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Sample records for db kationoobmennoe razdelenie

  1. Instant InnoDB

    CERN Document Server

    Reid, Matt

    2013-01-01

    This book is a complete reference guide, designed to provide you with answers and solutions to all the common problems you encounter within InnoDB, helping you achieve higher performance and greater stability in your InnoDB databases.The ""InnoDB Quick Reference Guide"" features content for all skill levels of MySQL administrators, developers, and engineers.

  2. Mastering MariaDB

    CERN Document Server

    Razzoli, Federico

    2014-01-01

    This book is intended for intermediate users who want to learn how to administrate a MariaDB server or a set of servers. It is aimed at MariaDB users, and hence working knowledge of MariaDB is a prerequisite.

  3. Instant MongoDB

    CERN Document Server

    Nayak, Amol

    2013-01-01

    Get to grips with a new technology, understand what it is and what it can do for you, and then get to work with the most important features and tasks. MongoDB Starter is a fast and practical guide designed to help you start developing high-performance and scalable applications using MongoDB.MongoDB Starter is ideal for developers who are new to MongoDB and who need a no-nonsense guide on how to start working with it. No knowledge of MongoDB is required to follow this book, but some knowledge of C++ would be helpful.

  4. Scaling CouchDB

    CERN Document Server

    Holt, Bradley

    2011-01-01

    This practical guide offers a short course on scaling CouchDB to meet the capacity needs of your distributed application. Through a series of scenario-based examples, this book lets you explore several methods for creating a system that can accommodate growth and meet expected demand. In the process, you learn about several tools that can help you with replication, load balancing, clustering, and load testing and monitoring. Apply performance tips for tuning your databaseReplicate data, using Futon and CouchDB's RESTful interfaceDistribute CouchDB's workload through load balancingLearn option

  5. dbVar

    Data.gov (United States)

    U.S. Department of Health & Human Services — dbVar is a database of genomic structural variation. It accepts data from all species and includes clinical data. It can accept diverse types of events, including...

  6. dbSNP

    Data.gov (United States)

    U.S. Department of Health & Human Services — dbSNP is a database of single nucleotide polymorphisms (SNPs) and multiple small-scale variations that include insertions/deletions, microsatellites, and...

  7. MELCOR DB Construction for the Severe Accident Analysis DB

    Energy Technology Data Exchange (ETDEWEB)

    Song, Y. M.; Ahn, K. I. [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2011-10-15

    The Korea Atomic Energy Research Institute (KAERI) has been constructing a severe accident analysis database (DB) under a National Nuclear R and D Program. In particular, an MAAP (commercial code being widely used in industries for integrated severe accident analysis) DB for many scenarios including a station blackout (SBO) has been completed. This paper shows the MELCOR DB construction process with examples of SBO scenarios, and the results will be used for a comparison with the MAAP DB

  8. MongoDB high availability

    CERN Document Server

    Mehrabani, Afshin

    2014-01-01

    This book has a perfect balance of concepts and their practical implementation along with solutions to make a highly available MongoDB server with clear instructions and guidance. If you are using MongoDB in a production environment and need a solution to make a highly available MongoDB server, this book is ideal for you. Familiarity with MongoDB is expected so that you understand the content of this book.

  9. Scaling MongoDB

    CERN Document Server

    Chodorow, Kristina

    2011-01-01

    Create a MongoDB cluster that will to grow to meet the needs of your application. With this short and concise book, you'll get guidelines for setting up and using clusters to store a large volume of data, and learn how to access the data efficiently. In the process, you'll understand how to make your application work with a distributed database system. Scaling MongoDB will help you: Set up a MongoDB cluster through shardingWork with a cluster to query and update dataOperate, monitor, and backup your clusterPlan your application to deal with outages By following the advice in this book, you'l

  10. CottonDB Enhancement

    Institute of Scientific and Technical Information of China (English)

    YU Jing; KOHEL Russell; HINZE Lori; FRELICHOWSKI James; XU Zhan-you; YU John Z; PERCY Richard

    2008-01-01

    @@ CottonDB (www.cottondb,org) was initiated in 1995.It is a database that contains genomic,genetic,and taxonomic information for cotton (Gossypium spp.).It serves both as an archival database and as a dynamic database,which incorporates new data and user resources.CottonDB is maintained at the Southern Plains Agricultural Research Center in College Station,TX.The project includes a website and database creating a repository of information for over 450,000 gene,EST,and conting sequences; genetic and physical map data; nearly 10,000 DNA primers; and 9,000 germplasm accessions.

  11. DB2 9 for Developers

    CERN Document Server

    Gunning, Philip K

    2008-01-01

    Written by an "in-the-trenches" consultant, this guide hails the newest version of DB2 as a major release, highlighting the large number of totally new features, most notably the addition of XML capabilities. Packed with the information DB2 developers and administrators need to know when implementing version 9, the discussion covers upgrading from prior releases of DB2, converting relational data to XML data, and how DB2 supports industry standard schemas. With detailed examples and useful scripts, users learn how to develop DB2 XML applications, design an XML database, and tune the

  12. Amazon SimpleDB LITE

    CERN Document Server

    Chaganti, Prabhakar

    2011-01-01

    This focused book is an extracted LITE version of Packt's full: Amazon SimpleDB Developer Guide. It concentrates on getting a grounding in the value of SimpleDB, and shows how to set up an AWS account, enable a SimpleDB service for the account, and install and set up libraries for Java, PHP, and Python. If you are a developer wanting to get to grips with a primer into SimpleDB, then this book is for you. You do not need to know anything about SimpleDB to read and learn from this book, and no basic knowledge is strictly necessary.

  13. RavenDB high performance

    CERN Document Server

    Ritchie, Brian

    2013-01-01

    RavenDB High Performance is comprehensive yet concise tutorial that developers can use to.This book is for developers & software architects who are designing systems in order to achieve high performance right from the start. A basic understanding of RavenDB is recommended, but not required. While the book focuses on advanced topics, it does not assume that the reader has a great deal of prior knowledge of working with RavenDB.

  14. MariaDB cookbook

    CERN Document Server

    Bartholomew, Daniel

    2014-01-01

    A practical cookbook, filled with advanced recipes , and plenty of code and commands used for illustration,which will make your learning curve easy and quick.This book is for anyone who wants to learn more about databases in general or MariaDB in particular. Some familiarity with SQL databases is assumed, but the recipes are approachable to almost anyone with basic database skills.

  15. Dicty_cDB: VHJ619 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available DB: 0 Number of Sequences: 97611 Number of extensions: 0 Number of successful extensions: 0 Number of sequences better... than 10.0: 0 Number of HSP's better than 10.0 without gapping: 0 Number of HSP's successfully ga...er of Sequences: 92845959 Number of Hits to DB: 0 Number of sequences better than

  16. Dicty_cDB: VHF574 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available f Hits to DB: 0 Number of Sequences: 97611 Number of extensions: 0 Number of successful extensions: 0 Number of sequences better... than 10.0: 0 Number of HSP's better than 10.0 without gapping: 0 Number of HSP's succes...1 -3 Number of Sequences: 92845959 Number of Hits to DB: 0 Number of sequences better

  17. Dicty_cDB: VHI754 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available f Hits to DB: 0 Number of Sequences: 97611 Number of extensions: 0 Number of successful extensions: 0 Number of sequences better... than 10.0: 0 Number of HSP's better than 10.0 without gapping: 0 Number of HSP's succes...1 -3 Number of Sequences: 92845959 Number of Hits to DB: 0 Number of sequences better

  18. Dicty_cDB: VHF379 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available its to DB: 0 Number of Sequences: 97611 Number of extensions: 0 Number of successful extensions: 0 Number of sequences better... than 10.0: 0 Number of HSP's better than 10.0 without gapping: 0 Number of HSP's successfu...3 Number of Sequences: 92845959 Number of Hits to DB: 0 Number of sequences better

  19. Dicty_cDB: SSM379 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available astall] WARNING: [000.000] Unable to open /db/DNA.DATA/b/est_rest3.seq.nsq [blastall] ERROR: [000.000] ReadDBOpenMHdrAndSeqFiles: fai...led to map files [blastall] WARNING: [000.000] Unable to open /db/DNA.DATA/b/est_re

  20. Dicty_cDB: SHL888 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available es. 36 0.19 9 AV734847 |AV734847.1 Homo sapiens cDNA clone:cdAAGH02, 5'end, expressed in human pheochromoc...ytoma. 48 0.28 1 DB493756 |DB493756.1 Homo sapiens hypothalamus cDNA, RIKEN full-le

  1. MongoDB and PHP

    CERN Document Server

    Francia, Steve

    2012-01-01

    What would happen if you optimized a data store for the operations application developers actually use? You'd arrive at MongoDB, the reliable document-oriented database. With this concise guide, you'll learn how to build elegant database applications with MongoDB and PHP. Written by the Chief Solutions Architect at 10gen-the company that develops and supports this open source database-this book takes you through MongoDB basics such as queries, read-write operations, and administration, and then dives into MapReduce, sharding, and other advanced topics. Get out of the relational database rut,

  2. Dicty_cDB: SSI750 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available P43331 SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3 ;, mRNA sequence. 44 0.033 2 BE192240 |BE192240.2 db89d06.x1 Well...W:SMD3_HUMAN P43331 SMALL NUCLEAR RIBONUCLEOPROTEIN SM D3 ;, mRNA sequence. 44 0.034 2 BE506983 |BE506983.1 db89d06.y1 Well

  3. PKCδ regulates hepatic triglyceride accumulation and insulin signaling in Lepr(db/db) mice.

    Science.gov (United States)

    Zhang, Jian; Burrington, Christine M; Davenport, Samantha K; Johnson, Andrew K; Horsman, Melissa J; Chowdhry, Saleem; Greene, Michael W

    2014-08-08

    PKCδ has been linked to key pathophysiological features of non-alcoholic fatty liver disease (NAFLD). Yet, our knowledge of PKCδ's role in NAFLD development and progression in obese models is limited. PKCδ(-/-)/Lepr(db)(/)(db) mice were generated to evaluate key pathophysiological features of NAFLD in mice. Hepatic histology, oxidative stress, apoptosis, gene expression, insulin signaling, and serum parameters were analyzed in Lepr(db)(/)(db) and PKCδ(-/-)/Lepr(db)(/)(db) mice. The absence of PKCδ did not abrogate the development of obesity in Lepr(db)(/)(db) mice. In contrast, serum triglyceride levels and epididymal white adipose tissue weight normalized to body weight were reduced in PKCδ(-/-)/Lepr(db)(/)(db) mice compared Lepr(db)(/)(db) mice. Analysis of insulin signaling in mice revealed that hepatic Akt and GSK3β phosphorylation were strongly stimulated by insulin in PKCδ(-/-)/Lepr(db)(/)(db) compared Lepr(db)(/)(db) mice. PKCδ may be involved in the development of obesity-associated NAFLD by regulating hepatic lipid metabolism and insulin signaling.

  4. Mibefradil reduces blood glucose concentration in db/db mice

    Directory of Open Access Journals (Sweden)

    Yujie Lu

    2014-01-01

    Full Text Available OBJECTIVE: Numerous recent studies suggest that abnormal intracellular calcium concentration ([Ca2+]i is a common defect in diabetic animal models and patients. Abnormal calcium handling is an important mechanism in the defective pancreatic β-cell function in type 2 diabetes. T-type Ca2+ channel antagonists lower blood glucose in type 2 diabetes, but the mechanism remains unknown. METHODS: We examined the effect of the Ca2+ channel antagonist mibefradil on blood glucose in male db/db mice and phenotypically normal heterozygous mice by intraperitoneal injection. RESULTS: Mibefradil (15 mg/kg, i.p., b.i.d. caused a profound reduction of fasting blood glucose from 430.92±20.46 mg/dl to 285.20±5.74 mg/dl in three days. The hypoglycemic effect of mibefradil was reproduced by NNC 55-0396, a compound structurally similar to mibefradil but more selective for T-type Ca2+ channels, but not by the specific L-type Ca2+ channel blocker nicardipine. Mibefradil did not show such hypoglycemic effects in heterozygous animals. In addition, triglycerides, basal insulin and food intake were significantly decreased by mibefradil treatment in the db/db mice but not in the controls. Western blot analysis, immunohistochemistry and immunofluorescence staining showed a significantly increased expression of T-type Ca2+ channel α-subunits Cav3.1 and Cav3.2 in liver and brain tissues from db/db mice compared to those from heterozygous animals. CONCLUSIONS: Collectively, these results suggest that T-type Ca2+ channels are potential therapeutic targets for antidiabetic drugs.

  5. Astragaloside IV ameliorates renal injury in db/db mice

    Science.gov (United States)

    Sun, Huili; Wang, Wenjing; Han, Pengxun; Shao, Mumin; Song, Gaofeng; Du, Heng; Yi, Tiegang; Li, Shunmin

    2016-09-01

    Diabetic nephropathy is a lethal complication of diabetes mellitus and a major type of chronic kidney disease. Dysregulation of the Akt pathway and its downstream cascades, including mTOR, NFκB, and Erk1/2, play a critical role in the development of diabetic nephropathy. Astragaloside IV is a major component of Huangqi and exerts renal protection in a mouse model of type 1 diabetes. The current study was undertaken to investigate the protective effects of diet supplementation of AS-IV on renal injury in db/db mice, a type 2 diabetic mouse model. Results showed that administration of AS-IV reduced albuminuria, ameliorated changes in the glomerular and tubular pathology, and decreased urinary NAG, NGAL, and TGF-β1 in db/db mice. AS-IV also attenuated the diabetes-related activation of Akt/mTOR, NFκB, and Erk1/2 signaling pathways without causing any detectable hepatotoxicity. Collectively, these findings showed AS-IV to be beneficial to type 2 diabetic nephropathy, which might be associated with the inhibition of Akt/mTOR, NFκB and Erk1/2 signaling pathways.

  6. Dicty_cDB: SFK465 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available er of successful extensions: 462 Number of sequences better than 10.0: 0 Number of HSP's better than 10.0 wi...r of Hits to DB: 7,939,383 Number of extensions: 416863 Number of successful extensions: 21980 Number of sequences better

  7. Dicty_cDB: VFM414 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available extensions: 0 Number of sequences better than 10.0: 0 Number of HSP's better than 10.0 without gapping: 0 Nu...trix: blastn matrix:1 -3 Number of Sequences: 102105510 Number of Hits to DB: 0 Number of sequences better

  8. Dicty_cDB: VHP866 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available equences: 97611 Number of extensions: 0 Number of successful extensions: 0 Number of sequences better than 1...845959 Number of Hits to DB: 0 Number of sequences better than 10.0: 0 Length of ...0.0: 0 Number of HSP's better than 10.0 without gapping: 0 Number of HSP's successfully gapped in prelim tes

  9. Dicty_cDB: SFK133 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available sful extensions: 462 Number of sequences better than 10.0: 0 Number of HSP's better than 10.0 without gappin... DB: 7,939,383 Number of extensions: 416863 Number of successful extensions: 21980 Number of sequences better

  10. Dicty_cDB: SFK442 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ensions: 0 Number of sequences better than 10.0: 0 Number of HSP's better than 10.0 without gapping: 0 Numbe...x: blastn matrix:1 -3 Number of Sequences: 92845959 Number of Hits to DB: 0 Number of sequences better

  11. Dicty_cDB: SFK484 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available of extensions: 0 Number of successful extensions: 0 Number of sequences better than 10.0: 0 Number of HSP's better...ces: 92845959 Number of Hits to DB: 0 Number of sequences better than 10.0: 0 Length of query: 146 Length of

  12. Dicty_cDB: VSH547 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available xtensions: 0 Number of sequences better than 10.0: 0 Number of HSP's better than 10.0 without gapping: 0 Num...x: blastn matrix:1 -3 Number of Sequences: 102105510 Number of Hits to DB: 0 Number of sequences better than

  13. Dicty_cDB: VHL529 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available s: 97611 Number of extensions: 0 Number of successful extensions: 0 Number of sequences better than 10.0: 0 Number of HSP's better...Number of Hits to DB: 0 Number of sequences better than 10.0: 0 Length of query:

  14. Dicty_cDB: SFK265 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 0.711 1.31 Matrix: blastn matrix:1 -3 Gap Penalties: Existence: 5, Extension: 2 Number of Hits to DB: 0 Numb...s found ****** Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalt

  15. Dicty_cDB: SSL755 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available map 6245135-6357017 strain AX4, complete sequence. 36 0.082 9 CA982933 |CA982933.1 AGENCOURT_11279987 Wellc...e:XL094h21, 3' end, single read. 48 0.30 1 BE506694 |BE506694.1 db85g10.y1 Wellcome CRC pSK animal cap Xenop

  16. Dicty_cDB: VHK631 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available lastn matrix:1 -3 Gap Penalties: Existence: 5, Extension: 2 Number of Hits to DB: 0 Number of Sequences: 976...ambda K H 0.310 0.121 0.355 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence:

  17. Dicty_cDB: SSG859 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 711 1.31 Matrix: blastn matrix:1 -3 Gap Penalties: Existence: 5, Extension: 2 Number of Hits to DB: 0 Number...18 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension

  18. Mesenteric resistance arteries in type 2 diabetic db/db mice undergo outward remodeling.

    Directory of Open Access Journals (Sweden)

    Flavia M Souza-Smith

    Full Text Available OBJECTIVE: Resistance vessel remodeling is controlled by myriad of hemodynamic and neurohormonal factors. This study characterized structural and molecular remodeling in mesenteric resistance arteries (MRAs in diabetic (db/db and control (Db/db mice. METHODS: Structural properties were assessed in isolated MRAs from 12 and 16 wk-old db/db and Db/db mice by pressure myography. Matrix regulatory proteins were measured by Western blot analysis. Mean arterial pressure and superior mesenteric blood flow were measured in 12 wk-old mice by telemetry and a Doppler flow nanoprobe, respectively. RESULTS: Blood pressure was similar between groups. Lumen diameter and medial cross-sectional area were significantly increased in 16 wk-old db/db MRA compared to control, indicating outward hypertrophic remodeling. Moreover, wall stress and cross-sectional compliance were significantly larger in diabetic arteries. These remodeling indices were associated with increased expression of matrix regulatory proteins matrix metalloproteinase (MMP-9, MMP-12, tissue inhibitors of matrix metalloproteinase (TIMP-1, TIMP-2, and plasminogen activator inhibitor-1 (PAI-1 in db/db arteries. Finally, superior mesenteric artery blood flow was increased by 46% in 12 wk-old db/db mice, a finding that preceded mesenteric resistance artery remodeling. CONCLUSIONS: These data suggest that flow-induced hemodynamic changes may supersede the local neurohormonal and metabolic milieu to culminate in hypertrophic outward remodeling of type 2 DM mesenteric resistance arteries.

  19. Mesenteric Resistance Arteries in Type 2 Diabetic db/db Mice Undergo Outward Remodeling

    Science.gov (United States)

    Souza-Smith, Flavia M.; Katz, Paige S.; Trask, Aaron J.; Stewart, James A.; Lord, Kevin C.; Varner, Kurt J.; Vassallo, Dalton V.; Lucchesi, Pamela A.

    2011-01-01

    Objective Resistance vessel remodeling is controlled by myriad of hemodynamic and neurohormonal factors. This study characterized structural and molecular remodeling in mesenteric resistance arteries (MRAs) in diabetic (db/db) and control (Db/db) mice. Methods Structural properties were assessed in isolated MRAs from 12 and 16 wk-old db/db and Db/db mice by pressure myography. Matrix regulatory proteins were measured by Western blot analysis. Mean arterial pressure and superior mesenteric blood flow were measured in 12 wk-old mice by telemetry and a Doppler flow nanoprobe, respectively. Results Blood pressure was similar between groups. Lumen diameter and medial cross-sectional area were significantly increased in 16 wk-old db/db MRA compared to control, indicating outward hypertrophic remodeling. Moreover, wall stress and cross-sectional compliance were significantly larger in diabetic arteries. These remodeling indices were associated with increased expression of matrix regulatory proteins matrix metalloproteinase (MMP)-9, MMP-12, tissue inhibitors of matrix metalloproteinase (TIMP)-1, TIMP-2, and plasminogen activator inhibitor-1 (PAI-1) in db/db arteries. Finally, superior mesenteric artery blood flow was increased by 46% in 12 wk-old db/db mice, a finding that preceded mesenteric resistance artery remodeling. Conclusions These data suggest that flow-induced hemodynamic changes may supersede the local neurohormonal and metabolic milieu to culminate in hypertrophic outward remodeling of type 2 DM mesenteric resistance arteries. PMID:21829729

  20. Dicty_cDB: VHD884 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available -Sampling_GS-31-01-01-1P3-1P8KB marine metagenome genomic clone 1061005829372 3', genomic survey...3-1P8KB marine metagenome genomic clone 1061001949010 3', genomic survey sequence. 48 0.074 1 DB745988 |DB74...1-01-2P2KB marine metagenome genomic clone 1061002566945 5', genomic survey sequence. 46 0.29 1 ER314627 |ER...314627.1 1092344130575 Global-Ocean-Sampling_GS-34-01-01-1P5-1P8KB marine metagenome genomic clone 1061001445481 3', genomic survey...obal-Ocean-Sampling_GS-31-01-01-1P3-1P8KB marine metagenome genomic clone 1061002047837 5', genomic survey s

  1. Dicty_cDB: AFL585 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available SP's gapped (non-prelim): 0 length of query: 130 length of database: 80,480,566 effective HSP length: 17 effective length of query...ences: 102105510 Number of Hits to DB: 0 Number of sequences better than 10.0: 0 Length of query...: 130 Length of database: 101,790,757,118 Length adjustment: 22 Effective length of query: 10

  2. Dicty_cDB: AFM760 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available P's gapped (non-prelim): 0 length of query: 176 length of database: 80,480,566 effective HSP length: 17 effective length of query...n matrix:1 -3 Number of Sequences: 102105510 Number of Hits to DB: 0 Number of sequences better than 10.0: 0 Length of query...: 176 Length of database: 101,790,757,118 Length adjustment: 22 Effective length of query: 1

  3. Dicty_cDB: VSE362 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ter than 10.0: 0 Number of HSP's better than 10.0 without gapping: 0 Number of HSP'...mber of extensions: 746480 Number of successful extensions: 104742 Number of sequences better than 10.0: 0 L... of Hits to DB: 870 Number of Sequences: 97611 Number of extensions: 870 Number of successful extensions: 246 Number of sequences bet

  4. Dicty_cDB: VHI565 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available : 0 Number of Sequences: 97611 Number of extensions: 0 Number of successful extensions: 0 Number of sequences better... than 10.0: 0 Number of HSP's better than 10.0 without gapping: 0 Number of HSP's successfully gappe...772 Number of sequences better than 10.0: 0 Length of query: 121 Length of database: 95,242,211,685 Length a...of Sequences: 92845959 Number of Hits to DB: 68,262,994 Number of extensions: 660

  5. Dicty_cDB: SSK760 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available nstitute Human BAC Library) complete sequence. 46 0.48 1 BE189076 |BE189076.2 db68f12.x1 Wellcome CRC pSK eg...g Xenopus laevis cDNA clone IMAGE:3378191 3', mRNA sequence. 30 0.52 3 BI444834 |BI444834.1 daa94h07.x3 Well

  6. Dicty_cDB: AFK350 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available mbda K H 1.37 0.711 1.31 Matrix: blastn matrix:1 -3 Gap Penalties: Existence: 5, Extension: 2 Number of Hits...**** Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Exi...stence: 11, Extension: 1 Number of Sequences: 3039690 Number of Hits to DB: 40,592,

  7. Dicty_cDB: Contig-U05578-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available taurus cDNA 3', mRNA sequence. 44 5.0 1 ( DB873960 ) Lipochromis sp. 'matumbi hunter' cDNA clone:hm791... 4...4 5.0 1 ( DB870335 ) Lipochromis sp. 'matumbi hunter' cDNA clone:hm746... 44 5.0 ...1 ( DB865397 ) Lipochromis sp. 'matumbi hunter' cDNA clone:hm791... 44 5.0 1 ( DB861503 ) Lipochromis sp. 'matumbi hunter

  8. Getting started with MariaDB

    CERN Document Server

    Bartholomew, Daniel

    2013-01-01

    A practical, hands-on, beginner-friendly guide to installing and using MariaDB.Getting Started with MariaDB is for anyone who wants to learn more about databases in general or MariaDB in particular. No prior database experience is required. It is assumed that you have basic knowledge of software installation, editing files with a text editor, and using the command line and terminal.

  9. Improved cerebral energetics and ketone body metabolism in db/db mice.

    Science.gov (United States)

    Andersen, Jens V; Christensen, Sofie K; Nissen, Jakob D; Waagepetersen, Helle S

    2017-03-01

    It is becoming evident that type 2 diabetes mellitus is affecting brain energy metabolism. The importance of alternative substrates for the brain in type 2 diabetes mellitus is poorly understood. The aim of this study was to investigate whether ketone bodies are relevant candidates to compensate for cerebral glucose hypometabolism and unravel the functionality of cerebral mitochondria in type 2 diabetes mellitus. Acutely isolated cerebral cortical and hippocampal slices of db/db mice were incubated in media containing [U-(13)C]glucose, [1,2-(13)C]acetate or [U-(13)C]β-hydroxybutyrate and tissue extracts were analysed by mass spectrometry. Oxygen consumption and ATP synthesis of brain mitochondria of db/db mice were assessed by Seahorse XFe96 and luciferin-luciferase assay, respectively. Glucose hypometabolism was observed for both cerebral cortical and hippocampal slices of db/db mice. Significant increased metabolism of [1,2-(13)C]acetate and [U-(13)C]β-hydroxybutyrate was observed for hippocampal slices of db/db mice. Furthermore, brain mitochondria of db/db mice exhibited elevated oxygen consumption and ATP synthesis rate. This study provides evidence of several changes in brain energy metabolism in type 2 diabetes mellitus. The increased hippocampal ketone body utilization and improved mitochondrial function in db/db mice, may act as adaptive mechanisms in order to maintain cerebral energetics during hampered glucose metabolism.

  10. CouchDB the definitive guide

    CERN Document Server

    Anderson, J; Slater, Noah

    2010-01-01

    Three of CouchDB's creators show you how to use this document-oriented database as a standalone application framework or with high-volume, distributed applications. With its simple model for storing, processing, and accessing data, CouchDB is ideal for web applications that handle huge amounts of loosely structured data. That alone would stretch the limits of a relational database, yet CouchDB offers an open source solution that's reliable, scales easily, and responds quickly. CouchDB works with self-contained data that has loose or ad-hoc connections. It's a model that fits many real-world

  11. Dicty_cDB: Contig-U01012-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available seq; ddbjhum22.seq; ddbjhum3.seq; ddbjhum4.seq; ddbjhum5.seq; ddbjhum6.seq; ddbjhum7.seq; ddbjhum8.seq; ddbjhum9.seq; /db/DDBJNEW....DATA/a/new_ddbjhum.seq; ddbjpri.seq; /db/DDBJNEW.DATA/a/new...d3.seq; ddbjrod4.seq; ddbjrod5.seq; ddbjrod6.seq; ddbjrod7.seq; ddbjrod8.seq; ddbjrod9.seq; /db/DDBJNEW.DATA.../a/new_ddbjrod.seq; ddbjmam.seq; /db/DDBJNEW.DATA/a/new_ddbjmam.seq; ddbjvrt1.seq...; ddbjvrt2.seq; ddbjvrt3.seq; ddbjvrt4.seq; ddbjvrt5.seq; ddbjvrt6.seq; /db/DDBJNEW.DATA/a/new_ddbjvrt.seq;

  12. Dicty_cDB: Contig-U06177-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available jhum5.seq; ddbjhum6.seq; ddbjhum7.seq; ddbjhum8.seq; ddbjhum9.seq; /db/DDBJNEW.DATA/a/new_ddbjhum.seq; ddbjp...ri1.seq; ddbjpri2.seq; /db/DDBJNEW.DATA/a/new_ddbjpri.seq; ddbjrod1.seq; ddbjrod1...rod7.seq; ddbjrod8.seq; ddbjrod9.seq; /db/DDBJNEW.DATA/a/new_ddbjrod.seq; ddbjmam...1.seq; ddbjmam2.seq; /db/DDBJNEW.DATA/a/new_ddbjmam.seq; ddbjvrt1.seq; ddbjvrt2.seq; ddbjvrt3.seq; ddbjvrt4....seq; ddbjvrt5.seq; ddbjvrt6.seq; ddbjvrt7.seq; ddbjvrt8.seq; /db/DDBJNEW.DATA/a/new_ddbjvrt.seq; ddbjinv1.se

  13. Dicty_cDB: Contig-U03642-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 9 Cotton Lambda Zap Express Library Gossyp... 44 5.1 1 ( DB869360 ) Lipochromis sp. 'matumbi hunter...' cDNA clone:hm736... 44 5.1 1 ( DB869335 ) Lipochromis sp. 'matumbi hunter' cDNA clone:hm...734... 44 5.1 1 ( DB864756 ) Lipochromis sp. 'matumbi hunter' cDNA clone:hm783... 44 5.1 1 ( DB860882 ) Lipochromis sp. 'matumbi hunt...er' cDNA clone:hm736... 44 5.1 1 ( DB860855 ) Lipochromis sp. 'matumbi hunter' cDNA

  14. Dicty_cDB: Contig-U15580-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available lone:VS... 50 0.31 1 ( DB918201 ) Idiosepius paradoxus cDNA, clone:Ip_aB_031_J12,... 5... 50 0.31 1 ( DB918037 ) Idiosepius paradoxus cDNA, clone:Ip_aB_031_B19, 5... 50 0.31 1 ( DB917576 ) Idiosepius... paradoxus cDNA, clone:Ip_aB_029_M04, 5... 50 0.31 1 ( DB917237 ) Idiosepius paradoxus cDNA, clone:Ip..._aB_028_M04, 5... 50 0.31 1 ( DB914554 ) Idiosepius paradoxus cDNA, clone:Ip_aB_0...16_L17, 5... 50 0.31 1 ( DB911920 ) Idiosepius paradoxus cDNA, clone:Ip_aB_003_N02, 5... 50 0.31 1 ( DB911747 ) Idiosepius

  15. Dicty_cDB: VSK261 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available XXXXXXXXCCCNAAAAAAAAAAAAAAATAAAAAATAAAAA ATAAAAAAAGCAATTATTAATA sequence update 2001. 3.22 Translated Amino ...Seq.d/ 36 0.067 SSM263 (SSM263Q) /CSM/SS/SSM2-C/SSM263Q.Seq.d/ 36 0.067 own update 2003. 1.10 Homology vs DN...477258.1 603847884F1 CSEQRBN22 Gallus gallus cDNA clone ChEST839h22 5', mRNA sequence. 36 6.7 2 dna update 2... of Sequences: 3019103 Number of Hits to DB: 16,926,333 protein update 2009. 3.26 PSORT - 5' end seq. ID VSK

  16. Dicty_cDB: VSI483 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ATATAAATATATTAAAAAAAAAAXXXXXXXXXXCGNACG CG sequence update 2001. 3.22 Translated Amino Acid sequence nk*LIKY...VSI555Q) /CSM/VS/VSI5-C/VSI555Q.Seq.d/ 44 2e-04 own update 2009. 4. 4 Homology vs...8489804391 X1: 11 (21.8 bits) S2: 20 (40.1 bits) Dictyostelium discoideum cDNA Project Home dna update 2009....Sequences: 3019103 Number of Hits to DB: 6,396,198 protein update 2009. 3.24 PSORT - 5' end seq. ID VSI483F

  17. Dicty_cDB: VHL120 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 7 0.711 1.31 Gapped Lambda K H 1.37 0.711 1.31 Matrix: blastn matrix:1 -3 Gap Penalties: Existence: 5, Extension: 2 Number... of Hits to DB: 484 Number of Sequences: 97611 Number of extensions: 484 Number of successful extensions: 10 Number... of sequences better than 10.0: 0 Number of HSP's better than 10.0 without gapping: 0 Number... of HSP's successfully gapped in prelim test: 0 Number of HSP's that attempt...ed gapping in prelim test: 10 Number of HSP's gapped (non-prelim): 0 length of query: 133 length of database

  18. Dicty_cDB: VSI493 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available matrix:1 -3 Gap Penalties: Existence: 5, Extension: 2 Number of Hits to DB: 8 Number... of Sequences: 97611 Number of extensions: 8 Number of successful extensions: 5 Number of sequences better than 10.0: 0 Number... of HSP's better than 10.0 without gapping: 0 Number of HSP's successfully gapped in prelim test: 0 Number... of HSP's that attempted gapping in prelim test: 5 Number of HSP's gapped (non-prelim): ...logy vs DNA ***** No hits found ****** Lambda K H 1.37 0.711 1.31 Matrix: blastn matrix:1 -3 Number of Sequences: 105743758 Number

  19. Dicty_cDB: AFM786 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available matrix:1 -3 Gap Penalties: Existence: 5, Extension: 2 Number of Hits to DB: 4764 Number of Sequences: 97611 Number... of extensions: 4764 Number of successful extensions: 1588 Number of sequences better than 10.0: 0 Number... of HSP's better than 10.0 without gapping: 0 Number of HSP's successfully gapped in prelim test: 0 Number... of HSP's that attempted gapping in prelim test: 1588 Number of HSP's gapped (n...**** No hits found ****** Lambda K H 1.37 0.711 1.31 Matrix: blastn matrix:1 -3 Number of Sequences: 102105510 Number

  20. Dicty_cDB: VSF561 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: ...vs CSM-cDNA ***** No hits found ****** Lambda K H 1.37 0.711 1.31 Gapped Lambda K H 1.37 0.711 1.31 Matrix: ...blastn matrix:1 -3 Gap Penalties: Existence: 5, Extension: 2 Number of Hits to DB: 0 Number of Sequences: 97

  1. IBM DB2 97 Advanced Administration Cookbook

    CERN Document Server

    Neagu, Adrian

    2012-01-01

    This cookbook has recipes written in a simple, easy to understand format, with lots of screenshots and insightful tips and hints. If you are a DB2 Database Administrator who wants to understand and get hands on with the underlying aspects of database administration, then this book is for you. This book assumes that you have a basic understanding of DB2 database concepts.

  2. Getting started with OrientDB

    CERN Document Server

    Tesoriero, Claudio

    2013-01-01

    A standard tutorial aimed at making you an OrientDB expert, through the use of practical examples, explained in a step-by-step format.Getting Started with OrientDB 1.3.0 is great for database designers, developers, and systems engineers. It is assumed that you are familiar with NoSQL concepts, Java, and networking principles.

  3. Impaired Muscle Regeneration in Ob/ob and Db/db Mice

    Directory of Open Access Journals (Sweden)

    Mai-Huong Nguyen

    2011-01-01

    Full Text Available In obesity and type 2 diabetes, efficient skeletal muscle repair following injury may be required, not only for restoring muscle structure and function, but also for maintaining exercise capacity and insulin sensitivity. The hypothesis of this study was that muscle regeneration would be impaired in ob/ob and db/db mice, which are common mouse models of obesity and type 2 diabetes. Muscle injury was produced by cardiotoxin injection, and regeneration was assessed by morphological and immunostaining techniques. Muscle regeneration was delayed in ob/ob and db/db mice, but not in a less severe model of insulin resistance – feeding a high-fat diet to wild-type mice. Angiogenesis, cell proliferation, and myoblast accumulation were also impaired in ob/ob and db/db mice, but not the high-fat diet mice. The impairments in muscle regeneration were associated with impaired macrophage accumulation; macrophages have been shown previously to be required for efficient muscle regeneration. Impaired regeneration in ob/ob and db/db mice could be due partly to the lack of leptin signaling, since leptin is expressed both in damaged muscle and in cultured muscle cells. In summary, impaired muscle regeneration in ob/ob and db/db mice was associated with reduced macrophage accumulation, angiogenesis, and myoblast activity, and could have implications for insulin sensitivity in the skeletal muscle of obese and type 2 diabetic patients.

  4. Dicty_cDB: Contig-U01243-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available jhum7.seq; ddbjhum8.seq; ddbjhum9.seq; /db/DDBJNEW.DATA/a/new_ddbjhum.seq; ddbjpri.seq; /db/DDBJNEW.DATA/a/n...d13.seq; ddbjrod2.seq; ddbjrod3.seq; ddbjrod4.seq; ddbjrod5.seq; ddbjrod6.seq; ddbjrod7.seq; ddbjrod8.seq; d...dbjrod9.seq; /db/DDBJNEW.DATA/a/new_ddbjrod.seq; ddbjmam.seq; /db/DDBJNEW.DATA/a/new_ddbjmam.seq; ddbjvrt1.s...eq; ddbjvrt2.seq; ddbjvrt3.seq; ddbjvrt4.seq; ddbjvrt5.seq; ddbjvrt6.seq; /db/DDBJNEW....DATA/a/new_ddbjvrt.seq; ddbjinv1.seq; ddbjinv2.seq; ddbjinv3.seq; ddbjinv4.seq; ddbjinv5.seq; ddbjinv6.seq; /db/DDBJNEW.

  5. Dicty_cDB: Contig-U14108-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available q; ddbjhum5.seq; ddbjhum6.seq; ddbjhum7.seq; ddbjhum8.seq; ddbjhum9.seq; /db/DDBJNEW.DATA/a/new_ddbjhum.seq;...seq; ddbjrod7.seq; ddbjrod8.seq; ddbjrod9.seq; /db/DDBJNEW.DATA/a/new_ddbjrod.seq; ddbjmam.seq; /db/DDBJNEW....DATA/a/new_ddbjmam.seq; ddbjvrt1.seq; ddbjvrt2.seq; ddbjvrt3.seq; ddbjvrt4.seq; ddbjvrt5.seq; ddbjvrt6.seq; /db/DDBJNEW....jinv4.seq; ddbjinv5.seq; ddbjinv6.seq; /db/DDBJNEW.DATA/a/new_ddbjinv.seq; ddbjpln1.seq; ddbjpln10.seq; ddbj... ddbjpln9.seq; /db/DDBJNEW.DATA/a/new_ddbjpln.seq; ddbjbct1.seq; ddbjbct2.seq; ddbjbct3.seq; ddbjbct4.seq; d

  6. Dicty_cDB: Contig-U04482-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 5.seq; ddbjhum6.seq; ddbjhum7.seq; ddbjhum8.seq; ddbjhum9.seq; /db/DDBJNEW.DATA/a/new_ddbjhum.seq; ddbjpri1....seq; ddbjpri2.seq; /db/DDBJNEW.DATA/a/new_ddbjpri.seq; ddbjrod1.seq; ddbjrod10.se....seq; ddbjrod9.seq; /db/DDBJNEW.DATA/a/new_ddbjrod.seq; ddbjmam1.seq; ddbjmam2.seq; /db/DDBJNEW.... ddbjvrt6.seq; ddbjvrt7.seq; ddbjvrt8.seq; /db/DDBJNEW.DATA/a/new_ddbjvrt.seq; ddbjinv1.seq; ddbjinv2.seq; d...dbjinv3.seq; ddbjinv4.seq; ddbjinv5.seq; ddbjinv6.seq; ddbjinv7.seq; /db/DDBJNEW.DATA/a/new_ddbjinv.seq; ddb

  7. Dicty_cDB: Contig-U02361-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ipochromis sp. 'matumbi hunter' cDNA clone:hm799... 46 3.3 1 ( DB874581 ) Lipochromis sp. 'matumbi hunter...' cDNA clone:hm797... 46 3.3 1 ( DB873827 ) Lipochromis sp. 'matumbi hunter' cDNA cl...one:hm786... 46 3.3 1 ( DB870860 ) Lipochromis sp. 'matumbi hunter' cDNA clone:hm753... 46 3.3 1 ( DB870788 ...) Lipochromis sp. 'matumbi hunter' cDNA clone:hm752... 46 3.3 1 ( DB867028 ) Lipochromis sp. 'matumbi hunt...er' cDNA clone:hm709... 46 3.3 1 ( DB865449 ) Lipochromis sp. 'matumbi hunter' cDNA

  8. Dicty_cDB: SSH704 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available SS (Link to library) SSH704 (Link to dictyBase) ssh704 - - - SSH704P (Link to Original site) SSH704F 228 SSH...704Z 260 SSH704P 488 - - Show SSH704 Library SS (Link to library) Clone ID SSH704 (...Link to dictyBase) Atlas ID ssh704 NBRP ID - dictyBase ID - Link to Contig - Original site URL http://dictyc...db.biol.tsukuba.ac.jp/CSM/SS/SSH7-A/SSH704Q.Seq.d/ Representative seq. ID SSH704P... (Link to Original site) Representative DNA sequence >SSH704 (SSH704Q) /CSM/SS/SSH7-A/SSH704Q.Seq.d/ GGTGGTT

  9. MongoDB the definitive guide

    CERN Document Server

    Chodorow, Kristina

    2010-01-01

    How does MongoDB help you manage a huMONGOus amount of data collected through your web application? With this authoritative introduction, you'll learn the many advantages of using document-oriented databases, and discover why MongoDB is a reliable, high-performance system that allows for almost infinite horizontal scalability. Written by engineers from 10gen, the company that develops and supports this open source database, MongoDB: The Definitive Guide provides guidance for database developers, advanced configuration for system administrators, and an overview of the concepts and use cases f

  10. Dicty_cDB: Contig-U00805-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available dult female blood fed... 44 8.2 1 ( EG594390 ) SSH-94 Common bean supression subtractive hybridi... 44 8.2 1 ( DB919135 ) Idiosepius... paradoxus cDNA, clone:Ip_aB_034_E12, 5... 44 8.2 1 ( DB919106 ) Idiosepius paradoxu...s cDNA, clone:Ip_aB_034_D05, 5... 44 8.2 1 ( DB916651 ) Idiosepius paradoxus cDNA

  11. Dicty_cDB: Contig-U04578-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available clon... 42 4.6 1 ( DY887051 ) CeleSEQ2921 Cunninghamella elegans pBluescript (E... 42 4.6 1 ( DB919550 ) Idiosepius... paradoxus cDNA, clone:Ip_aB_035_H22, 5... 42 4.6 1 ( DB919510 ) Idiosepius paradoxus cDNA, clone:Ip..._aB_035_G02, 5... 42 4.6 1 ( DB917576 ) Idiosepius paradoxus cDNA, clone:Ip_aB_02

  12. Dicty_cDB: Contig-U06579-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available opore... 46 0.61 1 ( BE189537 ) db66g05.x1 Wellcome CRC pSK egg Xenopus laevis cD...... 46 0.61 1 ( BE189318 ) db64a10.x1 Wellcome CRC pSK egg Xenopus laevis cD... 46 0.61 1 ( BE188809 ) db59h10.x1 Well

  13. Dicty_cDB: Contig-U08185-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 0b18, 5' end,... 44 1.7 2 ( DB870607 ) Lipochromis sp. 'matumbi hunter' cDNA clone:hm751... 38 2.0 2 ( AV995...Lipochromis sp. 'matumbi hunter' cDNA clone:hm750... 38 2.1 2 ( DB868045 ) Lipochromis sp. 'matumbi hunter' ...ratus clone R3-112B16, WO... 46 2.6 4 ( DB869433 ) Lipochromis sp. 'matumbi hunter

  14. Dicty_cDB: Contig-U05180-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ipochromis sp. 'matumbi hunter' cDNA clone:hm791... 44 6.3 1 ( DB865465 ) Lipochromis sp. 'matumbi hunter...' cDNA clone:hm791... 44 6.3 1 ( DB864300 ) Lipochromis sp. 'matumbi hunter' cDNA cl...art li... 44 6.3 1 ( EB319027 ) CNSN01-F-008856-501 Normalized CNS library (juven... 44 6.3 1 ( DB874029 ) L

  15. Dicty_cDB: Contig-U15394-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available .011 12 ( DB912555 ) Idiosepius paradoxus cDNA, clone:Ip_aB_006_L23, 5... 42 0.011 2 ( AU087262 ) Plasmodium...7590 ) Dictyostelium discoideum iplA gene for inositol 1... 34 0.012 5 ( DB911197 ) Idiosepius paradoxus cDN...tis vinifera contig VV78X048242.8, whole genome... 52 0.016 4 ( DB918216 ) Idiosepius paradoxus cDNA, clone:... Dictyostelium discoideum developmental protein DG... 34 0.049 5 ( DB915718 ) Idiosepius

  16. Dicty_cDB: Contig-U05475-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available . 46 1.3 1 ( DY594159 ) KIDNEYF042327N20 POSSUM_01-POSSUM-KIDNEY-2KB Tric... 46 1.3 1 ( DB871834 ) Lipochromis sp. 'matumbi hunter...' cDNA clone:hm764... 46 1.3 1 ( DB870676 ) Lipochromis sp. 'matumbi hunter...' cDNA clone:hm750... 46 1.3 1 ( DB864953 ) Lipochromis sp. 'matumbi hunter' cDNA clone:hm78..... 44 5.3 1 ( DN683050 ) CGX27-G02.x1d-t SHGC-CGX Gasterosteus aculeatus c... 44 5.3 1 ( DB874016 ) Lipochromis sp. 'matumbi hunter

  17. Validity of leptin receptor-deficiency (db/db) type 2 diabetes mellitus mice as a model of secondary osteoporosis

    Science.gov (United States)

    Huang, Le; You, Yong-Ke; Zhu, Tracy Y.; Zheng, Li-Zhen; Huang, Xiao-Ru; Chen, Hai-Yong; Yao, Dong; Lan, Hui-Yao; Qin, Ling

    2016-06-01

    This study aimed to evaluate the validation of the leptin receptor-deficient mice model for secondary osteoporosis associated with type 2 diabetes mellitus (T2DM) at bone micro-architectural level. Thirty three 36-week old male mice were divided into four groups: normal control (db/m) (n = 7), leptin receptor-deficient T2DM (db/db) (n = 8), human C-reactive protein (CRP) transgenic normal control (crp/db/m) (n = 7), and human CRP transgenic T2DM (crp/db/db) (n = 11). Lumber vertebrae (L5) and bilateral lower limbs were scanned by micro-CT to analyze trabecular and cortical bone quality. Right femora were used for three-point bending to analyze the mechanical properties. Trabecular bone quality at L5 was better in db/db or crp/db/db group in terms of bone mineral density (BMD), bone volume fraction, connectivity density, trabecular number and separation (all p  0.05). Maximum loading and energy yield in mechanical test were similar among groups while the elastic modulus in db/db and crp/db/db significantly lower than db/m. The leptin-receptor mice is not a proper model for secondary osteoporosis associated with T2DM.

