of free sphingoid base accumulation after fumonisin B1 treatment; however, it was accompanied by a lack of fumonisin B1-induced SPHK induction. The fumonisin B1-induced SPT was unaffected by lack of iNOS gene. Deletion of iNOS gene did not prevent fumonisin B1-dependent induction of inflammatory cytokines, namely tumor necrosis factor α, interferon γ and interleukin-12. The lack of fumonisin B1-induced SPHK induction in Nos-KO was supported by a similar effect on phosphorylated metabolites of sphingoid bases; the equilibrium between sphingoid bases and their phosphates is maintained by SPHK. We therefore conclude that iNOS induction produced by fumonisin B1 modulates SPHK activity; the lack of iNOS prevents generation of sphingosine 1-phosphate and deprives cells from its protective effects.
doi:10.1016/j.tox.2006.09.010
PMCID: PMC1850950  PMID: 17095132

Results 1-9 (9)