  18. The Research Applications of db/db Mouse%db/db小鼠的实验室应用

    Institute of Scientific and Technical Information of China (English)

    吴静; 王华旻; 李晶; 门秀丽

    2013-01-01

    The db/db mice are perfect animal models of type 2 diabetes which have been widely used. The phenotypes of severe obesity, hyperphagia, polydipsia, and polyuria are due to a spontaneous mutation of the leptin receptor ( Lepr) . The course of the disease is markedly influenced by genetic background, which is more serious in the C57BLKS/J background. And there are many other spontaneous mutations in different sites of Lepr, which produce a series of animal models of obesity, including db / db mice, db /db mice, dbpas/dbpas mice, Zucker fa/fa rats, and Koletsky fa/fa rats, etc. These rodents appear similar hyperphagia and severe obesity, but different levels of blood glucose, kidney damage and reproductive ability, providing profuse material to investigate the complex function of Lepr. Here we review the history of the discovery of the leptin signaling pathway, the abnormal phenotypes of db/db mice in metabolic, reproductive, immune, etc. Discuss their research applications, reproductive strategy , genotyping guideline, the phenotypic diversity of those animal models with Lepr spontaneous mutation and their mutation patterns, respectively.%db/db小鼠为广泛应用的2型糖尿病动物模型,由瘦素受体(leptin receptor,Lepr)的自发性突变引起极度肥胖、多食、消渴、多尿.其表型的严重程度受基因背景的影响,在C57BLKS/J背景下更严重.Lepr还在其它多个位点发生自发性突变,产生一系列肥胖动物,包括db3J/db3J小鼠、db5J/db5J小鼠、dbpas/dbpas小鼠、Zucker fa/fa大鼠和Koletsky fak/fak大鼠等.这些啮齿动物在食欲旺盛和严重肥胖方面表型相似,但在血糖、肾脏损伤及生殖能力等方面的表型不尽相同,为探讨Lepr的复杂功能提供了丰富的素材.本文将就瘦素信号通路的发现史,db/db小鼠在代谢、生殖、免疫等方面的异常表型,其实验室应用、繁殖与鉴定策略,其它自发性突变动物的表型差异及对应的Lepr突变模式等进行较全面的综述.

  19. Dicty_cDB: Contig-U15437-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available F-SAU3A-T3-M-P18.AB1 Blood stage Plasmodium ... 40 0.002 2 ( DB919709 ) Idiosepius paradoxus cDNA, clone:Ip_...* SEQUENCI... 34 0.071 2 ( DB918224 ) Idiosepius paradoxus cDNA, clone:Ip_aB_031_K12, 5... 36 0.071 2 ( CV28

  20. Dicty_cDB: Contig-U09423-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available o rerio genomic clone DKEY-124M2, genomic sur... 54 0.006 1 ( DB920051 ) Idiosepius paradoxus cDNA, clone:Ip..._aB_036_P20, 5... 54 0.006 1 ( DB919413 ) Idiosepius paradoxus cDNA, clone:Ip_aB_035_B18, 5... 54 0.006 1 (

  1. Dicty_cDB: Contig-U15891-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available OSSUM_01-POSSUM-LIVER-2KB Tricho... 54 1e-21 7 ( DB919968 ) Idiosepius paradoxus cDNA, clone:Ip_aB_036_M01, ...84 6e-19 4 ( EY099278 ) CAZI24167.fwd CAZI Artemisia annua normalized lea... 50 8e-19 4 ( DB920027 ) Idiosepius

  2. Dicty_cDB: Contig-U14706-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 76 e-130 1 ( DB913693 ) Idiosepius paradoxus cDNA, clone:Ip_aB_014_D11, 5... 58 7e-17 3 ( CX081125 ) EHAAC72...4 Sea urchin larva cDNA library MPM... 64 7e-09 2 ( DB919037 ) Idiosepius paradox

  3. Dicty_cDB: Contig-U16123-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available in gene, partial cds. 36 1.2 4 ( BV482695 ) rnq67c08.b1 Clint Pan troglodytes verus STS genom... 38 1.2 3 ( DB913696 ) Idiosepius....7 3 ( AY191013 ) Dictyostelium discoideum autophagy protein 6 (apg... 40 2.9 2 ( DB911467 ) Idiosepius para

  4. Dicty_cDB: Contig-U12325-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ing_GS-30-02-01-1... 52 0.055 1 ( DY887210 ) CeleSEQ3135 Cunninghamella elegans pBluescript (E... 42 0.14 2 ( DB911478 ) Idiosepius... paradoxus cDNA, clone:Ip_aB_002_H13, 5... 38 0.17 2 ( DB911959 ) Idiosepius

  5. Dicty_cDB: Contig-U15567-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available DN100954 ) 1000348 MARC 4PIG Sus scrofa cDNA 5', mRNA sequence. 46 6.9 1 ( DB919136 ) Idiosepius paradoxus ...cDNA, clone:Ip_aB_034_E13, 5... 46 6.9 1 ( DB918741 ) Idiosepius paradoxus cDNA,

  6. Dicty_cDB: Contig-U11897-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available icus DNA, BAC clone: RNB1-279A02, 3'... 46 3.3 1 ( DB916884 ) Idiosepius paradoxu...s cDNA, clone:Ip_aB_027_L18, 5... 46 3.3 1 ( DB916498 ) Idiosepius paradoxus cDNA, clone:Ip_aB_026_I23, 5...

  7. Dicty_cDB: Contig-U06765-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ... 50 0.059 1 ( DC199146 ) Plasmodium berghei cDNA clone:LV009447, liver sta... 50 0.059 1 ( DB917901 ) Idiosepius... paradoxus cDNA, clone:Ip_aB_030_L13, 5... 50 0.059 1 ( DB912130 ) Idiosepius

  8. Dicty_cDB: Contig-U09769-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available Bluescript (... 50 0.13 1 ( DB874496 ) Lipochromis sp. 'matumbi hunter' cDNA clone:hm796... 50 0.13 1 ( DB86...2401 ) Lipochromis sp. 'matumbi hunter' cDNA clone:hm759... 50 0.13 1 ( AC175917

  9. Dicty_cDB: Contig-U16371-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 6 0.64 2 ( BJ690967 ) Ptyochromis sp. 'redtail sheller' cDNA clone:no60... 46 0.64 2 ( DB871470 ) Lipochromis sp. 'matumbi hunter...( DB867711 ) Lipochromis sp. 'matumbi hunter' cDNA clone:hm717... 46 1.0 2 ( AC145267 ) Mus musculus BAC clo

  10. Dicty_cDB: Contig-U03911-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 12ST096_338113 Tall fescue, Festuca arun... 44 6e-08 4 ( DB872213 ) Lipochromis sp. 'matumbi hunter...' cDNA clone:hm769... 56 6e-08 2 ( DB866234 ) Lipochromis sp. 'matumbi hunter' cDNA clone:

  11. Improved insulin sensitivity and islet function after PPARdelta activation in diabetic db/db mice.

    Science.gov (United States)

    Winzell, Maria Sörhede; Wulff, Erik Max; Olsen, Grith Skytte; Sauerberg, Per; Gotfredsen, Carsten F; Ahrén, Bo

    2010-01-25

    The peroxisome proliferator-activated receptors (PPARs) are transcription factors belonging to the nuclear receptor superfamily. Several reports have shown that PPARdelta is involved in lipid metabolism, increasing fat oxidation and depleting lipid accumulation. Whether PPARdelta is involved in the regulation of glucose metabolism is not completely understood. In this study, we examined effects of long-term PPARdelta activation on glycemic control, islet function and insulin sensitivity in diabetic db/db mice. Male db/db mice were administered orally once daily with a selective and partial PPARdelta agonist (NNC 61-5920, 30 mg/kg) for eight weeks; control mice received vehicle. Fasting and non-fasting plasma glucose were reduced, reflected in reduced hemoglobinA(1c) (3.6+/-1.6% vs. 5.4+/-1.8 in db/db controls, Pdiabetic db/db mice. This suggests that activation of PPARdelta improves glucose metabolism and may therefore potentially be target for treatment of type 2 diabetes.

  12. Acarbose Accelerates Wound Healing via Akt/eNOS Signaling in db/db Mice

    Directory of Open Access Journals (Sweden)

    Xue Han

    2017-01-01

    Full Text Available Refractory wound is a dreaded complication of diabetes and is highly correlated with EPC dysfunction caused by hyperglycemia. Acarbose is a widely used oral glucose-lowering drug exclusively for T2DM. Previous studies have suggested the beneficial effect of acarbose on improving endothelial dysfunction in patients with T2DM. However, no data have been reported on the beneficial efficacy of acarbose in wound healing impairment caused by diabetes. We herein investigated whether acarbose could improve wound healing in T2DM db/db mice and the possible mechanisms involved. Acarbose hastened wound healing and enhanced angiogenesis, accompanied by increased circulating EPC number in db/db mice. In vitro, a reversed BM-EPC dysfunction was observed after the administration of acarbose in db/db mice, as reflected by tube formation assay. In addition, a significantly increased NO production was also witnessed in BM-EPCs from acarbose treated db/db mice, with decreased O2 levels. Akt inhibitor could abolish the beneficial effect of acarbose on high glucose induced EPC dysfunction in vitro, accompanied by reduced eNOS activation. Acarbose displayed potential effect in promoting wound healing and improving angiogenesis in T2DM mice, which was possibly related to the Akt/eNOS signaling pathway.

  13. C57BL/KsJ-db/db-ApcMin/+ Mice Exhibit an Increased Incidence of Intestinal Neoplasms

    Directory of Open Access Journals (Sweden)

    Yoshinobu Hirose

    2011-11-01

    Full Text Available The numbers of obese people and diabetic patients are ever increasing. Obesity and diabetes are high-risk conditions for chronic diseases, including certain types of cancer, such as colorectal cancer (CRC. The aim of this study was to develop a novel animal model in order to clarify the pathobiology of CRC development in obese and diabetic patients. We developed an animal model of obesity and colorectal cancer by breeding the C57BL/KsJ-db/db (db/db mouse, an animal model of obesity and type II diabetes, and the C57BL/6J-ApcMin/+ (Min/+ mouse, a model of familial adenomatous polyposis. At 15 weeks of age, the N9 backcross generation of C57BL/KsJ-db/db-ApcMin/+ (db/db-Min/+ mice developed an increased incidence and multiplicity of adenomas in the intestinal tract when compared to the db/m-Min/+ and m/m-Min/+ mice. Blood biochemical profile showed significant increases in insulin (8.3-fold to 11.7-fold, cholesterol (1.2-fold to 1.7-fold, and triglyceride (1.2-fold to 1.3-fold in the db/db-Min/+ mice, when compared to those of the db/m-Min/+ and m/m-Min/+ mice. Increases (1.4-fold to 2.6-fold in RNA levels of insulin-like growth factor (IGF-1, IRF-1R, and IGF-2 were also observed in the db/db-Min/+ mice. These results suggested that the IGFs, as well as hyperlipidemia and hyperinsulinemia, promoted adenoma formation in the db/db-Min/+ mice. Our results thus suggested that the db/db-Min/+ mice should be invaluable for studies on the pathogenesis of CRC in obese and diabetes patients and the therapy and prevention of CRC in these patients.

  14. Dicty_cDB: Contig-U16254-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available . 222 3e-60 2 ( DB911423 ) Idiosepius paradoxus cDNA, clone:Ip_aB_002_E22, 5... 109 3e-60 4 ( EB681956 ) KP1...-59 5 ( DY333092 ) OB_MEa0009D11.r OB_MEa Ocimum basilicum cDNA clon... 139 4e-59 6 ( DB919840 ) Idiosepius ...8 3 ( AF351199 ) Dictyostelium sphaerocephalum 18S ribosomal RNA g... 214 7e-58 2 ( DB912577 ) Idiosepius pa...167 8e-57 5 ( DB915267 ) Idiosepius paradoxus cDNA, clone:Ip_aB_018_N03, 5... 115... tabacum vacuolar H+-ATPase B subunit mR... 88 2e-54 8 ( DB915413 ) Idiosepius paradoxus cDNA, clone:Ip_aB_0

  15. Zinc Prevents the Development of Diabetic Cardiomyopathy in db/db Mice

    Directory of Open Access Journals (Sweden)

    Shudong Wang

    2017-03-01

    Full Text Available Diabetic cardiomyopathy (DCM is highly prevalent in type 2 diabetes (T2DM patients. Zinc is an important essential trace metal, whose deficiency is associated with various chronic ailments, including vascular diseases. We assessed T2DM B6.BKS(D-Leprdb/J (db/db mice fed for six months on a normal diet containing three zinc levels (deficient, adequate, and supplemented, to explore the role of zinc in DCM development and progression. Cardiac function, reflected by ejection fraction, was significantly decreased, along with increased left ventricle mass and heart weight to tibial length ratio, in db/db mice. As a molecular cardiac hypertrophy marker, atrial natriuretic peptide levels were also significantly increased. Cardiac dysfunction and hypertrophy were accompanied by significantly increased fibrotic (elevated collagen accumulation as well as transforming growth factor β and connective tissue growth factor levels and inflammatory (enhanced expression of tumor necrosis factor alpha, interleukin-1β, caspase recruitment domain family member 9, and B-cell lymphoma/leukemia 10, and activated p38 mitogen-activated protein kinase responses in the heart. All these diabetic effects were exacerbated by zinc deficiency, and not affected by zinc supplementation, respectively. Mechanistically, oxidative stress and damage, mirrored by the accumulation of 3-nitrotyrosine and 4-hydroxy-2-nonenal, was significantly increased along with significantly decreased expression of Nrf2 and its downstream antioxidants (NQO-1 and catalase. This was also exacerbated by zinc deficiency in the db/db mouse heart. These results suggested that zinc deficiency promotes the development and progression of DCM in T2DM db/db mice. The exacerbated effects by zinc deficiency on the heart of db/db mice may be related to further suppression of Nrf2 expression and function.

  16. Ginsenoside Rb1 ameliorates liver fat accumulation by upregulating perilipin expression in adipose tissue of db/db obese mice

    Directory of Open Access Journals (Sweden)

    Xizhong Yu

    2015-07-01

    Conclusion: G-Rb1 may improve insulin sensitivity in obese and diabetic db/db mice by reducing hepatic fat accumulation and suppressing adipocyte lipolysis; these effects may be mediated via the upregulation of perilipin expression in adipocytes.

  17. Protective effects of astragaloside IV on db/db mice with diabetic retinopathy.

    Directory of Open Access Journals (Sweden)

    Yuzhi Ding

    Full Text Available Diabetic retinopathy (DR is a common diabetic eye disease which is well-known as the result of microvascular retinal changes. Although the potential biological functions of astragaloside IV (AS IV have long been described in traditional system of medicine, its protective effect on DR remains unclear. This study aims to investigate the function and mechanism of AS IV on type 2 diabetic db/db mice.Db/db mice were treated with AS IV (4.5 mg/kg or 9 mg/kg or physiological saline by oral gavage for 20 weeks along with db/m mice. In each group, retinal ganglion cell (RGC function was measured by pattern electroretinogram (ERG and apoptosis was determined by Terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL staining. Blood and retina aldose reductase (AR activity were quantified by chemiluminescence analysis. The expressions of phosporylated-ERK1/2, NF-κB were determined by Western blot analysis. Furthermore, the expression of related downstream proteins were quantified by Label-based Mouse Antibody Array.Administration of AS IV significantly improved the amplitude in pattern ERG and reduced the apoptosis of RGCs.in db/db mice. Furthermore, downregulation of AR activity, ERK1/2 phosphorylation, NF-κB and related cytokine were observed in AS IV treatment group.Our study indicated that AS IV, as an inhibitor of AR, could prevent the activation of ERK1/2 phosporylation and NF-kB and further relieve the RGCs disfunction in db/db mice with DR. It has provided a basis for investigating the clinical efficacy of AR inhibitors in preventing DR.

  18. DBA2J db/db mice are susceptible to early albuminuria and glomerulosclerosis that correlate with systemic insulin resistance.

    Science.gov (United States)

    Østergaard, Mette V; Pinto, Vanda; Stevenson, Kirsty; Worm, Jesper; Fink, Lisbeth N; Coward, Richard J M

    2017-02-01

    Diabetic nephropathy (DN) is the leading cause of kidney failure in the world. To understand important mechanisms underlying this condition, and to develop new therapies, good animal models are required. In mouse models of type 1 diabetes, the DBA/2J strain has been shown to be more susceptible to develop kidney disease than other common strains. We hypothesized this would also be the case in type 2 diabetes. We studied db/db and wild-type (wt) DBA/2J mice and compared these with the db/db BLKS/J mouse, which is currently the most widely used type 2 DN model. Mice were analyzed from age 6 to 12 wk for systemic insulin resistance, albuminuria, and glomerular histopathological and ultrastructural changes. Body weight and nonfasted blood glucose were increased by 8 wk in both genders, while systemic insulin resistance commenced by 6 wk in female and 8 wk in male db/db DBA/2J mice. The urinary albumin-to-creatinine ratio (ACR) was closely linked to systemic insulin resistance in both sexes and was increased ~50-fold by 12 wk of age in the db/db DBA/2J cohort. Glomerulosclerosis, foot process effacement, and glomerular basement membrane thickening were observed at 12 wk of age in db/db DBA/2J mice. Compared with db/db BLKS/J mice, db/db DBA/2J mice had significantly increased levels of urinary ACR, but similar glomerular histopathological and ultrastructural changes. The db/db DBA/2J mouse is a robust model of early-stage albuminuric DN, and its levels of albuminuria correlate closely with systemic insulin resistance. This mouse model will be helpful in defining early mechanisms of DN and ultimately the development of novel therapies. Copyright © 2017 the American Physiological Society.

  19. Getting started with LevelDB

    CERN Document Server

    Dent, Andy

    2013-01-01

    The book is a concise guide for using LevelDB. It explains database concepts and the use of C++, ranging from the basics all the way to high level topics in an easy to follow, step-by-step format.The book is meant for developers who want an embedded database for their applications. Experienced programmers can pick up on the sophisticated data mapping patterns and tuning tips.Getting Started with LevelDB requires a minimal background in programming in C++ or Objective-C for OS/X or iOS and familiarity with XCode. Therefore it teaches enough C++ to use LevelDB without presuming any C++ knowledge

  20. Effects of phlorizin on vascular complications in diabetes db/db mice

    Institute of Scientific and Technical Information of China (English)

    SHEN Lin; YOU Bei-an; GAO Hai-qing; LI Bao-ying; YU Fei; PEI Fei

    2012-01-01

    Background Diabetic macrovascular complications are important causes of cardiovascular and cerebrovascular diseases and also one of the major causes of morbidity and mortality in patients with type 2 diabetes mellitus (T2DM).Phlorizin has been reported to be effective in reducing the blood glucose level in diabetic mellitus,while little is known about its effects on vascular complications.This study aimed to observe the effects of phlorizin on the aorta of diabetes db/db mice and explore its mechanism.Methods Diabetic db/db mice (n=16) and age-matched db/m mice (n=8) were divided into three groups:normal control group (CC group,db/m mice,n=8),untreated diabetic group (DM group,db/db mice,n=8) and diabetic group treated by phlorizin (DMT group,db/db mice,n=8).Phlorizin (20 mg/kg body weight) was given in normal saline solution intragastrically for 10 weeks.Animals were weighed weekly.At the 10th weekend,all mice were fasted overnight and then sacrificed.Fasting blood was collected,and the aortas were dissected.The blood samples were analyzed for fasting blood glucose (FBG),serum advanced glycation end products (AGEs),malondialdehyde (MDA) and superoxide dismutase (SOD) activity,the aortic ultrastructure was studied.Results The weight and serum concentration of FBG,AGEs,and MDA in the DM group were higher than that in the CC group (P <0.01 ),and they were significantly lower in the DMT group (P <0.05).Serum SOD activity was lower than that in the CC group (P <0.01),and it is significantly higher in the DMT group (P <0.05).The severity of aorta damage in the DMT group was less than that in the DM group.Conclusions Phlorizin protected the db/db mice from diabetic macrovascular complications,attributed to the decreasing of blood glucose and AGEs level,and its antioxidant potential.This study may provide a new natural medicine for treating diabetic macrovascular complications.

  1. Dicty_cDB: Contig-U04683-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 1 ( DN523042 ) 1266489 MARC 7BOV Bos taurus cDNA 3', mRNA sequence. 46 1.9 1 ( DB916246 ) Idiosepius... paradoxus cDNA, clone:Ip_aB_025_M24, 5... 46 1.9 1 ( DB916080 ) Idiosepius paradoxus cDN...A, clone:Ip_aB_025_F18, 5... 46 1.9 1 ( DB916077 ) Idiosepius paradoxus cDNA, clone:Ip_aB_025_F15, 5... 46 1

  2. Dicty_cDB: Contig-U14844-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available um falciparum strain 3D7, chromosome 9; s... 44 0.012 9 ( DB911747 ) Idiosepius paradoxus cDNA, clone:Ip_aB_...003_E09, 5... 44 0.012 2 ( DB911920 ) Idiosepius paradoxus cDNA, clone:Ip_aB_003_N02, 5... 44 0.012 2 ( AC11... ) BB170019A20F12.5 Bee Brain Normalized/Subtracted ... 34 0.013 3 ( DB918201 ) Idiosepius paradoxus cDNA, c

  3. Dicty_cDB: Contig-U16002-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available Dictyostelium discoideum cDNA clone:dds19d18, 5' ... 38 3.3 2 ( DB916077 ) Idiosepius paradoxus cDNA, clone:..., 5' e... 46 3.6 2 ( EL906265 ) INIT2_11_B01.b1_A006 G5 trophont cDNA (INIT2) Ich... 46 3.6 2 ( DB916080 ) Idiosepius...tage Plasmodi... 42 4.3 3 ( EK576016 ) 1095521191381 Global-Ocean-Sampling_GS-32-01-01-1... 32 4.3 2 ( DB916246 ) Idiosepius...aculeatus ... 46 6.6 1 ( DN720777 ) CNB135-F10.x1d-t SHGC-CNB Gasterosteus aculeatus ... 46 6.6 1 ( DB915443 ) Idiosepius

  4. Effect of curcumin supplementation on blood glucose, plasma insulin, and glucose homeostasis related enzyme activities in diabetic db/db mice.

    Science.gov (United States)

    Seo, Kwon-Il; Choi, Myung-Sook; Jung, Un Ju; Kim, Hye-Jin; Yeo, Jiyoung; Jeon, Seon-Min; Lee, Mi-Kyung

    2008-09-01

    We investigated the effect of curcumin on insulin resistance and glucose homeostasis in male C57BL/KsJ-db/db mice and their age-matched lean non-diabetic db/+ mice. Both db/+ and db/db mice were fed with or without curcumin (0.02%, wt/wt) for 6 wks. Curcumin significantly lowered blood glucose and HbA 1c levels, and it suppressed body weight loss in db/db mice. Curcumin improved homeostasis model assessment of insulin resistance and glucose tolerance, and elevated the plasma insulin level in db/db mice. Hepatic glucokinase activity was significantly higher in the curcumin-supplemented db/db group than in the db/db group, whereas glucose-6-phosphatase and phosphoenolpyruvate carboxykinase activities were significantly lower. In db/db mice, curcumin significantly lowered the hepatic activities of fatty acid synthase, beta-oxidation, 3-hydroxy-3-methylglutaryl coenzyme reductase, and acyl-CoA: cholesterol acyltransferase. Curcumin significantly lowered plasma free fatty acid, cholesterol, and triglyceride concentrations and increased the hepatic glycogen and skeletal muscle lipoprotein lipase in db/db mice. Curcumin normalized erythrocyte and hepatic antioxidant enzyme activities (superoxide dismutase, catalase, gluthathione peroxidase) in db/db mice that resulted in a significant reduction in lipid peroxidation. However, curcumin showed no effect on the blood glucose, plasma insulin, and glucose regulating enzyme activities in db/+ mice. These results suggest that curcumin seemed to be a potential glucose-lowering agent and antioxidant in type 2 diabetic db/db mice, but had no affect in non-diabetic db/+ mice.

  5. Improved cerebral energetics and ketone body metabolism in db/db mice

    DEFF Research Database (Denmark)

    Andersen, Jens V; Christensen, Sofie K; Nissen, Jakob D

    2017-01-01

    It is becoming evident that type 2 diabetes mellitus is affecting brain energy metabolism. The importance of alternative substrates for the brain in type 2 diabetes mellitus is poorly understood. The aim of this study was to investigate whether ketone bodies are relevant candidates to compensate...... metabolism in type 2 diabetes mellitus. The increased hippocampal ketone body utilization and improved mitochondrial function in db/db mice, may act as adaptive mechanisms in order to maintain cerebral energetics during hampered glucose metabolism....

  6. Dicty_cDB: Contig-U16170-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available e R3-4012K8, WO... 44 0.31 5 ( DB915479 ) Idiosepius paradoxus cDNA, clone:Ip_aB_019_H19, 5... 44 0.32 2 ( B...lone: QflA-12636, 5' e... 44 0.34 2 ( DB915181 ) Idiosepius paradoxus cDNA, clone:Ip_aB_018_I21, 5... 44 0.3

  7. Dicty_cDB: Contig-U03772-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ( AM437561 ) Vitis vinifera contig VV78X271076.15, whole genom... 38 0.011 4 ( DB917492 ) Idiosepius parado...11 5 ( DB917153 ) Idiosepius paradoxus cDNA, clone:Ip_aB_028_I04, 5... 40 0.011 2...EQUENCING IN PROGRESS... 38 0.010 6 ( AL356014 ) Arabidopsis thaliana DNA chromosome 3, BAC clone ... 44 0.0

  8. The db/db mouse, a model for diabetic dyslipidemia: molecular characterization and effects of Western diet feeding.

    Science.gov (United States)

    Kobayashi, K; Forte, T M; Taniguchi, S; Ishida, B Y; Oka, K; Chan, L

    2000-01-01

    Diabetic dyslipidemia is a major factor contributing to the accelerated atherosclerosis in type 2 diabetes mellitus. Although several mouse models are available, the plasma lipoproteins in response to diet have not been fully characterized in these animals. In this study, we have characterized the plasma lipoproteins and related apolipoproteins, as well as the vascular lipases, in diabetes (db/db) mice and their nondiabetic controls (+/?) in the C57BL/KsJ strain. Within 6 weeks of age, db/db mice developed significant obesity, fasting hyperglycemia, and hyperinsulinemia. By FPLC analysis, db/db mice showed a prominent peak in the low-density lipoprotein (LDL) range that was absent in +/? mice, although high-density lipoprotein (HDL) was the predominant species in both groups of animals. Postheparin lipoprotein lipase (LPL) activity in db/db mice was 28% of the level in +/? mice. Upon feeding a human-like 0.15% (wt/wt) cholesterol and 21% (wt/wt) fat "Western" diet, db/db mice developed elevated plasma cholesterol, accompanied by an exaggerated apolipoprotein E (apoE) response compared with +/? mice. FPLC analysis showed that the marked hypercholesterolemic response in db/db mice was the result of a massive increase in the LDL region, which overshadowed a moderate increase in HDL. We next isolated lipoproteins by ultracentrifugation and characterized them by nondenaturing gradient gel electrophoresis. With regular chow, db/db mice had almost exclusively small dense LDL with a peak size at 21.4 nm, as compared with 26.6 nm in nondiabetic controls. On the Western diet, the small dense LDLs persisted but larger particles also appeared in db/db mice, whereas the size distribution in +/? mice was unchanged by the diet. Our results suggest that db/db mice fed a Western diet have a plasma lipoprotein phenotype that shows some similarities to that in patients with type 2 diabetes mellitus, and that db/db mice are a useful model to study the pathogenesis and treatment of

  9. Systemic immune modulation induced by alcoholic beverage intake in obese-diabetes (db/db) mice.

    Science.gov (United States)

    Lee, Hyunah; Jang, Ik-Soon; Park, Junsoo; Kim, Seol-Hee; Baek, So-Young; Go, Sung-Ho; Lee, Seung-Hoon

    2013-03-01

    Alcohol over-consumption is generally immunosuppressive. In this study, the effects of single or repetitive alcohol administration on the systemic immunity of db/db mice were observed to clarify the possible mechanisms for the increased susceptibility of obese individuals to alcohol-related immunological health problems. Alcohol (as a form of commercially available 20% distilled-alcoholic beverage) was orally administered one-time or seven times over 2 weeks to db/db mice and normal C57BL/6J mice. Immunologic alterations were analyzed by observation of body weight and animal activity, along with proportional changes of splenocytes for natural killer cells, macrophages, and T and B lymphocytes. Modulation of plasma cytokine level and immune-related genes were also ascertained by micro-bead assay and a microarray method, respectively. The immune micro-environment of db/db mice was an inflammatory state and adaptive cellular immunity was significantly suppressed. Low-dose alcohol administration reversed the immune response, decreasing inflammatory responses and the increment of adaptive immunity mainly related to CD4(+) T cells, but not CD8(+) T cells, to normal background levels. Systemic immune modulation due to alcohol administration in the obese-diabetic mouse model may be useful in the understanding of the induction mechanism, which will aid the development of therapeutics for related secondary diseases.

  10. Asiago spectroscopic classification of ASASSN-15db

    Science.gov (United States)

    Ochner, P.; Pastorello, A.; Benetti, S.; Cappellaro, E.; Elias-Rosa, N.; Tartaglia, L.; Terreran, G.; Tomasella, L.; Turatto, M.

    2015-02-01

    The Asiago Transient Classification Program (Tomasella et al. 2014, AN, 335, 841) reports the spectroscopic observation of ASASSN-15db in NGC 5996. The observation was performed with the Asiago 1.82m Copernico Telescope (+AFOSC; range 340-820 nm; resolution 1.4 nm), equipped with the CCD Andor IKON L936.

  11. Lepr(db/db Mice with senescence marker protein-30 knockout (Lepr(db/dbSmp30(Y/- exhibit increases in small dense-LDL and severe fatty liver despite being fed a standard diet.

    Directory of Open Access Journals (Sweden)

    Yoshitaka Kondo

    Full Text Available BACKGROUND/AIMS: The senescence marker protein-30 (SMP30 is a 34 kDa protein originally identified in rat liver that shows decreased levels with age. Several functional studies using SMP30 knockout (Smp30(Y/- mice established that SMP30 functions as an antioxidant and protects against apoptosis. To address the potential role of SMP30 in nonalcoholic fatty liver disease (NAFLD pathogenesis, we established Smp30(Y/- mice on a Lepr(db/db background (Lepr(db/dbSmp30(Y/- mice. RESEARCH DESIGN/PRINCIPAL FINDINGS: Male Lepr(db/dbSmp30(Y/- mice were fed a standard diet (340 kcal/100 g, fat 5.6% for 16 weeks whereupon the lipid/lipoprotein profiles, hepatic expression of genes related to lipid metabolism and endoplasmic reticulum stress markers were analyzed by HPLC, quantitative RT-PCR and western blotting, respectively. Changes in the liver at a histological level were also investigated. The amount of SMP30 mRNA and protein in livers was decreased in Lepr(db/dbSmp30(Y/+ mice compared with Lepr(db/+Smp30(Y/+ mice. Compared with Lepr(db/dbSmp30(Y/+ mice, 24 week old Lepr(db/dbSmp30(Y/- mice showed: i increased small dense LDL-cho and decreased HDL-cho levels; ii fatty liver accompanied by numerous inflammatory cells and increased oxidative stress; iii decreased mRNA expression of genes involved in fatty acid oxidation (PPARα and lipoprotein uptake (LDLR and VLDLR but increased CD36 levels; and iv increased endoplasmic reticulum stress. CONCLUSION: Our data strongly suggest that SMP30 is closely associated with NAFLD pathogenesis, and might be a possible therapeutic target for NAFLD.

  12. Full-thickness splinted skin wound healing models in db/db and heterozygous mice: implications for wound healing impairment.

    Science.gov (United States)

    Park, Shin Ae; Teixeira, Leandro B C; Raghunathan, Vijay Krishna; Covert, Jill; Dubielzig, Richard R; Isseroff, Roslyn Rivkah; Schurr, Michael; Abbott, Nicholas L; McAnulty, Jonathan; Murphy, Christopher J

    2014-01-01

    The excisional dorsal full-thickness skin wound model with or without splinting is widely utilized in wound healing studies using diabetic or normal mice. However, the effects of splinting on dermal wound healing have not been fully characterized, and there are limited data on the direct comparison of wound parameters in the splinted model between diabetic and normal mice. We compared full-thickness excisional dermal wound healing in db/db and heterozygous mice by investigating the effects of splinting, semi-occlusive dressing, and poly(ethylene glycol) treatment. Two 8-mm full-thickness wounds were made with or without splinting in db/db and heterozygous mice. Body weights, splint maintenance, wound contraction, wound closure, and histopathological parameters including reepithelialization, wound bed collagen deposition, and inflammation were compared between groups. Our results show that silicone splint application effectively reduced wound contraction in heterozygous and db/db mice. Splinted wounds, as opposed to nonsplinted wounds, exhibited no significant differences in wound closure between heterozygous and db/db mice. Finally, polyethylene glycol and the noncontact dressing had no significant effect on wound healing in heterozygous or db/db mice. We believe these findings will help investigators in selection of the appropriate wound model and data interpretation with fully defined parameters.

  13. IBM DB2 97 Advanced Application Developer Cookbook

    CERN Document Server

    Saraswatipura, Mohankumar

    2012-01-01

    This cookbook has recipes written in a simple, easy to understand format with lots of screenshots and insightful tips and hints. If you are an IBM DB2 application developer who would like to exploit advanced features provided by DB2 to design and implement high quality applications, then this book is for you. This book assumes you have a basic understanding of the DB2 application development.

  14. The Application of the Transactions Control in DB2 with DB Query Analyzer%DB Query Analyzer中的事务管理在DB2中的应用

    Institute of Scientific and Technical Information of China (English)

    马根峰

    2011-01-01

    事务控制是数据库应用系统中的关键技术之一,概述了事务控制的概念以及《DB Query Analyzer》中的事务控制,以一个具体的实例,给出了《DB Query Analyzer》中的事务控制在DB2中的使用方法.

  15. lexiDB:a scalable corpus database management system

    OpenAIRE

    Coole, Matt; Rayson, Paul Edward; Mariani, John Amedeo

    2016-01-01

    lexiDB is a scalable corpus database management system designed to fulfill corpus linguistics retrieval queries on multi-billion-word multiply-annotated corpora. It is based on a distributed architecture that allows the system to scale out to support ever larger text collections. This paper presents an overview of the architecture behind lexiDB as well as a demonstration of its functionality. We present lexiDB's performance metrics based on the AWS (Amazon Web Services) infrastructure with tw...

  16. RavenDB 2.x beginner's guide

    CERN Document Server

    Tannir, Khaled

    2013-01-01

    Written in a friendly, example-driven Beginner's Guide format, there are plenty of step-by-step instructions and examples that are designed to help you get started with RavenDB. If you are a .NET developer, new to document-oriented databases, and you wish to learn how to build applications using NoSQL databases, then this book is for you. Experience with relational database systems will be helpful, but not necessary.

  17. Novel small-molecule AMPK activator orally exerts beneficial effects on diabetic db/db mice

    Energy Technology Data Exchange (ETDEWEB)

    Li, Yuan-Yuan; Yu, Li-Fang; Zhang, Li-Na; Qiu, Bei-Ying; Su, Ming-Bo; Wu, Fang; Chen, Da-Kai; Pang, Tao; Gu, Min; Zhang, Wei; Ma, Wei-Ping; Jiang, Hao-Wen; Li, Jing-Ya, E-mail: jyli@mail.shcnc.ac.cn; Nan, Fa-Jun, E-mail: fjnan@mail.shcnc.ac.cn; Li, Jia, E-mail: jli@mail.shcnc.ac.cn

    2013-12-01

    AMP-activated protein kinase (AMPK), which is a pivotal guardian of whole-body energy metabolism, has become an attractive therapeutic target for metabolic syndrome. Previously, using a homogeneous scintillation proximity assay, we identified the small-molecule AMPK activator C24 from an optimization based on the original allosteric activator PT1. In this paper, the AMPK activation mechanism of C24 and its potential beneficial effects on glucose and lipid metabolism on db/db mice were investigated. C24 allosterically stimulated inactive AMPK α subunit truncations and activated AMPK heterotrimers by antagonizing autoinhibition. In primary hepatocytes, C24 increased the phosphorylation of AMPK downstream target acetyl-CoA carboxylase dose-dependently without changing intracellular AMP/ATP ratio, indicating its allosteric activation in cells. Through activating AMPK, C24 decreased glucose output by down-regulating mRNA levels of phosphoenolpyruvate carboxykinase (PEPCK) and glucose-6-phosphatase (G6Pase) in primary hepatocytes. C24 also decreased the triglyceride and cholesterol contents in HepG2 cells. Due to its improved bioavailability, chronic oral treatment with multiple doses of C24 significantly reduced blood glucose and lipid levels in plasma, and improved the glucose tolerance of diabetic db/db mice. The hepatic transcriptional levels of PEPCK and G6Pase were reduced. These results demonstrate that this orally effective activator of AMPK represents a novel approach to the treatment of metabolic syndrome. - Highlights: • C24 activates AMPK through antagonizing autoinhibition within α subunit. • C24 activates AMPK in hepatocytes and decreases glucose output via AMPK. • C24 exerts beneficial effects on diabetic db/db mice. • C24 represents a novel therapeutic for treatment of metabolic syndrome.

  18. Bile acid sequestration reduces plasma glucose levels in db/db mice by increasing its metabolic clearance rate.

    Directory of Open Access Journals (Sweden)

    Maxi Meissner

    Full Text Available AIMS/HYPOTHESIS: Bile acid sequestrants (BAS reduce plasma glucose levels in type II diabetics and in murine models of diabetes but the mechanism herein is unknown. We hypothesized that sequestrant-induced changes in hepatic glucose metabolism would underlie reduced plasma glucose levels. Therefore, in vivo glucose metabolism was assessed in db/db mice on and off BAS using tracer methodology. METHODS: Lean and diabetic db/db mice were treated with 2% (wt/wt in diet Colesevelam HCl (BAS for 2 weeks. Parameters of in vivo glucose metabolism were assessed by infusing [U-(13C]-glucose, [2-(13C]-glycerol, [1-(2H]-galactose and paracetamol for 6 hours, followed by mass isotopologue distribution analysis, and related to metabolic parameters as well as gene expression patterns. RESULTS: Compared to lean mice, db/db mice displayed an almost 3-fold lower metabolic clearance rate of glucose (p = 0.0001, a ∼300% increased glucokinase flux (p = 0.001 and a ∼200% increased total hepatic glucose production rate (p = 0.0002. BAS treatment increased glucose metabolic clearance rate by ∼37% but had no effects on glucokinase flux nor total hepatic or endogenous glucose production. Strikingly, BAS-treated db/db mice displayed reduced long-chain acylcarnitine content in skeletal muscle (p = 0.0317 but not in liver (p = 0.189. Unexpectedly, BAS treatment increased hepatic FGF21 mRNA expression 2-fold in lean mice (p = 0.030 and 3-fold in db/db mice (p = 0.002. CONCLUSIONS/INTERPRETATION: BAS induced plasma glucose lowering in db/db mice by increasing metabolic clearance rate of glucose in peripheral tissues, which coincided with decreased skeletal muscle long-chain acylcarnitine content.

  19. Probucol inhibited Nox2 expression and attenuated podocyte injury in type 2 diabetic nephropathy of db/db mice.

    Science.gov (United States)

    Zhou, Guangyu; Wang, Yanqiu; He, Ping; Li, Detian

    2013-01-01

    The present study was conducted to investigate the effects of probucol on the progression of diabetic nephropathy and the underlying mechanism in type 2 diabetic db/db mice. Eight weeks db/db mice were treated with regular diet or probucol-containing diet (1%) for 12 weeks. Non-diabetic db/m mice were used as controls. We examined body weight, blood glucose, and urinary albumin. At 20 weeks, experimental mice were sacrificed and their blood and kidneys were extracted for the analysis of blood chemistry, kidney histology, oxidative stress marker, and podocyte marker. As a result, 24 h urinary albumin excretions were reduced after probucol treatment. There were improvements of extracellular matrix accumulation and fibronectin and collagen IV deposition in glomeruli in the probucol-treated db/db mice. The reduction of nephrin and the loss of podocytes were effectively prevented by probucol in db/db mice. Furthermore, probucol significantly decreased the production of thiobarbituric acid-reactive substances (TBARS), an index of reactive oxygen species (ROS) generation and down-regulated the expression of Nox2. Taken together, our findings support that probucol may have the potential to protect against type 2 diabetic nephropathy via amelioration of podocyte injury and reduction of oxidative stress.

  20. Comparison of gene expression changes induced by biguanides in db/db mice liver.

    Science.gov (United States)

    Heishi, Masayuki; Hayashi, Koji; Ichihara, Junji; Ishikawa, Hironori; Kawamura, Takao; Kanaoka, Masaharu; Taiji, Mutsuo; Kimura, Toru

    2008-08-01

    Large-scale clinical studies have shown that the biguanide drug metformin, widely used for type 2 diabetes, to be very safe. By contrast, another biguanide, phenformin, has been withdrawn from major markets because of a high incidence of serious adverse effects. The difference in mode of action between the two biguanides remains unclear. To gain insight into the different modes of action of the two drugs, we performed global gene expression profiling using the livers of obese diabetic db/db mice after a single administration of phenformin or metformin at levels sufficient to cause a significant reduction in blood glucose level. Metformin induced modest expression changes, including G6pc in the liver as previously reported. By contrast, phenformin caused changes in expression level of many additional genes. We used a knowledge-based bioinformatic analysis to study the effects of phenformin. Differentially expressed genes identified in this study constitute a large gene network, which may be related to cell death, inflammation or wound response. Our results suggest that the two biguanides show a similar hypoglycemic effect in db/db mice, but phenformin induces a greater stress on the liver even a short time after a single administration. These findings provide a novel insight into the cause of the relatively high occurrence of serious adverse effect after phenformin treatment.

  1. Dicty_cDB: Contig-U04669-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 1 ( DB758584 ) Apis mellifera head cDNA, RIKEN full-length enric... 42 7.7 1 ( CU624043 ) Theobroma cacao, ...mRNA sequence (KZ0ABE13YJ12FM1). 42 7.7 1 ( CU591562 ) Theobroma cacao, mRNA sequ

  2. Dicty_cDB: Contig-U04158-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available .9 1 ( DB911979 ) Idiosepius paradoxus cDNA, clone:Ip_aB_005_A09, 5... 44 8.9 1 ( CO418025 ) Mdfrt3032m24.y1.... 44 8.9 1 ( DN419404 ) LIB4215-059-R1-K1-H6 LIB4215 Canis lupus familiar... 44 8

  3. Dicty_cDB: Contig-U02962-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available m gastrula/neurula pCMVS... 44 2.2 1 ( FF450896 ) G178P60133RE10.T0 Acorn worm gastrula/neurula pCM... 44 2....2 1 ( DB913305 ) Idiosepius paradoxus cDNA, clone:Ip_aB_013_B17, 5... 40 4.4 2 (

  4. Carnosine enhances diabetic wound healing in the db/db mouse model of type 2 diabetes.

    Science.gov (United States)

    Ansurudeen, Ishrath; Sunkari, Vivekananda Gupta; Grünler, Jacob; Peters, Verena; Schmitt, Claus Peter; Catrina, Sergiu-Bogdan; Brismar, Kerstin; Forsberg, Elisabete Alcantara

    2012-07-01

    Diabetes mellitus (DM) is a progressive disorder with severe late complications. Normal wound healing involves a series of complex and well-orchestrated molecular events dictated by multiple factors. In diabetes, wound healing is grossly impaired due to defective, and dysregulated cellular and molecular events at all phases of wound healing resulting in chronic wounds that fail to heal. Carnosine, a dipeptide of alanine and histidine and an endogenous antioxidant is documented to accelerate healing of wounds and ulcers. However, not much is known about its role in wound healing in diabetes. Therefore, we studied the effect of carnosine in wound healing in db/db mice, a mice model of Type 2 DM. Six millimeter circular wounds were made in db/db mice and analyzed for wound healing every other day. Carnosine (100 mg/kg) was injected (I.P.) every day and also applied locally. Treatment with carnosine enhanced wound healing significantly, and wound tissue analysis showed increased expression of growth factors and cytokines genes involved in wound healing. In vitro studies with human dermal fibroblasts and microvascular-endothelial cells showed that carnosine increases cell viability in presence of high glucose. These effects, in addition to its known role as an antioxidant and a precursor for histamine synthesis, provide evidence for a possible therapeutic use of carnosine in diabetic wound healing.

  5. Dicty_cDB: Contig-U01479-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 1_A034 Shoot tip pitch canker susce... 50 0.19 1 ( DB880069 ) Populus nigra mRNA,...19 1 ( BZ114256 ) CH230-255O15.TV CHORI-230 Segment 2 Rattus norveg... 50 0.19 1 ( DR016697 ) STRS1_11_D08.g

  6. Comparing MongoDB to SQL Server, Replicated

    NARCIS (Netherlands)

    K. Azizi

    2014-01-01

    htmlabstractParker et al [1] studied the performance difference between MongoDB and Microsoft SQL Server on basis of a number of insert, update and select scenarios. As the result of their study, they conclude that MongoDB has got a better performance when it comes to insert, update and simple

  7. PRISMA/DB: A Parallel Main-Memory Relational DBMS

    NARCIS (Netherlands)

    Apers, Peter M.G.; Flokstra, Jan; van den Berg, Carel A.; Grefen, P.W.P.J.; Wilschut, A.N.; Kersten, Martin L.; van den Berg, C.A.

    1992-01-01

    PRISMA/DB, a full-fledged parallel, main memory relational database management system (DBMS) is described. PRISMA/DB's high performance is obtained by the use of parallelism for query processing and main memory storage of the entire database. A flexible architecture for experimenting with functional

  8. Klaim-DB: A Modeling Language for Distributed Database Applications

    DEFF Research Database (Denmark)

    Wu, Xi; Li, Ximeng; Lluch Lafuente, Alberto;

    2015-01-01

    We present the modelling language, Klaim-DB, for distributed database applications. Klaim-DB borrows the distributed nets of the coordination language Klaim but essentially re-incarnates the tuple spaces of Klaim as databases, and provides high-level language abstractions for the access and manip...

  9. Comparing MongoDB to SQL Server, Replicated

    NARCIS (Netherlands)

    Azizi, K.

    2014-01-01

    Parker et al [1] studied the performance difference between MongoDB and Microsoft SQL Server on basis of a number of insert, update and select scenarios. As the result of their study, they conclude that MongoDB has got a better performance when it comes to insert, update and simple queries. However,

  10. Database design and SQL for DB2

    CERN Document Server

    Cooper, James

    2013-01-01

    Thorough and updated coverage of database design and SQL for DB2 are the focus of this guide for the relational database-management system used on IBM i computer systems. Suitable for classroom instruction or self-study, this book explains the most widely used database language and the way that language is implemented on a variety of computer platforms. Topics covered include database concepts, SQL inquiries, web applications, and database security, and the material is reinforced by numerous illustrations, examples, and exercises.

  11. Swietenia mahagony extract shows agonistic activity to PPARγ and gives ameliorative effects on diabetic db/db mice

    Institute of Scientific and Technical Information of China (English)

    Dan-dan LI; Xu SHEN; Hua-liang JIANG; Jun-hua CHEN; Qing CHEN; Guo-wei LI; Jing CHEN; Jian-min YUE; Min-li CHEN; Xiao-ping WANG; Jian-hua SHEN

    2005-01-01

    Aim: To search the peroxisome proliferator-activated receptor γ (PPARγ) agonists from Swietenia mahagony extract (SmE) and observe the possible ameliorative effects of SmE on diabetic db/db mice. Methods: The PPARγ agonistic activity of SmE was screened by yeast-two hybrid system. The blood glucose levels of diabetic db/db mice were measured using a blood glucose level monitor and the data were statistically analyzed by NDST8.8W software. Results: By using the clinical drug rosiglitazone as a positive control, it was found that the PPARγ agonistic activity of SmE at a concentration of 50 μg/L was approximately half that of 35.7 μg/L (0.1 μmol/L) of rosiglitazone. At the dose of 1000 mg/kg, SmE remark ably decreased the blood glucose concentration of db/db mice from (15.26±2.98) to (7.58±2.20) mmol/L, and reduced the blood glucose levels by 55.49% compared with the control group (P<0.01). Conclusion: SmE shows agonistic activity to PPARγ and can ameliorate the blood glucose levels of diabetic db/db mice. SmE may be thus used as a potential agent for diabetes therapy.

  12. Neuronal histamine decreases fat accumulation and up-regulates UCP family in db/db obese mice

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    To examine anti-obesity and-diabetic effects of neuronal histamine especially in leptin resistant states, we investigated the effects of chronic central treatment with histamine on lipid, glucose and energy metabolism of db/db obese mice, which are genetically leptin receptor mutated mice. Chronic centrally treatment with histamine (0.05 μmol*g-1 body weight*d-1 for 7 days) decreased body weight, food intake in db/db obese mice, and decreased body fat weight, serum concentration of glucose compared with pair-fed db/db obese mice. Neuronal histamine also suppressed ob mRNA in the white adipose tissue (WAT), serum leptin and increased UCPs mRNA expression in brown adipose tissue (BAT) and in WAT compared with pair-fed controls. These above effects of the histamine were attenuated in these mice with combination of targeted disruption of the histamine H1 receptor gene. In conclusion, neuronal histamine can regulate body fat deposition, serum glucose, leptin, BAT and WAT UCPs expression even in leptin insensitive db/db obese mice.

  13. Diabetes (db/db mutation-induced endometrial epithelial lipoapoptosis: Ultrastructural and cytochemical analysis of reproductive tract atrophy

    Directory of Open Access Journals (Sweden)

    Garris David R

    2005-04-01

    Full Text Available Abstract Background The diabetes (db/db mutation in C57BL/KsJ mice promotes a progressive cytolipidemia within the endometrial epithelial (EE layer of the female reproductive tract which results in premature cellular and organ atrophy. The current studies focus on the ultrastructural and cytochemical changes which promote nuclear apoptosis and cytostructural disruption following the expression of endometrial hypercytolipidemia which promotes diabetes-associated organoinvolution and manifest infertility. Methods Control (normal:+/+ and diabetes (db/db genotype groups were prepared for high resolution light microscopic analysis of cytolipidemia and nuclear apoptosis (TUNEL-labeled 3'-DNA fragmentation indices and compared to the transmission electron (TEM microscopic analysis of endometrial tissue samples collected from 8–16 week-old groups. Results Compared to controls, db/db mutation expression induced a dramatic increase in EE cytolipid vacuole volume and density within the epithelial endometrial layer. TEM analysis revealed that cytolipid vacuole accumulations initially aggregated at the baso-polar regions of UEE cells in response to the systemic hyperglycemic/hypertriglyceridemic conditions which characterized the (db/db groups. Progressive cytoplasmic movement of the lipid pools into perinuclear compartments of affected EE cells induced nuclear isolation from organelles that were displaced towards peripheral cytoplasmic compartments. Cytochemical analysis of lipid vacuole accumulations indicated attraction towards, and incorporation within, the nuclear envelope of hyperlipidemic cells. Co-localization of nuclear apoptotic 3'-DNA fragments within identified hyperlipidemic EE cells was coincident with the cytochemical and ultrastructural identification of lipid penetration through the nuclear envelope in db/db mutants. Conclusion These results are the first cytochemical indication that the metabolic disturbances in db/db mutants which

  14. Generalized Soft-and-Hard/DB Boundary

    CERN Document Server

    Lindell, Ismo V

    2016-01-01

    A novel class of boundary conditions is introduced as a generalization of the previously defined class of soft-and-hard/DB (SHDB) boundary conditions. It is shown that the conditions for the generalized soft-and-hard/DB (GSHDB) boundary arise most naturally in a simple and straightforward manner by applying four-dimensional differential-form and dyadic formalism. At a given boundary surface, the GSHDB conditions are governed by two one-forms. In terms of Gibbsian 3D vector and dyadic algebra the GSHDB conditions are defined in terms of two vectors tangential to the boundary surface and two scalars. Considering plane-wave reflection from the GSHDB boundary, for two eigenpolarizations, the GSHDB boundary can be replaced by the PEC or PMC boundary. Special attention is paid to the problem of plane waves matched to the GSHDB boundary, defined by a 2D dispersion equation for the wave vector, making the reflection dyadic indeterminate. Examples of dispersion curves for various chosen parameters of the GSHDB boundar...

  15. Soy Leaf Extract Containing Kaempferol Glycosides and Pheophorbides Improves Glucose Homeostasis by Enhancing Pancreatic β-Cell Function and Suppressing Hepatic Lipid Accumulation in db/db Mice.

    Science.gov (United States)

    Li, Hua; Ji, Hyeon-Seon; Kang, Ji-Hyun; Shin, Dong-Ha; Park, Ho-Yong; Choi, Myung-Sook; Lee, Chul-Ho; Lee, In-Kyung; Yun, Bong-Sik; Jeong, Tae-Sook

    2015-08-19

    This study investigated the molecular mechanisms underlying the antidiabetic effect of an ethanol extract of soy leaves (ESL) in db/db mice. Control groups (db/+ and db/db) were fed a normal diet (ND), whereas the db/db-ESL group was fed ND with 1% ESL for 8 weeks. Dietary ESL improved glucose tolerance and lowered plasma glucose, glycated hemoglobin, HOMA-IR, and triglyceride levels. The pancreatic insulin content of the db/db-ESL group was significantly greater than that of the db/db group. ESL supplementation altered pancreatic IRS1, IRS2, Pdx1, Ngn3, Pax4, Ins1, Ins2, and FoxO1 expression. Furthermore, ESL suppressed lipid accumulation and increased glucokinase activity in the liver. ESL primarily contained kaempferol glycosides and pheophorbides. Kaempferol, an aglycone of kaempferol glycosides, improved β-cell proliferation through IRS2-related FoxO1 signaling, whereas pheophorbide a, a product of chlorophyll breakdown, improved insulin secretion and β-cell proliferation through IRS1-related signaling with protein kinase A in MIN6 cells. ESL effectively regulates glucose homeostasis by enhancing IRS-mediated β-cell insulin signaling and suppressing SREBP-1-mediated hepatic lipid accumulation in db/db mice.

  16. PPT-DB: the protein property prediction and testing database.

    Science.gov (United States)

    Wishart, David S; Arndt, David; Berjanskii, Mark; Guo, An Chi; Shi, Yi; Shrivastava, Savita; Zhou, Jianjun; Zhou, You; Lin, Guohui

    2008-01-01

    The protein property prediction and testing database (PPT-DB) is a database housing nearly 30 carefully curated databases, each of which contains commonly predicted protein property information. These properties include both structural (i.e. secondary structure, contact order, disulfide pairing) and dynamic (i.e. order parameters, B-factors, folding rates) features that have been measured, derived or tabulated from a variety of sources. PPT-DB is designed to serve two purposes. First it is intended to serve as a centralized, up-to-date, freely downloadable and easily queried repository of predictable or 'derived' protein property data. In this role, PPT-DB can serve as a one-stop, fully standardized repository for developers to obtain the required training, testing and validation data needed for almost any kind of protein property prediction program they may wish to create. The second role that PPT-DB can play is as a tool for homology-based protein property prediction. Users may query PPT-DB with a sequence of interest and have a specific property predicted using a sequence similarity search against PPT-DB's extensive collection of proteins with known properties. PPT-DB exploits the well-known fact that protein structure and dynamic properties are highly conserved between homologous proteins. Predictions derived from PPT-DB's similarity searches are typically 85-95% correct (for categorical predictions, such as secondary structure) or exhibit correlations of >0.80 (for numeric predictions, such as accessible surface area). This performance is 10-20% better than what is typically obtained from standard 'ab initio' predictions. PPT-DB, its prediction utilities and all of its contents are available at http://www.pptdb.ca.

  17. Red raspberry (Rubus idaeus L.) intake decreases oxidative stress in obese diabetic (db/db) mice.

    Science.gov (United States)

    Noratto, Giuliana D; Chew, Boon P; Atienza, Liezl M

    2017-07-15

    Red raspberry fruit intake was investigated on obese diabetic (db/db) mice for 8weeks. Animals fed isocaloric diets (5.3% freeze-dried raspberry, or control) were assessed for obesity-diabetes-disease risk biomarkers. Results showed that raspberry intake improved antioxidant status and lessened plasma interleukin (IL)-6 (0.3-fold of control, p0.05). Plasma levels of total cholesterol (T-CHL), low density lipoprotein-cholesterol (LDL-CHL), and resistin were higher in the raspberry group. Overall, the enhanced detoxifying cell defenses exerted by raspberry intake might be due to its polyphenolics and fibre. This study demonstrates in vivo that raspberry intake, at a dose that can be achieved by human consumption, might protect against diabetes-induced oxidative stress.

  18. CouchDB NoSQL databáze

    OpenAIRE

    2016-01-01

    This bachelor work deals with CouchDB database system. The main objective is to characterize the basic features and architecture of CouchDB and to show a practical example of how to work with that database system from two perspectives. To achieve that aim were studied official documents and other literature, providing a sufficient amount of information to write this. The contribution of this work lies in the fact that it serves as a guide for CouchDB, especially for Czech readers, because in ...

  19. Molecular signatures database (MSigDB) 3.0.

    Science.gov (United States)

    Liberzon, Arthur; Subramanian, Aravind; Pinchback, Reid; Thorvaldsdóttir, Helga; Tamayo, Pablo; Mesirov, Jill P

    2011-06-15

    Well-annotated gene sets representing the universe of the biological processes are critical for meaningful and insightful interpretation of large-scale genomic data. The Molecular Signatures Database (MSigDB) is one of the most widely used repositories of such sets. We report the availability of a new version of the database, MSigDB 3.0, with over 6700 gene sets, a complete revision of the collection of canonical pathways and experimental signatures from publications, enhanced annotations and upgrades to the web site. MSigDB is freely available for non-commercial use at http://www.broadinstitute.org/msigdb.

  20. Dicty_cDB: Contig-U00745-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available erosum cDNA clone 6... 58 3e-04 1 ( CN216337 ) 30227 Suspension culture Solanum t...R, mRNA seque... 58 3e-04 1 ( AC233065 ) Solanum lycopersicum chromosome 9 clone C09SLe001... 58 3e-04 1 ( DN938633 ) 30227.2 Suspens...ion culture Solanum tuberosum cDNA... 58 3e-04 1 ( DB702841 ) Solanum lycopersicum

  1. Dicty_cDB: Contig-U13694-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available N142696 ) WOUND1_11_D06.g1_A002 Wounded leaves Sorghum bico... 42 0.001 2 ( DB861...0.001 2 ( CN143316 ) WOUND1_15_B04.g1_A002 Wounded leaves Sorghum bico... 42 0.00...ssue Osmerus mo... 42 0.001 2 ( CN150824 ) WOUND1_71_E05.g1_A002 Wounded leaves Sorghum bico... 42 0.001 2 (

  2. The PKD inhibitor CID755673 enhances cardiac function in diabetic db/db mice.

    Directory of Open Access Journals (Sweden)

    Kylie Venardos

    Full Text Available The development of diabetic cardiomyopathy is a key contributor to heart failure and mortality in obesity and type 2 diabetes (T2D. Current therapeutic interventions for T2D have limited impact on the development of diabetic cardiomyopathy. Clearly, new therapies are urgently needed. A potential therapeutic target is protein kinase D (PKD, which is activated by metabolic insults and implicated in the regulation of cardiac metabolism, contractility and hypertrophy. We therefore hypothesised that PKD inhibition would enhance cardiac function in T2D mice. We first validated the obese and T2D db/db mouse as a model of early stage diabetic cardiomyopathy, which was characterised by both diastolic and systolic dysfunction, without overt alterations in left ventricular morphology. These functional characteristics were also associated with increased PKD2 phosphorylation in the fed state and a gene expression signature characteristic of PKD activation. Acute administration of the PKD inhibitor CID755673 to normal mice reduced both PKD1 and 2 phosphorylation in a time and dose-dependent manner. Chronic CID755673 administration to T2D db/db mice for two weeks reduced expression of the gene expression signature of PKD activation, enhanced indices of both diastolic and systolic left ventricular function and was associated with reduced heart weight. These alterations in cardiac function were independent of changes in glucose homeostasis, insulin action and body composition. These findings suggest that PKD inhibition could be an effective strategy to enhance heart function in obese and diabetic patients and provide an impetus for further mechanistic investigations into the role of PKD in diabetic cardiomyopathy.

  3. Salvianolic Acid B Ameliorates Hyperglycemia and Dyslipidemia in db/db Mice through the AMPK Pathway

    Directory of Open Access Journals (Sweden)

    Ming-Qing Huang

    2016-12-01

    Full Text Available Background/Aims: Salvianolic acid B (Sal B, a major polyphenolic compound of Salvia miltiorrhiza Bunge, has been shown to possess potential antidiabetic activities. However, the action mechanism of SalB in type 2 diabetes has not been investigated extensively. The present study was designed to investigate the effects of Sal B on diabetes-related metabolic changes in a spontaneous model of type 2 diabetes, as well as its potential molecular mechanism. Methods: Male C57BL/KsJ-db/db mice were orally treated with Sal B (50 and 100 mg/kg or metformin (positive drug, 300 mg/kg for 6 weeks. Results: Both doses of Sal B significantly decreased fasting blood glucose, serum insulin, triglyceride and free fatty acid levels, reduced hepatic gluconeogenic gene expression and improved insulin intolerance in db/db mice. High dose Sal B also significantly improved glucose intolerance, increased hepatic glycolytic gene expression and muscle glycogen content, and ameliorated histopathological alterations of pancreas, similar to metformin. Sal B treatment resulted in increased phosphorylated AMP-activated protein kinase (p-AMPK protein expression in skeletal muscle and liver, increased glucose transporter 4 (GLUT4 and glycogen synthase protein expressions in skeletal muscle, and increased peroxisome proliferator-activated receptor alpha (PPARα and phosphorylated acetyl CoA carboxylase (p-ACC protein expressions in liver. Conclusion: Our data suggest that Sal B displays beneficial effects in the prevention and treatment of type 2 diabetes at least in part via modulation of the AMPK pathway.

  4. Oral green tea catechins transiently lower plasma glucose concentrations in female db/db mice.

    Science.gov (United States)

    Wein, Silvia; Schrader, Eva; Rimbach, Gerald; Wolffram, Siegfried

    2013-04-01

    Polyphenols, including green tea catechins, are secondary plant compounds often discussed in the context of health-promoting potential. Evidence for such effects is mainly derived from epidemiological and cell culture studies. The aim of the present study was to investigate antidiabetic, antiadipogenic, and anti-inflammatory effects at nonpharmacological doses in an obese diabetic mouse model that exerts early relevant clinical signs of non-insulin-dependent diabetes mellitus. Female db/db mice received a flavonoid-poor diet either without additive, with rosiglitazone (RSG, 0.02 g/kg diet), or with green tea extract (low-dose green tea extract [LGTE] and high-dose green tea extract [HGTE], 0.1 and 1 g/kg diet). Food and water were freely available. The body weight was monitored weekly. Blood was sampled (12-h fasted) from the tail vein on day 28 and analyzed for glucose, cholesterol, triacylglycerol, nonesterified fatty acids, insulin, adiponectin, and soluble intercellular adhesion molecule-1 (sICAM-1). Blood glucose was also analyzed on day 14. Furthermore, sICAM-1 release was investigated in tumor necrosis factor alpha-stimulated EAhy926 cells. After 14 days, fasting glycemia was improved by RSG or HGTE supplementation compared to controls. However, at the end of the study (day 28), only RSG exhibited glucose-lowering effects and induced plasma adiponectin concentrations, paralleled by higher body weight gain and reduced periuterine fat pads compared to controls. However, only GTE treatment reduced sICAM-1 release in vitro and in vivo. Nonpharmacological HGTE supplementation in db/db mice caused (1) no adiponectin-inducing or antiadipogenic effects, (2) reduced sICAM-1 release, thereby potentially exerting anti-inflammatory effects in the progressive diabetic state, and (3) a transient improvement in glycemia.

  5. Impaired Corpus Cavernosum Relaxation Is Accompanied by Increased Oxidative Stress and Up-Regulation of the Rho-Kinase Pathway in Diabetic (Db/Db) Mice.

    Science.gov (United States)

    Priviero, Fernanda B M; Toque, Haroldo A F; Nunes, Kenia Pedrosa; Priolli, Denise G; Teixeira, Cleber E; Webb, R Clinton

    2016-01-01

    Basal release of nitric oxide from endothelial cells modulates contractile activity in the corpus cavernosum via inhibition of the RhoA/Rho-kinase signaling pathway. We aimed to investigate nitric oxide bioavailability, oxidative stress and the Rho-kinase pathway in the relaxation of the corpus cavernosum of an obese and diabetic model of mice (db/db mice). We hypothesized that in db/db mice impaired relaxation induced by Rho-kinase inhibitor is accompanied by diminished NO bioavailability, increased oxidative stress and upregulation of the RhoA/Rho-kinase signalling pathway. Cavernosal strips from male lean and non-diabetic db/+ and db/db mice were mounted in myographs and isometric force in response to Rho-kinase inhibitor Y-27632 was recorded. Enzyme activity and protein expression of oxidative stress markers and key molecules of the RhoA/Rho-kinase pathway were analyzed. The Rho-kinase inhibitor Y-27632 concentration-dependently caused corpus cavernosum relaxation and inhibited cavernosal contractions. Nonetheless, a rightward shift in the curves obtained in corpus cavernosum of db/db mice was observed. Compared to db/+, this strain presented increased active RhoA, higher MYPT-1 phosphorylation stimulated by phenylephrine, and increased expression of ROKα and Rho-GEFs. Further, we observed normal expression of endothelial and neuronal NOS in corpus cavernosum of db/db mice. However, nitrate/nitrate (NOx) levels were diminished, suggesting decreased NO bioavailability. We measured the oxidant status and observed increased lipid peroxidation, with decreased SOD activity and expression. In conclusion, our data demonstrate that in db/db mice, upregulation of the RhoA/Rho-kinase signalling pathway was accompanied by decreased NO bioavailability and increased oxidative stress contributing to impaired relaxation of the corpus cavermosum of db/db mice.

  6. Impaired Corpus Cavernosum Relaxation Is Accompanied by Increased Oxidative Stress and Up-Regulation of the Rho-Kinase Pathway in Diabetic (Db/Db Mice.

    Directory of Open Access Journals (Sweden)

    Fernanda B M Priviero

    Full Text Available Basal release of nitric oxide from endothelial cells modulates contractile activity in the corpus cavernosum via inhibition of the RhoA/Rho-kinase signaling pathway. We aimed to investigate nitric oxide bioavailability, oxidative stress and the Rho-kinase pathway in the relaxation of the corpus cavernosum of an obese and diabetic model of mice (db/db mice. We hypothesized that in db/db mice impaired relaxation induced by Rho-kinase inhibitor is accompanied by diminished NO bioavailability, increased oxidative stress and upregulation of the RhoA/Rho-kinase signalling pathway. Cavernosal strips from male lean and non-diabetic db/+ and db/db mice were mounted in myographs and isometric force in response to Rho-kinase inhibitor Y-27632 was recorded. Enzyme activity and protein expression of oxidative stress markers and key molecules of the RhoA/Rho-kinase pathway were analyzed. The Rho-kinase inhibitor Y-27632 concentration-dependently caused corpus cavernosum relaxation and inhibited cavernosal contractions. Nonetheless, a rightward shift in the curves obtained in corpus cavernosum of db/db mice was observed. Compared to db/+, this strain presented increased active RhoA, higher MYPT-1 phosphorylation stimulated by phenylephrine, and increased expression of ROKα and Rho-GEFs. Further, we observed normal expression of endothelial and neuronal NOS in corpus cavernosum of db/db mice. However, nitrate/nitrate (NOx levels were diminished, suggesting decreased NO bioavailability. We measured the oxidant status and observed increased lipid peroxidation, with decreased SOD activity and expression. In conclusion, our data demonstrate that in db/db mice, upregulation of the RhoA/Rho-kinase signalling pathway was accompanied by decreased NO bioavailability and increased oxidative stress contributing to impaired relaxation of the corpus cavermosum of db/db mice.

  7. The business value of DB2 for z/OS IBM DB2 analytics accelerator and optimizer

    CERN Document Server

    Campbell, John; Li, Ruiping; Parekh, Surekha; Purcell, Terry

    2013-01-01

    Celebrating the 30th anniversary of the first release of DB2, this book highlights the important milestones, capabilities, and impacts of the database management software for IBM's mainframe operating system. Special focus is given to IBM DB2 Analytics Accelerator, covering the key design and operational aspects that enable IBM DB2 for z/OS clients to benefit from faster performance, reduced CPU usage, and lower costs. The second half of the book discusses performance enhancements and cost-saving measures in the version 10 release and is rich with hints and tips for a successful upgrade. A spe

  8. SolveDB: Integrating Optimization Problem Solvers Into SQL Databases

    DEFF Research Database (Denmark)

    Siksnys, Laurynas; Pedersen, Torben Bach

    2016-01-01

    Many real-world decision problems involve solving optimization problems based on data in an SQL database. Traditionally, solving such problems requires combining a DBMS with optimization software packages for each required class of problems (e.g. linear and constraint programming) -- leading...... to workflows that are cumbersome, complex, inefficient, and error-prone. In this paper, we present SolveDB - a DBMS for optimization applications. SolveDB supports solvers for different problem classes and offers seamless data management and optimization problem solving in a pure SQL-based setting. This allows...... for much simpler and more effective solutions of database-based optimization problems. SolveDB is based on the 3-level ANSI/SPARC architecture and allows formulating, solving, and analysing solutions of optimization problems using a single so-called solve query. SolveDB provides (1) an SQL-based syntax...

  9. StarDB: a large-scale DBMS for strings

    KAUST Repository

    Sahli, Majed

    2015-08-01

    Strings and applications using them are proliferating in science and business. Currently, strings are stored in file systems and processed using ad-hoc procedural code. Existing techniques are not flexible and cannot efficiently handle complex queries or large datasets. In this paper, we demonstrate StarDB, a distributed database system for analytics on strings. StarDB hides data and system complexities and allows users to focus on analytics. It uses a comprehensive set of parallel string operations and provides a declarative query language to solve complex queries. StarDB automatically tunes itself and runs with over 90% efficiency on supercomputers, public clouds, clusters, and workstations. We test StarDB using real datasets that are 2 orders of magnitude larger than the datasets reported by previous works.

  10. Eukaryotic Pathogen Database Resources (EuPathDB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — EuPathDB Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Diseases is a portal for accessing genomic-scale datasets associated with...

  11. Download - Plabrain DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...escription Download License Update History of This Database Site Policy | Contact Us Download - Plabrain DB | LSDB Archive ...

  12. dbSNP: the NCBI database of genetic variation.

    Science.gov (United States)

    Sherry, S T; Ward, M H; Kholodov, M; Baker, J; Phan, L; Smigielski, E M; Sirotkin, K

    2001-01-01

    In response to a need for a general catalog of genome variation to address the large-scale sampling designs required by association studies, gene mapping and evolutionary biology, the National Center for Biotechnology Information (NCBI) has established the dbSNP database [S.T.Sherry, M.Ward and K. Sirotkin (1999) Genome Res., 9, 677-679]. Submissions to dbSNP will be integrated with other sources of information at NCBI such as GenBank, PubMed, LocusLink and the Human Genome Project data. The complete contents of dbSNP are available to the public at website: http://www.ncbi.nlm.nih.gov/SNP. The complete contents of dbSNP can also be downloaded in multiple formats via anonymous FTP at ftp://ncbi.nlm.nih.gov/snp/.

  13. GigaDB: announcing the GigaScience database

    Directory of Open Access Journals (Sweden)

    Sneddon Tam P

    2012-07-01

    Full Text Available Abstract With the launch of GigaScience journal, here we provide insight into the accompanying database GigaDB, which allows the integration of manuscript publication with supporting data and tools. Reinforcing and upholding GigaScience’s goals to promote open-data and reproducibility of research, GigaDB also aims to provide a home, when a suitable public repository does not exist, for the supporting data or tools featured in the journal and beyond.

  14. GigaDB: announcing the GigaScience database.

    Science.gov (United States)

    Sneddon, Tam P; Li, Peter; Edmunds, Scott C

    2012-07-12

    With the launch of GigaScience journal, here we provide insight into the accompanying database GigaDB, which allows the integration of manuscript publication with supporting data and tools. Reinforcing and upholding GigaScience's goals to promote open-data and reproducibility of research, GigaDB also aims to provide a home, when a suitable public repository does not exist, for the supporting data or tools featured in the journal and beyond.

  15. DB2 10.1 fundamentals certification study guide

    CERN Document Server

    Sanders, Roger E

    2014-01-01

    Beginning with an explanation of the certification process and working through fundamental exam objectives, this guide gives test-takers all they need to know to pass IBM's DB2 10.1 Fundamentals certification exam (Exam 610). All the subjects covered on the exam are included: planning, security, data concurrency, working with databases and database objects, working with data using SQL and XQuery, working with DB2 tables, views, and indexes-and more. The book concludes with an

  16. LocSigDB: a database of protein localization signals

    OpenAIRE

    Negi, Simarjeet; Pandey, Sanjit; Srinivasan, Satish M; Mohammed, Akram; Guda, Chittibabu

    2015-01-01

    LocSigDB (http://genome.unmc.edu/LocSigDB/) is a manually curated database of experimental protein localization signals for eight distinct subcellular locations; primarily in a eukaryotic cell with brief coverage of bacterial proteins. Proteins must be localized at their appropriate subcellular compartment to perform their desired function. Mislocalization of proteins to unintended locations is a causative factor for many human diseases; therefore, collection of known sorting signals will hel...

  17. LocSigDB: a database of protein localization signals.

    Science.gov (United States)

    Negi, Simarjeet; Pandey, Sanjit; Srinivasan, Satish M; Mohammed, Akram; Guda, Chittibabu

    2015-01-01

    LocSigDB (http://genome.unmc.edu/LocSigDB/) is a manually curated database of experimental protein localization signals for eight distinct subcellular locations; primarily in a eukaryotic cell with brief coverage of bacterial proteins. Proteins must be localized at their appropriate subcellular compartment to perform their desired function. Mislocalization of proteins to unintended locations is a causative factor for many human diseases; therefore, collection of known sorting signals will help support many important areas of biomedical research. By performing an extensive literature study, we compiled a collection of 533 experimentally determined localization signals, along with the proteins that harbor such signals. Each signal in the LocSigDB is annotated with its localization, source, PubMed references and is linked to the proteins in UniProt database along with the organism information that contain the same amino acid pattern as the given signal. From LocSigDB webserver, users can download the whole database or browse/search for data using an intuitive query interface. To date, LocSigDB is the most comprehensive compendium of protein localization signals for eight distinct subcellular locations. Database URL: http://genome.unmc.edu/LocSigDB/

  18. Jicama (Pachyrhizus erosus) extract increases insulin sensitivity and regulates hepatic glucose in C57BL/Ksj-db/db mice

    OpenAIRE

    Park, Chan Joo; Lee, Hyun-Ah; Han, Ji-Sook

    2015-01-01

    This study investigated the effect of jicama extract on hyperglycemia and insulin sensitivity in an animal model of type 2 diabetes. Male C57BL/Ksj-db/db mice were divided into groups subsequently fed a regular diet (controls), or diet supplemented with jicama extract, and rosiglitazone. After 6 weeks, blood levels of glucose and glycosylated hemoglobin were significantly lower in animals administered the jicama extract than the control group. Additionally, glucose and insulin tolerance tests...

  19. DB2 9 for Linux, Unix, and Windows database administration certification study guide

    CERN Document Server

    Sanders, Roger E

    2007-01-01

    In DB2 9 for Linux, UNIX, and Windows Database Administration Certification Study Guide, Roger E. Sanders-one of the world's leading DB2 authors and an active participant in the development of IBM's DB2 certification exams-covers everything a reader needs to know to pass the DB2 9 UDB DBA Certification Test (731).This comprehensive study guide steps you through all of the topics that are covered on the test, including server management, data placement, database access, analyzing DB2 activity, DB2 utilities, high availability, security, and much more. Each chapter contains an extensive set of p

  20. Pluronic L-81 ameliorates diabetic symptoms in db/db mice through transcriptional regulation of microsomal triglyceride transfer protein

    Institute of Scientific and Technical Information of China (English)

    Wo-Shing Au; Li-Wei Lu; Sidney Tam; Otis King Hung Ko; Billy KC Chow; Ming-Liang He; Samuel S Ng; Chung-Man Yeung; Ching-Chiu Liu; Hsiang-Fu Kung; Marie C Lin

    2009-01-01

    AIM: To test whether oral L-81 treatment could improve the condition of mice with diabetes and to investigate how L-81 regulates microsomal triglyceride transfer protein (MTP) activity in the liver.METHODS: Genetically diabetic (db /db ) mice were fed on chow supplemented with or without L-81 for 4 wk. The body weight, plasma glucose level, plasma lipid profile, and adipocyte volume of the db /db mice were assessed after treatment. Toxicity of L-81 was also evaluated. To understand the molecular mechanism,HepG2 cells were treated with L-81 and the effects on apolipoprotein B (apoB) secretion and mRNA level of the MTP gene were assessed. RESULTS: Treatment of db /db mice with L-81 significantly reduced and nearly normalized their body weight, hyperphagia and polydipsia. L-81 also markedly decreased the fasting plasma glucose level, improved glucose tolerance, and attenuated the elevated levels of plasma cholesterol and triglyceride. At the effective dosage, little toxicity was observed. Treatment of HepG2 cells with L-81 not only inhibited apoB secretion, but also significantly decreased the mRNA level of the MTP gene. Similar to the action of insulin, L-81 exerted its effect on the MTP promoter. CONCLUSION: L-81 represents a promising candidate in the development of a selective insulin-mimetic molecule and an anti-diabetic agent.

  1. Anti-diabetic effect of amorphastilbol through PPARα/γ dual activation in db/db mice

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Woojung; Ham, Jungyeob; Kwon, Hak Cheol [Natural Medicine Center, KIST Gangneung Institute, Gangneung 210-340 (Korea, Republic of); Kim, Yong Kee, E-mail: yksnbk@sookmyung.ac.kr [College of Pharmacy, Sookmyung Women’s University, Seoul 140-742 (Korea, Republic of); Kim, Su-Nam, E-mail: snkim@kist.re.kr [Natural Medicine Center, KIST Gangneung Institute, Gangneung 210-340 (Korea, Republic of)

    2013-03-01

    Highlights: ► Amorphastilbol stimulates the transcriptional activities of both PPARα and PPARγ. ► Amorphastilbol improves glucose and lipid impairment in db/db mice. ► There are no side effects, such as hepatomegaly, in amorphastilbol-treated mice. ► Amorphastilbol can be used as a potential therapeutic agent against T2DM. - Abstract: Peroxisome proliferator-activated receptors (PPARs) have been considered as desirable targets for metabolic syndrome treatments, even though their specific agonists have several side effects, including body weight gain, edema, and tissue failure. The effects of amorphastilbol (APH) on glucose- and lipid metabolism were investigated with in vitro 3T3-L1 adipocyte systems and in vivo db/db mice model. APH selectively stimulates the transcriptional activities of both PPARα and PPARγ, which are able to enhance fatty acid oxidation and glucose utilization. Furthermore, APH improves glucose and lipid impairment in db/db mice. More importantly, there are no significant side effects, such as weight gain or hepatomegaly, in APH-treated animals, implying that APH do not adversely affect liver or lipid metabolism. All our data suggest that APH can be used as potential therapeutic agents against type 2 diabetes and related metabolic disorders, including obesity, by enhancing glucose and lipid metabolism.

  2. Pitavastatin suppresses diethylnitrosamine-induced liver preneoplasms in male C57BL/KsJ-db/db obese mice

    Directory of Open Access Journals (Sweden)

    Kochi Takahiro

    2011-06-01

    Full Text Available Abstract Background Obesity and related metabolic abnormalities, including inflammation and lipid accumulation in the liver, play a role in liver carcinogenesis. Adipocytokine imbalances, such as decreased serum adiponectin levels, are also involved in obesity-related liver tumorigenesis. In the present study, we examined the effects of pitavastatin - a drug used for the treatment of hyperlipidemia - on the development of diethylnitrosamine (DEN-induced liver preneoplastic lesions in C57BL/KsJ-db/db (db/db obese mice. Methods Male db/db mice were administered tap water containing 40 ppm DEN for 2 weeks and were subsequently fed a diet containing 1 ppm or 10 ppm pitavastatin for 14 weeks. Results At sacrifice, feeding with 10 ppm pitavastatin significantly inhibited the development of hepatic premalignant lesions, foci of cellular alteration, as compared to that in the untreated group by inducing apoptosis, but inhibiting cell proliferation. Pitavastatin improved liver steatosis and activated the AMPK-α protein in the liver. It also decreased free fatty acid and aminotransferases levels, while increasing adiponectin levels in the serum. The serum levels of tumor necrosis factor (TNF-α and the expression of TNF-α and interleukin-6 mRNAs in the liver were decreased by pitavastatin treatment, suggesting attenuation of the chronic inflammation induced by excess fat deposition. Conclusions Pitavastatin is effective in inhibiting the early phase of obesity-related liver tumorigenesis and, therefore, may be useful in the chemoprevention of liver cancer in obese individuals.

  3. DPP-4 inhibitor des-F-sitagliptin treatment increased insulin exocytosis from db/db mice {beta} cells

    Energy Technology Data Exchange (ETDEWEB)

    Nagamatsu, Shinya, E-mail: shinya@ks.kyorin-u.ac.jp [Department of Biochemistry, Kyorin University School of Medicine, Mitaka, Tokyo 181-8611 (Japan); Ohara-Imaizumi, Mica; Nakamichi, Yoko; Aoyagi, Kyota; Nishiwaki, Chiyono [Department of Biochemistry, Kyorin University School of Medicine, Mitaka, Tokyo 181-8611 (Japan)

    2011-09-09

    Highlights: {yields} Anti-diabetic new drug, DPP-4 inhibitor, can affect the insulin exocytosis. {yields} DPP-4 inhibitor treatment altered syntaxin 1 expression. {yields} Treatment of db/db mice with DPP-4 inhibitor increased insulin release. -- Abstract: Incretin promotes insulin secretion acutely. Recently, orally-administered DPP-4 inhibitors represent a new class of anti-hyperglycemic agents. Indeed, inhibitors of dipeptidyl peptidase-IV (DPP-4), sitagliptin, has just begun to be widely used as therapeutics for type 2 diabetes. However, the effects of sitagliptin-treatment on insulin exocytosis from single {beta}-cells are yet unknown. We therefore investigated how sitagliptin-treatment in db/db mice affects insulin exocytosis by treating db/db mice with des-F-sitagliptin for 2 weeks. Perfusion studies showed that 2 weeks-sitagliptin treatment potentiated insulin secretion. We then analyzed insulin granule motion and SNARE protein, syntaxin 1, by TIRF imaging system. TIRF imaging of insulin exocytosis showed the increased number of docked insulin granules and increased fusion events from them during first-phase release. In accord with insulin exocytosis data, des-F-sitagliptin-treatment increased the number of syntaxin 1 clusters on the plasma membrane. Thus, our data demonstrated that 2-weeks des-F-sitagliptin-treatment increased the fusion events of insulin granules, probably via increased number of docked insulin granules and that of syntaxin 1 clusters.

  4. Qing-Hua Granule induces GLP-1 secretion via bitter taste receptor in db/db mice.

    Science.gov (United States)

    Li, Junyan; Xu, Jie; Hou, Ruifang; Jin, Xin; Wang, Jingyi; Yang, Na; Yang, Li; Liu, Li; Tao, Feng; Lu, Hao

    2017-05-01

    Qing-Hua Granule (QHG), the modified formulation of a classical Chinese prescription named Gegen Qinlian Decoction, was clinically employed to treat type 2 diabetes mellitus (T2DM) through regulation of glucagon-like peptide-1 (GLP-1). However, the potential mechanism is unknown. We investigate whether QHG induces GLP-1 secretion via activation of bitter taste receptor (TAS2R) pathway in the gastrointestinal tract of db/db mice. The db/db mice were intragastrically (i.g.) administered QHG (low/medium/high dose) once daily for 8 weeks. GLP-1 secretion was evaluated. The bitter receptor signaling pathway, which regulates GLP-1 secretion, including TAS2R5 (a subtype of TAS2R), α-gustducin (Gαgust), 1-phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta-2 (PLCβ2), transient receptor potential cation channel subfamily M member 5 (TRPM5), was assessed by quantitative real-time polymerase chain reaction (qRT-PCR), Western blot and immunohistochemistry (IHC). The biochemical observations of ileum and pancreas tissue were detected histopathologically. Acquity Ultra Performance LCTM - Micromass ZQ 2000 (UPLC-MS) was used for the phytochemical analysis. QHG exhibited significant and dose-dependent effect on GLP-1 secretion in db/db mice, along with significant up-regulation of TAS2R5 mRNA level and activation of TAS2R pathway (ptaste receptor pathway. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  5. The idiosyncrasies of (BBIM-alkane)DB30C10 MIMs

    Science.gov (United States)

    Ghosh, Sabari; Chaudhuri, Tandrima; Padmanaban, E.; Mukhopadhyay, Chhanda

    2015-10-01

    In this present study we explore the mechanically interlocked molecules (MIMs) resulting from the combination of the BBIM(bis-benzimidazolium)-alkane systems with DB30C10 (Dibenzo-30-crown-10) in solvent acetonitrile. The (BBIM-alkane)DB30C10 systems chosen for the study are (BBIM)DB30C10, (BBIM-methane)DB30C10, (BBIM-ethane)DB30C10, (BBIM-propane)DB30C10 and (BBIM-butane)DB30C10. 1H NMR, 2D-NMR (COSY and NOESY), Monte Carlo calculations and HRMS have been done on the studied assemblies. Even though (BBIM)DB30C10 and (BBIM-methane)DB30C10 form normal threaded structures, in (BBIM-ethane)DB30C10, (BBIM-propane)DB30C10 and (BBIM-butane)DB30C10 systems the respective axles are cradled inside the crown ether. That is, the axles BBIM-ethane, BBIM-propane and BBIM-butane are cradled inside the boat-like cavity of DB30C10.

  6. Dicty_cDB: Contig-U13178-1 [Dicty_cDB

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  1. Coronary Arterioles in Type 2 Diabetic (db/db) Mice Undergo a Distinct Pattern of Remodeling Associated with Decreased Vessel Stiffness

    Science.gov (United States)

    Katz, Paige S.; Trask, Aaron J.; Souza-Smith, Flavia M.; Hutchinson, Kirk R.; Galantowicz, Maarten L.; Lord, Kevin C.; Stewart, James A.; Cismowski, Mary J.; Varner, Kurt J.; Lucchesi, Pamela A.

    2011-01-01

    Background Little is known about the impact of type 2 diabetes mellitus (DM) on coronary arteriole remodeling. The aim of this study was to determine the mechanisms that underlie coronary arteriole structural remodeling in type 2 diabetic (db/db) mice. Methods and Results Passive structural properties of septal coronary arterioles isolated from 12- and 16-wk-old diabetic db/db and control mice were assessed by pressure myography. Coronary arterioles from 12-wk-old db/db mice were structurally similar to age-matched controls. By 16-wks of age, coronary wall thickness was increased in db/db arterioles (p < 0.01), while luminal diameter was reduced (Control: 118±5μm; db/db: 102±4μm, p < 0.05), augmenting the wall-to-lumen ratio by 58% (Control: 5.9±0.6; db/db: 9.5±0.4, p < 0.001). Inward hypertrophic remodeling was accompanied by a 56% decrease in elastic modulus (p < 0.05, indicating decreased vessel coronary wall stiffness) and a ~30% reduction in coronary flow reserve in diabetic mice. Interestingly, aortic pulse wave velocity and femoral artery incremental modulus were increased (p < 0.05) in db/db mice, indicating macrovascular stiffness. Molecular tissue analysis revealed increased elastin-to-collagen ratio in diabetic coronaries when compared to control and a decrease in the same ratio in the diabetic aortas. Conclusions These data show that coronary arterioles isolated from type 2 diabetic mice undergo inward hypertrophic remodeling associated with decreased stiffness and increased elastin-to-collagen ratio which results in a decreased coronary flow reserve. This study suggests that coronary microvessels undergo a different pattern of remodeling from macrovessels in type 2 DM. PMID:21744279

  2. InterProScan Result: DB670049 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB670049 DB670049_2_ORF1 A67A4A4AD4AA3090 PANTHER PTHR11405:SF3 CARBAMOYL-PHOSPHATE...cess (GO:0006520)|Molecular Function: carboxyl- or carbamoyltransferase activity (GO:0016743) ...

  3. MannDB: A microbial annotation database for protein characterization

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, C; Lam, M; Smith, J; Zemla, A; Dyer, M; Kuczmarski, T; Vitalis, E; Slezak, T

    2006-05-19

    MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins) are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. MannDB comprises a large number of genomes and comprehensive protein sequence analyses representing organisms listed as high

  4. Antihyperglycemic and Antiobesity Effects of JAL2 on db/db Mice

    Directory of Open Access Journals (Sweden)

    In-Seung Lee

    2016-01-01

    Full Text Available Lonicera japonica Thunb. (LJT and Rehmannia glutinosa Libosch. (RGL have been used traditionally as a herbal medicine in Korean medicine. Using LC/Q-TOF was performed to profile the two herbal medicines and the mixture of LJR and RGL (JAL2, ratio 1 : 1. We performed oral glucose tolerance test (OGTT and plasma GLP-1 and insulin secretion by multiplex assays to investigate antidiabetic effects of LJT, RGL, and JAL2 in db/db mice, the mice model of type 2 diabetes mellitus (T2DM. Also, the antiobesity-related factors such as plasma peptide YY (PYY, triglyceride, total cholesterol, HDL, LDL, and weight of liver, epididymal, and retroperitoneal fat tissue were investigated. Through the multiplex assay, it was found that JAL2 treatment more efficiently attenuated high levels of blood glucose by stimulating GLP-1 secretion and reduced LDL concentration and weight of liver and retroperitoneal fat tissue compared to LJT or RGL treated separately. These results suggest that the JAL2 has antidiabetes and antiobesity effects in T2DM mice model.

  5. NaoXinTong Inhibits the Development of Diabetic Retinopathy in db/db Mice

    Directory of Open Access Journals (Sweden)

    Mengyang Liu

    2015-01-01

    Full Text Available Buchang NaoXinTong capsule (NXT is a Chinese Materia Medica standardized product extracted from 16 Chinese traditional medical herbs and widely used for treatment of patients with cerebrovascular and cardiovascular diseases in China. Formation of microaneurysms plays an important role in the development of diabetic retinopathy. In this study, we investigated if  NXT can protect diabetic mice against the development of diabetic retinopathy. The db/db mice (~6 weeks old, a diabetic animal model, were divided into two groups and fed normal chow or plus NXT for 14 weeks. During the treatment, fasting blood glucose levels were monthly determined. After treatment, retinas were collected to determine retinal thickness, accumulation of carbohydrate macromolecules, and caspase-3 (CAS-3 expression. Our results demonstrate that administration of NXT decreased fasting blood glucose levels. Associated with the decreased glucose levels, NXT blocked the diabetes-induced shrink of multiple layers, such as photoreceptor layer and outer nuclear/plexiform layers, in the retina. NXT also inhibited the diabetes-induced expression of CAS-3 protein and mRNA, MMP-2/9 and TNFα mRNA, accumulation of carbohydrate macromolecules, and formation of acellular capillaries in the retina. Taken together, our study shows that NXT can inhibit the development of diabetic retinopathy and suggests a new potential application of NXT in clinic.

  6. Anti-diabetic and hypolipidemic effects of Sargassum yezoense in db/db mice.

    Science.gov (United States)

    Kim, Su-Nam; Lee, Woojung; Bae, Gyu-Un; Kim, Yong Kee

    2012-08-10

    Peroxisome proliferator-activated receptors (PPARs) have been considered to be desirable targets for metabolic syndrome, even though their specific agonists have several side effects including body weight gain, edema and tissue failure. Previously, we have reported in vitro effects of Sargassum yezoense (SY) and its ingredients, sargaquinoic acid (SQA) and sargahydroquinoic acid (SHQA), on PPARα/γ dual transcriptional activation. In this study, we describe in vivo pharmacological property of SY on metabolic disorders. SY treatment significantly improved glucose and lipid impairment in db/db mice model. More importantly, there are no significant side effects such as body weight gain and hepatomegaly in SY-treated animals, indicating little side effects of SY in liver and lipid metabolism. In addition, SY led to a decrease in the expression of G6Pase for gluconeogenesis in liver responsible for lowering blood glucose level and an increase in the expression of UCP3 in adipose tissue for the reduction of total and LDL-cholesterol level. Altogether, our data suggest that SY would be a potential therapeutic agent against type 2 diabetes and related metabolic disorders by ameliorating the glucose and lipid metabolism.

  7. AphanoDB: a genomic resource for Aphanomyces pathogens

    Directory of Open Access Journals (Sweden)

    Wincker Patrick

    2007-12-01

    Full Text Available Abstract Background The Oomycete genus Aphanomyces comprises devastating plant and animal pathogens. However, little is known about the molecular mechanisms underlying pathogenicity of Aphanomyces species. In this study, we report on the development of a public database called AphanoDB which is dedicated to Aphanomyces genomic data. As a first step, a large collection of Expressed Sequence Tags was obtained from the legume pathogen A. euteiches, which was then processed and collected into AphanoDB. Description Two cDNA libraries of A. euteiches were created: one from mycelium growing on synthetic medium and one from mycelium grown in contact to root tissues of the model legume Medicago truncatula. From these libraries, 18,684 expressed sequence tags were obtained and assembled into 7,977 unigenes which were compared to public databases for annotation. Queries on AphanoDB allow the users to retrieve information for each unigene including similarity to known protein sequences, protein domains and Gene Ontology classification. Statistical analysis of EST frequency from the two different growth conditions was also added to the database. Conclusion AphanoDB is a public database with a user-friendly web interface. The sequence report pages are the main web interface which provides all annotation details for each unigene. These interactive sequence report pages are easily available through text, BLAST, Gene Ontology and expression profile search utilities. AphanoDB is available from URL: http://www.polebio.scsv.ups-tlse.fr/aphano/.

  8. IBM DB2信息管理解决方案概览

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    @@ IBM信息管理产品可以分为数据库(DB2UDB/Informix),商业智能(DB2 OLAP和Intelligent Miner,Warehouse Manager,Redbrick),内容管理Content Management),DB2信息集成软件(Information Integrator)和DB2数据库工具五大类.

  9. Repin1 deficiency improves insulin sensitivity and glucose metabolism in db/db mice by reducing adipose tissue mass and inflammation.

    Science.gov (United States)

    Kunath, Anne; Hesselbarth, Nico; Gericke, Martin; Kern, Matthias; Dommel, Sebastian; Kovacs, Peter; Stumvoll, Michael; Blüher, Matthias; Klöting, Nora

    2016-09-09

    Replication initiator 1 (Repin1) is a zinc finger protein playing a role in insulin sensitivity, body fat mass and lipid metabolism by regulating the expression key genes of glucose and lipid metabolism. Here, we tested the hypothesis that introgression of a Repin1 deletion into db/db mice improves glucose metabolism in vivo. We generated a whole body Repin1 deficient db/db double knockout mouse (Rep1(-/-)x db/db) and systematically characterized the consequences of Repin1 deficiency on insulin sensitivity, glucose and lipid metabolism parameters and fat mass. Hyperinsulinemic-euglycemic clamp studies revealed significantly improved insulin sensitivity in Rep1(-/-)x db/db mice, which are also characterized by lower HbA1c, lower body fat mass and reduced adipose tissue (AT) inflammation area. Our study provides evidence that loss of Repin1 in db/db mice improves insulin sensitivity and reduces chronic hyperglycemia most likely by reducing fat mass and AT inflammation. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Update History of This Database - dbQSNP | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us dbQSNP Update History of This Database Date Update contents 2017/02/16 dbQSNP English archiv...e Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - dbQSNP | LSDB Archive ...

  11. Update History of This Database - DB-SPIRE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us DB-SPIRE Update History of This Database Date Update contents 2017/02/16 DB-SPIRE English ar...ase Description Download License Update History of This Database Site Policy | Contact Us Update History of This Database - DB-SPIRE | LSDB Archive ...

  12. Molecular signatures database (MSigDB) 3.0

    Science.gov (United States)

    Liberzon, Arthur; Subramanian, Aravind; Pinchback, Reid; Thorvaldsdóttir, Helga; Tamayo, Pablo; Mesirov, Jill P.

    2011-01-01

    Motivation: Well-annotated gene sets representing the universe of the biological processes are critical for meaningful and insightful interpretation of large-scale genomic data. The Molecular Signatures Database (MSigDB) is one of the most widely used repositories of such sets. Results: We report the availability of a new version of the database, MSigDB 3.0, with over 6700 gene sets, a complete revision of the collection of canonical pathways and experimental signatures from publications, enhanced annotations and upgrades to the web site. Availability and Implementation: MSigDB is freely available for non-commercial use at http://www.broadinstitute.org/msigdb. Contact: gsea@broadinstitute.org PMID:21546393

  13. HieranoiDB: a database of orthologs inferred by Hieranoid

    Science.gov (United States)

    Kaduk, Mateusz; Riegler, Christian; Lemp, Oliver; Sonnhammer, Erik L. L.

    2017-01-01

    HieranoiDB (http://hieranoiDB.sbc.su.se) is a freely available on-line database for hierarchical groups of orthologs inferred by the Hieranoid algorithm. It infers orthologs at each node in a species guide tree with the InParanoid algorithm as it progresses from the leaves to the root. Here we present a database HieranoiDB with a web interface that makes it easy to search and visualize the output of Hieranoid, and to download it in various formats. Searching can be performed using protein description, identifier or sequence. In this first version, orthologs are available for the 66 Quest for Orthologs reference proteomes. The ortholog trees are shown graphically and interactively with marked speciation and duplication nodes that show the inferred evolutionary scenario, and allow for correct extraction of predicted orthologs from the Hieranoid trees. PMID:27742821

  14. XTalkDB: a database of signaling pathway crosstalk

    Science.gov (United States)

    Sam, Sarah A.; Teel, Joelle; Tegge, Allison N.; Bharadwaj, Aditya; Murali, T.M.

    2017-01-01

    Analysis of signaling pathways and their crosstalk is a cornerstone of systems biology. Thousands of papers have been published on these topics. Surprisingly, there is no database that carefully and explicitly documents crosstalk between specific pairs of signaling pathways. We have developed XTalkDB (http://www.xtalkdb.org) to fill this very important gap. XTalkDB contains curated information for 650 pairs of pathways from over 1600 publications. In addition, the database reports the molecular components (e.g. proteins, hormones, microRNAs) that mediate crosstalk between a pair of pathways and the species and tissue in which the crosstalk was observed. The XTalkDB website provides an easy-to-use interface for scientists to browse crosstalk information by querying one or more pathways or molecules of interest. PMID:27899583

  15. ReadDB Provides Efficient Storage for Mapped Short Reads

    Directory of Open Access Journals (Sweden)

    Gifford David K

    2011-07-01

    Full Text Available Abstract Background The advent of high-throughput sequencing has enabled sequencing based measurements of cellular function, with an individual measurement potentially consisting of more than 108 reads. While tools are available for aligning sets of reads to genomes and interpreting the results, fewer tools have been developed to address the storage and retrieval requirements of large collections of aligned datasets. We present ReadDB, a network accessible column store database system for aligned high-throughput read datasets. Results ReadDB stores collections of aligned read positions and provides a client interface to support visualization and analysis. ReadDB is implemented as a network server that responds to queries on genomic intervals in an experiment with either the set of contained reads or a histogram based interval summary. Tests on datasets ranging from 105 to 108 reads demonstrate that ReadDB performance is generally within a factor of two of local-storage based methods and often three to five times better than other network-based methods. Conclusions ReadDB is a high-performance foundation for ChIP-Seq and RNA-Seq analysis. The client-server model provides convenient access to compute cluster nodes or desktop visualization software without requiring a shared network filesystem or large amounts of local storage. The client code provides a simple interface for fast data access to visualization or analysis. ReadDB provides a new way to store genome-aligned reads for use in applications where read sequence and alignment mismatches are not needed.

  16. NGSmethDB 2017: enhanced methylomes and differential methylation.

    Science.gov (United States)

    Lebrón, Ricardo; Gómez-Martín, Cristina; Carpena, Pedro; Bernaola-Galván, Pedro; Barturen, Guillermo; Hackenberg, Michael; Oliver, José L

    2017-01-04

    The 2017 update of NGSmethDB stores whole genome methylomes generated from short-read data sets obtained by bisulfite sequencing (WGBS) technology. To generate high-quality methylomes, stringent quality controls were integrated with third-part software, adding also a two-step mapping process to exploit the advantages of the new genome assembly models. The samples were all profiled under constant parameter settings, thus enabling comparative downstream analyses. Besides a significant increase in the number of samples, NGSmethDB now includes two additional data-types, which are a valuable resource for the discovery of methylation epigenetic biomarkers: (i) differentially methylated single-cytosines; and (ii) methylation segments (i.e. genome regions of homogeneous methylation). The NGSmethDB back-end is now based on MongoDB, a NoSQL hierarchical database using JSON-formatted documents and dynamic schemas, thus accelerating sample comparative analyses. Besides conventional database dumps, track hubs were implemented, which improved database access, visualization in genome browsers and comparative analyses to third-part annotations. In addition, the database can be also accessed through a RESTful API. Lastly, a Python client and a multiplatform virtual machine allow for program-driven access from user desktop. This way, private methylation data can be compared to NGSmethDB without the need to upload them to public servers. Database website: http://bioinfo2.ugr.es/NGSmethDB. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. License - Plabrain DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Plabrain DB License to Use This Database Last updated : 2010/12/16 You may use this database in compliance w...se and the requirements you must follow in using this database.... The license for this database is specified in the Creative Commons Attribution-Share Alike 2.1 Japan... . If you use data from this database, please be sure attribute this database as follows: Plabrain DB © 2010.... The summary of the Creative Commons Attribution-Share Alike 2.1 Japan is found here . With regard to this database

  18. 50 tips and tricks for MongoDB developers

    CERN Document Server

    Chodorow, Kristina

    2011-01-01

    Getting started with MongoDB is easy, but once you begin building applications with it, you'll face some complex issues. What are the tradeoffs between normalized and denormalized data? How do you handle replica set failure and failover? This collection of MongoDB tips, tricks, and hacks helps you resolve issues with everything from application design and implementation to data safety and monitoring. You get specific guidance in five topic areas directly from engineers at 10gen, the company that develops and supports this open source database: Application Design Tips: What to keep in mind wh

  19. PHP and MongoDB Web Development Beginner's Guide

    CERN Document Server

    Islam, Rubayeet

    2011-01-01

    The book follows a "Code first, explain later" approach, using practical examples in PHP to demonstrate unique features of MongoDB. This book is packed with step-by-step instructions and practical examples, along with challenges to test and improve your knowledge. This book assumes that you are experienced in web application development using PHP, HTML, and CSS. Having working knowledge of using a relational database system such as MySQL will help you grasp some of the concepts quicker, but it is not strictly mandatory. No prior knowledge of MongoDB is required.

  20. 阿利吉仑对2型糖尿病db/db小鼠肾脏损伤的保护作用%Protective effect of aliskiren on type 2 diabetic nephropathy in db/db mice

    Institute of Scientific and Technical Information of China (English)

    周光宇; 苏雪松; 杜丰; 李德天

    2011-01-01

    目的 观察肾素抑制剂阿利吉仑对2型糖尿病db/db小鼠肾脏损伤的保护作用.方法 8周龄db/db和db/m小鼠行单侧肾切除,16周进入实验,分为4组:db/m小鼠对照组(db/m组)、db/db糖尿病小鼠对照组(db/db组)、db/db糖尿病小鼠阿利吉仑3 mg·kg-1·d-1治疗组(db/db+A3组)和db/db糖尿病小鼠阿利吉仑25 mg·kg-1·d-1治疗组(db/db+A25组).阿利吉仑溶于磷酸盐缓冲液( PBS,350 mg/L)皮下泵入(0.25 μl/h)给药,疗程4周.治疗前后检测体质量、血糖、糖化血红蛋白、尿蛋白量、血压水平;PAS染色观察肾脏组织学变化;ELISA法检测肾皮质转化生长因子β1 (TGF-β1)和纤溶酶原激活抑制因子1(PAI-1)含量;间接免疫荧光检测肾小球Ⅳ型胶原( ColⅣ)和纤连蛋白(FN)表达;实时定量PCR检测TGF-β1、PAI-1、ColⅣ、FN和肾素mRNA表达;放射免疫法检测肾皮质肾素活性和血管紧张素Ⅱ(AngⅡ)水平.结果 与db/m组小鼠比较,db/db组小鼠有大量蛋白尿,肾小球细胞外基质沉积增加,TGF-β1、PAI-1、ColⅣ和FN蛋白及mRNA表达增加,同时肾皮质肾素mRNA、肾素活性和AngⅡ水平增高(均P<0.05).阿利吉仑25 mg·kg-1·d-1治疗在没有影响血压情况下,显著减少db/db小鼠24 h尿蛋白量,减少肾小球细胞外基质沉积,减少TGF-β1、PAI-1、ColⅣ、FN蛋白和mRNA表达,同时降低肾皮质肾素活性和AngⅡ水平(均P<0.05).结论 阿利吉仑对2型糖尿病db/db小鼠肾脏损伤有保护作用.%Objective To investigate the effect of aliskiren on type 2 diabetic nephropathy in db/db mice.Methods Eight-week old db/db and db/m mice were subjected to right nephrectomy to hasten the development of diabetic nephropathy.At age of 16 weeks,they were divided into four groups:db/m group (normal control),db/db group ( diabetic control),db/db+ A3 group (db/db mice treated with aliskiren 3 mg·kg-1"d-1) and db/db+A25 group (db/db mice treated with aliskiren 25 mg "kg-1 "d-1).Body

  1. DB2 11 the ultimate database for cloud, analytics, and mobile

    CERN Document Server

    Campbell, John; Jones, Gareth; Parekh, Surekha; Yothers, Jay

    2014-01-01

    Building on the prior book ""DB2 11: The Database for Big Data and Analytics,"" published in 2013, this book is written particularly for new and existing DB2 for z/OS customers and users who want to learn as much as they can about the new software version before migrating their organizations to DB2 11 for z/OS. The book begins with a technical overview of DB2 11 features and explains how the new functions in DB2 11 can help enterprise customers address the challenges they face with the explosion of data and information. There has been rapid growth in the variety, volume, and velocity of dat

  2. Dicty_cDB: Contig-U15345-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ... 34 6.2 3 ( CD404691 ) Gm_ck2768 Soybean induced by Salicylic Acid Glyci... 42 6.2 2 ( AC212861 ) Pongo a... clone SOYBE... 42 6.6 2 ( CD400493 ) Gm_ck22354 Soybean induced by Salicylic Acid Glyc... 42 6.6 2 ( CU9290...... 42 6.8 2 ( CD405526 ) Gm_ck29180 Soybean induced by Salicylic Acid Glyc... 42... 6.9 2 ( CD410160 ) Gm_ck37673 Soybean induced by Salicylic Acid Glyc... 42 6.9 2 ( DB980377 ) Glycine max c...DNA, clone: GMFL02-21-A24, 3'end. 42 6.9 2 ( CD395438 ) Gm_ck15456 Soybean induced by Salicylic Acid Glyc...

  3. Dicty_cDB: Contig-U16283-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available A004D12 of library AZ0AA from... 155 7e-82 6 ( FE856401 ) CAFU609.fwd CAFU Pichia stipitis oxygen limited d....unninghamella elegans pBluescript (E... 176 3e-71 5 ( FE855138 ) CAFT711.rev CAFT Pichia stipitis oxygen limited...TP synthase beta subuni... 109 2e-51 7 ( FE855128 ) CAFT706.rev CAFT Pichia stipitis oxygen limited...erobic dextrose... 147 2e-50 6 ( FE855139 ) CAFT711.fwd CAFT Pichia stipitis oxygen limited... DB915475 ) Idiosepius paradoxus cDNA, clone:Ip_aB_019_H14, 5... 105 2e-50 6 ( FE855260 ) CAFT778.fwd CAFT Pichia stipitis oxygen lim

  4. Dicty_cDB: Contig-U15634-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 91 ) CS00-C3-702-045-E06-CT.F Sweet orange fruit, deve... 46 1e-12 4 ( EC755644 ) PPE00009879 Agenco...urt Biosciences Agen-0020 Non-n... 66 1e-12 4 ( EC757836 ) PPE00008054 Agencourt Bioscien...ces Agen-0020 Non-n... 66 2e-12 4 ( EC758873 ) PPE00006126 Agencourt Biosciences Agen-0020 Non-n... 66 2e-12...8 6e-10 3 ( EC756583 ) PPE00008621 Agencourt Biosciences Agen-0020 Non-n... 66 6e-10 3 ( DB997675 ) Quercus ..... 50 2e-06 2 ( AP004967 ) Lotus japonicus genomic DNA, chromosome 1, clone:... 52 4e-06 2 ( EC756528 ) PPE00010451 Agenco

  5. Dicty_cDB: Contig-U13156-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 4e-17 1 ( DR059902 ) RTNIT1_20_A12.g1_A029 Roots minus nitrogen Pinus ... 52 0.033 1 ( CO176742 ) NDL1_63_H...ts minus phosphorous Pi... 44 8.1 1 ( DR161605 ) RTFE1_12_G03.g1_A029 Roots minus i...ron Pinus taeda... 44 8.1 1 ( DR058830 ) RTNIT1_14_D10.b1_A029 Roots minus nitrogen Pinus ... 44 8.1 1 ( DB5...39865 ) Homo sapiens hippocampus cDNA, RIKEN full-length ... 44 8.1 1 ( CO367317 ) RTK1_33_C10.g1_A029 Roots...11 ) EST1072886 Normalized pine embryo library, Lib_D ... 44 8.1 1 ( DR166655 ) RTPHOS1_13_C10.g1_A029 Roo

  6. Dicty_cDB: Contig-U16468-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ric... 48 2e-08 3 ( ES226010 ) MpSG_ag5_A23 Myzus persicae, tobacco lineage, aph... 46 2e-08 3 ( DB732624 ) ...Apis mellifera head cDNA, RIKEN full-length enric... 48 2e-08 3 ( ES223551 ) MpHnorm_ag3_F06 Myzus persicae,... tobacco lineage, ... 46 3e-08 3 ( ES220707 ) MpGV_ag1_G04 Myzus persicae, line G006, PLRV infe... 46 3e-08 ...3 ( ES220854 ) MpGV_ag1_M17 Myzus persicae, line G006, PLRV infe... 46 3e-08 3 ( DW011463 ) w13m9_M13F Myz...us persicae, tobacco lineage, whole... 46 3e-08 3 ( ES225317 ) MpSG_ag2_L04 Myzus p

  7. Dicty_cDB: Contig-U12691-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 1 AE009441_2344( AE009441 |pid:none) Pyrobaculum aerophilum str. IM2... 35 4.1 FJ611395_1( FJ611395 |pid:none) Plethodon... fourchensis voucher DBS ... 34 5.4 FJ611471_1( FJ611471 |pid:none) Plethodon fourchensis vouche...r DBS ... 34 5.4 FJ611385_1( FJ611385 |pid:none) Plethodon fourchensis voucher DB...S ... 34 5.4 FJ611465_1( FJ611465 |pid:none) Plethodon fourchensis voucher DBS ... 34 5.4 FJ611400_1( FJ611400 |pid:none) Plethodon... fourchensis voucher DBS ... 34 5.4 FJ611415_1( FJ611415 |pid:none) Plethodon fourche

  8. Dicty_cDB: Contig-U08743-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ( FG764070 ) G1146P324FM6.T0 Anolis carolinensis pooled normal... 54 0.001 2 ( D...B775134 ) Apis mellifera head cDNA, RIKEN full-length enric... 56 0.004 1 ( FG779811 ) G1147P347FH16.T0 Anolis caroline...nsis pooled norma... 54 0.014 1 ( FG766620 ) G1147P341RG4.T0 Anolis carolinensis pooled normal...... 54 0.014 1 ( FG766572 ) G1147P341FG4.T0 Anolis carolinensis pooled normal... 54 ...0.014 1 ( FG764118 ) G1146P324RM6.T0 Anolis carolinensis pooled normal... 54 0.014 1 ( FG722743 ) G1144P319FK5.T0 Anolis caroline

  9. Dicty_cDB: Contig-U11064-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available DN... 51 1e-04 FJ647224_2( FJ647224 |pid:none) Murine coronavirus MHV-3, complete... 51 1e-04 AE014188_327( ...licase polyprotein 1ab; Short... 51 2e-04 AF391541_1( AF391541 |pid:none) Bovine coronavirus isolate BCoV-EN...omonas mendocina ymp, comp... 51 2e-04 DQ915164_2( DQ915164 |pid:none) Bovine coronavirus isolate Alpaca,......avirus R-AH187, comple... 51 2e-04 DQ811784_2( DQ811784 |pid:none) Bovine coronav...irus DB2, complete g... 51 2e-04 AB354579_1( AB354579 |pid:none) Bovine coronavirus

  10. Diet supplementation with green tea extract epigallocatechin gallate prevents progression to glucose intolerance in db/db mice

    Directory of Open Access Journals (Sweden)

    Ortsäter Henrik

    2012-02-01

    Full Text Available Abstract Background Green tea was suggested as a therapeutic agent for the treatment of diabetes more than 70 years ago, but the mechanisms behind its antidiabetic effect remains elusive. In this work, we address this issue by feeding a green tea extract (TEAVIGO™ with a high content of epigallocatechin gallate (EGCG or the thiazolidinedione PPAR-γ agonist rosiglitazone, as positive control, to db/db mice, an animal model for diabetes. Methods Young (7 week-old db/db mice were randomized and assigned to receive diets supplemented with or without EGCG or rosiglitazone for 10 weeks. Fasting blood glucose, body weight and food intake was measured along the treatment. Glucose and insulin levels were determined during an oral glucose tolerance test after 10 weeks of treatment. Pancreata were sampled at the end of the study for blinded histomorphometric analysis. Islets were isolated and their mRNA expression analyzed by quantitative RT-PCR. Results The results show that, in db/db mice, EGCG improves glucose tolerance and increases glucose-stimulated insulin secretion. EGCG supplementation reduces the number of pathologically changed islets of Langerhans, increases the number and the size of islets, and heightens pancreatic endocrine area. These effects occurred in parallel with a reduction in islet endoplasmic reticulum stress markers, possibly linked to the antioxidative capacity of EGCG. Conclusions This study shows that the green tea extract EGCG markedly preserves islet structure and enhances glucose tolerance in genetically diabetic mice. Dietary supplementation with EGCG could potentially contribute to nutritional strategies for the prevention and treatment of type 2 diabetes.

  11. A novel MitoNEET ligand, TT01001, improves diabetes and ameliorates mitochondrial function in db/db mice.

    Science.gov (United States)

    Takahashi, Takehiro; Yamamoto, Masashi; Amikura, Kazutoshi; Kato, Kozue; Serizawa, Takashi; Serizawa, Kanako; Akazawa, Daisuke; Aoki, Takumi; Kawai, Koji; Ogasawara, Emi; Hayashi, Jun-Ichi; Nakada, Kazuto; Kainoh, Mie

    2015-02-01

    The mitochondrial outer membrane protein mitoNEET is a binding protein of the insulin sensitizer pioglitazone (5-[[4-[2-(5-ethylpyridin-2-yl)ethoxy]phenyl]methyl]-1,3-thiazolidine-2,4-dione) and is considered a novel target for the treatment of type II diabetes. Several small-molecule compounds have been identified as mitoNEET ligands using structure-based design or virtual docking studies. However, there are no reports about their therapeutic potential in animal models. Recently, we synthesized a novel small molecule, TT01001 [ethyl-4-(3-(3,5-dichlorophenyl)thioureido)piperidine-1-carboxylate], designed on the basis of pioglitazone structure. In this study, we assessed the pharmacological properties of TT01001 in both in vitro and in vivo studies. We found that TT01001 bound to mitoNEET without peroxisome proliferator-activated receptor-γ activation effect. In type II diabetes model db/db mice, TT01001 improved hyperglycemia, hyperlipidemia, and glucose intolerance, and its efficacy was equivalent to that of pioglitazone, without the pioglitazone-associated weight gain. Mitochondrial complex II + III activity of the skeletal muscle was significantly increased in db/db mice. We found that TT01001 significantly suppressed the elevated activity of the complex II + III. These results suggest that TT01001 improved type II diabetes without causing weight gain and ameliorated mitochondrial function of db/db mice. This is the first study that demonstrates the effects of a mitoNEET ligand on glucose metabolism and mitochondrial function in an animal disease model. These findings support targeting mitoNEET as a potential therapeutic approach for the treatment of type II diabetes.

  12. Anti-diabetic and hypolipidemic effects of Sargassum yezoense in db/db mice

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Su-Nam, E-mail: snkim@kist.re.kr [Natural Medicine Center, KIST Gangneung Institute, Gangneung 210-340 (Korea, Republic of); Lee, Woojung [Natural Medicine Center, KIST Gangneung Institute, Gangneung 210-340 (Korea, Republic of); Bae, Gyu-Un [College of Pharmacy, Sookmyung Women' s University, Seoul 140-742 (Korea, Republic of); Research Center for Cell Fate Control, Sookmyung Women' s University, Seoul 140-742 (Korea, Republic of); Kim, Yong Kee, E-mail: yksnbk@sookmyung.ac.kr [College of Pharmacy, Sookmyung Women' s University, Seoul 140-742 (Korea, Republic of)

    2012-08-10

    Highlights: Black-Right-Pointing-Pointer Sargassum yezoense (SY) treatment improved glucose and lipid impairment in vivo. Black-Right-Pointing-Pointer This pharmacological action is associated with PPAR{alpha}/{gamma} dual activation. Black-Right-Pointing-Pointer It decreases the expression of G6Pase for gluconeogenesis in liver. Black-Right-Pointing-Pointer It increases the expression of UCP3 for lipid metabolism in adipose tissue. Black-Right-Pointing-Pointer There are no significant side effects such as body weight gain and hepatomegaly. -- Abstract: Peroxisome proliferator-activated receptors (PPARs) have been considered to be desirable targets for metabolic syndrome, even though their specific agonists have several side effects including body weight gain, edema and tissue failure. Previously, we have reported in vitro effects of Sargassum yezoense (SY) and its ingredients, sargaquinoic acid (SQA) and sargahydroquinoic acid (SHQA), on PPAR{alpha}/{gamma} dual transcriptional activation. In this study, we describe in vivo pharmacological property of SY on metabolic disorders. SY treatment significantly improved glucose and lipid impairment in db/db mice model. More importantly, there are no significant side effects such as body weight gain and hepatomegaly in SY-treated animals, indicating little side effects of SY in liver and lipid metabolism. In addition, SY led to a decrease in the expression of G6Pase for gluconeogenesis in liver responsible for lowering blood glucose level and an increase in the expression of UCP3 in adipose tissue for the reduction of total and LDL-cholesterol level. Altogether, our data suggest that SY would be a potential therapeutic agent against type 2 diabetes and related metabolic disorders by ameliorating the glucose and lipid metabolism.

  13. EST Table: DB670702 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB670702 E_FL_BmN-_18P12_F_0 10/09/28 99 %/165 aa ref|NP_001106143.1| ribosome-asso...RSSA_ANOGA 10/09/10 83 %/165 aa gnl|Amel|GB19082-PA 10/09/10 86 %/165 aa gi|91089051|ref|XP_970069.1| PREDIC

  14. EST Table: DB673030 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB673030 E_FL_BmN-_26N13_F_0 10/09/28 100 %/188 aa ref|NP_001106143.1| ribosome-ass...1| ribosomal protein SA [Bombyx mori] 10/09/01 82 %/187 aa FBpp0243730|DwilGK14587-PA 10/08/28 65 %/187 aa B

  15. EuPathDB: the eukaryotic pathogen genomics database resource

    Science.gov (United States)

    Aurrecoechea, Cristina; Barreto, Ana; Basenko, Evelina Y.; Brestelli, John; Brunk, Brian P.; Cade, Shon; Crouch, Kathryn; Doherty, Ryan; Falke, Dave; Fischer, Steve; Gajria, Bindu; Harb, Omar S.; Heiges, Mark; Hertz-Fowler, Christiane; Hu, Sufen; Iodice, John; Kissinger, Jessica C.; Lawrence, Cris; Li, Wei; Pinney, Deborah F.; Pulman, Jane A.; Roos, David S.; Shanmugasundram, Achchuthan; Silva-Franco, Fatima; Steinbiss, Sascha; Stoeckert, Christian J.; Spruill, Drew; Wang, Haiming; Warrenfeltz, Susanne; Zheng, Jie

    2017-01-01

    The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polysomal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data. Forthcoming upgrades include user workspaces for private integration of data with existing EuPathDB data and improved integration and presentation of host–pathogen interactions. PMID:27903906

  16. ArchDB 2014: structural classification of loops in proteins

    Science.gov (United States)

    Bonet, Jaume; Planas-Iglesias, Joan; Garcia-Garcia, Javier; Marín-López, Manuel A.; Fernandez-Fuentes, Narcis; Oliva, Baldo

    2014-01-01

    The function of a protein is determined by its three-dimensional structure, which is formed by regular (i.e. β-strands and α-helices) and non-periodic structural units such as loops. Compared to regular structural elements, non-periodic, non-repetitive conformational units enclose a much higher degree of variability—raising difficulties in the identification of regularities, and yet represent an important part of the structure of a protein. Indeed, loops often play a pivotal role in the function of a protein and different aspects of protein folding and dynamics. Therefore, the structural classification of protein loops is an important subject with clear applications in homology modelling, protein structure prediction, protein design (e.g. enzyme design and catalytic loops) and function prediction. ArchDB, the database presented here (freely available at http://sbi.imim.es/archdb), represents such a resource and has been an important asset for the scientific community throughout the years. In this article, we present a completely reworked and updated version of ArchDB. The new version of ArchDB features a novel, fast and user-friendly web-based interface, and a novel graph-based, computationally efficient, clustering algorithm. The current version of ArchDB classifies 149,134 loops in 5739 classes and 9608 subclasses. PMID:24265221

  17. ProOpDB: Prokaryotic Operon DataBase.

    Science.gov (United States)

    Taboada, Blanca; Ciria, Ricardo; Martinez-Guerrero, Cristian E; Merino, Enrique

    2012-01-01

    The Prokaryotic Operon DataBase (ProOpDB, http://operons.ibt.unam.mx/OperonPredictor) constitutes one of the most precise and complete repositories of operon predictions now available. Using our novel and highly accurate operon identification algorithm, we have predicted the operon structures of more than 1200 prokaryotic genomes. ProOpDB offers diverse alternatives by which a set of operon predictions can be retrieved including: (i) organism name, (ii) metabolic pathways, as defined by the KEGG database, (iii) gene orthology, as defined by the COG database, (iv) conserved protein domains, as defined by the Pfam database, (v) reference gene and (vi) reference operon, among others. In order to limit the operon output to non-redundant organisms, ProOpDB offers an efficient method to select the most representative organisms based on a precompiled phylogenetic distances matrix. In addition, the ProOpDB operon predictions are used directly as the input data of our Gene Context Tool to visualize their genomic context and retrieve the sequence of their corresponding 5' regulatory regions, as well as the nucleotide or amino acid sequences of their genes.

  18. denovo-db: a compendium of human de novo variants.

    Science.gov (United States)

    Turner, Tychele N; Yi, Qian; Krumm, Niklas; Huddleston, John; Hoekzema, Kendra; F Stessman, Holly A; Doebley, Anna-Lisa; Bernier, Raphael A; Nickerson, Deborah A; Eichler, Evan E

    2017-01-04

    Whole-exome and whole-genome sequencing have facilitated the large-scale discovery of de novo variants in human disease. To date, most de novo discovery through next-generation sequencing focused on congenital heart disease and neurodevelopmental disorders (NDDs). Currently, de novo variants are one of the most significant risk factors for NDDs with a substantial overlap of genes involved in more than one NDD. To facilitate better usage of published data, provide standardization of annotation, and improve accessibility, we created denovo-db (http://denovo-db.gs.washington.edu), a database for human de novo variants. As of July 2016, denovo-db contained 40 different studies and 32,991 de novo variants from 23,098 trios. Database features include basic variant information (chromosome location, change, type); detailed annotation at the transcript and protein levels; severity scores; frequency; validation status; and, most importantly, the phenotype of the individual with the variant. We included a feature on our browsable website to download any query result, including a downloadable file of the full database with additional variant details. denovo-db provides necessary information for researchers to compare their data to other individuals with the same phenotype and also to controls allowing for a better understanding of the biology of de novo variants and their contribution to disease. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. SOI-Based 3dB MMI Splitter

    Institute of Scientific and Technical Information of China (English)

    魏红振; 余金中; 刘忠立; 张晓峰; 史伟; 房昌水

    2000-01-01

    A type of SOI-based MMI 3dB splitter has been demonstrated. The geometry was analyzed and designed by effective index method and guide mode method. The fabrication tolerance was analyzed too. The device was fabricated and near-field output was obtained. The device shows large width tolerance, low loss and low power uniformity.

  20. CastorDB: a comprehensive knowledge base for Ricinus communis

    Directory of Open Access Journals (Sweden)

    Chattoo Bharat B

    2011-09-01

    Full Text Available Abstract Background Ricinus communis is an industrially important non-edible oil seed crop, native to tropical and subtropical regions of the world. Although, R. communis genome was assembled in 4X draft by JCVI, and is predicted to contain 31,221 proteins, the function of most of the genes remains to be elucidated. A large amount of information of different aspects of the biology of R. communis is available, but most of the data are scattered one not easily accessible. Therefore a comprehensive resource on Castor, Castor DB, is required to facilitate research on this important plant. Findings CastorDB is a specialized and comprehensive database for the oil seed plant R. communis, integrating information from several diverse resources. CastorDB contains information on gene and protein sequences, gene expression and gene ontology annotation of protein sequences obtained from a variety of repositories, as primary data. In addition, computational analysis was used to predict cellular localization, domains, pathways, protein-protein interactions, sumoylation sites and biochemical properties and has been included as derived data. This database has an intuitive user interface that prompts the user to explore various possible information resources available on a given gene or a protein. Conclusion CastorDB provides a user friendly comprehensive resource on castor with particular emphasis on its genome, transcriptome, and proteome and on protein domains, pathways, protein localization, presence of sumoylation sites, expression data and protein interacting partners.

  1. EST Table: DB668879 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB668879 E_FL_BmN-_12J04_F_0 10/09/28 62 %/173 aa ref|XP_002431503.1| enzymatic pol...yprotein; Endonuclease; Reverse transcriptase, putative [Pediculus humanus corporis] gb|EEB18765.1| enzymati

  2. EST Table: DB668639 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB668639 E_FL_BmN-_11H24_F_0 11/12/09 n.h 10/09/28 64 %/130 aa ref|XP_002431503.1| enzyma...tic polyprotein; Endonuclease; Reverse transcriptase, putative [Pediculus humanus corporis] gb|EEB18765.1| enzyma

  3. EuPathDB: the eukaryotic pathogen genomics database resource.

    Science.gov (United States)

    Aurrecoechea, Cristina; Barreto, Ana; Basenko, Evelina Y; Brestelli, John; Brunk, Brian P; Cade, Shon; Crouch, Kathryn; Doherty, Ryan; Falke, Dave; Fischer, Steve; Gajria, Bindu; Harb, Omar S; Heiges, Mark; Hertz-Fowler, Christiane; Hu, Sufen; Iodice, John; Kissinger, Jessica C; Lawrence, Cris; Li, Wei; Pinney, Deborah F; Pulman, Jane A; Roos, David S; Shanmugasundram, Achchuthan; Silva-Franco, Fatima; Steinbiss, Sascha; Stoeckert, Christian J; Spruill, Drew; Wang, Haiming; Warrenfeltz, Susanne; Zheng, Jie

    2017-01-04

    The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polysomal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data. Forthcoming upgrades include user workspaces for private integration of data with existing EuPathDB data and improved integration and presentation of host-pathogen interactions.

  4. CastorDB: a comprehensive knowledge base for Ricinus communis

    Science.gov (United States)

    2011-01-01

    Background Ricinus communis is an industrially important non-edible oil seed crop, native to tropical and subtropical regions of the world. Although, R. communis genome was assembled in 4X draft by JCVI, and is predicted to contain 31,221 proteins, the function of most of the genes remains to be elucidated. A large amount of information of different aspects of the biology of R. communis is available, but most of the data are scattered one not easily accessible. Therefore a comprehensive resource on Castor, Castor DB, is required to facilitate research on this important plant. Findings CastorDB is a specialized and comprehensive database for the oil seed plant R. communis, integrating information from several diverse resources. CastorDB contains information on gene and protein sequences, gene expression and gene ontology annotation of protein sequences obtained from a variety of repositories, as primary data. In addition, computational analysis was used to predict cellular localization, domains, pathways, protein-protein interactions, sumoylation sites and biochemical properties and has been included as derived data. This database has an intuitive user interface that prompts the user to explore various possible information resources available on a given gene or a protein. Conclusion CastorDB provides a user friendly comprehensive resource on castor with particular emphasis on its genome, transcriptome, and proteome and on protein domains, pathways, protein localization, presence of sumoylation sites, expression data and protein interacting partners. PMID:21914200

  5. The double-layered chemical structure in DB white dwarfs

    CERN Document Server

    Althaus, L G

    2004-01-01

    We study the structure and evolution of white dwarf stars with helium-rich atmospheres (DB) in a self-consistent way with the predictions of time-dependent element diffusion. Our treatment of diffusion includes gravitational settling and chemical and thermal diffusion. OPAL radiative opacities for arbitrary metallicity and carbon-and oxygen-rich compositions are employed. Emphasis is placed on the evolution of the diffusion-modeled double-layered chemical structure. This structure, which is characterized by a pure helium envelope atop an intermediate remnant shell rich in helium, carbon and oxygen, is expected for pulsating DB white dwarfs, assuming that they are descendants of hydrogen-deficient PG1159 post-AGB stars. We find that, depending on the stellar mass, if DB white dwarf progenitors are formed with a helium content smaller than \\approx 10^-3 M_*, a single-layered configuration is expected to emerge during the DB pulsation instability strip. We also explore the consequences of diffusively evolving ch...

  6. TheHiveDB image data management and analysis framework.

    Science.gov (United States)

    Muehlboeck, J-Sebastian; Westman, Eric; Simmons, Andrew

    2014-01-06

    The hive database system (theHiveDB) is a web-based brain imaging database, collaboration, and activity system which has been designed as an imaging workflow management system capable of handling cross-sectional and longitudinal multi-center studies. It can be used to organize and integrate existing data from heterogeneous projects as well as data from ongoing studies. It has been conceived to guide and assist the researcher throughout the entire research process, integrating all relevant types of data across modalities (e.g., brain imaging, clinical, and genetic data). TheHiveDB is a modern activity and resource management system capable of scheduling image processing on both private compute resources and the cloud. The activity component supports common image archival and management tasks as well as established pipeline processing (e.g., Freesurfer for extraction of scalar measures from magnetic resonance images). Furthermore, via theHiveDB activity system algorithm developers may grant access to virtual machines hosting versioned releases of their tools to collaborators and the imaging community. The application of theHiveDB is illustrated with a brief use case based on organizing, processing, and analyzing data from the publically available Alzheimer Disease Neuroimaging Initiative.

  7. TheHiveDB image data management and analysis framework

    Directory of Open Access Journals (Sweden)

    J-Sebastian eMuehlboeck

    2014-01-01

    Full Text Available The hive database system (theHiveDB is a web-based brain imaging database, collaboration and activity system which has been designed as an imaging workflow management system capable of handling cross-sectional and longitudinal multi-center studies. It can be used to organize and integrate existing data from heterogeneous projects as well as data from ongoing studies. It has been conceived to guide and assist the researcher throughout the entire research process, integrating all relevant types of data across modalities (i.e. brain imaging, clinical and genetic data. TheHiveDB is a modern activity and resource management system capable of scheduling image processing on both private compute resources and the cloud. The activity component supports common image archival and management tasks as well as established pipeline processing (e.g. Freesurfer for extraction of scalar measures from magnetic resonance images. Furthermore, via theHiveDB activity system algorithm developers may grant access to virtual machines hosting versioned releases of their tools to collaborators and the imaging community. The application of theHiveDB is illustrated with a brief use case based on organizing, processing, and analyzing data from the publically available Alzheimer Disease Neuroimaging Initiative (ADNI.

  8. Web development with MongoDB and Node.js

    CERN Document Server

    Krol, Jason

    2014-01-01

    This book is designed for developers of any skill level that want to get up and running using Node.js and MongoDB to build full featured web applications. A basic understanding of JavaScript and HTML is the only requirement for this book.

  9. DemaDb: an integrated dematiaceous fungal genomes database.

    Science.gov (United States)

    Kuan, Chee Sian; Yew, Su Mei; Chan, Chai Ling; Toh, Yue Fen; Lee, Kok Wei; Cheong, Wei-Hien; Yee, Wai-Yan; Hoh, Chee-Choong; Yap, Soon-Joo; Ng, Kee Peng

    2016-01-01

    Many species of dematiaceous fungi are associated with allergic reactions and potentially fatal diseases in human, especially in tropical climates. Over the past 10 years, we have isolated more than 400 dematiaceous fungi from various clinical samples. In this study, DemaDb, an integrated database was designed to support the integration and analysis of dematiaceous fungal genomes. A total of 92 072 putative genes and 6527 pathways that identified in eight dematiaceous fungi (Bipolaris papendorfii UM 226, Daldinia eschscholtzii UM 1400, D. eschscholtzii UM 1020, Pyrenochaeta unguis-hominis UM 256, Ochroconis mirabilis UM 578, Cladosporium sphaerospermum UM 843, Herpotrichiellaceae sp. UM 238 and Pleosporales sp. UM 1110) were deposited in DemaDb. DemaDb includes functional annotations for all predicted gene models in all genomes, such as Gene Ontology, EuKaryotic Orthologous Groups, Kyoto Encyclopedia of Genes and Genomes (KEGG), Pfam and InterProScan. All predicted protein models were further functionally annotated to Carbohydrate-Active enzymes, peptidases, secondary metabolites and virulence factors. DemaDb Genome Browser enables users to browse and visualize entire genomes with annotation data including gene prediction, structure, orientation and custom feature tracks. The Pathway Browser based on the KEGG pathway database allows users to look into molecular interaction and reaction networks for all KEGG annotated genes. The availability of downloadable files containing assembly, nucleic acid, as well as protein data allows the direct retrieval for further downstream works. DemaDb is a useful resource for fungal research community especially those involved in genome-scale analysis, functional genomics, genetics and disease studies of dematiaceous fungi. Database URL: http://fungaldb.um.edu.my.

  10. Astaxanthin Attenuates the Apoptosis of Retinal Ganglion Cells in db/db Mice by Inhibition of Oxidative Stress

    Directory of Open Access Journals (Sweden)

    Xiao-Li Kang

    2013-03-01

    Full Text Available Diabetic retinopathy is a common diabetic eye disease caused by changes in retinal ganglion cells (RGCs. It is an ocular manifestation of systemic disease, which affects up to 80% of all patients who have had diabetes for 10 years or more. The genetically diabetic db/db mouse, as a model of type-2 diabetes, shows diabetic retinopathy induced by apoptosis of RGCs. Astaxanthin is a carotenoid with powerful antioxidant properties that exists naturally in various plants, algae and seafood. Here, astaxanthin was shown to reduce the apoptosis of RGCs and improve the levels of oxidative stress markers, including superoxide anion, malondialdehyde (MDA, a marker of lipid peroxidation, 8-hydroxy-2-deoxyguanosine (8-OHdG, indicator of oxidative DNA damage and MnSOD (manganese superoxide dismutase activity in the retinal tissue of db/db mouse. In addition, astaxanthin attenuated hydrogen peroxide(H2O2-induced apoptosis in the transformed rat retinal ganglion cell line RGC-5. Therefore, astaxanthin may be developed as an antioxidant drug to treat diabetic retinopathy.

  11. DbUnit在数据库测试中的应用%Application of DbUnit in Database Testing

    Institute of Scientific and Technical Information of China (English)

    胡银保

    2012-01-01

    在实现测试驱动开发过程中,DbUnit工具是专门针对数据库测试的单元测试框架,它是对JUnit的一个扩展.DbUnit测试允许程序员在整个测试过程中自由地管理和控制数据库,将其置于一个可知的状态.在明确测试机制、搭建好测试环境的基础之上,围绕数据库备份、植入测试数据集进行单元测试、使数据库恢复到测试前状态等问题进行分析和探讨,以期建立一个良好的测试流程.%In the process of realizing Test-Driven development,DbUnit tool is a kind of unit test framework especially for database testing which is an extension of JUnit.In the process of DbUnit testing,programmer can manage and control database freely,place it in a knowable state.The problems such as database backup,implanting data to test,database recovery are analyzed on the base of clearifying the test mechanism and building the test environment,so as to build a good test process.

  12. Oligomannuronate-Chromium (Ⅲ) Complex Ameliorates Insulin Resistance in C57BL/KsJ-db/db Mice

    Institute of Scientific and Technical Information of China (English)

    HAO Cui; HAO Jiejie; WANG Wei; LI Guangsheng; ZENG Yangyang; WANG Peipei; ZHAO Xia; YU Guangli

    2011-01-01

    Diabetes mellitus is the most common metabolic disease and its prevalence is increasing in many countries year by year.More than 90% of diabetes patients are type 2 diabetes,which is caused by insulin resistance and beta-cell dysfunction.In this paper,the oligomannuronate-chromium (Ⅲ) complex (OM2) was prepared and its effect and mechanism on attenuating insulin resistance in diabetic C57BL/KsJ-db/db mice were studied.The results indicated that oral intake of OM2 (50mgkg1d-1) for 42d decreased blood glucose and lipid concentration,which was associated with the reduced serum insulin concentration and insulin resistance.According to western blot assay,OM2 could activate AMPK pathway to regulate glycogen synthesis,gluconeogenesis and lipid metabolism in the liver,and attenuate the hyperglycemic symptom in db/db mice.The effects of OM2 on attenuating insulin resistance were comparable to that of the established antidiabetic drug metformin,and OM2 showed less adverse effect than metformin in vivo.Based on the effectiveness and low toxicity,OM2 may potentially be used for prevention and treatment of type 2 diabetes mellitus.

  13. Acceleration of biliary cholesterol secretion restores glycemic control and alleviates hypertriglyceridemia in obese db/db mice.

    Science.gov (United States)

    Su, Kai; Sabeva, Nadezhda S; Wang, Yuhuan; Liu, Xiaoxi; Lester, Joshua D; Liu, Jingjing; Liang, Shuang; Graf, Gregory A

    2014-01-01

    Recent studies support a role for cholesterol in the development of obesity and nonalcoholic fatty liver disease. Mice lacking the ABCG5 ABCG8 (G5G8) sterol transporter have reduced biliary cholesterol secretion and are more susceptible to steatosis, hepatic insulin resistance, and loss of glycemic control when challenged with a high-fat diet. We hypothesized that accelerating G5G8-mediated biliary cholesterol secretion would correct these phenotypes in obese mice. Obese (db/db) male and their lean littermates were administered a cocktail of control adenovirus or adenoviral vectors encoding ABCG5 and ABCG8 (AdG5G8). Three days after viral administration, measures of lipid and glucose homeostasis were determined, and tissues were collected for biochemical analyses. AdG5G8 increased biliary cholesterol and fecal sterol elimination. Fasting glucose and triglycerides declined, and glucose tolerance improved in obese mice expressing G5G8 compared with mice receiving control adenovirus. These changes were associated with a reduction in phosphorylated eukaryotic initiation factor 2α and c-Jun N-terminal kinase in liver, suggesting alleviation of endoplasmic reticulum stress. Phosphorylated insulin receptor and protein kinase B were increased, indicating restored hepatic insulin signaling. However, there was no reduction in hepatic triglycerides after the 3-day treatment period. Accelerating biliary cholesterol secretion restores glycemic control and reduces plasma triglycerides in obese db/db mice.

  14. Dicty_cDB: Contig-U12726-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available DY298864 ) IC0AAA96DA07RM1 CitNFL Citrus clementina cDNA 5',... 48 0.10 1 ( DY298348 ) IC0AAA95BD07RM1 CitNFL Citrus clementi...na cDNA 5',... 48 0.10 1 ( DY294893 ) IC0AAA86DB10RM1 CitNFL Citrus clementi...na cDNA 5',... 48 0.10 1 ( DY291995 ) IC0AAA79CG12RM1 CitNFL Citrus clementina cDNA 5',... 48 0....10 1 ( DY282181 ) IC0AAA56AB08RM1 CitNFL Citrus clementina cDNA 5',... 48 0.10 1 ( DY279712 ) IC0AAA4AF10RM1 CitNFL Citrus clementi...na cDNA 5', ... 48 0.10 1 ( DY277548 ) IC0AAA44AG01RM1 CitNFL Citrus clementi

  15. Dicty_cDB: Contig-U03262-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 2 ) Mus musculus B16 F10Y cells cDNA, RIKEN full-leng... 46 2.3 1 ( ET080496 ) QM0AAB9DD12RM1 CCER1 Citrus clementi...Z971886 ) PUDDF61TD ZM_0.6_1.0_KB Zea mays genomic clone ZM... 46 2.3 1 ( DY280275 ) IC0AAA50DB02RM1 CitNFL Citrus clementi...na cDNA 5',... 46 2.3 1 ( DY261480 ) KN0AAP3YA03FM1 Fruit-TF Citrus clementina cDNA 5'... 46 ...2.3 1 ( DY256661 ) KN0AAA1BE10ZM1 AbsAOv1 Citrus clementina cDNA 5',... 46 2.3 1 ( CX307061 ) C18025D05Rv Dr...ought2 Citrus reshni cDNA clone C18... 46 2.3 1 ( CX292158 ) C04011B12SK FlavFr1 Citrus clementi

  16. Effect of echinacoside on kidney fibrosis by inhibition of TGF-β1/Smads signaling pathway in the db/db mice model of diabetic nephropathy

    Directory of Open Access Journals (Sweden)

    Tang FJ

    2017-09-01

    Full Text Available Fengjuan Tang,1 Yarong Hao,1 Xue Zhang,1 Jian Qin2 1Department of Geriatrics, 2Central Laboratory, Renmin Hospital of Wuhan University, Hubei, People’s Republic of China Abstract: Kidney fibrosis and renal tubular epithelial-to-mesenchymal transition (EMT are the main pathological changes of diabetic nephropathy (DN, which eventually leads to end-stage renal disease. Previous studies have suggested that echinacoside (ECH is antifibrotic in the liver. However, the effect of ECH on kidney fibrosis in DN and its mechanisms are unknown. This study was performed to explore the effect of ECH on kidney fibrosis and also the molecular mechanisms of ECH in a db/db mice model of DN. Our results showed that, relative to db/db mice, the mice in the ECH group had an improved general state and reduced blood glucose and 24-hour urinary protein levels. The deterioration of renal function was delayed due to treatment with ECH. We also observed that ECH can improve histopathological findings in the kidneys of db/db mice, including collagen deposition, mesangial cell and mesangial matrix hyperplasia, basement membrane thickening, and podocyte reduction. Moreover, ECH inhibited the TGF-β1/Smads signaling pathway, downregulated fibronectin (FN, collagen IV, and alpha-smooth muscle actin (α-SMA levels, and upregulated E-cadherin level in the db/db mice model of DN. Our findings indicate that ECH has a therapeutic effect on DN, including the inhibition of renal tubular EMT and kidney fibrosis. Furthermore, ECH inhibits kidney fibrosis through regulation of the TGF-β1/Smads signaling pathway. Keywords: diabetic nephropathies, echinacoside, db/db mice, kidney fibrosis, EMT, TGF-β1/Smads signaling pathway

  17. Phosphatidylinositol 3-kinase/Akt signaling pathway activates the WNK-OSR1/SPAK-NCC phosphorylation cascade in hyperinsulinemic db/db mice.

    Science.gov (United States)

    Nishida, Hidenori; Sohara, Eisei; Nomura, Naohiro; Chiga, Motoko; Alessi, Dario R; Rai, Tatemitsu; Sasaki, Sei; Uchida, Shinichi

    2012-10-01

    Metabolic syndrome patients have insulin resistance, which causes hyperinsulinemia, which in turn causes aberrant increased renal sodium reabsorption. The precise mechanisms underlying this greater salt sensitivity of hyperinsulinemic patients remain unclear. Abnormal activation of the recently identified with-no-lysine kinase (WNK)-oxidative stress-responsive kinase 1 (OSR1)/STE20/SPS1-related proline/alanine-rich kinase (SPAK)-NaCl cotransporter (NCC) phosphorylation cascade results in the salt-sensitive hypertension of pseudohypoaldosteronism type II. Here, we report a study of renal WNK-OSR1/SPAK-NCC cascade activation in the db/db mouse model of hyperinsulinemic metabolic syndrome. Thiazide sensitivity was increased, suggesting greater activity of NCC in db/db mice. In fact, increased phosphorylation of OSR1/SPAK and NCC was observed. In both SpakT243A/+ and Osr1T185A/+ knock-in db/db mice, which carry mutations that disrupt the signal from WNK kinases, increased phosphorylation of NCC and elevated blood pressure were completely corrected, indicating that phosphorylation of SPAK and OSR1 by WNK kinases is required for the increased activation and phosphorylation of NCC in this model. Renal phosphorylated Akt was increased in db/db mice, suggesting that increased NCC phosphorylation is regulated by the phosphatidylinositol 3-kinase/Akt signaling cascade in the kidney in response to hyperinsulinemia. A phosphatidylinositol 3-kinase inhibitor (NVP-BEZ235) corrected the increased OSR1/SPAK-NCC phosphorylation. Another more specific phosphatidylinositol 3-kinase inhibitor (GDC-0941) and an Akt inhibitor (MK-2206) also inhibited increased NCC phosphorylation. These results indicate that the phosphatidylinositol 3-kinase/Akt signaling pathway activates the WNK-OSR1/SPAK-NCC phosphorylation cascade in db/db mice. This mechanism may play a role in the pathogenesis of salt-sensitive hypertension in human hyperinsulinemic conditions, such as the metabolic syndrome.

  18. PI3K/Akt Signaling Pathway Activates the WNK-OSR1/SPAK-NCC Phosphorylation Cascade in Hyperinsulinemic db/db Mice

    Science.gov (United States)

    Nishida, Hidenori; Sohara, Eisei; Nomura, Naohiro; Chiga, Motoko; Alessi, Dario R; Rai, Tatemitsu; Sasaki, Sei; Uchida, Shinichi

    2013-01-01

    Metabolic syndrome patients have insulin resistance, which causes hyperinsulinemia, which in turn causes aberrant increased renal sodium reabsorption. The precise mechanisms underlying this greater salt-sensitivity of hyperinsulinemic patients remain unclear. Abnormal activation of the recently-identified WNK kinase-OSR1/SPAK kinases-NCC transporter phosphorylation cascade results in the salt-sensitive hypertension of pseudohypoaldosteronism type II. Here, we report a study of renal WNK-OSR1/SPAK-NCC cascade activation in the db/db mouse model of hyperinsulinemic metabolic syndrome. Thiazide sensitivity was increased, suggesting greater activity of NCC in db/db mice. In fact, increased phosphorylation of OSR1/SPAK and NCC was observed. In both SpakT243A/+ and Osr1T185A/+ knock-in db/db mice, which carry mutations that disrupt the signal from WNK kinases, increased phosphorylation of NCC and elevated blood pressure were completely corrected, indicating that phosphorylation of SPAK and OSR1 by WNK kinases is required for the increased activation and phosphorylation of NCC in this model. Renal phosphorylated Akt was increased in db/db mice, suggesting that increased NCC phosphorylation is regulated by the PI3K/Akt signaling cascade in the kidney in response to hyperinsulinemia. A PI3K inhibitor (NVP-BEZ235) corrected the increased OSR1/SPAK-NCC phosphorylation. Another more specific PI3K inhibitor (GDC-0941) and an Akt inhibitor (MK-2206) also inhibited increased NCC phosphorylation. These results indicate that the PI3K/Akt signaling pathway activates the WNK-OSR1/SPAK-NCC phosphorylation cascade in db/db mice. This mechanism may play a role in the pathogenesis of salt-sensitive hypertension in human hyperinsulinemic conditions such as the metabolic syndrome. PMID:22949526

  19. Berberine-loaded solid lipid nanoparticles are concentrated in the liver and ameliorate hepatosteatosis in db/db mice

    Directory of Open Access Journals (Sweden)

    Xue M

    2015-08-01

    Full Text Available Mei Xue,1,2,* Liang Zhang,3,* Ming-xing Yang,1 Wei Zhang,1 Xiu-min Li,1,2 Zhi-min Ou,1 Zhi-peng Li,1,2 Su-huan Liu,1 Xue-jun Li,1 Shu-yu Yang1 1Xiamen Diabetes Institute, the First Affiliated Hospital of Xiamen University, Xiamen, 2Department of Pharmacology, Beijing University of Chinese Medicine, Chao Yang District, Beijing, 3Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China *These authors contributed equally to this work Abstract: Berberine (BBR shows very low plasma levels after oral administration due to its poor absorption by the gastrointestinal tract. We have previously demonstrated that BBR showed increased gastrointestinal absorption and enhanced antidiabetic effects in db/db mice after being entrapped into solid lipid nanoparticles (SLNs. However, whether BBR-loaded SLNs (BBR-SLNs also have beneficial effects on hepatosteatosis is not clear. We investigated the effects of BBR-SLNs on lipid metabolism in the liver using histological staining and reverse transcription polymerase chain reaction analysis. The results showed that oral administration of BBR-SLNs inhibited the increase of body weight and decreased liver weight in parallel with the reduction of serum alanine transaminase and liver triglyceride levels in db/db mice. The maximum drug concentration in the liver was 20-fold higher than that in the blood. BBR-SLNs reduced fat accumulation and lipid droplet sizes significantly in the liver, as indicated by hematoxylin and eosin and Oil Red O staining. The expression of lipogenic genes, including fatty acid synthase (FAS, stearoyl-CoA desaturase (SCD1, and sterol regulatory element-binding protein 1c (SREBP1c were downregulated, while lipolytic gene carnitine palmitoyltransferase-1 (CPT1 was upregulated in BBR-SLN-treated livers. In summary, we have uncovered an unexpected effect of BBR-SLNs on hepatosteatosis treatment through the inhibition of lipogenesis and the induction

  20. GigaDB: promoting data dissemination and reproducibility.

    Science.gov (United States)

    Sneddon, Tam P; Zhe, Xiao Si; Edmunds, Scott C; Li, Peter; Goodman, Laurie; Hunter, Christopher I

    2014-01-01

    Often papers are published where the underlying data supporting the research are not made available because of the limitations of making such large data sets publicly and permanently accessible. Even if the raw data are deposited in public archives, the essential analysis intermediaries, scripts or software are frequently not made available, meaning the science is not reproducible. The GigaScience journal is attempting to address this issue with the associated data storage and dissemination portal, the GigaScience database (GigaDB). Here we present the current version of GigaDB and reveal plans for the next generation of improvements. However, most importantly, we are soliciting responses from you, the users, to ensure that future developments are focused on the data storage and dissemination issues that still need resolving. Database URL: http://www.gigadb.org.

  1. Getting Started with GEO, CouchDB, and Nodejs

    CERN Document Server

    Thompson, Mick

    2011-01-01

    Today's mobile devices have GPS and standard APIs to give you access to coordinates-but what can you do with that data? With this concise book, application developers learn how to work with location data quickly and easily, using Node.js, CouchDB, and other open source tools and libraries. Node.js makes it simple to run event code on the Web, and the CouchDB document-oriented database lets you store location data and perform complex queries on it quickly. You'll learn how to get started with these tools, and then use them together to build an example project called MapChat, using HTML and Ja

  2. Rapid Screening of chloramphenicol in Turbot with photobacterium phosphoreum DB

    Institute of Scientific and Technical Information of China (English)

    Zhu Lanlan; Wang Jingxue; Lin Hong; Wang Yaqun; Wang Jing; Mei Cexia

    2009-01-01

    A new, simple, rapid microbial assay was put forward for the detection of chloramphenicol (CAP) residues in Turbot muscles using luminescent bacteria DB (Photobacterium phosphoreum) as test organism. By the luminescence inhibition of DB, the concentrations of CAP were determined. CAP spiked in Turbot muscle tissues ranging from 0.5 to 100μg/kg was extracted using ethyl acetate and hexane. The method had a good recovery of 93.69% with a minimum detection limit of 0.65μg/kg. It can be performed within 30min following simple extraction. The method therefore proved to be advantageous over chromatographic procedures as it was inexpensive, quite sensitive and can be adopted for rapid screening of CAP in Turbot tissues.

  3. Update History of This Database - D-HaploDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us D-HaploDB Up...date History of This Database Date Update contents 2011/09/22 D-HaploDB English archive site is ...his Database Database Description Download License Update History of This Databas...e Site Policy | Contact Us Update History of This Database - D-HaploDB | LSDB Archive ...

  4. Update History of This Database - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGDBj - Ortholog DB Up...date History of This Database Date Update contents 2014/05/12 PGDBj Ortholog DB Englis...a SEF URLs by Artio About This Database Database Description Download License Upd...ate History of This Database Site Policy | Contact Us Update History of This Database - PGDBj - Ortholog DB | LSDB Archive ...

  5. Scalable Web Application using Node.JS and CouchDB

    OpenAIRE

    Paudyal, Umesh

    2011-01-01

    This report presents design and implementation of a protoype application using server side javascript programming language, node.JS and couchDB as backend database. It scales and evaluates the developed prototype application and the couchDB for their scalability and performance. The report concludes that node.JS is a suitable framework for development of scalable web servers and couchDB as a backend database, though natively not distributed and scalable, can be scaled and distributed across m...

  6. EST Table: DB670370 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB670370 E_FL_BmN-_17N09_F_0 10/09/28 79 %/179 aa dbj|BAA76304.1| endonuclease and ...h 10/09/10 n.h 10/09/10 n.h 10/09/10 47 %/171 aa gi|270015323|gb|EFA11771.1| hypothetical protein TcasGA2_TC004098 [Tribolium castaneum] NM_001099615 BmN- ...

  7. Analyzing GAIAN Database (GaianDB) on a Tactical Network

    Science.gov (United States)

    2015-11-30

    NAME(S) AND ADDRESS(ES) US Army Research Laboratory ATTN: RDRL-CIN-T 2800 Powder Mill Road Adelphi, MD 20783-1138 8. PERFORMING ORGANIZATION...with the second-generation CSRs, we discovered that Internet Protocol (IP) encapsulation of GaianDB traffic in radio frequency (RF) transmissions...create a network bridge or, in our case, create an ad-hoc network by encapsulating raw packets (which contain preambles and Ethernet frames) inside

  8. EST Table: DB672736 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB672736 E_FL_BmN-_25P16_F_0 10/09/28 80 %/174 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  9. EST Table: DB670781 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB670781 E_FL_BmN-_19D22_F_0 10/09/28 97 %/112 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  10. EST Table: DB670034 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB670034 E_FL_BmN-_16K20_F_0 10/09/28 97 %/112 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  11. EST Table: DB672143 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB672143 E_FL_BmN-_23P18_F_0 10/09/28 97 %/115 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  12. EST Table: DB671186 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB671186 E_FL_BmN-_20J15_F_0 10/09/28 97 %/107 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  13. EST Table: DB670705 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB670705 E_FL_BmN-_18P15_F_0 10/09/28 97 %/112 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  14. EST Table: DB672816 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB672816 E_FL_BmN-_26D13_F_0 10/09/28 97 %/136 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  15. EST Table: DB669357 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB669357 E_FL_BmN-_14F05_F_0 10/09/28 79 %/167 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  16. EST Table: DB670427 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB670427 E_FL_BmN-_18A11_F_0 10/09/28 79 %/158 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  17. EST Table: DB669833 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB669833 E_FL_BmN-_15O19_F_0 10/09/28 97 %/127 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  18. EST Table: DB670674 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB670674 E_FL_BmN-_18N22_F_0 10/09/28 97 %/112 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  19. EST Table: DB668643 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB668643 E_FL_BmN-_11I07_F_0 10/09/28 97 %/102 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  20. EST Table: DB670460 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB670460 E_FL_BmN-_18C06_F_0 10/09/28 97 %/106 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  1. EST Table: DB671394 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB671394 E_FL_BmN-_21D22_F_0 10/09/28 97 %/130 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  2. EST Table: DB672479 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB672479 E_FL_BmN-_25C19_F_0 10/09/28 97 %/132 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  3. EST Table: DB669351 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB669351 E_FL_BmN-_14E22_F_0 10/09/28 97 %/136 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  4. EST Table: DB669958 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB669958 E_FL_BmN-_16G15_F_0 10/09/28 69 %/101 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  5. EST Table: DB673346 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB673346 E_FL_BmN-_27L23_F_0 10/09/28 82 %/199 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  6. EST Table: DB669384 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB669384 E_FL_BmN-_14G18_F_0 10/09/28 81 %/181 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  7. EST Table: DB669536 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB669536 E_FL_BmN-_14P04_F_0 10/09/28 78 %/142 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  8. EST Table: DB672087 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB672087 E_FL_BmN-_23M10_F_0 10/09/28 79 %/162 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  9. EST Table: DB670050 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB670050 E_FL_BmN-_16L17_F_0 10/09/28 97 %/104 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  10. EST Table: DB672158 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB672158 E_FL_BmN-_24A24_F_0 10/09/28 74 %/122 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  11. EST Table: DB673321 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB673321 E_FL_BmN-_27K18_F_0 10/09/28 73 %/115 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  12. EST Table: DB672727 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB672727 E_FL_BmN-_25P06_F_0 10/09/28 97 %/115 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  13. EST Table: DB670043 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB670043 E_FL_BmN-_16L08_F_0 10/09/28 78 %/156 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  14. EST Table: DB671704 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB671704 E_FL_BmN-_22G04_F_0 10/09/28 82 %/193 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  15. EST Table: DB670066 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB670066 E_FL_BmN-_16M17_F_0 10/09/28 80 %/177 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  16. EST Table: DB671548 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB671548 E_FL_BmN-_21N19_F_0 10/09/28 78 %/160 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  17. EST Table: DB671621 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB671621 E_FL_BmN-_22B23_F_0 10/09/28 78 %/166 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  18. EST Table: DB670261 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB670261 E_FL_BmN-_17H02_F_0 10/09/28 97 %/112 aa dbj|BAD35018.1| coat protein [Bombyx mori Macula-like late...nt virus] 10/09/01 n.h 10/08/28 n.h 10/09/10 n.h 10/09/10 n.h 10/09/10 n.h AU002603 BmN- ...

  19. Protein (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGD... The IDs of clusters that the amino acid sequences belong to in each taxon are indicated. Data file File name: pgd...bj_ortholog_db_cyanobacteria_protein.zip File URL: ftp://ftp.biosciencedbc.jp/archive/pgdbj-ortholog-db/LATEST/pgd...ch URL http://togodb.biosciencedbc.jp/togodb/view/pgdbj_ortholog_db_cyanobacteria_protein#en Data acquisitio...ase Database Description Download License Update History of This Database Site Policy | Contact Us Protein (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive ...

  20. Magnolia officinalis Extract Contains Potent Inhibitors against PTP1B and Attenuates Hyperglycemia in db/db Mice

    Directory of Open Access Journals (Sweden)

    Jing Sun

    2015-01-01

    Full Text Available Protein tyrosine phosphatase 1B (PTP1B is an established therapeutic target for type 2 diabetes mellitus (T2DM and obesity. The aim of this study was to investigate the inhibitory activity of Magnolia officinalis extract (ME on PTP1B and its anti-T2DM effects. Inhibition assays and inhibition kinetics of ME were performed in vitro. 3T3-L1 adipocytes and C2C12 myotubes were stimulated with ME to explore its bioavailability in cell level. The in vivo studies were performed on db/db mice to probe its anti-T2DM effects. In the present study, ME inhibited PTP1B in a reversible competitive manner and displayed good selectivity against PTPs in vitro. Furthermore, ME enhanced tyrosine phosphorylation levels of cellular proteins, especially the insulin-induced tyrosine phosphorylations of insulin receptor β-subunit (IRβ and ERK1/2 in a dose-dependent manner in stimulated 3T3-L1 adipocytes and C2C12 myotubes. Meanwhile, ME enhanced insulin-stimulated GLUT4 translocation. More importantly, there was a significant decrease in fasting plasma glucose level of db/db diabetic mice treated orally with 0.5 g/kg ME for 4 weeks. These findings indicated that improvement of insulin sensitivity and hypoglycemic effects of ME may be attributed to the inhibition of PTP1B. Thereby, we pioneered the inhibitory potential of ME targeted on PTP1B as anti-T2DM drug discovery.

  1. db/db Mice Exhibit Features of Human Type 2 Diabetes That Are Not Present in Weight-Matched C57BL/6J Mice Fed a Western Diet

    Directory of Open Access Journals (Sweden)

    Susan J. Burke

    2017-01-01

    Full Text Available To understand features of human obesity and type 2 diabetes mellitus (T2D that can be recapitulated in the mouse, we compared C57BL/6J mice fed a Western-style diet (WD to weight-matched genetically obese leptin receptor-deficient mice (db/db. All mice were monitored for changes in body composition, glycemia, and total body mass. To objectively compare diet-induced and genetic models of obesity, tissue analyses were conducted using mice with similar body mass. We found that adipose tissue inflammation was present in both models of obesity. In addition, distinct alterations in metabolic flexibility were evident between WD-fed mice and db/db mice. Circulating insulin levels are elevated in each model of obesity, while glucagon was increased only in the db/db mice. Although both WD-fed and db/db mice exhibited adaptive increases in islet size, the db/db mice also displayed augmented islet expression of the dedifferentiation marker Aldh1a3 and reduced nuclear presence of the transcription factor Nkx6.1. Based on the collective results put forth herein, we conclude that db/db mice capture key features of human T2D that do not occur in WD-fed C57BL/6J mice of comparable body mass.

  2. A Response Surface Methodology Approach to Investigate the Effect of Sulfur Dioxide, pH, and Ethanol on DbCD and DbVPR Gene Expression and on the Volatile Phenol Production in Dekkera/Brettanomyces bruxellensis CBS2499.

    Science.gov (United States)

    Valdetara, Federica; Fracassetti, Daniela; Campanello, Alessia; Costa, Carlo; Foschino, Roberto; Compagno, Concetta; Vigentini, Ileana

    2017-01-01

    Dekkera/Brettanomyces bruxellensis, the main spoilage yeast in barrel-aged wine, metabolize hydroxycinnamic acids into off-flavors, namely ethylphenols. Recently, both the enzymes involved in this transformation, the cinnamate decarboxylase (DbCD) and the vinylphenol reductase (DbVPR), have been identified. To counteract microbial proliferation in wine, sulfur dioxide (SO2) is used commonly to stabilize the final product, but limiting its use is advised to preserve human health and boost sustainability in winemaking. In the present study, the influence of SO2 was investigated in relation with pH and ethanol factors on the expression of DbCD and DbVPR genes and volatile phenol production in D. bruxellensis CBS2499 strain under different model wines throughout a response surface methodology (RSM). In order to ensure an exact quantification of DbCD and DbVPR expression, an appropriate housekeeping gene was sought among DbPDC, DbALD, DbEF, DbACT, and DbTUB genes by GeNorm and Normfinder algorithms. The latter gene showed the highest expression stability and it was chosen as the reference housekeeping gene in qPCR assays. Even though SO2 could not be commented as main factor because of its statistical irrelevance on the response of DbCD gene, linear interactions with pH and ethanol concurred to define a significant effect (p bruxellensis spoilage.

  3. Oral administration of Nitraria retusa ethanolic extract enhances hepatic lipid metabolism in db/db mice model 'BKS.Cg-Dock7(m)+/+ Lepr(db/)J' through the modulation of lipogenesis-lipolysis balance.

    Science.gov (United States)

    Zar Kalai, Feten; Han, Junkyu; Ksouri, Riadh; Abdelly, Chedly; Isoda, Hiroko

    2014-10-01

    The medicinal plants can be used in the prevention or treatment of many diseases. Several studies concerning the potential of bioactive components in plants and food products and their link to obesity and related metabolic disorders, have been gaining big interest. Diabetes is a serious metabolic syndrome. Searching for alternative natural bioactive molecules is considered main strategy to manage diabetes through weight management. In the present study, an edible halophyte Nitraria retusa was selected and in vivo experiment was conducted using db/db model mice. We orally administrated its ethanol extract (NRE) to BKS.Cg-Dock7(m)+/+ Lepr(db/)J mice model for a period of 4 weeks. The effect was evaluated on the body weight and adiposity changes and on the biochemical parameters of db/db NRE-treated mice. The molecular mechanism underlying the anti-obesity effect was investigated by testing the gene expression related to hepatic lipid metabolism. NRE was found to significantly supress increases in body and fat mass weight, decreases triglycerides and LDL-cholesterol levels and enhances gene expression related to lipid homeostasis in liver showing anti-obesity actions. Our findings, indicate that NRE possesses potential anti-obesity effects in BKS.Cg-Dock7(m)+/+ Lepr(db/)J model mice and may relieve obesity-related symptoms including hyperlipidemia through modulating the lipolysis-lipogenesis balance. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. InterProScan Result: DB669691 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB669691 DB669691_3_ORF2 B6716AD6F9104644 PANTHER PTHR10132 ALPHA-/EPSILON-SARCOGLYCAN (ALPHA-/EPSILO...N-SG) 6.4e-18 T IPR008908 Sarcoglycan alphaepsilon Cellular Component: sarcoglycan complex (GO:0016012) ...

  5. Update History of This Database - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...List Contact us MicrobeDB.jp Update History of This Database Date Update contents 2017/06/29 Archive V2 is r...ion Download License Update History of This Database Site Policy | Contact Us Update History of This Database - MicrobeDB.jp | LSDB Archive ...

  6. Transformasi Skema Basis Data Relasional Menjadi Model Data Berorientasi Dokumen pada MongoDB

    Directory of Open Access Journals (Sweden)

    I Gede Winaya

    2016-01-01

    Full Text Available MongoDB is a database that uses document-oriented data storage models. In fact, to  migrate from a relational database to NoSQL databases such as MongoDB is not an easy matter especially if the data are extremely complex. Based on the documentation that has been done by several global companies related to the use of MongoDB, it can be concluded that the process of migration from RDBMS to MongoDB require quite a long time. One process that takes quite a lot is transformation of relational database schema into a document-oriented data model on MongoDB.             This research discusses the development transformation system of relational database schema to the document oriented data model in MongoDB. The process of transformation is done by utilizing the structure and relationships between tables in the scheme as the main parameters of the modeling algorithm. In the process of the modeling documents, it necessary to adjustments the specifications of MongoDB document that formed document model can be implemented in MongoDB.             Document models are formed from transformation process can be a single document, embedded document, referenced document or combination of these. Document models are formed depending on the type, rules, and the value of the relationships cardinality between tables in the relational database schema.

  7. InterProScan Result: DB674426 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB674426 DB674426_4_ORF1 4B0C8A5F848582EF PFAM PF04683 Proteasom_Rpn13 NA ? IPR006773 unintegrated Cellular... Component: nucleus (GO:0005634)|Cellular Component: cytoplasm (GO:0005737) ...

  8. Index of /data/pgdbj-ortholog-db/20170307 [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Index of /data/pgdbj-ortholog-db/20170307 Name Last modified Size Description Parent Directory - README.html... 07-Mar-2017 15:07 23K README_e.html 07-Mar-2017 15:08 20K pgdbj_ortholog_db_cy..>

  9. InterProScan Result: DB674426 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB674426 DB674426_4_ORF1 4B0C8A5F848582EF PFAM PF04683 Proteasom_Rpn13 NA ? IPR006773 unintegrated Cellular... Component: nucleus (GO:0005634)|Cellular Component: cytoplasm (GO:0005737) ...

  10. InterProScan Result: DB673798 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB673798 DB673798_4_ORF1 AEE38DD3F2A2B877 PRINTS PR00385 P450 5.8e-05 T IPR001128 Cytochrome P450 Molecular... Function: monooxygenase activity (GO:0004497)|Molecular Function: iron ion binding (GO:0005506)|Molecular... Function: electron carrier activity (GO:0009055)|Molecular Function: heme binding (GO:0020037) ...

  11. BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology.

    Science.gov (United States)

    Gilson, Michael K; Liu, Tiqing; Baitaluk, Michael; Nicola, George; Hwang, Linda; Chong, Jenny

    2016-01-04

    BindingDB, www.bindingdb.org, is a publicly accessible database of experimental protein-small molecule interaction data. Its collection of over a million data entries derives primarily from scientific articles and, increasingly, US patents. BindingDB provides many ways to browse and search for data of interest, including an advanced search tool, which can cross searches of multiple query types, including text, chemical structure, protein sequence and numerical affinities. The PDB and PubMed provide links to data in BindingDB, and vice versa; and BindingDB provides links to pathway information, the ZINC catalog of available compounds, and other resources. The BindingDB website offers specialized tools that take advantage of its large data collection, including ones to generate hypotheses for the protein targets bound by a bioactive compound, and for the compounds bound by a new protein of known sequence; and virtual compound screening by maximal chemical similarity, binary kernel discrimination, and support vector machine methods. Specialized data sets are also available, such as binding data for hundreds of congeneric series of ligands, drawn from BindingDB and organized for use in validating drug design methods. BindingDB offers several forms of programmatic access, and comes with extensive background material and documentation. Here, we provide the first update of BindingDB since 2007, focusing on new and unique features and highlighting directions of importance to the field as a whole.

  12. myPhyloDB: a local web server for the storage and analysis of metagenomics data

    Science.gov (United States)

    myPhyloDB is a user-friendly personal database with a browser-interface designed to facilitate the storage, processing, analysis, and distribution of metagenomics data. MyPhyloDB archives raw sequencing files, and allows for easy selection of project(s)/sample(s) of any combination from all availab...

  13. Original Dataset - dbQSNP | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us dbQSNP Original Dataset Data detail Data name Original Dataset DOI 10.18908/lsdba.nbdc00042-...This Database Site Policy | Contact Us Original Dataset - dbQSNP | LSDB Archive ... ...switchLanguage; BLAST Search Image Search Home About Archive Update History Data

  14. DB2数据库设计及优化技术研究%The Design and Optimization of DB2 Database

    Institute of Scientific and Technical Information of China (English)

    刘姝

    2011-01-01

    DB2数据库是IBM公司研制的一种大型的关系型数据库,它在大数据量存储中具有很高的效率和很好的安全性。本文研究了基于DB2数据库的设计和数据库的一些优化技术。对数据库设计和优化的规则做了研究。%DB2 database is a large relational database which is developed by IBM,it has high efficiency and good security in a large amount of data storage.In this paper,database design and some optimization techniques are researched based on the DB2 database.Some rules of database design and optimization are researched.

  15. Plant DB link - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGDBj Registered... Description Download License Update History of This Database Site Policy | Contact Us Plant DB link - PGDBj Registered

  16. Temperature Dependence of Characteristics for Multimode Interference Based 3-dB Coupler in SOI

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    The temperature dependence of characteristics for multimode interference(MMI) based 3-dB coupler in silicon-on-insulator is analyzed, which originates from the relatively high thermo-optic coefficient of silicon. For restricted interference 3-dB MMI coupler, the output power uniformity is ideally 0 at room temperature and becomes 0.32dB when temperature rises up to 550K.For symmetric interference 3-dB MMI coupler, the power uniformity keeps ideally 0 due to its intrinsic symmetric interference mechanism. With the temperature rising, the excess loss of the both devices increases. The performance deterioration due to temperature variety is more obvious to restricted interference MMI 3-dB coupler, comparing with that of symmetric interference MMI 3-dB coupler.

  17. DB2 9 for Linux, Unix, and Windows database administration upgrade certification study guide

    CERN Document Server

    Sanders, Roger E

    2007-01-01

    Written by one of the world's leading DB2 authors who is an active participant in the development of the DB2 certification exams, this resource covers everything a database adminstrator needs to know to pass the DB2 9 for Linux, UNIX, and Windows Database Administration Certification Upgrade exam (Exam 736). This comprehensive study guide discusses all exam topics: server management, data placement, XML concepts, analyzing activity, high availability, database security, and much more. Each chapter contains an extensive set of practice questions along with carefully explained answers. Both information-technology professionals who have experience as database administrators and have a current DBA certification on version 8 of DB2 and individuals who would like to learn the new features of DB2 9 will benefit from the information in this reference guide.

  18. The role of leptin and its short-form receptor in inflammation in db/db mice infused with peritoneal dialysis fluid.

    Science.gov (United States)

    Leung, Joseph C K; Chan, Loretta Y Y; Lam, Man Fai; Tang, Sydney C W; Chow, Chui Wa; Lim, Ai Ing; Lai, Kar Neng

    2012-08-01

    In peritoneal dialysis (PD), the peritoneal membrane exhibits structural and functional changes following continuous exposure to the non-physiological peritoneal dialysis fluid (PDF). In this study, we examined the effect of PDF on peritoneal adipose tissue in a diabetic milieu. Six-week-old db/db mice and their non-diabetic littermates (db/m) were subjected to uninephrectomy. All animals then received intra-abdominal infusion of lactated Ringer's solution (Ringer) or 1.5% glucose-containing PDF (Dianeal) twice daily. Mice were sacrificed 4 weeks later. Parietal and visceral adipose tissues were harvested for examining gene and protein expression of adiponectin, leptin, monocyte chemotactic protein-1, vascular endothelial growth factor, tumor necrosis factor alpha (TNF-α), transforming growth factor beta and interleukin 6 (IL-6). Expression of TNF-α and F4/80+ macrophage accumulation in adipose tissues was assessed by immunohistochemical staining. Modulation of leptin synthesis and leptin receptors expression and the relevant signaling pathways were also determined by quantitative reverse transcription-polymerase chain reaction, immunoblotting or enzyme-linked immunosorbent assay. Compared to Ringer infusion, Dianeal infusion significantly increased serum leptin but decreased adiponectin in db/db mice. Increased expression of leptin, TNF-α and IL-6 was observed in visceral but not in parietal adipose tissue. Dianeal infusion also increased F4/80+ macrophage accumulation and enhanced the expression of pro-inflammatory cytokines including IL-6 and TNF-α in the visceral adipose tissue. Compared to db/m mice, infusion with Dianeal exhibited a more deleterious effect on db/db mice, characterized by an upregulation of short-form leptin receptor ObRa and activation of the mitogen-activated protein kinase signaling pathway. In conclusion, PD-induced hyperleptinemia amplifies the inflammatory response of adipose tissue through short-form leptin receptor when the long

  19. The temperature dependence of the retention index for n-alkyl esters of acetic, propionic, cyclohexanecarboxylic, benzoic and phenylacetic acid on DB-1 and DB-5 capillary columns

    Directory of Open Access Journals (Sweden)

    DUSAN Z. MIJIN

    2006-06-01

    Full Text Available The temperature dependence of the retention index was studied for n-alkyl esters of acetic, propionic, cyclohexanecarboxylic, benzoic and phenylacetic acid on DB-1 and DB-5 capillary columns. The study was performed over various temperature ranges depending on the volatility of the ester. Two linear equations of the temperature dependence of the retention data on the column temperature and its reciprocal as variables were studied. Agood linearity of the retention index versus column temperature was found.

  20. Chemotherapy of second stage human African trypanosomiasis: comparison between the parenteral diamidine DB829 and its oral prodrug DB868 in vervet monkeys.

    Science.gov (United States)

    Thuita, John K; Wolf, Kristina K; Murilla, Grace A; Bridges, Arlene S; Boykin, David W; Mutuku, James N; Liu, Qiang; Jones, Susan K; Gem, Charles O; Ching, Shelley; Tidwell, Richard R; Wang, Michael Z; Paine, Mary F; Brun, Reto

    2015-02-01

    Human African trypanosomiasis (HAT, sleeping sickness) ranks among the most neglected tropical diseases based on limited availability of drugs that are safe and efficacious, particularly against the second stage (central nervous system [CNS]) of infection. In response to this largely unmet need for new treatments, the Consortium for Parasitic Drug Development developed novel parenteral diamidines and corresponding oral prodrugs that have shown cure of a murine model of second stage HAT. As a rationale for selection of one of these compounds for further development, the pharmacokinetics and efficacy of intramuscular (IM) active diamidine 2,5-bis(5-amidino-2-pyridyl)furan (DB829; CPD-0802) and oral prodrug2,5-bis[5-(N-methoxyamidino)-2-pyridyl]furan (DB868) were compared in the vervet monkey model of second stage HAT. Treatment was initiated 28 days post-infection of monkeys with T. b. rhodesiense KETRI 2537. Results showed that IM DB829 at 5 mg/kg/day for 5 consecutive days, 5 mg/kg/day every other day for 5 doses, or 2.5 mg/kg/day for 5 consecutive days cured all monkeys (5/5). Oral DB868 was less successful, with no cures (0/2) at 3 mg/kg/day for 10 days and cure rates of 1/4 at 10 mg/kg/day for 10 days and 20 mg/kg/day for 10 days; in total, only 2/10 monkeys were cured with DB868 dose regimens. The geometric mean plasma Cmax of IM DB829 at 5 mg/kg following the last of 5 doses was 25-fold greater than that after 10 daily oral doses of DB868 at 20 mg/kg. These data suggest that the active diamidine DB829, administered IM, should be considered for further development as a potential new treatment for second stage HAT.

  1. Evaluation of loganin, iridoid glycoside from Corni Fructus, on hepatic and renal glucolipotoxicity and inflammation in type 2 diabetic db/db mice.

    Science.gov (United States)

    Yamabe, Noriko; Noh, Jeong Sook; Park, Chan Hum; Kang, Ki Sung; Shibahara, Naotoshi; Tanaka, Takashi; Yokozawa, Takako

    2010-12-01

    Previously, we have reported that Corni Fructus possessed hypoglycemic and hypocholesterolemic effects in streptozotocin-induced type 1 diabetic rats and diet-induced hypercholesterolemic rats. Herein, we have focused on the effect and mechanism of loganin, a major iridoid glycoside of Corni Fructus, on the type 2 diabetic db/db mice. Loganin was orally administered to db/db mice at a dose of 20 or 100 mg/kg body weight daily for 8 weeks. The biochemical factors and expressions of protein and mRNA related to lipid metabolism, inflammation, advanced glycation endproducts, and its receptor were measured. In loganin-treated db/db mice, hyperglycemia and dyslipidemia were ameliorated in both the serum and hepatic tissue; however, in the kidney, only triglyceride was reduced. The enhanced oxidative stress was alleviated by loganin through a decrease in thiobarbituric acid-reactive substances (liver and kidney) and reactive oxygen species (serum, liver, and kidney), as well as augmentation of the oxidized to reduced glutathione ratio (liver and kidney). The marked lipid-regulatory effect of loganin was exerted in the liver of type 2 diabetic mice via suppressing mRNA expressions related to lipid synthesis and adjusting the abnormal expression of peroxisome proliferator-activated receptor α and sterol regulatory-element binding protein in the nucleus. Furthermore, loganin inhibited advanced glycation endproduct formation and the expression of its receptor, and nuclear factor-kappa B-induced inflammation in the hepatic tissue of db/db mice. Loganin exhibits protective effects against hepatic injury and other diabetic complications associated with abnormal metabolic states and inflammation caused by oxidative stress and advanced glycation endproduct formation.

  2. Hepato-protective effects of loganin, iridoid glycoside from Corni Fructus, against hyperglycemia-activated signaling pathway in liver of type 2 diabetic db/db mice.

    Science.gov (United States)

    Park, Chan Hum; Tanaka, Takashi; Kim, Ji Hyun; Cho, Eun Ju; Park, Jong Cheol; Shibahara, Naotoshi; Yokozawa, Takako

    2011-11-28

    Accumulating evidence indicates that uncontrolled diabetes leads to the progression of diabetic complications such as liver disorder. The present study was carried out to elucidate the protective role of loganin extracted from Corni Fructus against hepatic oxidative stress caused by type 2 diabetes. Loganin (20 or 100mg/kg body weight/day, p.o.) was administered every day for 8 weeks to db/db mice, and its effect was assessed on comparison with vehicle-treated db/db and m/m mice. The administration of loganin led to a decrease in glucose and elevation of leptin in serum. The diabetic oxidative stress was attenuated by loganin through inhibitions of reactive oxygen species production and lipid peroxidation in the serum and liver. The expression of proteins induced by oxidative stress was significantly up-regulated in the liver of diabetic db/db mice; however, the expressions of both Nox-4 and p22(phox) were decreased significantly by loganin administration. Loganin showed a crucial effect in the inflammation-activated signaling pathway through the regulation of NF-κB, COX-2, and iNOS. It was also found to regulate the anti-inflammatory factors Nrf-2 and HO-1 in hepatic tissue. Moreover, expression of MCP-1 was significantly down-regulated in the loganin-treated db/db mice. Furthermore, loganin administration showed a protective effect against apoptosis by the regulation of Bcl-2 and cytochrome c. The present study demonstrated that the administration of loganin isolated from Corni Fructus had a protective effect against hepatic oxidative stress under type 2 diabetes through regulations of protein expressions related to oxidative stress, inflammation, and apoptosis.

  3. cuticleDB: a relational database of Arthropod cuticular proteins

    Directory of Open Access Journals (Sweden)

    Willis Judith H

    2004-09-01

    Full Text Available Abstract Background The insect exoskeleton or cuticle is a bi-partite composite of proteins and chitin that provides protective, skeletal and structural functions. Little information is available about the molecular structure of this important complex that exhibits a helicoidal architecture. Scores of sequences of cuticular proteins have been obtained from direct protein sequencing, from cDNAs, and from genomic analyses. Most of these cuticular protein sequences contain motifs found only in arthropod proteins. Description cuticleDB is a relational database containing all structural proteins of Arthropod cuticle identified to date. Many come from direct sequencing of proteins isolated from cuticle and from sequences from cDNAs that share common features with these authentic cuticular proteins. It also includes proteins from the Drosophila melanogaster and the Anopheles gambiae genomes, that have been predicted to be cuticular proteins, based on a Pfam motif (PF00379 responsible for chitin binding in Arthropod cuticle. The total number of the database entries is 445: 370 derive from insects, 60 from Crustacea and 15 from Chelicerata. The database can be accessed from our web server at http://bioinformatics.biol.uoa.gr/cuticleDB. Conclusions CuticleDB was primarily designed to contain correct and full annotation of cuticular protein data. The database will be of help to future genome annotators. Users will be able to test hypotheses for the existence of known and also of yet unknown motifs in cuticular proteins. An analysis of motifs may contribute to understanding how proteins contribute to the physical properties of cuticle as well as to the precise nature of their interaction with chitin.

  4. HDACiDB: a database for histone deacetylase inhibitors

    Directory of Open Access Journals (Sweden)

    Murugan K

    2015-04-01

    Full Text Available Kasi Murugan,1 Shanmugasamy Sangeetha,2 Shanmugasamy Ranjitha,2 Antony Vimala,2 Saleh Al-Sohaibani,1 Gopal Rameshkumar21Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia; 2Bioinformatics Laboratory, Anna University K. Balachander Research Centre, MIT Campus of Anna University Chennai, Chennai, IndiaAbstract: An histone deacetylase (HDAC inhibitor database (HDACiDB was constructed to enable rapid access to data relevant to the development of epigenetic modulators (HDAC inhibitors [HDACi], helping bring precision cancer medicine a step closer. Thousands of HDACi targeting HDACs are in various stages of development and are being tested in clinical trials as monotherapy and in combination with other cancer agents. Despite the abundance of HDACi, information resources are limited. Tools for in silico experiments on specific HDACi prediction, for designing and analyzing the generated data, as well as custom-made specific tools and interactive databases, are needed. We have developed an HDACiDB that is a composite collection of HDACi and currently comprises 1,445 chemical compounds, including 419 natural and 1,026 synthetic ones having the potential to inhibit histone deacetylation. Most importantly, it will allow application of Lipinski’s rule of five drug-likeness and other physicochemical property-based screening of the inhibitors. It also provides easy access to information on their source of origin, molecular properties, drug likeness, as well as bioavailability with relevant references cited. Being the first comprehensive database on HDACi that contains all known natural and synthetic HDACi, the HDACiDB may help to improve our knowledge concerning the mechanisms of actions of available HDACi and enable us to selectively target individual HDAC isoforms and establish a new paradigm for intelligent epigenetic cancer drug design. The database is freely available on the http

  5. PineappleDB: An online pineapple bioinformatics resource

    Directory of Open Access Journals (Sweden)

    Fairbairn David J

    2005-10-01

    Full Text Available Abstract Background A world first pineapple EST sequencing program has been undertaken to investigate genes expressed during non-climacteric fruit ripening and the nematode-plant interaction during root infection. Very little is known of how non-climacteric fruit ripening is controlled or of the molecular basis of the nematode-plant interaction. PineappleDB was developed to provide the research community with access to a curated bioinformatics resource housing the fruit, root and nematode infected gall expressed sequences. Description PineappleDB is an online, curated database providing integrated access to annotated expressed sequence tag (EST data for cDNA clones isolated from pineapple fruit, root, and nematode infected root gall vascular cylinder tissues. The database currently houses over 5600 EST sequences, 3383 contig consensus sequences, and associated bioinformatic data including splice variants, Arabidopsis homologues, both MIPS based and Gene Ontology functional classifications, and clone distributions. The online resource can be searched by text or by BLAST sequence homology. The data outputs provide comprehensive sequence, bioinformatic and functional classification information. Conclusion The online pineapple bioinformatic resource provides the research community with access to pineapple fruit and root/gall sequence and bioinformatic data in a user-friendly format. The search tools enable efficient data mining and present a wide spectrum of bioinformatic and functional classification information. PineappleDB will be of broad appeal to researchers investigating pineapple genetics, non-climacteric fruit ripening, root-knot nematode infection, crassulacean acid metabolism and alternative RNA splicing in plants.

  6. SilkDB: a knowledgebase for silkworm biology and genomics

    DEFF Research Database (Denmark)

    Wang, Jing; Xia, Qingyou; He, Ximiao

    2005-01-01

    of ESTs from Bombyx mandarina, a wild progenitor of B.mori, and a collection of genes from other Lepidoptera. Comparative analysis results between the domestic and wild silkworm, between B.mori and other Lepidoptera, and between B.mori and the two sequenced insects, fruitfly and mosquito, are displayed...... by using B.mori genome sequence as a reference framework. Designed as a basic platform, SilkDB strives to provide a comprehensive knowledgebase about the silkworm and present the silkworm genome and related information in systematic and graphical ways for the convenience of in-depth comparative studies...

  7. EST Table: DB676926 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB676926 E_FL_BmN-_25C14_R_0 10/09/28 90 %/140 aa ref|NP_001037470.1| protein ultra...spiracle homolog [Bombyx mori] sp|P49700.1|USP_BOMMO RecName: Full=Protein ultraspiracle homolog; AltName: F...1|gene:AGAP002095 10/09/10 44 %/133 aa gnl|Amel|GB16648-PA 10/09/10 42 %/127 aa gi|121308144|emb|CAL25729.1| ultraspiracle nuclear receptor [Tribolium castaneum] BJ988216 BmN- ...

  8. EST Table: DB675523 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB675523 E_FL_BmN-_20I20_R_0 10/09/28 89 %/128 aa ref|NP_001037470.1| protein ultra...spiracle homolog [Bombyx mori] sp|P49700.1|USP_BOMMO RecName: Full=Protein ultraspiracle homolog; AltName: F...1|gene:AGAP002095 10/09/10 41 %/122 aa gnl|Amel|GB16648-PA 10/09/10 44 %/115 aa gi|121308144|emb|CAL25729.1| ultraspiracle nuclear receptor [Tribolium castaneum] BJ988216 BmN- ...

  9. 吡格列酮对db/db小鼠骨骼肌蛋白酪氨酸磷酸酶1B表达的影响%The Effects of Pioglitazone on Expression of Protein Tyrosine Phosphatase 1 B in Muscle of db/db Mice

    Institute of Scientific and Technical Information of China (English)

    卢斌; 顾萍; 邵加庆; 杜宏; 王坚

    2012-01-01

    目的 探讨吡格列酮对db/db小鼠骨骼肌蛋白酪氨酸磷酸酶1B( protein tyrosine phosphatase 1B,PTP1B)表达水平的影响.方法 将20只4周龄db/db小鼠随机分为两组(吡格列酮组和db/db对照组),每组10只,分别给予吡格列酮10mg/kg.d和安慰剂灌胃.另设10只同周龄db/m小鼠,给予安慰剂灌胃作为非糖尿病对照(db/m对照组).每周监测体重、血糖,4周后用蛋白印迹法检测各组小鼠骨骼肌组织中PTP1 B蛋白含量.结果 db/db组小鼠骨骼肌PTP1B表达显著高于db/m组,给予吡格列酮干预,血糖、胰岛素抵抗指数显著低于db/db组(P<0.05),骨骼肌PTP1B表达水平亦显著降低(P<0.05).结论吡格列酮改善胰岛素抵抗,可能与降低骨骼肌PTP1B蛋白表达有关.%Objective To explore the effects of pioglitazone on expression of protein tyrosine phosphatase 1B in muscle of db/db mice. Methods Twenty db/db mice aged 4 weeks were randomized to pioglitazone group ( PIO group) and db/db group, fed with 10mg/kg·d pioglitazone and placebo respectively. Ten age-matched db/misty mice were concurrently treated with placebo as non-diabetic control group (db/m group). Body weight and blood glucose were measured every week. After 4 weeks'treatment, the expression of PTP1B in muscle of mice were determined with Western blotting. Results The expression of PTP1B in muscle of db/db mice significantly increased compared with db/m( P < 0. 05 ). Pioglitazone treatment significantly decreased fasting blood glucose and HOMA-IR. The expression of PTP1B in muscle of pioglitazone-treated mice obviously decreased compared with db/db group ( P < 0.05 ). Conclusion Pioglitazone treatment could improve insulin resistance possibly by reducing the expression level of PTP1B in the muscle.

  10. Serotonin- and Dopamine-Related Gene Expression in db/db Mice Islets and in MIN6 β-Cells Treated with Palmitate and Oleate

    Science.gov (United States)

    Cataldo, L. R.; Olmos, P.; Galgani, J. E.; Valenzuela, R.; Aranda, E.; Cortés, V. A.; Santos, J. L.

    2016-01-01

    High circulating nonesterified fatty acids (NEFAs) concentration, often reported in diabetes, leads to impaired glucose-stimulated insulin secretion (GSIS) through not yet well-defined mechanisms. Serotonin and dopamine might contribute to NEFA-dependent β-cell dysfunction, since extracellular signal of these monoamines decreases GSIS. Moreover, palmitate-treated β-cells may enhance the expression of the serotonin receptor Htr2c, affecting insulin secretion. Additionally, the expression of monoamine-oxidase type B (Maob) seems to be lower in islets from humans and mice with diabetes compared to nondiabetic islets, which may lead to increased monoamine concentrations. We assessed the expression of serotonin- and dopamine-related genes in islets from db/db and wild-type (WT) mice. In addition, the effect of palmitate and oleate on the expression of such genes, 5HT content, and GSIS in MIN6 β-cell was determined. Lower Maob expression was found in islets from db/db versus WT mice and in MIN6 β-cells in response to palmitate and oleate treatment compared to vehicle. Reduced 5HT content and impaired GSIS in response to palmitate (−25%; p < 0.0001) and oleate (−43%; p < 0.0001) were detected in MIN6 β-cells. In conclusion, known defects of GSIS in islets from db/db mice and MIN6 β-cells treated with NEFAs are accompanied by reduced Maob expression and reduced 5HT content. PMID:27366756

  11. Impaired endothelial calcium signaling is responsible for the defective dilation of mesenteric resistance arteries from db/db mice to acetylcholine.

    Science.gov (United States)

    Chen, Hua; Kold-Petersen, Henrik; Laher, Ismael; Simonsen, Ulf; Aalkjaer, Christian

    2015-11-15

    We aimed at assessing the role of endothelial cell calcium for the endothelial dysfunction of mesenteric resistance arteries of db/db mice (a model of type 2 diabetes) and determine whether treatment with sulfaphenazole, improves endothelial calcium signaling and function. Pressure myography was used to study acetylcholine (ACh) -induced vasodilation. Intracellular calcium ([Ca(2+)]i) transients was measured by confocal laser scanning microscopy and smooth muscle membrane potential with sharp microelectrodes. The impaired dilation to ACh observed in mesenteric resistance arteries from db/db mice was improved by treatment of the mice with sulfaphenazole for 8 weeks. The impaired dilation to ACh was associated with decreased endothelial [Ca(2+)]i and smooth muscle hyperpolarization. Sulfaphenazole applied in vitro improved endothelial mediated dilation of arteries from db/db mice both in the absence and the presence of inhibitors of nitric oxide and cyclooxygenase. Sulfaphenazole also increased the percentage of endothelial cells with ACh induced increases of [Ca(2+)]i. The study shows that impaired endothelial [Ca(2+)]i control can explain the reduced endothelial function in arteries from diabetic mice and that sulfaphenazole treatment improves endothelial [Ca(2+)]i responses to ACh and consequently endothelium-dependent vasodilation. These observations provide mechanistic insight into endothelial dysfunction in diabetes.

  12. A PPARγ, NF-κB and AMPK-Dependent Mechanism May Be Involved in the Beneficial Effects of Curcumin in the Diabetic db/db Mice Liver

    Directory of Open Access Journals (Sweden)

    Lizbeth M. Jiménez-Flores

    2014-06-01

    Full Text Available Turmeric (Curcuma longa is a rhizomatous herbaceous perennial plant of the ginger family which has been used to treat biliary disorders, anorexia, cough, rheumatism, cancer, sinusitis, hepatic disorders, hyperglycemia, obesity, and diabetes in both Ayurvedic and Traditional Chinese Medicine. Suggested mechanisms of action include the modulation of signal transduction cascades and effects on gene expression, however they remain to be elucidated. In this study, the expression of some proteins responsible for transcription factors, inflammation, and metabolic control were evaluated by western blot in 15-week-old db/db mice livers treated with curcumin 0.75% mixed in their diet for 8 weeks. In addition, nitrosative stress was evaluated. Curcumin increased the expression of AMPK and PPARγ, and diminished NF-κB protein in db/db mice. However, it did not modify the expression of PGC-1α or SIRT1. Nitrosative stress present in db/db mice livers was determined by a unique nitrotyrosylated protein band (75 kDa and was not reverted with curcumin. In conclusion, curcumin regulates the expression of AMPK, PPARγ, and NF-κB; suggesting a beneficial effect for treatment of T2DM complications. In order to observe best beneficial effects it is desirable to administer curcumin in the earlier states of T2DM.

  13. A PPARγ, NF-κB and AMPK-dependent mechanism may be involved in the beneficial effects of curcumin in the diabetic db/db mice liver.

    Science.gov (United States)

    Jiménez-Flores, Lizbeth M; López-Briones, Sergio; Macías-Cervantes, Maciste H; Ramírez-Emiliano, Joel; Pérez-Vázquez, Victoriano

    2014-06-18

    Turmeric (Curcuma longa) is a rhizomatous herbaceous perennial plant of the ginger family which has been used to treat biliary disorders, anorexia, cough, rheumatism, cancer, sinusitis, hepatic disorders, hyperglycemia, obesity, and diabetes in both Ayurvedic and Traditional Chinese Medicine. Suggested mechanisms of action include the modulation of signal transduction cascades and effects on gene expression, however they remain to be elucidated. In this study, the expression of some proteins responsible for transcription factors, inflammation, and metabolic control were evaluated by western blot in 15-week-old db/db mice livers treated with curcumin 0.75% mixed in their diet for 8 weeks. In addition, nitrosative stress was evaluated. Curcumin increased the expression of AMPK and PPARγ, and diminished NF-κB protein in db/db mice. However, it did not modify the expression of PGC-1α or SIRT1. Nitrosative stress present in db/db mice livers was determined by a unique nitrotyrosylated protein band (75 kDa) and was not reverted with curcumin. In conclusion, curcumin regulates the expression of AMPK, PPARγ, and NF-κB; suggesting a beneficial effect for treatment of T2DM complications. In order to observe best beneficial effects it is desirable to administer curcumin in the earlier states of T2DM.

  14. Physical-Property Measurements on Core samples from Drill-Holes DB-1 and DB-2, Blue Mountain Geothermal Prospect, North-Central Nevada

    Science.gov (United States)

    Ponce, David A.; Watt, Janet T.; Casteel, John; Logsdon, Grant

    2009-01-01

    From May to June 2008, the U.S. Geological Survey (USGS) collected and measured physical properties on 36 core samples from drill-hole Deep Blue No. 1 (DB-1) and 46 samples from drill-hole Deep Blue No. 2 (DB-2) along the west side of Blue Mountain about 40 km west of Winnemucca, Nev. These data were collected as part of an effort to determine the geophysical setting of the Blue Mountain geothermal prospect as an aid to understanding the geologic framework of geothermal systems throughout the Great Basin. The physical properties of these rocks and other rock types in the area create a distinguishable pattern of gravity and magnetic anomalies that can be used to infer their subsurface geologic structure. Drill-holes DB-1 and DB-2 were spudded in alluvium on the western flank of Blue Mountain in 2002 and 2004, respectively, and are about 1 km apart. Drill-hole DB-1 is at a ground elevation of 1,325 m and was drilled to a depth of 672 m and drill-hole DB-2 is at a ground elevation of 1,392 m and was drilled to a depth of 1522 m. Diameter of the core samples is 6.4 cm. These drill holes penetrate Jurassic and Triassic metasedimentary rocks predominantly consisting of argillite, mudstone, and sandstone; Tertiary diorite and gabbro; and younger Tertiary felsic dikes.

  15. The Extract of Litsea japonica Reduced the Development of Diabetic Nephropathy via the Inhibition of Advanced Glycation End Products Accumulation in db/db Mice

    Directory of Open Access Journals (Sweden)

    Eunjin Sohn

    2013-01-01

    Full Text Available Increasing evidence indicates that advanced glycation end products (AGEs contribute to the pathogenesis of diabetic nephropathy. The aim of this study was to investigate the protective effect of L. japonica extract (LJE against renal damage in the db/db mouse. LJE (100 or 250 mg/kg per day was given to diabetic mice for 12 weeks. Body weight, blood glucose levels, glycated hemoglobin (HbA1c levels, and proteinuria were examined. In in vitro assay of the inhibition of AGE formation, immunohistochemical analysis of podocyte loss and AGE accumulations were performed. In 20-week-old db/db mice, severe hyperglycemia developed, and proteinuria was significantly increased. Diabetes induced markedly morphological alterations to the renal glomerular cells. AGE accumulations and podocyte loss were detected in renal glomeruli. LJE treatment significantly reduced proteinuria and AGE accumulations in diabetic mice. Moreover, the loss of nephrin, an important slit diaphragm component in the kidneys, was restored by LJE treatment. Our studies suggest that LJE might be beneficial for the treatment of diabetic nephropathy. The ability of LJE to attenuate proteinuria and podocyte dysfunction may be mediated by the inhibition of AGE accumulation in the context of diabetic nephropathy in db/db mice.

  16. Effects of eugenol-reduced clove extract on glycogen phosphorylase b and the development of diabetes in db/db mice.

    Science.gov (United States)

    Sanae, Fujiko; Kamiyama, Ogusa; Ikeda-Obatake, Kyoko; Higashi, Yasuhiko; Asano, Naoki; Adachi, Isao; Kato, Atsushi

    2014-02-01

    We found that the 50% aqueous EtOH extract of clove (Syzygium aromaticum) had potent dose-dependent inhibitory activity toward glycogen phosphorylase b and glucagon-stimulated glucose production in primary rat hepatocytes. Among the components, eugeniin inhibited glycogen phosphorylase b and glucagon-stimulated glucose production in primary rat hepatocytes, with IC50 values of 0.14 and 4.7 μM, respectively. In sharp contrast, eugenol showed no significant inhibition toward glycogen phosphorylase b, even at a concentration of 400 μM. Eugenol-reduced clove extracts (erCE) were prepared and when fed to a db/db mouse they clearly suppressed the blood glucose and HbA1c levels. Furthermore, plasma triglyceride and non-esterified fatty acid levels in 5% and 10% erCE-fed db/db mice were significantly lowered, compared with control db/db mice without erCE supplementation. These results suggested that dietary supplementation with the erCE could beneficially modify glucose and lipid metabolism and contribute to the prevention of the progress of hyperglycemia and metabolic syndrome.

  17. Caulerpa lentillifera extract ameliorates insulin resistance and regulates glucose metabolism in C57BL/KsJ-db/db mice via PI3K/AKT signaling pathway in myocytes.

    Science.gov (United States)

    Sharma, Bhesh Raj; Kim, Hyun Jung; Rhyu, Dong Young

    2015-02-15

    Glucose homeostasis is distorted by defects of the PI3K/AKT and AMPK pathways in insulin-sensitive tissues, allowing the accumulation of glucose in the blood. The purpose of this study was to assess the effects and mechanisms by which ethanol extract of Caulerpa lentillifera (CLE) regulates glucose metabolism in C57BL/KsJ-db/db (db/db) mice. Mice were administered CLE (250 or 500 mg/kg BW) or rosiglitazone (RSG, 10 mg/kg BW) for 6 weeks. Then, oral glucose tolerance test (OGTT) and intraperitoneal insulin tolerance test (IPITT) were performed, and blood glucose was measured in db/db mice. Levels of insulin and insulin resistance factors in plasma, glycogen content in the liver, and IRS, PI3K, AKT, and GLUT4 expressions in skeletal muscles were measured in db/db mice. Glucose uptake and insulin signaling molecules were measured in L6 myocytes, using fluorometry and Western blotting. CLE significantly decreased fasting blood glucose, glucose level in OGTT and IPITT, plasma insulin, homeostatic model assessment-insulin resistant (HOMA-IR), TNF-α, IL-6, FFA, TG and TC levels, and hepatic glycogen content in db/db mice. CLE significantly increased the activation of IRS, AKT, PI3K, and GLUT4, which are the key effector molecules of the PI3K/AKT pathway in L6 myocytes and the skeletal muscles of db/db mice. The enhanced glucose uptake by CLE was abolished by treatment with a PI3K inhibitor (LY294002), but not by an AMPK inhibitor (compound C) in L6 myocytes. CLE regulated glucose uptake and homeostasis via the PI3K/AKT pathway in myocytes and db/db mice, respectively. Our results suggest that CLE could be a potential candidate for the prevention of diabetes.

  18. Procurement of Beams in Multiple D&B Bridge Projects

    Directory of Open Access Journals (Sweden)

    CT. Ramanathan

    2010-06-01

    Full Text Available Selected infrastructure development projects are being implemented by Design and Build (D&B pocurement system in Sabah (East Malaysia by the Public Works Department (PWD. In the first phase 45 bridge replacement projects were awarded in 5 packages. These simultaneous multiple Bridge projects are for the development of the backward areas and hence their timely completion is utmost important. Procurement and production of bridge beams have been the critical element of construction in these rural areas and no researches has been reported on various aspects of procurement of the bridge beams in multiple D&B projects. The aspects of procurement researched in this work include the determination of a common beam element for the ease of procurement and the optimization of the construction methodology, the finalization and purchasing plate dimensions to suite the manufacturer's production range, the delivery of materials, the planning and monitoring of fabrication, the preparation and assembly, and the erection and launching of beams. The beams are optimized using element optimization techniques. The most important problems in fabricating steel girders were in planning and scheduling of materials for the fabrication and the fabrication process. Findings in all the aspects of production of steel girders are highlighted through a case study of six long span bridges at various locations in Sabah. Solutions drawn from lessons learnt which minimize wastages, and aids in timely completion of beams in multiple bridge construction are discussed.

  19. GiSAO.db: a database for ageing research

    Directory of Open Access Journals (Sweden)

    Grillari Johannes

    2011-05-01

    Full Text Available Abstract Background Age-related gene expression patterns of Homo sapiens as well as of model organisms such as Mus musculus, Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster are a basis for understanding the genetic mechanisms of ageing. For an effective analysis and interpretation of expression profiles it is necessary to store and manage huge amounts of data in an organized way, so that these data can be accessed and processed easily. Description GiSAO.db (Genes involved in senescence, apoptosis and oxidative stress database is a web-based database system for storing and retrieving ageing-related experimental data. Expression data of genes and miRNAs, annotation data like gene identifiers and GO terms, orthologs data and data of follow-up experiments are stored in the database. A user-friendly web application provides access to the stored data. KEGG pathways were incorporated and links to external databases augment the information in GiSAO.db. Search functions facilitate retrieval of data which can also be exported for further processing. Conclusions We have developed a centralized database that is very well suited for the management of data for ageing research. The database can be accessed at https://gisao.genome.tugraz.at and all the stored data can be viewed with a guest account.

  20. MiR-138 promotes smooth muscle cells proliferation and migration in db/db mice through down-regulation of SIRT1

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Juan [Department of Gynecology, Changzhou Maternity and Children Health Hospital, Changzhou, Jiangsu 213003 (China); Li, Li; Yun, Hui-fang [Department of Anesthesiology, Changzhou No. 2 People' s Hospital, Changzhou, Jiangsu 213003 (China); Han, Ye-shan, E-mail: yeshanhan123@163.com [Department of Anesthesiology, Changzhou No. 2 People' s Hospital, Changzhou, Jiangsu 213003 (China)

    2015-08-07

    Background: Diabetic vascular smooth muscle cells (VSMCs) exhibit significantly increased rates of proliferation and migration, which was the most common pathological change in atherosclerosis. In addition, the study about the role for miRNAs in the regulation of VSMC proliferation is just beginning to emerge and additional miRNAs involved in VSMC proliferation modulation should be identified. Methods: The expression of miR-138 and SIRT1 were examined in SMCs separated from db/db mice and in SMC lines C-12511 exposed to high glucose with qRT-PCR and western blot. The regulation of miR-138 on the expression of SMCs was detected with luciferase report assay. VSMCs proliferation and migration assays were performed to examine the effect of miR-138 inhibitor on VSMCs proliferation and migration. Results: We discovered that higher mRNA level of miR-138 and reduced expression of SIRT1 were observed in SMCs separated from db/db mice and in SMC lines C-12511. Moreover, luciferase report assay showed that the activity of SIRT1 3′-UTR was highly increased by miR-138 inhibitor and reduced by miR-138 mimic. In addition, we examined that the up-regulation of NF-κB induced by high glucose in SMCs was reversed by resveratrol and miR-138 inhibitor. MTT and migration assays showed that miR-138 inhibitor attenuated the proliferation and migration of smooth muscle cells. Conclusion: In this study, we revealed that miR-138 might promote proliferation and migration of SMC in db/db mice through suppressing the expression of SIRT1. - Highlights: • Higher mRNA level of miR-138 was observed in SMCs from db/db mice. • The mRNA and protein level of SIRT1 in SMCs from db/db mice were greatly reduced. • miR-138 could regulate the expression of SIRT1 in SMCs. • SIRT1 overexpression reversed the up-regulation of acetylized p65 and NF-κB induced by high glucose. • MiR-138 inhibitor reversed VSMCs proliferation and migration induced by high glucose.

  1. Aldose reductase inhibition suppresses azoxymethane-induced colonic premalignant lesions in C57BL/KsJ-db/db mice.

    Science.gov (United States)

    Saxena, Ashish; Shoeb, Mohammad; Tammali, Ravinder; Ramana, Kota V; Srivastava, Satish K

    2014-12-01

    Type-2 diabetes and obesity-related metabolic abnormalities are major risk factors for the development of colon cancer. In the present study, we examined the effects of polyol pathway enzyme aldose reductase (AR) inhibitor, fidarestat, on the development of azoxymethane (AOM)-induced colonic premalignant lesions in C57BL/KsJ-db/db obese mice. Our results indicate that fidarestat given in the drinking water caused a significant reduction in the total number of colonic premalignant lesions in the AOM treated obese mice. Further, the expression levels of PKC-β2, AKT, COX-2 and iNOS in the colonic mucosa of AOM-treated mice were significantly decreased by fidarestat. The serum levels of IL-1α, IP-10, MIG, TNF-α and VEGF are significantly suppressed in AOM + fidarestat treated obese mice. Fidarestat also decreased the expression of COX-2, iNOS, XIAP, survivin, β-catenin and NF-κB in high glucose-treated HT29 colon cancer cells. In conclusion, our results indicate that fidarestat inhibits the development of colonic premalignant lesions in an obesity-related colon cancer and is chemopreventive to colorectal carcinogenesis in obese individuals. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  2. Jicama (Pachyrhizus erosus) extract increases insulin sensitivity and regulates hepatic glucose in C57BL/Ksj-db/db mice.

    Science.gov (United States)

    Park, Chan Joo; Lee, Hyun-Ah; Han, Ji-Sook

    2016-01-01

    This study investigated the effect of jicama extract on hyperglycemia and insulin sensitivity in an animal model of type 2 diabetes. Male C57BL/Ksj-db/db mice were divided into groups subsequently fed a regular diet (controls), or diet supplemented with jicama extract, and rosiglitazone. After 6 weeks, blood levels of glucose and glycosylated hemoglobin were significantly lower in animals administered the jicama extract than the control group. Additionally, glucose and insulin tolerance tests showed that jicama extract increased insulin sensitivity. The homeostatic index of insulin resistance was lower in the jicama extract-treated group than in the diabetic control group. Administration of jicama extract significantly enhanced the expressions of the phosphorylated AMP-activated protein kinase and Akt substrate of 160 kDa, and plasma membrane glucose transporter type 4 in skeletal muscle. Jicama extract administration also decreased the expressions of glucose 6-phosphatase and phosphoenol pyruvate carboxykinase in the liver. Jicama extract may increases insulin sensitivity and inhibites the gluconeogenesis in the liver.

  3. Potential hypoglycemic effect of an ethanol extract of Gynostemma pentaphyllum in C57BL/KsJ-db/db mice.

    Science.gov (United States)

    Yeo, Jiyoung; Kang, Young-Jin; Jeon, Seon-Min; Jung, Un Ju; Lee, Mi-Kyung; Song, Hebok; Choi, Myung-Sook

    2008-12-01

    This study was conducted to evaluate the antihyperglycemic effect of an extract of Gynostemma pentaphyllum Makino, containing standardized concentrations of gypenosides, in C57BL/KSJ-db/db mice. For 5 weeks, animals were provided a standard AIN-76 diet (normal control) with rosiglitazone (0.005%, wt/wt) or two different doses of G. pentaphyllum ethanol extract (GPE) of the plant leaves (0.0025% and 0.01%, wt/wt). After the experimental period, the blood glucose levels of the high-dose GPE- and rosiglitazone-supplemented groups were significantly lower than that of the control group. The plasma insulin concentrations of the GPE-supplemented mice were significantly elevated compared to the control group. The GPE and rosiglitazone treatments profoundly affected the intraperitoneal insulin tolerance test compared to the control group, but not the intraperitoneal glucose tolerance test. In the evaluation of effects on hepatic glucose metabolism, the ratios of glucokinase/glucose-6-phosphatase activities in the high-dose GPE- and rosiglitazone-supplemented groups were prominently higher than that of the control group. The histology of the pancreatic islets revealed that the insulin-positive beta-cell numbers were higher in the high-dose GPE- and rosiglitazone-supplemented groups than in the control group. These results suggest that the supplementation of high-dose GPE (0.01%) in the diet lowers the blood glucose level by altering the hepatic glucose metabolic enzyme activities.

  4. Administration of Danhong Injection to diabetic db/db mice inhibits the development of diabetic retinopathy and nephropathy.

    Science.gov (United States)

    Liu, Mengyang; Pan, Quan; Chen, Yuanli; Yang, Xiaoxiao; Zhao, Buchang; Jia, Lifu; Zhu, Yan; Zhang, Boli; Gao, Xiumei; Li, Xiaoju; Han, Jihong; Duan, Yajun

    2015-06-10

    Danhong Injection (DHI), a Chinese medicine for treatment of patients with coronary heart disease, inhibits primary abdominal aortic aneurysms in apoE deficient (apoE(-/-)) mice. Formation of microaneurysms plays an important role in the development of diabetic retinopathy and nephropathy. It remains unknown if DHI can reduce these diabetic complications. In this study, diabetic db/db mice in two groups were injected with saline and DHI, respectively, for 14 weeks. Blood and tissue samples were collected to determine serum glucose, lipids and tissue structure. DHI reduced diabetes-induced body weight gain, serum cholesterol and glucose levels. In retinas, DHI blocked the shrink of whole retina and retinal sub-layers by inhibiting expression of caspase 3, matrix metalloproteinase 2 (MMP-2) and MMP-9, accumulation of carbohydrate macromolecules and formation of acellular capillaries. DHI improved renal functions by inhibiting mesangial matrix expansion, expression of vascular endothelial growth factor A, fibronectin and advanced glycation end products in kidneys. Mechanistically, DHI induced expression of glucokinase, AMPKα/phosphorylated AMPKα, insulin receptor substrate 1, fibroblast growth factor 21 and peroxisome proliferator-activated γ. Expression of genes responsible for energy expenditure was also activated by DHI. Therefore, DHI inhibits diabetic retinopathy and nephropathy by ameliorating glucose metabolism and demonstrates a potential application in clinics.

  5. Dioscorea Extract (DA-9801) Modulates Markers of Peripheral Neuropathy in Type 2 Diabetic db/db Mice.

    Science.gov (United States)

    Moon, Eunjung; Lee, Sung Ok; Kang, Tong Ho; Kim, Hye Ju; Choi, Sang Zin; Son, Mi-Won; Kim, Sun Yeou

    2014-09-01

    The purpose of this study was to investigate the therapeutic effects of DA-9801, an optimized extract of Dioscorea species, on diabetic peripheral neuropathy in a type 2 diabetic animal model. In this study, db/db mice were treated with DA-9801 (30 and 100 mg/kg, daily, p.o.) for 12 weeks. DA-9801 reduced the blood glucose levels and increased the withdrawal latencies in hot plate tests. Moreover, it prevented nerve damage based on increased nerve conduction velocity and ultrastructural changes. Decrease of nerve growth factor (NGF) may have a detrimental effect on diabetic neuropathy. We previously reported NGF regulatory properties of the Dioscorea genus. In this study, DA-9801 induced NGF production in rat primary astrocytes. In addition, it increased NGF levels in the sciatic nerve and the plasma of type 2 diabetic animals. DA-9801 also increased neurite outgrowth and mRNA expression of Tieg1/Klf10, an NGF target gene, in PC12 cells. These results demonstrated the attenuation of diabetic peripheral neuropathy by oral treatment with DA-9801 via NGF regulation. DA-9801 is currently being evaluated in a phase II clinical study.

  6. PhilDB: the time series database with built-in change logging

    Directory of Open Access Journals (Sweden)

    Andrew MacDonald

    2016-03-01

    Full Text Available PhilDB is an open-source time series database that supports storage of time series datasets that are dynamic; that is, it records updates to existing values in a log as they occur. PhilDB eases loading of data for the user by utilising an intelligent data write method. It preserves existing values during updates and abstracts the update complexity required to achieve logging of data value changes. It implements fast reads to make it practical to select data for analysis. Recent open-source systems have been developed to indefinitely store long-period high-resolution time series data without change logging. Unfortunately, such systems generally require a large initial installation investment before use because they are designed to operate over a cluster of servers to achieve high-performance writing of static data in real time. In essence, they have a ‘big data’ approach to storage and access. Other open-source projects for handling time series data that avoid the ‘big data’ approach are also relatively new and are complex or incomplete. None of these systems gracefully handle revision of existing data while tracking values that change. Unlike ‘big data’ solutions, PhilDB has been designed for single machine deployment on commodity hardware, reducing the barrier to deployment. PhilDB takes a unique approach to meta-data tracking; optional attribute attachment. This facilitates scaling the complexities of storing a wide variety of data. That is, it allows time series data to be loaded as time series instances with minimal initial meta-data, yet additional attributes can be created and attached to differentiate the time series instances when a wider variety of data is needed. PhilDB was written in Python, leveraging existing libraries. While some existing systems come close to meeting the needs PhilDB addresses, none cover all the needs at once. PhilDB was written to fill this gap in existing solutions. This paper explores existing time

  7. Update History of This Database - Dicty_cDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available date History of This Database Date Update contents 2015/01/09 The original website information was up...[ Credits ] BLAST Search Image Search Home About Archive Update History Contact us Dicty_cDB Up...dated. 2010/03/29 Dicty_cDB English archive site is opened. 2009/8 Data is updated. 1996/12 Dicty_cDB(h...s by Artio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Up

  8. DB2 9 for zOS Database Administration Certification Study Guide

    CERN Document Server

    Lawson, Susan

    2008-01-01

    In order to become an IBM Certified Database Administrator - DB2 9 DBA for z/OS, you must pass two exams: DB2 9 Fundamentals Exam (Exam 730), and DB2 9 Database Administrator for z/OS (Exam 732)-the primary focus focus of this book. Written by two members of the team who participated in the actual writing of the exam, this specialized study guide covers every topic that you will need to know to pass Exam 732, including database design and implementation, operation and recovery, security and auditing, performance, as well as installation and migration/upgrade. But that is only the beginning.

  9. Protein (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us PGD... IDs of clusters that the amino acid sequences belong to in each taxon are indicated. Data file File name: pgd...bj_ortholog_db_viridiplantae_protein.zip File URL: ftp://ftp.biosciencedbc.jp/archive/pgdbj-ortholog-db/LATEST/pgd...RL http://togodb.biosciencedbc.jp/togodb/view/pgdbj_ortholog_db_viridiplantae_protein#en Data acquisition me...BI GI number of Amino Acid sequence RefSeq ID NCBI Reference Sequence ID Cluster (Kingdom) Cluster ID (rank: Kingd

  10. Download - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available criptions are about the downloadable data in this page. They might not correspond to the contents of the ori... name File Simple search and download 1 README README_e.html - 2 Protein (Viridiplantae) pgdbj_ortholog_db_v...iridiplantae_protein.zip (85 MB) Simple search and download 3 Cluster (Viridiplantae) pgdbj_ortholog_db_viri...diplantae_cluster.zip (15.6 MB) Simple search and download 4 Taxon (Viridiplantae...) pgdbj_ortholog_db_viridiplantae_taxon.zip (2.3 KB) Simple search and download 5 Protein (Cyanobacteria) pg

  11. 2型糖尿病模型db/db小鼠肾上腺超微结构观察%ULTRASTRUCTURE STUDY OF THE ADRENAL GLAND IN GENETICALLY OBESE DIABETIC db/db MICE

    Institute of Scientific and Technical Information of China (English)

    张松筠; 张庆九; 苏胜偶; 张力辉

    2006-01-01

    目的 观察人类2型糖尿病动物模型--C57BL/KsJ db/db(db/db)小鼠肾上腺超微结构变化.方法 糖尿病组为6周龄C57BL/KsJ(db+/db+)小鼠10只,尾静脉空腹血糖高于11.1 mmol/L,且肥胖.对照组为非糖尿病小鼠C57BL/KsJ(?/+)5只,尾静脉空腹血糖低于6.0 mmol/L,体质量正常.于30周龄及54周龄(成模第6月末和第12月末)时,在透射电镜下观察肾上腺皮质束状带超微结构.结果 糖尿病小鼠超微结构发生显著改变包括线粒体变性,脂滴减少,细胞核变型、染色质边集等.病变程度与病程正相关.结论 2型糖尿病所致肾上腺超微结构改变可能与糖尿病下丘脑-垂体-肾上腺皮质轴功能受损有关.

  12. Novel anti-diabetic effect of SCM-198 via inhibiting the hepatic NF-κB pathway in db/db mice.

    Science.gov (United States)

    Huang, Hui; Xin, Hong; Liu, Xinhua; Xu, Yajun; Wen, Danyi; Zhang, Yahua; Zhu, Yi Zhun

    2012-04-01

    There are reports of early evidence that suggest the involvement of chronic low-grade inflammation in the pathogenesis of Type 2 diabetes. Thus, substances that have effects in reducing inflammation could be potential drugs for Type 2 diabetes. Leonurine (4-guanidino-n-butyl syringate; SCM-198) is an alkaloid in HL (Herba leonuri), which was reported to possess anti-inflammatory properties. We hypothesize that SCM-198 may have beneficial effects on Type 2 diabetes. In the present study, we attempted to test this hypothesis by evaluating the anti-diabetic effect of SCM-198 and the possible underlying mechanisms of its effects in db/db mice. SCM-198 (50, 100 and 200 mg/kg of body weight), pioglitazone (50 mg/kg of body weight, as a positive control) or 1% CMC-Na (sodium carboxymethylcellulose) were administered to the db/db or db/m mice once daily for 3 weeks. After 3 weeks, SCM-198 (200 mg/kg of body weight) treatment significantly reduced the fasting blood glucose level and increased the plasma insulin concentration in the db/db mice, meanwhile it significantly lowered the plasma TAG (triacylglycerol) concentration and increased the HDL (high-density lipoprotein)-cholesterol concentration. Moreover, the dysregulated transcription of the hepatic glucose metabolic enzymes, including GK (glucokinase), G6Pase (glucose-6-phosphatase) and PEPCK (phosphoenolpyruvate carboxykinase), was recovered by an Akt-dependent pathway. The pro-inflammatory mediators {such as TNFα (tumour necrosis factor α), IL (interleukin)-6, IL-1β, degradation of IκB [inhibitor of NF-κB (nuclear factor-κB)] α and thereafter activation of NF-κB} were reversed by SCM-198 treatment in the db/db mice. The present study provides first evidence that SCM-198 exhibits anti-inflammatory activity and has an ameliorating effect on diabetic symptoms via inhibiting of NF-κB/IKK (IκB kinase) pathway. Consequently, we suggest that SCM-198 may be a prospective agent for prevention and

  13. 2型糖尿病模型db/db小鼠海马超微结构观察%The ultrastructure study of the hippocampus in genetically obese diabetic db/db mice

    Institute of Scientific and Technical Information of China (English)

    张松筠; 苏胜偶; 张庆九; 刘文淑; 杨天祝; 赵占胜

    2001-01-01

    Objective To observe the ultrastructure changes of genetically diabetic C57BL/KsJ(db/db) mice in hippocampus. Methods Diabetic group consisted of 5 obese C57BL/KsJ (db/db) mice of 6 weeks old with fasting blood glucose (FBG) higher than 11.1 mmol/L and normal group consisted of 5 normal weight C57BL/KsJ mice with FBG lower than 6.0 mmol/L. Mice were killed at 30 weeks old and hippocampus samples were embedded in Epon 812. Thin sections were cut with ultrathin microtome and observed with transmissional electron microscopes. Results Pyramidal cells of diabetic mice's hippocampus showed significant retrograde changes; synapses degenerated; myelin sheath broke up. Conclusion The significant pathological changes in hippocampus of diabetic mice may related to cognitive dysfunction.%目的 观察2型糖尿病动物模型——C57BL/KsJ(db/db)小鼠海马超微结构变化。方法 糖尿病组:6周龄C57BL/KsJ(db/db)小鼠5只,尾静脉空腹血糖高于11.1 mmol/L且肥胖;对照组:非糖尿病小鼠C57BL/KsJ 5只,尾静脉空腹血糖低于6.0 mmol/L,体重正常。于30周龄(成模第6个月末)时,灌注固定取脑,透射电镜下观察海马CA1区。结果 糖尿病小鼠海马超微结构发生显著改变包括锥体细胞退变、髓鞘崩解、突触变性等。结论 糖尿病所致海马超微结构改变可能与糖尿病学习记忆功能减退有关。

  14. H-InvDB in 2009: extended database and data mining resources for human genes and transcripts.

    Science.gov (United States)

    Yamasaki, Chisato; Murakami, Katsuhiko; Takeda, Jun-ichi; Sato, Yoshiharu; Noda, Akiko; Sakate, Ryuichi; Habara, Takuya; Nakaoka, Hajime; Todokoro, Fusano; Matsuya, Akihiro; Imanishi, Tadashi; Gojobori, Takashi

    2010-01-01

    We report the extended database and data mining resources newly released in the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). H-InvDB is a comprehensive annotation resource of human genes and transcripts, and consists of two main views and six sub-databases. The latest release of H-InvDB (release 6.2) provides the annotation for 219,765 human transcripts in 43,159 human gene clusters based on human full-length cDNAs and mRNAs. H-InvDB now provides several new annotation features, such as mapping of microarray probes, new gene models, relation to known ncRNAs and information from the Glycogene database. H-InvDB also provides useful data mining resources-'Navigation search', 'H-InvDB Enrichment Analysis Tool (HEAT)' and web service APIs. 'Navigation search' is an extended search system that enables complicated searches by combining 16 different search options. HEAT is a data mining tool for automatically identifying features specific to a given human gene set. HEAT searches for H-InvDB annotations that are significantly enriched in a user-defined gene set, as compared with the entire H-InvDB representative transcripts. H-InvDB now has web service APIs of SOAP and REST to allow the use of H-InvDB data in programs, providing the users extended data accessibility.

  15. Scientific Data Bases at Scale and SciDB

    CERN Document Server

    CERN. Geneva

    2013-01-01

    Abstract: As a general rule, scientists have shunned relational data management systems (RDBMS), choosing instead to “roll their own” on top of file system technology.  We first discuss why file systems are a poor choice for science data storage, especially as data volumes become large and scalability becomes important.   Then, we continue with the reasons why RDBMSs work poorly on most science applications.  These include a data model “impedance mismatch” and missing features. We discuss array DBMSs, and why they are a much better choice for science applications, and use SciDB as an exemplar of this new class of DBMSs.   Most science applications require a mix of data management and complex analytics.  In most cases, the analytics entail a sequence of linear algebra computations.  We discuss the possible ways of integrating a DBMS with statistical calculations, and conclude with the mechanism being used by S...

  16. SoyDB: a knowledge database of soybean transcription factors

    Directory of Open Access Journals (Sweden)

    Valliyodan Babu

    2010-01-01

    Full Text Available Abstract Background Transcription factors play the crucial rule of regulating gene expression and influence almost all biological processes. Systematically identifying and annotating transcription factors can greatly aid further understanding their functions and mechanisms. In this article, we present SoyDB, a user friendly database containing comprehensive knowledge of soybean transcription factors. Description The soybean genome was recently sequenced by the Department of Energy-Joint Genome Institute (DOE-JGI and is publicly available. Mining of this sequence identified 5,671 soybean genes as putative transcription factors. These genes were comprehensively annotated as an aid to the soybean research community. We developed SoyDB - a knowledge database for all the transcription factors in the soybean genome. The database contains protein sequences, predicted tertiary structures, putative DNA binding sites, domains, homologous templates in the Protein Data Bank (PDB, protein family classifications, multiple sequence alignments, consensus protein sequence motifs, web logo of each family, and web links to the soybean transcription factor database PlantTFDB, known EST sequences, and other general protein databases including Swiss-Prot, Gene Ontology, KEGG, EMBL, TAIR, InterPro, SMART, PROSITE, NCBI, and Pfam. The database can be accessed via an interactive and convenient web server, which supports full-text search, PSI-BLAST sequence search, database browsing by protein family, and automatic classification of a new protein sequence into one of 64 annotated transcription factor families by hidden Markov models. Conclusions A comprehensive soybean transcription factor database was constructed and made publicly accessible at http://casp.rnet.missouri.edu/soydb/.

  17. Wideband, 50 dB Attenuation Range Liquid Crystal Based Variable Optical Attenuator

    Institute of Scientific and Technical Information of China (English)

    J.J.; Pan; Henry; He; Eric; Zhang

    2003-01-01

    A compact variable optical attenuator, covering C and L bands with over 50 dB attenuation range, is realized using a single liquid crystal cell with a tilted fused silica coating compensating the cell's small residual birefringence.

  18. TropGENE-DB, a multi-tropical crop information system.

    Science.gov (United States)

    Ruiz, Manuel; Rouard, Mathieu; Raboin, Louis Marie; Lartaud, Marc; Lagoda, Pierre; Courtois, Brigitte

    2004-01-01

    TropGENE-DB, is a crop information system created to store genetic, molecular and phenotypic data of the numerous yet poorly documented tropical crop species. The most common data stored in TropGENE-DB are information on genetic resources (agro-morphological data, parentages, allelic diversity), molecular markers, genetic maps, results of quantitative trait loci analyses, data from physical mapping, sequences, genes, as well as the corresponding references. TropGENE-DB is organized on a crop basis with currently three running modules (sugarcane, cocoa and banana), with plans to create additional modules for rice, cotton, oil palm, coconut, rubber tree, pineapple, taro, yam and sorghum. The TropGENE-DB information system is accessible for consultation via the internet at http://tropgenedb.cirad.fr. Specific web consultation interfaces have been designed to allow quick consultations as well as complex queries.

  19. Download - D-HaploDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ... This Database Database Description Download License Update History of This Database Site Policy | Contact Us Download - D-HaploDB | LSDB Archive ...

  20. Download - Dicty_cDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...atabase Description Download License Update History of This Database Site Policy | Contact Us Download - Dicty_cDB | LSDB Archive ...

  1. Taxon (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...Artio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Taxon (Cyanobacteria) - PGDBj - Ortholog DB | LSDB Archive ...

  2. Taxon (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...Artio About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Taxon (Viridiplantae) - PGDBj - Ortholog DB | LSDB Archive ...

  3. Database Description - PGDBj - Ortholog DB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available data in the databases. By submitting queries to the PGDBj Ortholog DB with keywords or amino acid sequences, users...ding both model plants and crop plants. Following the links obtained, users can retrieve the actual entries

  4. A description of the Molecular Signatures Database (MSigDB) Web site.

    Science.gov (United States)

    Liberzon, Arthur

    2014-01-01

    Annotated lists of genes help researchers to prioritize their own lists of candidate genes and to plan follow-up studies. The Molecular Signatures Database (MSigDB) is one of the most widely used knowledge base repositories of annotated sets of genes involved in biochemical pathways, signaling cascades, expression profiles from research publications, and other biological concepts. Here we provide an overview of MSigDB and its online analytical tools.

  5. InterProScan Result: DB673798 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available DB673798 DB673798_4_ORF1 AEE38DD3F2A2B877 PRINTS PR00385 P450 5.8e-05 T IPR001128 Cytochrome P450 Mol...ecular Function: monooxygenase activity (GO:0004497)|Molecular Function: iron ion binding (GO:0005506)|Mol...ecular Function: electron carrier activity (GO:0009055)|Molecular Function: heme binding (GO:0020037) ...

  6. The NCBI dbGaP database of genotypes and phenotypes.

    Science.gov (United States)

    Mailman, Matthew D; Feolo, Michael; Jin, Yumi; Kimura, Masato; Tryka, Kimberly; Bagoutdinov, Rinat; Hao, Luning; Kiang, Anne; Paschall, Justin; Phan, Lon; Popova, Natalia; Pretel, Stephanie; Ziyabari, Lora; Lee, Moira; Shao, Yu; Wang, Zhen Y; Sirotkin, Karl; Ward, Minghong; Kholodov, Michael; Zbicz, Kerry; Beck, Jeffrey; Kimelman, Michael; Shevelev, Sergey; Preuss, Don; Yaschenko, Eugene; Graeff, Alan; Ostell, James; Sherry, Stephen T

    2007-10-01

    The National Center for Biotechnology Information has created the dbGaP public repository for individual-level phenotype, exposure, genotype and sequence data and the associations between them. dbGaP assigns stable, unique identifiers to studies and subsets of information from those studies, including documents, individual phenotypic variables, tables of trait data, sets of genotype data, computed phenotype-genotype associations, and groups of study subjects who have given similar consents for use of their data.

  7. AtomDB and PyAtomDB: Atomic Data and Modelling Tools for High Energy and Non-Maxwellian Plasmas

    Science.gov (United States)

    Foster, Adam; Smith, Randall K.; Brickhouse, Nancy S.; Cui, Xiaohong

    2016-04-01

    The release of AtomDB 3 included a large wealth of inner shell ionization and excitation data allowing accurate modeling of non-equilibrium plasmas. We describe the newly calculated data and compare it to published literature data. We apply the new models to existing supernova remnant data such as W49B and N132D. We further outline progress towards AtomDB 3.1, including a new energy-dependent charge exchange cross sections.We present newly developed models for the spectra of electron-electron bremsstrahlung and those due to non-Maxwellian electron distributions.Finally, we present our new atomic database access tools, released as PyAtomDB, allowing powerful use of the underlying fundamental atomic data as well as the spectral emissivities.

  8. SHBG-C57BL/ksJ-db/db: A New Mouse Model to Study SHBG Expression and Regulation During Obesity Development.

    Science.gov (United States)

    Saéz-López, Cristina; Rivera-Giménez, Marta; Hernández, Cristina; Simó, Rafael; Selva, David M

    2015-12-01

    Low plasma sex hormone-binding globulin (SHBG) levels in overweight individuals are a biomarker for the metabolic syndrome and are predictive of type 2 diabetes and cardiovascular disease risk. There are no in vivo models to study SHBG expression and regulation during obesity development. The main reason for this is that the obesity-prone rodent models cannot be used to study this issue, because rodents, unlike humans, do not express the SHBG gene in their livers. We have developed a unique mouse model that expresses the human SHBG, and it develops obesity, by crossing the human SHBG transgenic mice with the C57BL/ksJ-db/db mice. The results obtained with the SHBG-C57BL/ksJ-db/db mouse model have allowed us to determine that the SHBG overexpression in the C57BL/ksJ-db/db reduced the body weight gain but did not change the metabolic profile of these mice. Moreover, we elucidated the molecular mechanisms and transcription factors causing the SHBG down-regulation during obesity development, which involved changes in liver hepatocyte nuclear factor 4α and peroxisome proliferator-activated receptor-γ mRNA and protein levels. Furthermore, these results were confirmed using human liver biopsies. Importantly, we also showed that this model resembles what occurs in human obese subjects, because plasma SHBG and total testosterone levels where reduced in obese mice when compared with lean mice. Future research using this unique mouse model will determine the role of SHBG in the development and progression of obesity, type 2 diabetes, or fatty liver disease.

  9. A MongoDB-Based Management of Planar Spatial Data with a Flattened R-Tree

    Directory of Open Access Journals (Sweden)

    Longgang Xiang

    2016-07-01

    Full Text Available This paper addresses how to manage planar spatial data using MongoDB, a popular NoSQL database characterized as a document-oriented, rich query language and high availability. The core idea is to flatten a hierarchical R-tree structure into a tabular MongoDB collection, during which R-tree nodes are represented as collection documents and R-tree pointers are expressed as document identifiers. By following this strategy, a storage schema to support R-tree-based create, read, update, and delete (CRUD operations is designed and a module to manage planar spatial data by consuming and maintaining flattened R-tree structure is developed. The R-tree module is then seamlessly integrated into MongoDB, so that users could manipulate planar spatial data with existing command interfaces oriented to geodetic spatial data. The experimental evaluation, using real-world datasets with diverse coverage, types, and sizes, shows that planar spatial data can be effectively managed by MongoDB with our flattened R-tree and, therefore, the application extent of MongoDB will be greatly enlarged. Our work resulted in a MongoDB branch with R-tree support, which has been released on GitHub for open access.

  10. The Gypsy Database (GyDB) of mobile genetic elements: release 2.0.

    Science.gov (United States)

    Llorens, Carlos; Futami, Ricardo; Covelli, Laura; Domínguez-Escribá, Laura; Viu, Jose M; Tamarit, Daniel; Aguilar-Rodríguez, Jose; Vicente-Ripolles, Miguel; Fuster, Gonzalo; Bernet, Guillermo P; Maumus, Florian; Munoz-Pomer, Alfonso; Sempere, Jose M; Latorre, Amparo; Moya, Andres

    2011-01-01

    This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org.

  11. InterStoreDB: A Generic Integration Resource for Genetic and Genomic Data

    Institute of Scientific and Technical Information of China (English)

    Christopher G.Love; Ambrose E.Andongabo; Jun Wang; Pierre W.C.Carion; Christopher J.Rawlings; Graham J.King

    2012-01-01

    Associating phenotypic traits and quantitative trait loci (QTL) to causative regions of the underlying genome is a key goal in agricultural research.InterStoreDB is a suite of integrated databases designed to assist in this process.The individual databases are species independent and generic in design,providing access to curated datasets relating to plant populations,phenotypic traits,genetic maps,marker loci and QTL,with links to functional gene annotation and genomic sequence data.Each component database provides access to associated metadata,including data provenance and parameters used in analyses,thus providing users with information to evaluate the relative worth of any associations identified.The databases include CropStoreDB,for management of population,genetic map,QTL and trait measurement data,SeqStoreDB for sequence-related data and AlignStoreDB,which stores sequence alignment information,and allows navigation between genetic and genomic datasets.Genetic maps are visualized and compared using the CMAP tool,and functional annotation from sequenced genomes is provided via an EnsEMBL-based genome browser.This framework facilitates navigation of the multiple biological domains involved in genetics and genomics research in a transparent manner within a single portal.We demonstrate the value of InterStoreDB as a tool for Brassica research.InterStoreDB is available from:http:llwww.interstoredb.org

  12. Liraglutide reduces lipogenetic signals in visceral adipose of db/db mice with AMPK activation and Akt suppression

    Directory of Open Access Journals (Sweden)

    Shao Y

    2015-02-01

    Full Text Available Yimin Shao, Geheng Yuan, Junqing Zhang, Xiaohui Guo Department of Endocrinology, Peking University First Hospital, Beijing, People’s Republic of China Abstract: Liraglutide, a glucagon-like peptide-1 analog, has been proved to reduce body weight and visceral adipose tissue (VAT in human studies. In this study, we aimed at examining lipogenetic signal changes in VAT after weight-loss with liraglutide in db/db mice. The mice were divided into two groups: liraglutide-treated group (n=14, 8-week-old, fasting glucose. >10 mmol/L, liraglutide 300 µg/kg twice a day for 4 weeks and control group (n=14, saline. We found body weight gain and food intake were reduced after liraglutide treatment (P<0.05. Compared to the control group, the VAT weights were significantly lower in the treated group (2.32±0.37 g versus 3.20±0.30 g, P<0.01 than that in control group. In VAT, compared with control group, the lipogenetic transcription factors PPARγ and C/EBPα expressions were both reduced with pAMPK and pACC increased 3.5-fold and 2.31-fold respectively, while pAkt and pP38MAPK were reduced 0.38-fold and 0.62-fold respectively (P<0.01. In conclusion, VAT was reduced after weight loss with AMPK activation and Akt suppression with liraglutide treatment, which was associated with reduction of lipogenetic process in VAT. Keywords: liraglutide, visceral adipose tissue, AMP-activated protein kinase, lipogenesis

  13. Celastrol, an NF-κB inhibitor, improves insulin resistance and attenuates renal injury in db/db mice.

    Directory of Open Access Journals (Sweden)

    Jung Eun Kim

    Full Text Available The NF-κB pathway plays an important role in chronic inflammatory and autoimmune diseases. Recently, NF-κB has also been suggested as an important mechanism linking obesity, inflammation, and metabolic disorders. However, there is no current evidence regarding the mechanism of action of NF-κB inhibition in insulin resistance and diabetic nephropathy in type 2 diabetic animal models. We investigated the effects of the NF-κB inhibitor celastrol in db/db mice. The treatment with celastrol for 2 months significantly lowered fasting plasma glucose (FPG, HbA1C and homeostasis model assessment index (HOMA-IR levels. Celastrol also exhibited significant decreases in body weight, kidney/body weight and adiposity. Celastrol reduced insulin resistance and lipid abnormalities and led to higher plasma adiponectin levels. Celastrol treatment also significantly mitigated lipid accumulation and oxidative stress in organs including the kidney, liver and adipose tissue. The treated group also exhibited significantly lower creatinine levels and urinary albumin excretion was markedly reduced. Celastrol treatment significantly lowered mesangial expansion and suppressed type IV collagen, PAI-1 and TGFβ1 expressions in renal tissues. Celastrol also improved abnormal lipid metabolism, oxidative stress and proinflammatory cytokine activity in the kidney. In cultured podocytes, celastrol treatment abolished saturated fatty acid-induced proinflammatory cytokine synthesis. Taken together, celastrol treatment not only improved insulin resistance, glycemic control and oxidative stress, but also improved renal functional and structural changes through both metabolic and anti-inflammatory effects in the kidney. These results suggest that targeted therapy for NF-κB may be a useful new therapeutic approach for the management of type II diabetes and diabetic nephropathy.

  14. Portability, Salary and Asset Price Risk: A Continuous-Time Expected Utility Comparison of DB and DC Pension Plans

    Directory of Open Access Journals (Sweden)

    An Chen

    2015-03-01

    Full Text Available This paper compares two different types of private retirement plans from the perspective of a representative beneficiary: a defined benefit (DB and a defined contribution (DC plan. While salary risk is the main common risk factor in DB and DC pension plans, one of the key differences is that DB plans carry portability risks, whereas DC plans bear asset price risk. We model these tradeoffs explicitly in this paper and compare these two plans in a utility-based framework. Our numerical analysis focuses on answering the question of when the beneficiary is indifferent between the DB and DC plan. Most of our results confirm the findings in the existing literature, among which, e.g., portability losses considerably reduce the relative attractiveness of the DB plan. However, we also find that the attractiveness of the DB plan can decrease in the level of risk aversion, which is inconsistent with the existing literature.

  15. Insulin-sensitizing and cardiovascular effects of the sodium-hydrogen exchange inhibitor, cariporide, in the JCR: LA-cp rat and db/db mouse.

    Science.gov (United States)

    Russell, J C; Proctor, S D; Kelly, S E; Löhn, M; Busch, A E; Schäfer, S

    2005-12-01

    The effects of the sodium-hydrogen (Na/H) exchange inhibitor cariporide (HOE642), on insulin sensitivity and vascular function were studied in the JCR:LA-cp rat and the db/db mouse. In the insulin-resistant rat, cariporide reduced fasting insulin levels (42%, P JCR:LA-cp insulin-resistant rat, which develops advanced cardiovascular disease and ischemic myocardial lesions. It also improved vascular function in a similar mouse model of insulin resistance. These effects were markedly greater than those of ramipril.

  16. DTS(v)嵌入到DB(4,1;w)的研究%Embedding DTS(v) into DB(4,1; w)

    Institute of Scientific and Technical Information of China (English)

    田琛

    2005-01-01

    设(V,B)为一个DB(k,λ;v),(W,L)为一个DB(k',λ';v').如果V 并且L| v=B,即B={B:B∈L,B V},我们称(V,B)嵌入到了(W,L)中.主要给出了当k=3,k'=4,λ=λ'=1时,DTS(v)的嵌入谱的估计.同时,确定了小阶数的DTS(v)的嵌入谱.

  17. Protective effects of SGLT2 inhibitor luseogliflozin on pancreatic β-cells in obese type 2 diabetic db/db mice

    Energy Technology Data Exchange (ETDEWEB)

    Okauchi, Seizo, E-mail: okauchi@med.kawasaki-m.ac.jp; Shimoda, Masashi; Obata, Atsushi; Kimura, Tomohiko; Hirukawa, Hidenori; Kohara, Kenji; Mune, Tomoatsu; Kaku, Kohei; Kaneto, Hideaki

    2016-02-12

    It is well known that Sodium-Glucose Co-transporter 2 (SGLT2) inhibitors, new hypoglycemic agents, improve glycemic control by increasing urine glucose excretion, but it remained unclear how they exert protective effects on pancreatic β-cells. In this study, we examined the effects of SGLT2 inhibitor luseogliflozin on β-cell function and mass using obese type 2 diabetic db/db mice. Ten-week-old male diabetic db/db mice were treated with luseogliflozin 0.0025% or 0.01% in chow (Luse 0.0025% or Luse 0.01%) or vehicle (control) for 4 weeks. Urinary glucose excretion was increased in Luse groups (0.0025% and 0.01%) compared to control mice 3 days after the intervention. Fasting blood glucose levels were significantly lower in mice treated with Luse compared to control mice. Fasting serum insulin concentrations were significantly higher in mice treated with Luse compared to control mice. Triglyceride levels tended to be lower in Luse groups compared to control mice. In immunohistochemical study using pancreas tissues, β-cell mass was larger in Luse groups compared to control group which was due to the increase of β-cell proliferation and decrease of β-cell apoptosis. Furthermore, in gene analysis using isolated islets, insulin 1, insulin 2, MafA, PDX-1 and GLUT2 gene expression levels were significantly higher in Luse groups compared to control group. In contrast, expression levels of fibrosis-related gene such as TGFβ, fibronectin, collagen I and collagen III were significantly lower in Luse groups. In conclusion, SGLT2 inhibitor luseogliflozin ameliorates glycemic control and thus exerts protective effects on pancreatic β-cell mass and function. - Highlights: • SGLT2 inhibitor luseogliflozin ameliorates glycemic control in db/db mice. • Luseogliflozin increases β-cell proliferation and decreases β-cell apoptosis. • Luseogliflozin preserves various β-cell-specific gene expression. • Luseogliflozin decreases various fibrosis-related factors in db/db

  18. A Response Surface Methodology Approach to Investigate the Effect of Sulfur Dioxide, pH, and Ethanol on DbCD and DbVPR Gene Expression and on the Volatile Phenol Production in Dekkera/Brettanomyces bruxellensis CBS2499

    Directory of Open Access Journals (Sweden)

    Federica Valdetara

    2017-09-01

    Full Text Available Dekkera/Brettanomyces bruxellensis, the main spoilage yeast in barrel-aged wine, metabolize hydroxycinnamic acids into off-flavors, namely ethylphenols. Recently, both the enzymes involved in this transformation, the cinnamate decarboxylase (DbCD and the vinylphenol reductase (DbVPR, have been identified. To counteract microbial proliferation in wine, sulfur dioxide (SO2 is used commonly to stabilize the final product, but limiting its use is advised to preserve human health and boost sustainability in winemaking. In the present study, the influence of SO2 was investigated in relation with pH and ethanol factors on the expression of DbCD and DbVPR genes and volatile phenol production in D. bruxellensis CBS2499 strain under different model wines throughout a response surface methodology (RSM. In order to ensure an exact quantification of DbCD and DbVPR expression, an appropriate housekeeping gene was sought among DbPDC, DbALD, DbEF, DbACT, and DbTUB genes by GeNorm and Normfinder algorithms. The latter gene showed the highest expression stability and it was chosen as the reference housekeeping gene in qPCR assays. Even though SO2 could not be commented as main factor because of its statistical irrelevance on the response of DbCD gene, linear interactions with pH and ethanol concurred to define a significant effect (p < 0.05 on its expression. The DbCD gene was generally downregulated respect to a permissive growth condition (0 mg/L mol. SO2, pH 4.5 and 5% v/v ethanol; the combination of the factor levels that maximizes its expression (0.83-fold change was calculated at 0.25 mg/L mol. SO2, pH 4.5 and 12.5% (v/v ethanol. On the contrary, DbVPR expression was not influenced by main factors or by their interactions; however, its expression is maximized (1.80-fold change at the same conditions calculated for DbCD gene. While no linear interaction between factors influenced the off-flavor synthesis, ethanol and pH produced a significant effect as

  19. Identification of 13 DB + dM and 2 DC + dM binaries from the Sloan Digital Sky Survey

    NARCIS (Netherlands)

    Besselaar, E.J.M. van den; Roelofs, G.H.A.; Nelemans, G.A.; Augusteijn, T.; Groot, P.J.

    2005-01-01

    We present the identification of 13 DB + dM binaries and 2 DC + dM binaries from the Sloan Digital Sky Survey (SDSS). Before the SDSS only 2 DB + dM binaries and 1 DC + dM binary were known. At least three, possibly 8, of the new DB + dM binaries seem to have white dwarf temperatures well above 30 0

  20. MetPetDB: New Directions for Metamorphic Studies

    Science.gov (United States)

    Spear, F. S.; Adali, S.; Szymanski, B. K.; Hallett, B. K.; Waters, A. J.; Linder, Z. J.; Fyffe, M. E.; Goldfarb, D.; Barlett, K.

    2008-12-01

    It is estimated that less than 1% of the data collected on metamorphic rocks is published, and MetPetDB (database for metamorphic geochemistry) is being developed and populated to preserve these data and to foster new and innovative directions for scientific research and education. The data model is based on a sample of metamorphic rock and includes information about location, rock type, mineral assemblage, fabric, plus images of all types and mineral composition data. Mineral analyses are linked to locations on appropriate images so the spatial integrity of the data is preserved. Tools will be available for mineral recalculation, plotting, and thermobarometric applications. Derivative data such as peak P-T conditions, metamorphic P-T path, and cooling rate will also be stored. The database will be searchable based on any number of data fields, permitting rapid location of samples that can be used to test hypotheses and discover new relationships. For example: A student is designing a thesis project and MetPetDB will be a first resource to determine the types of rocks present in a region, the work that has been done on them, and links to the published findings. The Fe/Mg zoning in migmatitic garnets has been used to infer cooling rates. What is the range of cooling rates recorded by migmatitic garnets, and is there a correlation between peak metamorphic temperature and cooling rate? Is it possible that melting triggers rapid thrusting that causes the rapid cooling? A search on: rock type = migmatite plus Fe and Mg X-ray maps of garnet would reveal all samples that could be used in this study. A new geobarometer based on a specific mineral assemblage is proposed that permits pressures to be estimated to within 50 MPa. A search of the database for all samples with this assemblage plus analyses of the necessary minerals would provide a set of samples to which this new barometer can be applied. Recalculating pressures and temperatures for an entire region using new

  1. HBVPathDB: A database of HBV infection-related molecular interaction network

    Institute of Scientific and Technical Information of China (English)

    Yi Zhang; Xiao-Chen Bo; Jing Yang; Sheng-Qi Wang

    2005-01-01

    AIM: To describe molecules or genes interaction between hepatitis B viruses (HBV) and host, for understanding how virus' and host's genes and molecules are networked to form a biological system and for perceiving mechanism of HBV infection.METHODS: The knowledge of HBV infection-related reactions was organized into various kinds of pathways with carefully drawn graphs in HBVPathDB. Pathway information is stored with relational database management system (DBMS), which is currently the most efficient way to manage large amounts of data and query is implemented with powerful Structured Query Language (SQL). The search engine is written using Personal Home Page (PHP) with SQL embedded and web retrieval interface is developed for searching with Hypertext Markup Language (HTML).RESULTS: We present the first version of HBVPathDB,which is a HBV infection-related molecular interaction network database composed of 306 pathways with 1050molecules involved. With carefully drawn graphs, pathway information stored in HBVPathDB can be browsed in an intuitive way. We develop an easy-to-use interface for flexible accesses to the details of database. Convenient software is implemented to query and browse the pathway information of HBVPathDB. Four search page layout options-category search, gene search, description search,unitized search-are supported by the search engine ofthe database. The database is freely available at http://www.bio-inf, net/HBVPathDB/HBV/.CONCLUSION: The conventional perspective HBVPathDB have already contained a considerable amount of pathway information with HBV infection related, which is suitable for in-depth analysis of molecular interaction network of virus and host. HBVPathDB integrates pathway data-sets with convenient software for query, browsing,visualization, that provides users more opportunity to identify regulatory key molecules as potential drug targets and to explore the possible mechanism of HBV infection based on gene expression datasets.

  2. myPhyloDB: a local web server for the storage and analysis of metagenomic data.

    Science.gov (United States)

    Manter, Daniel K; Korsa, Matthew; Tebbe, Caleb; Delgado, Jorge A

    2016-01-01

    myPhyloDB v.1.1.2 is a user-friendly personal database with a browser-interface designed to facilitate the storage, processing, analysis, and distribution of microbial community populations (e.g. 16S metagenomics data). MyPhyloDB archives raw sequencing files, and allows for easy selection of project(s)/sample(s) of any combination from all available data in the database. The data processing capabilities of myPhyloDB are also flexible enough to allow the upload and storage of pre-processed data, or use the built-in Mothur pipeline to automate the processing of raw sequencing data. myPhyloDB provides several analytical (e.g. analysis of covariance,t-tests, linear regression, differential abundance (DESeq2), and principal coordinates analysis (PCoA)) and normalization (rarefaction, DESeq2, and proportion) tools for the comparative analysis of taxonomic abundance, species richness and species diversity for projects of various types (e.g. human-associated, human gut microbiome, air, soil, and water) for any taxonomic level(s) desired. Finally, since myPhyloDB is a local web-server, users can quickly distribute data between colleagues and end-users by simply granting others access to their personal myPhyloDB database. myPhyloDB is available athttp://www.ars.usda.gov/services/software/download.htm?softwareid=472 and more information along with tutorials can be found on our websitehttp://www.myphylodb.org. Database URL:http://www.myphylodb.org.

  3. Olmesartan Prevents Microalbuminuria in db/db Diabetic Mice Through Inhibition of Angiotensin II/p38/SIRT1-Induced Podocyte Apoptosis

    Directory of Open Access Journals (Sweden)

    Junhui Gu

    2016-11-01

    Full Text Available Background/Aims: Blockage of the renin-angiotensin II system (RAS prevents or delays albuminuria in diabetic patients. The aim of this study was to investigate the inhibitory mechanism of the angiotensin receptor blocker olmesartan on albuminuria in a murine model of diabetic nephropathy. Methods: Male db/db diabetic mice were fed with placebo or 20 mg/kg olmesartan by daily gavage for 12 weeks. Conditionally immortalized mouse podocytes were treated with glucose, angiotensin II, olmesartan or p38 inhibitor s8307 in different experimental conditions after differentiation. Results: Olmesartan reduced albuminuria in db/db mice without change in body weight and glycemia. The increase of apoptotic cells and decrease of podocytes in the diabetic glomerulus were prevented by olmesartan. Moreover, olmesartan restored silent mating type information regulation 1 (SIRT1 expression in diabetic glomeruli. Furthermore, olmesartan treatment suppressed p38 phosphorylation but did not restore adenosine 5‘-monophosphate-activated protein kinase (AMPK phosphorylation in the diabetic glomerulus. In vitro study revealed that olmesartan prevented angiotensin II/p38/SIRT1 induced podocyte apoptosis, but it only slightly prevented high glucose/AMPK/SIRT1 induced podocyte apoptosis. In addition, the p38 inhibitor s8307 reversed SIRT1 expression and angiotensin II induced podocyte apoptosis. Conclusions: Olmesartan reduced albuminuria in diabetic nephropathy through inhibiting angiotensin II/p38/SIRT1 triggered podocyte apoptosis.

  4. Olmesartan Prevents Microalbuminuria in db/db Diabetic Mice Through Inhibition of Angiotensin II/p38/SIRT1-Induced Podocyte Apoptosis.

    Science.gov (United States)

    Gu, Junhui; Yang, Ming; Qi, Na; Mei, Shuqin; Chen, Jiejian; Song, Shuwei; Jing, Ying; Chen, Meihan; He, Liangliang; Sun, Lijun; Hu, Huimin; Li, Lin; Wüthrich, Rudolf P; Wu, Ming; Mei, Changlin

    2016-01-01

    Blockage of the renin-angiotensin II system (RAS) prevents or delays albuminuria in diabetic patients. The aim of this study was to investigate the inhibitory mechanism of the angiotensin receptor blocker olmesartan on albuminuria in a murine model of diabetic nephropathy. Male db/db diabetic mice were fed with placebo or 20 mg/kg olmesartan by daily gavage for 12 weeks. Conditionally immortalized mouse podocytes were treated with glucose, angiotensin II, olmesartan or p38 inhibitor s8307 in different experimental conditions after differentiation. Olmesartan reduced albuminuria in db/db mice without change in body weight and glycemia. The increase of apoptotic cells and decrease of podocytes in the diabetic glomerulus were prevented by olmesartan. Moreover, olmesartan restored silent mating type information regulation 1 (SIRT1) expression in diabetic glomeruli. Furthermore, olmesartan treatment suppressed p38 phosphorylation but did not restore adenosine 5'-monophosphate-activated protein kinase (AMPK) phosphorylation in the diabetic glomerulus. In vitro study revealed that olmesartan prevented angiotensin II/p38/SIRT1 induced podocyte apoptosis, but it only slightly prevented high glucose/AMPK/SIRT1 induced podocyte apoptosis. In addition, the p38 inhibitor s8307 reversed SIRT1 expression and angiotensin II induced podocyte apoptosis. Olmesartan reduced albuminuria in diabetic nephropathy through inhibiting angiotensin II/p38/SIRT1 triggered podocyte apoptosis. © 2016 The Author(s) Published by S. Karger AG, Basel.

  5. The dbGaP data browser: a new tool for browsing dbGaP controlled-access genomic data

    Science.gov (United States)

    Wong, Kira M.; Langlais, Kristofor; Tobias, Geoffrey S.; Fletcher-Hoppe, Colette; Krasnewich, Donna; Leeds, Hilary S.; Rodriguez, Laura Lyman; Godynskiy, Georgy; Schneider, Valerie A.; Ramos, Erin M.; Sherry, Stephen T.

    2017-01-01

    The database of Genotypes and Phenotypes (dbGaP) Data Browser (https://www.ncbi.nlm.nih.gov/gap/ddb/) was developed in response to requests from the scientific community for a resource that enable view-only access to summary-level information and individual-level genotype and sequence data associated with phenotypic features maintained in the controlled-access tier of dbGaP. Until now, the dbGaP controlled-access environment required investigators to submit a data access request, wait for Data Access Committee review, download each data set and locally examine them for potentially relevant information. Existing unrestricted-access genomic data browsing resources (e.g. http://evs.gs.washington.edu/EVS/, http://exac.broadinstitute.org/) provide only summary statistics or aggregate allele frequencies. The dbGaP Data Browser serves as a third solution, providing researchers with view-only access to a compilation of individual-level data from general research use (GRU) studies through a simplified controlled-access process. The National Institutes of Health (NIH) will continue to improve the Browser in response to user feedback and believes that this tool may decrease unnecessary download requests, while still facilitating responsible genomic data-sharing. PMID:27899644

  6. C333H ameliorated insulin resistance through selectively modulating peroxisome proliferator-activated receptor γ in brown adipose tissue of db/db mice.

    Science.gov (United States)

    Zhang, Ning; Chen, Wei; Zhou, Xinbo; Zhou, Xiaolin; Xie, Xinni; Meng, Aimin; Li, Song; Wang, Lili

    2013-01-01

    Peroxisome proliferator-activated receptor γ (PPARγ) is a unique target for insulin sensitizer agents. These drugs have been used for the clinical treatment of type 2 diabetes for almost twenty years. However, serious safety issues are associated with the PPARγ agonist thiazolidinediones (TZDs). Selective PPARγ modulators (SPPARMs) which retain insulin sensitization without TZDs-like side effects are emerging as a promising new generation of insulin sensitizers. C333H is a novel structure compound synthesized by our laboratory. In diabetic rodent models, C333H has insulin-sensitizing and glucose-lowering activity comparable to that of TZDs, and causes no significant increase in body weight or adipose tissue weight in db/db mice. In diabetic db/db mice, C333H elevated circulating high molecular weight adiponectin isoforms, decreased PPARγ 273 serine phosphorylation in brown adipose tissue and selectively modulated the expression of a subset of PPARγ target genes in adipose tissue. In vitro, C333H weakly recruited coactivator and weakly dissociated corepressor activity. These findings suggest that C333H has similar properties to SPPARMs and may be a potential therapeutic agent for the treatment of type 2 diabetes.

  7. Impaired Mobilization of Vascular Reparative Bone Marrow Cells in Streptozotocin-Induced Diabetes but not in Leptin Receptor-Deficient db/db Mice.

    Science.gov (United States)

    Vasam, Goutham; Joshi, Shrinidh; Jarajapu, Yagna P R

    2016-05-18

    Diabetes is associated with impaired mobilization of bone marrow stem/progenitor cells that accelerate vascularization of ischemic areas. This study characterized mobilization of vascular reparative bone marrow progenitor cells in mouse models of diabetes. Age-matched control or streptozotocin (STZ)-induced diabetic, and db/db mice with lean-controls were studied. Mobilization induced by G-CSF, AMD3100 or ischemia was evaluated by flow cytometric enumeration of circulating Lin(-)Sca-1(+)cKit(+) (LSK) cells, and by colony forming unit (CFU) assay. The circulating WBCs and LSKs, and CFUs were reduced in both models with a shorter duration (10-12 weeks) of diabetes compared to their respective controls. Longer duration of STZ-diabetes (≥20 weeks) induced impairment of G-CSF- or AMD3100-mobilization (P mobilization by G-CSF or AMD3100 was either increased or unaffected (P mobilization, of LSK cells were impaired in both models. Leptin receptor antagonist, PESLAN-1, increased G-CSF- or AMD3100-mobilization of WBCs and LSKs, compared to the untreated. Leptin increased basal WBCs, decreased basal and AMD3100-mobilized LSK cells, and had no effect on G-CSF. These results suggest that mobilopathy is apparent in STZ-diabetes but not in db/db mice. Leptin receptor antagonism would be a promising approach for reversing diabetic bone marrow mobilopathy.

  8. ZiBuPiYin recipe protects db/db mice from diabetes-associated cognitive decline through improving multiple pathological changes.

    Directory of Open Access Journals (Sweden)

    Jing Chen

    Full Text Available Multiple organ systems, including the brain, which undergoes changes that may increase the risk of cognitive decline, are adversely affected by diabetes mellitus (DM. Here, we demonstrate that type 2 diabetes mellitus (T2DM db/db mice exhibited hippocampus-dependent memory impairment, which might associate with a reduction in dendritic spine density in the pyramidal neurons of brain, Aβ1-42 deposition in the prefrontal cortex (PFC and hippocampus, and a decreased expression of neurostructural proteins including microtubule-associated protein (MAP2, a marker of dendrites, and postsynaptic density 95 (PSD95, a marker of excitatory synapses. To investigate the effects of the ZiBuPiYin recipe (ZBPYR, a traditional Chinese medicine recipe, on diabetes-related cognitive decline (DACD, db/db mice received daily administration of ZBPYR over an experimental period of 6 weeks. We then confirmed that ZBPYR rescued learning and memory performance impairments, reversed dendritic spine loss, reduced Aβ1-42 deposition and restored the expression levels of MAP2 and PSD95. The present study also revealed that ZBPYR strengthened brain leptin and insulin signaling and inhibited GSK3β overactivity, which may be the potential mechanism or underlying targets of ZBPYR. These findings conclude that ZBPYR prevents DACD, most likely by improving dendritic spine density and attenuating brain leptin and insulin signaling pathway injury. Our findings provide further evidence for the effects of ZBPYR on DACD.

  9. Effect of long-term dietary arginyl-fructose (AF) on hyperglycemia and HbA1c in diabetic db/db mice.

    Science.gov (United States)

    Lee, Kwang-Hyoung; Ha, Kyoung-Soo; Jo, Sung-Hoon; Lee, Chong M; Kim, Young-Cheul; Chung, Kwang-Hoe; Kwon, Young-In

    2014-05-12

    We have previously reported that Amadori compounds exert anti-diabetic effects by lowering sucrose-induced hyperglycemia in normal Sprague-Dawley rats. In the present study we extended our recent findings to evaluate whether α-glucosidase inhibitor arginyl-fructose (AF) lowers blood glucose level in diabetic db/db mice, a genetic model for type 2 diabetes. The db/db mice were randomly assigned to high-carbohydrate diets (66.1% corn starch) with and without AF (4% in the diet) for 6 weeks. Changes in body weight, blood glucose level, and food intake were measured daily for 42 days. Dietary supplementation of AF resulted in a significant decrease of blood glucose level (p HbA1c, a better indicator of plasma glucose concentration over prolonged periods of time, was also significantly decreased for 6-week period (p diet), a positive control, also significantly alleviated the level of blood glucose, HbA1c, and body weight. These results indicate that AF Maillard reaction product improves postprandial hyperglycemia by suppressing glucose absorption as well as decreasing HbA1c level.

  10. Transfusion of CXCR4-primed endothelial progenitor cells reduces cerebral ischemic damage and promotes repair in db/db diabetic mice.

    Directory of Open Access Journals (Sweden)

    Ji Chen

    Full Text Available This study investigated the role of stromal cell-derived factor-1α (SDF-1α/CXC chemokine receptor 4 (CXCR4 axis in brain and endothelial progenitor cells (EPCs, and explored the efficacy of CXCR4 primed EPCs in treating ischemic stroke in diabetes. The db/db diabetic and db/+ mice were used in this study. Levels of plasma SDF-1α and circulating CD34+CXCR4+ cells were measured. Brain SDF-1α and CXCR4 expression were quantified at basal and after middle cerebral artery occlusion (MCAO. In in vitro study, EPCs were transfected with adenovirus carrying null (Ad-null or CXCR4 (Ad-CXCR4 followed with high glucose (HG treatment for 4 days. For pathway block experiments, cells were pre-incubated with PI3K inhibitor or nitric oxide synthase (NOS inhibitor for two hours. The CXCR4 expression, function and apoptosis of EPCs were determined. The p-Akt/Akt and p-eNOS/eNOS expression in EPCs were also measured. In in vivo study, EPCs transfected with Ad-null or Ad-CXCR4 were infused into mice via tail vein. On day 2 and 7, the cerebral blood flow, neurologic deficit score, infarct volume, cerebral microvascular density, angiogenesis and neurogenesis were determined. We found: 1 The levels of plasma SDF-1α and circulating CD34+CXCR4+ cells were decreased in db/db mice; 2 The basal level of SDF-1α and MCAO-induced up-regulation of SDF-1α/CXCR4 axis were reduced in the brain of db/db mice; 3 Ad-CXCR4 transfection increased CXCR4 expression in EPCs and enhanced EPC colonic forming capacity; 4 Ad-CXCR4 transfection prevented EPCs from HG-induced dysfunction (migration and tube formation and apoptosis via activation of PI3K/Akt/eNOS signal pathway; 4 Ad-CXCR4 transfection enhanced the efficacy of EPC infusion in attenuating infarct volume and promoting angiogenesis and neurogenesis. Our data suggest that Ad-CXCR4 primed EPCs have better therapeutic effects for ischemia stroke in diabetes than unmodified EPCs do.

  11. The capsicum transcriptome DB: a "hot" tool for genomic research.

    Science.gov (United States)

    Góngora-Castillo, Elsa; Fajardo-Jaime, Rubén; Fernández-Cortes, Araceli; Jofre-Garfias, Alba E; Lozoya-Gloria, Edmundo; Martínez, Octavio; Ochoa-Alejo, Neftalí; Rivera-Bustamante, Rafael

    2012-01-01

    Chili pepper (Capsicum annuum) is an economically important crop with no available public genome sequence. We describe a genomic resource to facilitate Capsicum annuum research. A collection of Expressed Sequence Tags (ESTs) derived from five C. annuum organs (root, stem, leaf, flower and fruit) were sequenced using the Sanger method and multiple leaf transcriptomes were deeply sampled using with GS-pyrosequencing. A hybrid assembly of 1,324,516 raw reads yielded 32,314 high quality contigs as validated by coverage and identity analysis with existing pepper sequences. Overall, 75.5% of the contigs had significant sequence similarity to entries in nucleic acid and protein databases; 23% of the sequences have not been previously reported for C. annuum and expand sequence resources for this species. A MySQL database and a user-friendly Web interface were constructed with search-tools that permit queries of the ESTs including sequence, functional annotation, Gene Ontology classification, metabolic pathways, and assembly information. The Capsicum Transcriptome DB is free available from http://www.bioingenios.ira.cinvestav.mx:81/Joomla/

  12. SinEx DB: a database for single exon coding sequences in mammalian genomes.

    Science.gov (United States)

    Jorquera, Roddy; Ortiz, Rodrigo; Ossandon, F; Cárdenas, Juan Pablo; Sepúlveda, Rene; González, Carolina; Holmes, David S

    2016-01-01

    Eukaryotic genes are typically interrupted by intragenic, noncoding sequences termed introns. However, some genes lack introns in their coding sequence (CDS) and are generally known as 'single exon genes' (SEGs). In this work, a SEG is defined as a nuclear, protein-coding gene that lacks introns in its CDS. Whereas, many public databases of Eukaryotic multi-exon genes are available, there are only two specialized databases for SEGs. The present work addresses the need for a more extensive and diverse database by creating SinEx DB, a publicly available, searchable database of predicted SEGs from 10 completely sequenced mammalian genomes including human. SinEx DB houses the DNA and protein sequence information of these SEGs and includes their functional predictions (KOG) and the relative distribution of these functions within species. The information is stored in a relational database built with My SQL Server 5.1.33 and the complete dataset of SEG sequences and their functional predictions are available for downloading. SinEx DB can be interrogated by: (i) a browsable phylogenetic schema, (ii) carrying out BLAST searches to the in-house SinEx DB of SEGs and (iii) via an advanced search mode in which the database can be searched by key words and any combination of searches by species and predicted functions. SinEx DB provides a rich source of information for advancing our understanding of the evolution and function of SEGs.Database URL: www.sinex.cl.

  13. MimoDB: a New Repository for Mimotope Data Derived from Phage Display Technology

    Directory of Open Access Journals (Sweden)

    Xianlong Wang

    2010-11-01

    Full Text Available Peptides selected from phage-displayed random peptide libraries are valuable in two aspects. On one hand, these peptides are candidates for new diagnostics, therapeutics and vaccines. On the other hand, they can be used to predict the networks or sites of protein-protein interactions. MimoDB, a new repository for these peptides, was developed, in which 10,716 peptides collected from 571 publications were grouped into 1,229 sets. Besides peptide sequences, other important information, such as the target, template, library and complex structure, was also included. MimoDB can be browsed and searched through a user-friendly web interface. For computational biologists, MimoDB can be used to derive customized data sets and benchmarks, which are useful for new algorithm development and tool evaluation. For experimental biologists, their results can be searched against the MimoDB database to exclude possible target-unrelated peptides. The MimoDB database is freely accessible at http://immunet.cn/mimodb/.

  14. Clone DB: an integrated NCBI resource for clone-associated data.

    Science.gov (United States)

    Schneider, Valerie A; Chen, Hsiu-Chuan; Clausen, Cliff; Meric, Peter A; Zhou, Zhigang; Bouk, Nathan; Husain, Nora; Maglott, Donna R; Church, Deanna M

    2013-01-01

    The National Center for Biotechnology Information (NCBI) Clone DB (http://www.ncbi.nlm.nih.gov/clone/) is an integrated resource providing information about and facilitating access to clones, which serve as valuable research reagents in many fields, including genome sequencing and variation analysis. Clone DB represents an expansion and replacement of the former NCBI Clone Registry and has records for genomic and cell-based libraries and clones representing more than 100 different eukaryotic taxa. Records provide details of library construction, associated sequences, map positions and information about resource distribution. Clone DB is indexed in the NCBI Entrez system and can be queried by fields that include organism, clone name, gene name and sequence identifier. Whenever possible, genomic clones are mapped to reference assemblies and their map positions provided in clone records. Clones mapping to specific genomic regions can also be searched for using the NCBI Clone Finder tool, which accepts queries based on sequence coordinates or features such as gene or transcript names. Clone DB makes reports of library, clone and placement data on its FTP site available for download. With Clone DB, users now have available to them a centralized resource that provides them with the tools they will need to make use of these important research reagents.

  15. dbSUPER: a database of super-enhancers in mouse and human genome.

    Science.gov (United States)

    Khan, Aziz; Zhang, Xuegong

    2016-01-04

    Super-enhancers are clusters of transcriptional enhancers that drive cell-type-specific gene expression and are crucial to cell identity. Many disease-associated sequence variations are enriched in super-enhancer regions of disease-relevant cell types. Thus, super-enhancers can be used as potential biomarkers for disease diagnosis and therapeutics. Current studies have identified super-enhancers in more than 100 cell types and demonstrated their functional importance. However, a centralized resource to integrate all these findings is not currently available. We developed dbSUPER (http://bioinfo.au.tsinghua.edu.cn/dbsuper/), the first integrated and interactive database of super-enhancers, with the primary goal of providing a resource for assistance in further studies related to transcriptional control of cell identity and disease. dbSUPER provides a responsive and user-friendly web interface to facilitate efficient and comprehensive search and browsing. The data can be easily sent to Galaxy instances, GREAT and Cistrome web-servers for downstream analysis, and can also be visualized in the UCSC genome browser where custom tracks can be added automatically. The data can be downloaded and exported in variety of formats. Furthermore, dbSUPER lists genes associated with super-enhancers and also links to external databases such as GeneCards, UniProt and Entrez. dbSUPER also provides an overlap analysis tool to annotate user-defined regions. We believe dbSUPER is a valuable resource for the biology and genetic research communities.

  16. Cytolipotoxicity-induced involution of the female reproductive tract following expression of obese (ob/ob) and diabetes (db/db) genotype mutations: progressive, hyperlipidemic transformation into adipocytic tissues.

    Science.gov (United States)

    Garris, David R; Garris, Bryan L

    2004-01-01

    Both diabetes (db/db) and obese (ob/ob) single gene mutations induce a progressive, hyperglycemic-hyperinsulinemic endometabolic environment which promotes hypercytolipidemic, utero-ovarian involution in C57BL/KsJ mice. The progressive expression of the induced diabetes-obesity syndrome (DOS) results in female reproductive sterility and eventual organoatrophy. In order to define the intra-cytoplasmic alterations induced by the progressive cytolipidemia on cellular vitality, utero-ovarian tissue samples were collected from both control (+/?) and littermate-matched ob/ob or db/db C57BL/KsJ mice at either 4 weeks (initial-onset DOS phase), 8 weeks (progressive, overt DOS phase), or 16 weeks (chronic-DOS phase) of age for cytolipid distribution analysis. All db/db and ob/ob mutant groups exhibited phenotypic obesity and systemic hyperglycemia-hyperinsulinemia relative to age-matched littermate +/? groups. In all db/db and ob/ob age groups, a progressive hypercytolipidemia was noted relative to +/? groups. When analyzed for lipid channeling, a progressive perinuclear mapping pattern of cytolipid distribution was noted. The primary locus of initial db/db and ob/ob cytolipid deposition was localized to the baso-polar regions in endometrial epithelia samples, or to the interstitium-thecal layer border of ovarian follicular compartments, during the initial-onset DOS phase. Progressively, intra-cytoplasmic lipid mobilization promoted a consistent perinuclear channeling of lipid vacuoles, ultimately isolating nuclear loci from the peripherally displaced cytoplasmic organelles within uterine epithelial layers. In db/db and ob/ob ovarian tissue samples, a progressive, gradient-related lipid infiltration of interstitial, thecal and, ultimately, granulosa cell layers promoted an enhanced rate of follicular-lipidemic atresia relative to +/? groups. In each tissue layer, the cytolipidemia promoted a dramatic perinuclear lipid-isolation barrier from intra-cytoplasmic organelle

  17. Connectivity between the OFF bipolar type DB3a and six types of ganglion cell in the marmoset retina.

    Science.gov (United States)

    Masri, Rania A; Percival, Kumiko A; Koizumi, Amane; Martin, Paul R; Grünert, Ulrike

    2016-06-15

    Parallel visual pathways originate at the first synapse in the retina, where cones make connections with cone bipolar cells that in turn contact ganglion cells. There are more ganglion cell types than bipolar types, suggesting that there must be divergence from bipolar to ganglion cells. Here we analyze the contacts between an OFF bipolar type (DB3a) and six ganglion cell types in the retina of the marmoset monkey (Callithrix jacchus). Ganglion cells were transfected via particle-mediated gene transfer of an expression plasmid for the postsynaptic density 95-green fluorescent protein (PSD95-GFP), and DB3a cells were labeled via immunohistochemistry. Ganglion cell types that fully or partially costratified with DB3a cells included OFF parasol, OFF midget, broad thorny, recursive bistratified, small bistratified, and large bistratified cells. On average, the number of DB3a contacts to parasol cells (18 contacts per axon terminal) is higher than that to other ganglion cell types (between four and seven contacts). We estimate that the DB3a output to OFF parasol cells accounts for at least 30% of the total DB3a output. Furthermore, we found that OFF parasol cells receive approximately 20% of their total bipolar input from DB3a cells, suggesting that other diffuse bipolar types also provide input to OFF parasol cells. We conclude that DB3a cells preferentially contact OFF parasol cells but also provide input to other ganglion cell types.

  18. Observational Assessment of Preschool Disruptive Behavior, Part II: Validity of the Disruptive Behavior Diagnostic Observation Schedule (DB-DOS)

    Science.gov (United States)

    Wakschlag, Lauren S.; Briggs-Gowan, Margaret J.; Hill, Carri; Danis, Barbara; Leventhal, Bennett L.; Keenan, Kate; Egger, Helen L.; Cicchetti, Domenic; Burns, James; Carter, Alice S.

    2008-01-01

    A study is conducted to determine whether the multidomain, multicontext Disruptive Behavior Diagnostic Observation Schedule (DB-DOS) is a valid observational method for assessing disruptive behavior of preschool children. It is concluded that the DB-DOS is a valid method for a direct observational assessment of clinically significant disruptive…

  19. Proteomic analysis of kidney and protective effects of grape seed procyanidin B2 in db/db mice indicate MFG-E8 as a key molecule in the development of diabetic nephropathy.

    Science.gov (United States)

    Zhang, Zhen; Li, Bao-Ying; Li, Xiao-Li; Cheng, Mei; Yu, Fei; Lu, Wei-da; Cai, Qian; Wang, Jun-Fu; Zhou, Rui-Hai; Gao, Hai-Qing; Shen, Lin

    2013-06-01

    Diabetic nephropathy, as a severe microvascular complication of diabetic mellitus, has become the leading cause of end-stage renal diseases. However, no effective therapeutic strategy has been developed to prevent renal damage progression to end stage renal disease. Hence, the present study evaluated the protective effects of grape seed procyanidin B2 (GSPB2) and explored its molecular targets underlying diabetic nephropathy by a comprehensive quantitative proteomic analysis in db/db mice. Here, we found that oral administration of GSPB2 significantly attenuated the renal dysfunction and pathological changes in db/db mice. Proteome analysis by isobaric tags for relative and absolute quantification (iTRAQ) identified 53 down-regulated and 60 up-regulated proteins after treatment with GSPB2 in db/db mice. Western blot analysis confirmed that milk fat globule EGF-8 (MFG-E8) was significantly up-regulated in diabetic kidney. MFG-E8 silencing by transfection of MFG-E8 shRNA improved renal histological lesions by inhibiting phosphorylation of extracellular signal-regulated kinase1/2 (ERK1⁄2), Akt and glycogen synthase kinase-3beta (GSK-3β) in kidneys of db/db mice. In contrast, over-expression of MFG-E8 by injection of recombinant MFG-E8 resulted in the opposite effects. GSPB2 treatment significantly decreased protein levels of MFG-E8, phospho-ERK1/2, phospho-Akt, and phospho-GSK-3β in the kidneys of db/db mice. These findings yield insights into the pathogenesis of diabetic nephropathy, revealing MFG-E8 as a new therapeutic target and indicating GSPB2 as a prospective therapy by down-regulation of MFG-E8, along with ERK1/2, Akt and GSK-3β signaling pathway.

  20. From ISIS to CouchDB: Databases and Data Models for Bibliographic Records

    Directory of Open Access Journals (Sweden)

    Luciano Ramalho

    2011-04-01

    Full Text Available For decades bibliographic data has been stored in non-relational databases, and thousands of libraries in developing countries still use ISIS databases to run their OPACs. Fast forward to 2010 and the NoSQL movement has shown that non-relational databases are good enough for Google, Amazon.com and Facebook. Meanwhile, several Open Source NoSQL systems have appeared. This paper discusses the data model of one class of NoSQL products, semistructured, document-oriented databases exemplified by Apache CouchDB and MongoDB, and why they are well-suited to collective cataloging applications. Also shown are the methods, tools, and scripts used to convert, from ISIS to CouchDB, bibliographic records of LILACS, a key Latin American and Caribbean health sciences index operated by the Pan-American Health Organization.

  1. PlantDB – a versatile database for managing plant research

    Directory of Open Access Journals (Sweden)

    Gruissem Wilhelm

    2008-01-01

    Full Text Available Abstract Background Research in plant science laboratories often involves usage of many different species, cultivars, ecotypes, mutants, alleles or transgenic lines. This creates a great challenge to keep track of the identity of experimental plants and stored samples or seeds. Results Here, we describe PlantDB – a Microsoft® Office Access database – with a user-friendly front-end for managing information relevant for experimental plants. PlantDB can hold information about plants of different species, cultivars or genetic composition. Introduction of a concise identifier system allows easy generation of pedigree trees. In addition, all information about any experimental plant – from growth conditions and dates over extracted samples such as RNA to files containing images of the plants – can be linked unequivocally. Conclusion We have been using PlantDB for several years in our laboratory and found that it greatly facilitates access to relevant information.

  2. Use of molecular variation in the NCBI dbSNP database.

    Science.gov (United States)

    Sherry, S T; Ward, M; Sirotkin, K

    2000-01-01

    While high quality information regarding variation in genes is currently available in locus-specific or specialized mutation databases, the need remains for a general catalog of genome variation to address the large-scale sampling designs required by association studies, gene mapping, and evolutionary biology. In response to this need, the National Center for Biotechnology Information (NCBI) has established the dbSNP database http://ncbi. nlm.nih.gov/SNP/ to serve as a generalized, central variation database. Submissions to dbSNP will be integrated with other sources of information at NCBI such as GenBank, PubMed, LocusLink, and the Human Genome Project data, and the complete contents of dbSNP are available to the public via anonymous FTP. Hum Mutat 15:68-75, 2000. Published 2000 Wiley-Liss, Inc.

  3. Antidiabetic and hypolipidemic effects of a novel dual peroxisome proliferator-activated receptor (PPAR) alpha/gamma agonist, E3030, in db/db mice and beagle dogs.

    Science.gov (United States)

    Kasai, Shunji; Inoue, Takashi; Yoshitomi, Hideki; Hihara, Taro; Matsuura, Fumiyoshi; Harada, Hitoshi; Shinoda, Masanobu; Tanaka, Isao

    2008-09-01

    We investigated the antidiabetic effects of E3030, which is a potent dual activator of peroxisome proliferator-activated receptor (PPAR) alpha and PPARgamma, in an animal model of diabetes, C57BL/KsJ-db/db mice (db/db mice), and the lipidemic effects of E3030 in beagle dogs, whose PPARalpha and PPARgamma transactivation responses to E3030 were similar to those of humans. E3030 activated human PPARalpha, mouse PPARalpha, dog PPARalpha, human PPARgamma, mouse PPARgamma, and dog PPARgamma with EC(50) values of 65, 920, 87, 34, 73, and 34 nM, respectively, in the chimeric GAL4-PPAR receptor transactivation reporter assay. In db/db mice orally administered E3030 decreased blood glucose, triglyceride (TG), non-esterified fatty acids (NEFA), and insulin levels and increased blood adiponectin levels during a 14-day experimental period. Significant effects on blood glucose and adiponectin levels were observed at a dose of 3 mg/kg or greater. Furthermore, significant effects on blood TG, NEFA, and insulin levels were observed at doses of 1 mg/kg or more. An oral glucose tolerance test (OGTT) performed on Day 15 showed that E3030 at 3 mg/kg improved glucose tolerance in this model. Fourteen days of oral treatment with E3030 at a dose of 0.03 mg/kg or greater showed remarkable TG- and non high-density lipoprotein (non-HDL) cholesterol-lowering effects in beagle dogs. These results were similar to those observed for the PPARalpha agonist fenofibrate. E3030 also reduced apo C-III levels on Days 7 and 14, and elevated lipoprotein lipase (LPL) levels on Day 15. These results indicate that the TG- and non-HDL cholesterol-lowering actions of E3030 involve combined effects on reduction of apo C-III and elevation of LPL, resulting in increased lipolysis. The experimental results in animals suggest that E3030 has potential for use in the treatment of various aspects of metabolic dysfunction in type 2 diabetes, including dyslipidemia, hyperglycemia, hyperinsulinemia, and impaired

  4. Xylobiose, an Alternative Sweetener, Ameliorates Diabetes-Related Metabolic Changes by Regulating Hepatic Lipogenesis and miR-122a/33a in db/db Mice

    Science.gov (United States)

    Lim, Eunjin; Lim, Ji Ye; Kim, Eunju; Kim, Yoo-Sun; Shin, Jae-Ho; Seok, Pu Reum; Jung, Sangwon; Yoo, Sang-Ho; Kim, Yuri

    2016-01-01

    Type 2 diabetes is a major public health concern worldwide. Xylobiose (XB) consists of two molecules of d-xylose and is a major disaccharide in xylooligosaccharides that are used as prebiotics. We hypothesized that XB could regulate diabetes-related metabolic and genetic changes via microRNA expression in db/db mice. For six weeks, C57BL/KsJ-db/db mice received 5% XB as part of the total sucrose content of their diet. XB supplementation improved glucose tolerance with reduced levels of OGTT AUC, fasting blood glucose, HbA1c, insulin, and HOMA-IR. Furthermore, XB supplementation decreased the levels of total triglycerides, total cholesterol, and LDL-C. The expression levels of miR-122a and miR-33a were higher and lower in the XB group, respectively. In the liver, expressions of the lipogenic genes, including, fatty acid synthase (FAS), peroxisome proliferator activated receptor γ (PPARγ), sterol regulatory element-binding protein-1C (SREBP-1C), sterol regulatory element-binding protein-2 (SREBP-2), acetyl-CoA carboxylase (ACC), HMG-CoA reductase (HMGCR), ATP-binding cassette transporter G5/G8 (ABCG5/8), cholesterol 7 alpha-hydroxylase (CYP7A1), and sterol 12-alpha-hydroxylase (CYP8B1), as well as oxidative stress markers, including superoxide dismutase 1 (SOD1), superoxide dismutase 2 (SOD2), glutathione peroxidase (GPX), and catalase, were also regulated by XB supplementation. XB supplementation inhibited the mRNA expressions levels of the pro-inflammatory cytokines, tumor necrosis factor (TNF)-α, interleukin (IL)-1β, interleukin (IL)-6, and monocyte chemoattractant protein (MCP)-1, as well as phosphorylation of c-Jun N-terminal kinase/stress activated protein kinase (JNK/SAPK), p38 mitogen-activated protein kinases (MAPK), and extracellular signal-regulated kinases 1/2 (ERK1/2). These data demonstrate that XB exhibits anti-diabetic, hypolipogenic, and anti-inflammatory effects via regulation of the miR-122a/33a axis in db/db mice. PMID:27929393

  5. Xylobiose, an Alternative Sweetener, Ameliorates Diabetes-Related Metabolic Changes by Regulating Hepatic Lipogenesis and miR-122a/33a in db/db Mice

    Directory of Open Access Journals (Sweden)

    Eunjin Lim

    2016-12-01

    Full Text Available Type 2 diabetes is a major public health concern worldwide. Xylobiose (XB consists of two molecules of d-xylose and is a major disaccharide in xylooligosaccharides that are used as prebiotics. We hypothesized that XB could regulate diabetes-related metabolic and genetic changes via microRNA expression in db/db mice. For six weeks, C57BL/KsJ-db/db mice received 5% XB as part of the total sucrose content of their diet. XB supplementation improved glucose tolerance with reduced levels of OGTT AUC, fasting blood glucose, HbA1c, insulin, and HOMA-IR. Furthermore, XB supplementation decreased the levels of total triglycerides, total cholesterol, and LDL-C. The expression levels of miR-122a and miR-33a were higher and lower in the XB group, respectively. In the liver, expressions of the lipogenic genes, including, fatty acid synthase (FAS, peroxisome proliferator activated receptor γ (PPARγ, sterol regulatory element-binding protein-1C (SREBP-1C, sterol regulatory element-binding protein-2 (SREBP-2, acetyl-CoA carboxylase (ACC, HMG-CoA reductase (HMGCR, ATP-binding cassette transporter G5/G8 (ABCG5/8, cholesterol 7 alpha-hydroxylase (CYP7A1, and sterol 12-alpha-hydroxylase (CYP8B1, as well as oxidative stress markers, including superoxide dismutase 1 (SOD1, superoxide dismutase 2 (SOD2, glutathione peroxidase (GPX, and catalase, were also regulated by XB supplementation. XB supplementation inhibited the mRNA expressions levels of the pro-inflammatory cytokines, tumor necrosis factor (TNF-α, interleukin (IL-1β, interleukin (IL-6, and monocyte chemoattractant protein (MCP-1, as well as phosphorylation of c-Jun N-terminal kinase/stress activated protein kinase (JNK/SAPK, p38 mitogen-activated protein kinases (MAPK, and extracellular signal-regulated kinases 1/2 (ERK1/2. These data demonstrate that XB exhibits anti-diabetic, hypolipogenic, and anti-inflammatory effects via regulation of the miR-122a/33a axis in db/db mice.

  6. GlycomeDB – integration of open-access carbohydrate structure databases

    Directory of Open Access Journals (Sweden)

    von der Lieth Claus-Wilhelm

    2008-09-01

    Full Text Available Abstract Background Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carbohydrate Structure Database (CCSD or CarbBank ceased in 1997, and since then several initiatives have developed independent databases with partially overlapping foci. For each database, different encoding schemes for residues and sequence topology were designed. Therefore, it is virtually impossible to obtain an overview of all deposited structures or to compare the contents of the various databases. Results We have implemented procedures which download the structures contained in the seven major databases, e.g. GLYCOSCIENCES.de, the Consortium for Functional Glycomics (CFG, the Kyoto Encyclopedia of Genes and Genomes (KEGG and the Bacterial Carbohydrate Structure Database (BCSDB. We have created a new database called GlycomeDB, containing all structures, their taxonomic annotations and references (IDs for the original databases. More than 100000 datasets were imported, resulting in more than 33000 unique sequences now encoded in GlycomeDB using the universal format GlycoCT. Inconsistencies were found in all public databases, which were discussed and corrected in multiple feedback rounds with the responsible curators. Conclusion GlycomeDB is a new, publicly available database for carbohydrate sequences with a unified, all-encompassing structure encoding format and NCBI taxonomic referencing. The database is updated weekly and can be downloaded free of charge. The JAVA application GlycoUpdateDB is also available for establishing and updating a local installation of GlycomeDB. With the advent of GlycomeDB, the distributed islands of knowledge in glycomics are now bridged to form a single resource.

  7. MorusDB: a resource for mulberry genomics and genome biology.

    Science.gov (United States)

    Li, Tian; Qi, Xiwu; Zeng, Qiwei; Xiang, Zhonghuai; He, Ningjia

    2014-01-01

    Mulberry is an important cultivated plant that has received the attention of biologists interested in sericulture and plant-insect interaction. Morus notabilis, a wild mulberry species with a minimal chromosome number is an ideal material for whole-genome sequencing and assembly. The genome and transcriptome of M. notabilis were sequenced and analyzed. In this article, a web-based and open-access database, the Morus Genome Database (MorusDB), was developed to enable easy-to-access and data mining. The MorusDB provides an integrated data source and an easy accession of mulberry large-scale genomic sequencing and assembly, predicted genes and functional annotations, expressed sequence tags (ESTs), transposable elements (TEs), Gene Ontology (GO) terms, horizontal gene transfers between mulberry and silkworm and ortholog and paralog groups. Transcriptome sequencing data for M. notabilis root, leaf, bark, winter bud and male flower can also be searched and downloaded. Furthermore, MorusDB provides an analytical workbench with some built-in tools and pipelines, such as BLAST, Search GO, Mulberry GO and Mulberry GBrowse, to facilitate genomic studies and comparative genomics. The MorusDB provides important genomic resources for scientists working with mulberry and other Moraceae species, which include many important fruit crops. Designed as a basic platform and accompanied by the SilkDB, MorusDB strives to be a comprehensive platform for the silkworm-mulberry interaction studies. Database URL: http://morus.swu.edu.cn/morusdb. © The Author(s) 2014. Published by Oxford University Press.

  8. DB90: A Fortran Callable Relational Database Routine for Scientific and Engineering Computer Programs

    Science.gov (United States)

    Wrenn, Gregory A.

    2005-01-01

    This report describes a database routine called DB90 which is intended for use with scientific and engineering computer programs. The software is written in the Fortran 90/95 programming language standard with file input and output routines written in the C programming language. These routines should be completely portable to any computing platform and operating system that has Fortran 90/95 and C compilers. DB90 allows a program to supply relation names and up to 5 integer key values to uniquely identify each record of each relation. This permits the user to select records or retrieve data in any desired order.

  9. Využití MongoDB s Node.js

    OpenAIRE

    Hejtmánková, Kateřina

    2015-01-01

    The aim of my thesis is to provide a collection of examples about document oriented MongoDB database using Node.js platform, specifically using the Mongoose program, for object-document mapping (ODM). The aim is met by analysis of Mongoose and Async module, which provides functions for more comprehensive asynchronous querying, needed for working with input/output to the MongoDB database in Node.js. The main merit of this thesis is (in the general sense) a demonstration of how to create a admi...

  10. License - dbQSNP | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us dbQSNP License License to Use This Database Last updated : 2017/02/16 You may use this datab...ase in compliance with the terms and conditions of the license described below. The license specifies the lice...nse terms regarding the use of this database and the requirements you must follow in using this database. The lice...follows: dbQSNP © Kenshi Hayashi (Research Center for Genetic Information, Medical Institute of Bioregulatio...d to this database, you are licensed to: freely access part or whole of this database, and acquire data; fre

  11. License - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us MicrobeDB.jp License License to Use This Database Last updated : 2017/06/29 You may use this... database in compliance with the terms and conditions of the license described below. The license specifies the lice...nse terms regarding the use of this database and the requirements you must follow in using this database. The lice...se as follows: MicrobeDB.jp © Ken Kurokawa (Center for Information Biology, National Institute of Genetics) lice... Creative Commons Attribution-Share Alike 4.0 International is found here . With regard to this database, you are lice

  12. License - DB-SPIRE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us DB-SPIRE License License to Use This Database Last updated : 2017/02/16 You may use this dat...abase in compliance with the terms and conditions of the license described below. The license specifies the lice...nse terms regarding the use of this database and the requirements you must follow in using this database. The lice...s follows: ... DB-SPIRE © Tamotsu Noguchi (National Institute of Advanced Industrial Science and Technology) lice...eative Commons Attribution-Share Alike 4.0 International is found here . With regard to this database, you are lice

  13. Index of /data/medaka-full-length-cdna-db/20110331 [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Index of /data/medaka-full-length-cdna-db/20110331 Name Last modified Size Descript...ion Parent Directory - README.html 06-Sep-2012 16:47 13K medaka_full_length_c..> 26-Aug-2011 15:54 99M medaka_full_leng...th_c..> 26-Aug-2011 15:52 814K medaka_full_length_c..> 26-Aug-2011 15:52 8.7M Index of /data/medaka-full-length-cdna-db/20110331 ...

  14. Comparison of multidimensional fuzzy set ordination with CCA and DB-RDA.

    Science.gov (United States)

    Roberts, David W

    2009-09-01

    Multidimensional fuzzy set ordination (MFSO) is an ordination algorithm based on the principles of fuzzy set theory that employs a dissimilarity matrix and environmental or experimental variables directly in the calculation of ordination coordinates. The objective is similar to constrained ordinations such as canonical correspondence analysis (CCA) and distance-based redundancy analysis (DB-RDA), although MFSO employs a different conceptual and algorithmic basis. Results from MFSO, CCA, and DB-RDA are compared on four data sets to determine the relative ability of the methods to identify and quantify environmental variable effect sizes on community variability. Models were fit by best all-subsets solutions and tested for significance by permutation tests. Methods were compared on the basis of variables selected and dimensionality of results and were evaluated on the basis of the correlation of the pair-wise distances of the derived ordination solutions to a Bray-Curtis dissimilarity matrix of the taxon data, and by cross-comparisons of the inertia explained by the fitted or derived values substituted into DB-RDA and CCA analyses. MFSO and DB-RDA achieved the highest correlation with the Bray-Curtis dissimilarity matrix on one data set each, and they tied for highest correlation on the two other data sets (differences set, tied for second on another, and achieved the lowest correlation on two data sets. When substituting MFSO- and DB-RDA-derived values into CCA, MFSO results achieved higher inertia explained on two of the four data sets; MFSO and DB-RDA achieved equivalent results on the other two. Substituting MFSO- or CCA-derived or fitted values into DB-RDA, MFSO results achieved higher inertia explained on all four data sets. While goodness-of-fit statistics were often similar across methods, the methods sometimes chose solutions of different dimensionality or employed different variables. In general, all algorithms performed well, finding relatively low

  15. Quantum Nondemolition Measurement of a Quantum Squeezed State Beyond the 3 dB Limit

    Science.gov (United States)

    Lei, C. U.; Weinstein, A. J.; Suh, J.; Wollman, E. E.; Kronwald, A.; Marquardt, F.; Clerk, A. A.; Schwab, K. C.

    2016-09-01

    We use a reservoir engineering technique based on two-tone driving to generate and stabilize a quantum squeezed state of a micron-scale mechanical oscillator in a microwave optomechanical system. Using an independent backaction-evading measurement to directly quantify the squeezing, we observe 4.7 ±0.9 dB of squeezing below the zero-point level surpassing the 3 dB limit of standard parametric squeezing techniques. Our measurements also reveal evidence for an additional mechanical parametric effect. The interplay between this effect and the optomechanical interaction enhances the amount of squeezing obtained in the experiment.

  16. DB2 9 for Linux, UNIX, and Windows Advanced Database Administration Certification Certification Study Guide

    CERN Document Server

    Sanders, Roger E

    2008-01-01

    Database administrators versed in DB2 wanting to learn more about advanced database administration activities and students wishing to gain knowledge to help them pass the DB2 9 UDB Advanced DBA certification exam will find this exhaustive reference invaluable. Written by two individuals who were part of the team that developed the certification exam, this comprehensive study guide prepares the student for challenging questions on database design; data partitioning and clustering; high availability diagnostics; performance and scalability; security and encryption; connectivity and networking; a

  17. PK/DB: database for pharmacokinetic properties and predictive in silico ADME models.

    Science.gov (United States)

    Moda, Tiago L; Torres, Leonardo G; Carrara, Alexandre E; Andricopulo, Adriano D

    2008-10-01

    The study of pharmacokinetic properties (PK) is of great importance in drug discovery and development. In the present work, PK/DB (a new freely available database for PK) was designed with the aim of creating robust databases for pharmacokinetic studies and in silico absorption, distribution, metabolism and excretion (ADME) prediction. Comprehensive, web-based and easy to access, PK/DB manages 1203 compounds which represent 2973 pharmacokinetic measurements, including five models for in silico ADME prediction (human intestinal absorption, human oral bioavailability, plasma protein binding, blood-brain barrier and water solubility). http://www.pkdb.ifsc.usp.br

  18. Partially hydrolyzed guar gum affects the expression of genes involved in host defense functions and cholesterol absorption in colonic mucosa of db/db male mice.

    Science.gov (United States)

    Yasukawa, Zenta; Naito, Yuji; Takagi, Tomohisa; Mizushima, Katsura; Tokunaga, Makoto; Ishihara, Noriyuki; R Juneja, Lekh; Yoshikawa, Toshikazu

    2012-07-01

    Biomedical evidence in the last 20 years has shown that the consumption of partially hydrolyzed guar gum may influence lipid and/or carbohydrate metabolism at many levels. Since intestine represents the first interface to interact with dietary partially hydrolyzed guar gum in vivo, we evaluated gene expression profiles in small intestinal mucosa of db/db mice fed with partially hydrolyzed guar gum in an effort to delineate its effect on the small intestine. DNA microarray and real-time PCR analyses were performed to evaluate the gene expression profiles in mice small intestinal mucosa. Among the 28,853 transcripts represented on the GeneChip® microarray, no more than 20 genes exhibited up- or down-regulation by 1.5-fold or more after four weeks following partially hydrolyzed guar gum consumption. No adverse effects were apparent. We detected up- or down-regulation of some genes known to be involved in host defense functions and cholesterol absorption.

  19. Rapid and efficient identification of the mouse leptin receptor mutation (C57BL/KsJ-db/db) by tetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) analysis.

    Science.gov (United States)

    Jung, Harry; Nam, Hajin; Suh, Jun-Gyo

    2016-03-01

    The C57BLKS/J-Lepr(db) mouse has a point mutation in the leptin receptor gene and is one of the most useful animal model for non-insulin dependent diabetes mellitus in human. Since the homozygote of C57BLKS/J-Lepr(db) mouse is infertile, detection of point mutation in the leptin receptor gene is important for efficient maintaining strains as well as mass production of homozygotes. To develop a rapid and efficient genotyping method for C57BLKS/J-Lepr(db) mouse, the tetra-primer amplification-refractory mutation system polymerase chain reaction (ARMS-PCR) was used. The 407 and 199 bp PCR products were amplified from normal (+/+) mice; while the 407 and 268 bp PCR products were amplified from homozygotes (db/db) mice; and the 407, 268, and 199 bp PCR products were amplified from heterozygotes (db/+) mice. This result showed that the tetra-primer ARMS-PCR analysis by us is suitable to detect point mutation of the leptin receptor gene. Taken together, our method will dramatically reduce animal use for maintenance of strains as well as production of homozygote in the C57BLKS/J-Lepr(db) strains.

  20. Hydrogen sulfide preconditions the db/db diabetic mouse heart against ischemia-reperfusion injury by activating Nrf2 signaling in an Erk-dependent manner.

    Science.gov (United States)

    Peake, Bridgette F; Nicholson, Chad K; Lambert, Jonathan P; Hood, Rebecca L; Amin, Hena; Amin, Sana; Calvert, John W

    2013-05-01

    Hydrogen sulfide (H2S) therapy protects nondiabetic animals in various models of myocardial injury, including acute myocardial infarction and heart failure. Here, we sought to examine whether H2S therapy provides cardioprotection in the setting of type 2 diabetes. H2S therapy in the form of sodium sulfide (Na2S) beginning 24 h or 7 days before myocardial ischemia significantly decreased myocardial injury in db/db diabetic mice (12 wk of age). In an effort to evaluate the signaling mechanism responsible for the observed cardioprotection, we focused on the role of nuclear factor E2-related factor (Nrf2) signaling. Our results indicate that diabetes does not alter the ability of H2S to increase the nuclear localization of Nrf2, but does impair aspects of Nrf2 signaling. Specifically, the expression of NADPH quinine oxidoreductase 1 was increased after the acute treatment, whereas the expression of heme-oxygenase-1 (HO-1) was only increased after 7 days of treatment. This discrepancy was found to be the result of an increased nuclear expression of Bach1, a known repressor of HO-1 transcription, which blocked the binding of Nrf2 to the HO-1 promoter. Further analysis revealed that 7 days of Na2S treatment overcame this impairment by removing Bach1 from the nucleus in an Erk1/2-dependent manner. Our findings demonstrate for the first time that exogenous administration of Na2S attenuates myocardial ischemia-reperfusion injury in db/db mice, suggesting the potential therapeutic effects of H2S in treating a heart attack in the setting of type 2 diabetes.

  1. The effective fraction isolated from Radix Astragali alleviates glucose intolerance, insulin resistance and hypertriglyceridemia in db/db diabetic mice through its anti-inflammatory activity

    Directory of Open Access Journals (Sweden)

    Hoo Ruby LC

    2010-08-01

    Full Text Available Abstract Background Macrophage infiltration in adipose tissue together with the aberrant production of pro-inflammatory cytokines has been identified as the key link between obesity and its related metabolic disorders. This study aims to isolate bioactive ingredients from the traditional Chinese herb Radix Astragali (Huangqi that alleviate obesity-induced metabolic damage through inhibiting inflammation. Methods Active fraction (Rx that inhibits pro-inflammatory cytokine production was identified from Radix Astragali by repeated bioactivity-guided high-throughput screening. Major constituents in Rx were identified by column chromatography followed by high-performance liquid chromatography (HPLC and mass-spectrometry. Anti-diabetic activity of Rx was evaluated in db/db mice. Results Treatment with Rx, which included calycosin-7-β-D-glucoside (0.9%, ononin (1.2%, calycosin (4.53% and formononetin (1.1%, significantly reduced the secretion of pro-inflammatory cytokines (TNF-α, IL-6 and MCP-1 in human THP-1 macrophages and lipopolysaccharide (LPS-induced activation of NF-κB in mouse RAW-Blue macrophages in a dose-dependent manner. Chronic administration of Rx in db/db obese mice markedly decreased the levels of both fed and fasting glucose, reduced serum triglyceride, and also alleviated insulin resistance and glucose intolerance when compared to vehicle-treated controls. The mRNA expression levels of inflammatory cell markers CD68 and F4/80, and cytokines MCP-1, TNF-α and IL-6 were significantly reduced in epididymal adipose tissue while the alternatively activated macrophage marker arginase I was markedly increased in the Rx-treated mice. Conclusion These findings suggest that suppression of the inflammation pathways in macrophages represents a valid strategy for high-throughput screening of lead compounds with anti-diabetic and insulin sensitizing properties, and further support the etiological role of inflammation in the pathogenesis of

  2. Preventive effects of branched-chain amino acid supplementation on the spontaneous development of hepatic preneoplastic lesions in C57BL/KsJ-db/db obese mice.

    Science.gov (United States)

    Terakura, Daishi; Shimizu, Masahito; Iwasa, Junpei; Baba, Atsushi; Kochi, Takahiro; Ohno, Tomohiko; Kubota, Masaya; Shirakami, Yohei; Shiraki, Makoto; Takai, Koji; Tsurumi, Hisashi; Tanaka, Takuji; Moriwaki, Hisataka

    2012-12-01

    Obesity and its associated disorders, such as non-alcoholic steatohepatitis, increase the risk of hepatocellular carcinoma. Branched-chain amino acids (BCAA), which improve protein malnutrition in patients with liver cirrhosis, reduce the risk of hepatocellular carcinoma in these patients with obesity. In the present study, the effects of BCAA supplementation on the spontaneous development of hepatic premalignant lesions, foci of cellular alteration, in db/db obese mice were examined. Male db/db mice were given a basal diet containing 3.0% of either BCAA or casein, a nitrogen-content-matched control of BCAA, for 36 weeks. On killing the mice, supplementation with BCAA significantly inhibited the development of foci of cellular alteration when compared with casein supplementation by inhibiting cell proliferation, but inducing apoptosis. BCAA supplementation increased the expression levels of peroxisome proliferator-activated receptor-γ, p21(CIP1) and p27(KIP1) messenger RNA and decreased the levels of c-fos and cyclin D1 mRNA in the liver. BCAA supplementation also reduced both the amount of hepatic triglyceride accumulation and the expression of interleukin (IL)-6, IL-1β, IL-18 and tumor necrosis factor-α mRNA in the liver. Increased macrophage infiltration was inhibited and the expression of IL-6, TNF-α, and monocyte chemoattractant protein-1 mRNA in the white adipose tissue were each decreased by BCAA supplementation. BCAA supplementation also reduced adipocyte size while increasing the expression of peroxisome proliferator-activated receptor-α, peroxisome proliferator-activated receptor-γ and adiponectin mRNA in the white adipose tissue compared with casein supplementation. These findings indicate that BCAA supplementation inhibits the early phase of obesity-related liver tumorigenesis by attenuating chronic inflammation in both the liver and white adipose tissue. BCAA supplementation may be useful in the chemoprevention of liver tumorigenesis in obese

  3. MiR-181c restrains nitration stress of endothelial cells in diabetic db/db mice through inhibiting the expression of FoxO1.

    Science.gov (United States)

    Yang, Guangwei; Wu, Yuanbo; Ye, Shandong

    2017-04-22

    Endothelial dysfunction played an important role in the progression of diabetes mellitus (DM). miR-181c has been implicated in many diseases, including DM. However, the molecular mechanisms of miR-181c regulate this process remained poorly understood. Healthy ICR mice were divided into control group (n = 10) and db/db DM group (n = 10). The expression of miR-181c and FoxO1 were both investigated in diabetic db/db mice or high glucose-induced endothelial cells (MAECs and END-D). Here we found that down-regulation of miR-181c and the activation of FoxO1/iNOS were observed in mice and endothelial cells. Furthermore, we verified that miR-181c directly targeted and inhibited FoxO1 gene expression by targeting its 3'-UTR through luciferase reporter assay. Knockdown of FoxO1 reversed the up-regulation of iNOS, nitrotyrosine and the down-regulation of p-eNOS(Ser1177)/eNOS in high glucose (30 mM)-induced MAECs cells. In addition, over-expression of miR-181c could reverse the enhanced nitration stress induced by high glucose, while this effect could be attenuated by pcDNA-FoxO1 in MAECs. These results shown that miR-181c attenuated nitration stress through regulating FoxO1 expression and affecting endothelial cell function, which offering a new target for the development of preventive or therapeutic agents against DM. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Telmisartan ameliorates insulin sensitivity by activating the AMPK/SIRT1 pathway in skeletal muscle of obese db/db mice

    Science.gov (United States)

    2012-01-01

    Background Telmisartan is a well-established angiotensin II type 1 receptor blocker that improves insulin sensitivity in animal models of obesity and insulin resistance, as well as in humans. Telmisartan has been reported to function as a partial agonist of the peroxisome proliferator-activated receptor (PPAR) γ, which is also targeted by the nicotinamide adenine dinucleotide (NAD)-dependent deacetylase (SIRT1). Here, we investigated the pathways through which telmisartan acts on skeletal muscle, in vitro as well as in vivo. Methods Nine-week-old male db/db mice were fed a 60% high-fat diet, with orally administrated either vehicle (carboxymethyl-cellulose, CMC), 5 mg/kg telmisartan, or 5 mg/kg telmisartan and 1 mg/kg GW9662, a selective irreversible antagonist of PPARγ, for 5 weeks. Effects of telmisartan on Sirt1 mRNA, AMPK phosphorylation, and NAD+/NADH ratio were determined in C2C12 cultured myocytes. Results and discussion Telmisartan treatment improved insulin sensitivity in obese db/db mice fed a high-fat diet and led to reduction in the size of hypertrophic pancreatic islets in these mice. Moreover, in vitro treatment with telmisartan led to increased expression of Sirt1 mRNA in C2C12 skeletal muscle cells; the increase in Sirt1 mRNA in telmisartan-treated C2C12 myoblasts occurred concomitantly with an increase in AMPK phosphorylation, an increase in NAD+/NADH ratio, and increases in the mRNA levels of PGC1α, FATP1, ACO, and GLUT4. Conclusions Our results indicate that telmisartan acts through a PPARγ-independent pathway, but at least partially exerts its effects by acting directly on skeletal muscle AMPK/SIRT1 pathways. PMID:23137106

  5. Telmisartan ameliorates insulin sensitivity by activating the AMPK/SIRT1 pathway in skeletal muscle of obese db/db mice

    Directory of Open Access Journals (Sweden)

    Shiota Asuka

    2012-11-01

    Full Text Available Abstract Background Telmisartan is a well-established angiotensin II type 1 receptor blocker that improves insulin sensitivity in animal models of obesity and insulin resistance, as well as in humans. Telmisartan has been reported to function as a partial agonist of the peroxisome proliferator-activated receptor (PPAR γ, which is also targeted by the nicotinamide adenine dinucleotide (NAD-dependent deacetylase (SIRT1. Here, we investigated the pathways through which telmisartan acts on skeletal muscle, in vitro as well as in vivo. Methods Nine-week-old male db/db mice were fed a 60% high-fat diet, with orally administrated either vehicle (carboxymethyl-cellulose, CMC, 5 mg/kg telmisartan, or 5 mg/kg telmisartan and 1 mg/kg GW9662, a selective irreversible antagonist of PPARγ, for 5 weeks. Effects of telmisartan on Sirt1 mRNA, AMPK phosphorylation, and NAD+/NADH ratio were determined in C2C12 cultured myocytes. Results and discussion Telmisartan treatment improved insulin sensitivity in obese db/db mice fed a high-fat diet and led to reduction in the size of hypertrophic pancreatic islets in these mice. Moreover, in vitro treatment with telmisartan led to increased expression of Sirt1 mRNA in C2C12 skeletal muscle cells; the increase in Sirt1 mRNA in telmisartan-treated C2C12 myoblasts occurred concomitantly with an increase in AMPK phosphorylation, an increase in NAD+/NADH ratio, and increases in the mRNA levels of PGC1α, FATP1, ACO, and GLUT4. Conclusions Our results indicate that telmisartan acts through a PPARγ-independent pathway, but at least partially exerts its effects by acting directly on skeletal muscle AMPK/SIRT1 pathways.

  6. Fermentation of purple Jerusalem artichoke extract to improve the α-glucosidase inhibitory effect in vitro and ameliorate blood glucose in db/db mice.

    Science.gov (United States)

    Wang, Zhiqiang; Hwang, Seung Hwan; Lee, Sun Youb; Lim, Soon Sung

    2016-06-01

    Jerusalem artichoke has inhibitory activity against α-glucosidase and decreases fasting serum glucose levels, which may be related to its fructan content. The biological activity of fructan can be influenced by the degree of polymerization. Thus, in this study, the inhibitory effects of original and fermented purple Jerusalem artichoke (PJA) on α-glucosidase were compared in vitro. Additionally, the anti-diabetes effect of Lactobacillus plantarum-fermented PJA (LJA) was studied in a non-insulin-dependent diabetes mellitus animal model (C57BIKsJ db/db). The water extract of PJA was fermented by L. plantarum, and two strains of Bacillus subtilis to compare their anti-α-glucosidase activities in vitro by α-glucosidase assays. The anti-diabetes effect of LJA was studied in a non-insulin-dependent diabetes mellitus animal model (C57BIKsJ db/db) for seven weeks. During the experiment, food intake, body weight, and fasting blood glucose were measured every week. At the end of the treatment period, several diabetic parameters and the intestinal α-glucosidase activity were measured. The LJA showed the highest α-glucosidase inhibitory activity in vitro. In the in vivo study, it resulted in a significantly lower blood glucose concentration than the control. Serum insulin and HDL cholesterol levels were significantly higher and the concentrations of triglycerides, non-esterified fatty acids, and total cholesterol were significant lower in mice treated with LJA after seven weeks. In addition, the intestinal α-glucosidase activity was partially inhibited. These results suggested that LJA regulates blood glucose and has potential use as a dietary supplement.

  7. New tools and methods for direct programmatic access to the dbSNP relational database.

    Science.gov (United States)

    Saccone, Scott F; Quan, Jiaxi; Mehta, Gaurang; Bolze, Raphael; Thomas, Prasanth; Deelman, Ewa; Tischfield, Jay A; Rice, John P

    2011-01-01

    Genome-wide association studies often incorporate information from public biological databases in order to provide a biological reference for interpreting the results. The dbSNP database is an extensive source of information on single nucleotide polymorphisms (SNPs) for many different organisms, including humans. We have developed free software that will download and install a local MySQL implementation of the dbSNP relational database for a specified organism. We have also designed a system for classifying dbSNP tables in terms of common tasks we wish to accomplish using the database. For each task we have designed a small set of custom tables that facilitate task-related queries and provide entity-relationship diagrams for each task composed from the relevant dbSNP tables. In order to expose these concepts and methods to a wider audience we have developed web tools for querying the database and browsing documentation on the tables and columns to clarify the relevant relational structure. All web tools and software are freely available to the public at http://cgsmd.isi.edu/dbsnpq. Resources such as these for programmatically querying biological databases are essential for viably integrating biological information into genetic association experiments on a genome-wide scale.

  8. Disease - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...sion V2 10.18908/lsdba.nbdc01181-007.V002 Update History V1 - Description of data contents The PDO annotatio...iption Download License Update History of This Database Site Policy | Contact Us Disease - MicrobeDB.jp | LSDB Archive ...

  9. GOLD - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...2 10.18908/lsdba.nbdc01181-008.V002 Update History V1 - Description of data contents Annotation results of p... Download License Update History of This Database Site Policy | Contact Us GOLD - MicrobeDB.jp | LSDB Archive ...

  10. Ultralow-loss 3-dB photonic crystal waveguide splitter

    DEFF Research Database (Denmark)

    Frandsen, Lars Hagedorn; Borel, Peter Ingo; Zhuang, Yanxin;

    2004-01-01

    A photonic crystal waveguide splitter that exhibits ultralow-loss 3-dB splitting for TE-polarized light is fabricated in silicon-on-insulator material by use of deep UV lithography. The high performance is achieved by use of a Y junction, which is designed to ensure single-mode operation, and low...

  11. Parallelism in a Main-Memory System: The Performance of PRISMA/DB

    NARCIS (Netherlands)

    Wilschut, A.N.; Flokstra, Jan; Apers, Peter M.G.

    1992-01-01

    his paper evaluates the performance of the parallel, main-memory DBMS, PRISMA/DB. First, an abstract architecture for parallel query execution is presented. A performance model for the execution of simple relational operations on this architecture is developed. The parameters in the model are set us

  12. MetaMetaDB: a database and analytic system for investigating microbial habitability.

    Directory of Open Access Journals (Sweden)

    Ching-chia Yang

    Full Text Available MetaMetaDB (http://mmdb.aori.u-tokyo.ac.jp/ is a database and analytic system for investigating microbial habitability, i.e., how a prokaryotic group can inhabit different environments. The interaction between prokaryotes and the environment is a key issue in microbiology because distinct prokaryotic communities maintain distinct ecosystems. Because 16S ribosomal RNA (rRNA sequences play pivotal roles in identifying prokaryotic species, a system that comprehensively links diverse environments to 16S rRNA sequences of the inhabitant prokaryotes is necessary for the systematic understanding of the microbial habitability. However, existing databases are biased to culturable prokaryotes and exhibit limitations in the comprehensiveness of the data because most prokaryotes are unculturable. Recently, metagenomic and 16S rRNA amplicon sequencing approaches have generated abundant 16S rRNA sequence data that encompass unculturable prokaryotes across diverse environments; however, these data are usually buried in large databases and are difficult to access. In this study, we developed MetaMetaDB (Meta-Metagenomic DataBase, which comprehensively and compactly covers 16S rRNA sequences retrieved from public datasets. Using MetaMetaDB, users can quickly generate hypotheses regarding the types of environments a prokaryotic group may be adapted to. We anticipate that MetaMetaDB will improve our understanding of the diversity and evolution of prokaryotes.

  13. dbSAP: single amino-acid polymorphism database for protein variation detection

    Science.gov (United States)

    Cao, Ruifang; Shi, Yan; Chen, Shuangguan; Ma, Yimin; Chen, Jiajun; Yang, Juan; Chen, Geng; Shi, Tieliu

    2017-01-01

    Millions of human single nucleotide polymorphisms (SNPs) or mutations have been identified so far, and these variants could be strongly correlated with phenotypic variations of traits/diseases. Among these variants, non-synonymous ones can result in amino-acid changes that are called single amino-acid polymorphisms (SAPs). Although some studies have tried to investigate the SAPs, only a small fraction of SAPs have been identified due to inadequately inferred protein variation database and the low coverage of mass spectrometry (MS) experiments. Here, we present the dbSAP database for conveniently accessing the comprehensive information and relationships of spectra, peptides and proteins of SAPs, as well as related genes, pathways, diseases and drug targets. In order to fully explore human SAPs, we built a customized protein database that contained comprehensive variant proteins by integrating and annotating the human SNPs and mutations from eight distinct databases (UniProt, Protein Mutation Database, HPMD, MSIPI, MS-CanProVar, dbSNP, Ensembl and COSMIC). After a series of quality controls, a total of 16 854 SAP peptides involving in 439 537 spectra were identified with large scale MS datasets from various human tissues and cell lines. dbSAP is freely available at http://www.megabionet.org/dbSAP/index.html. PMID:27903894

  14. AH-DB: collecting protein structure pairs before and after binding.

    Science.gov (United States)

    Chang, Darby Tien-Hao; Yao, Tsung-Ju; Fan, Chen-Yu; Chiang, Chih-Yun; Bai, Yi-Han

    2012-01-01

    This work presents the Apo-Holo DataBase (AH-DB, http://ahdb.ee.ncku.edu.tw/ and http://ahdb.csbb.ntu.edu.tw/), which provides corresponding pairs of protein structures before and after binding. Conformational transitions are commonly observed in various protein interactions that are involved in important biological functions. For example, copper-zinc superoxide dismutase (SOD1), which destroys free superoxide radicals in the body, undergoes a large conformational transition from an 'open' state (apo structure) to a 'closed' state (holo structure). Many studies have utilized collections of apo-holo structure pairs to investigate the conformational transitions and critical residues. However, the collection process is usually complicated, varies from study to study and produces a small-scale data set. AH-DB is designed to provide an easy and unified way to prepare such data, which is generated by identifying/mapping molecules in different Protein Data Bank (PDB) entries. Conformational transitions are identified based on a refined alignment scheme to overcome the challenge that many structures in the PDB database are only protein fragments and not complete proteins. There are 746,314 apo-holo pairs in AH-DB, which is about 30 times those in the second largest collection of similar data. AH-DB provides sophisticated interfaces for searching apo-holo structure pairs and exploring conformational transitions from apo structures to the corresponding holo structures.

  15. ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data.

    Science.gov (United States)

    Arnaiz, Olivier; Cain, Scott; Cohen, Jean; Sperling, Linda

    2007-01-01

    ParameciumDB (http://paramecium.cgm.cnrs-gif.fr) is a new model organism database associated with the genome sequencing project of the unicellular eukaryote Paramecium tetraurelia. Built with the core components of the Generic Model Organism Database (GMOD) project, ParameciumDB currently contains the genome sequence and annotations, linked to available genetic data including the Gif Paramecium stock collection. It is thus possible to navigate between sequences and stocks via the genes and alleles. Phenotypes, of mutant strains and of knockdowns obtained by RNA interference, are captured using controlled vocabularies according to the Entity-Attribute-Value model. ParameciumDB currently supports browsing of phenotypes, alleles and stocks as well as querying of sequence features (genes, UniProt matches, InterPro domains, Gene Ontology terms) and of genetic data (phenotypes, stocks, RNA interference experiments). Forms allow submission of RNA interference data and some bioinformatics services are available. Future ParameciumDB development plans include coordination of human curation of the near 40 000 gene models by members of the research community.

  16. Distribuciones de masas de estrellas PG; DO y DB: posibles conexiones evolutivas

    Science.gov (United States)

    Panei, J. A.; Althaus, L. G.; Miller Bertolami, M. M.; García-Berro, E.; Córsico, A. H.; Romero, A. D.; Kepler, S. O.; Rohrmann, R. D.

    A 20 % of white dwarf stars has hydrogen deficient atmospheres, known like no-DA white dwarfs. The results of this work allow for the first time to study a possible evolutionary connection between different low mass and hydrogen deficient post-AGB stars, like DO white dwarfs, PG 1159, O(He), DB and RCrB, among others. FULL TEXT IN SPANISH

  17. CyMSatDB: The Globe Artichoke (Cynara cardunculus var. scolymus) Microsatellite Database

    DEFF Research Database (Denmark)

    Portis, Ezio; Portis, Flavio; Valente, Luisa

    2015-01-01

    and for the construction of the first microsatellite marker database CyMSatDB (Cynara cardunculusMicroSatellite DataBase). Both perfect and compound SSRs were in-silico mined using the SciRoKo SSR-search module (http://kofler.or.at/bioinformatics/SciRoKo). On the whole, about 295,000 SSR motifs were identified which also...

  18. Arylimidamide DB766, a Potential Chemotherapeutic Candidate for Chagas' Disease Treatment ▿

    Science.gov (United States)

    Batista, Denise da Gama Jaén; Batista, Marcos Meuser; Oliveira, Gabriel Melo de; Amaral, Patrícia Borges do; Lannes-Vieira, Joseli; Britto, Constança Carvalho; Junqueira, Angela; Lima, Marli Maria; Romanha, Alvaro José; Sales Junior, Policarpo Ademar; Stephens, Chad E.; Boykin, David W.; Soeiro, Maria de Nazaré Correia

    2010-01-01

    Chagas' disease, a neglected tropical illness for which current therapy is unsatisfactory, is caused by the intracellular parasite Trypanosoma cruzi. The goal of this work is to investigate the in vitro and in vivo effects of the arylimidamide (AIA) DB766 against T. cruzi. This arylimidamide exhibits strong trypanocidal activity and excellent selectivity for bloodstream trypomastigotes and intracellular amastigotes (Y strain), giving IC50s (drug concentrations that reduce 50% of the number of the treated parasites) of 60 and 25 nM, respectively. DB766 also exerts striking effects upon different parasite stocks, including those naturally resistant to benznidazole, and displays higher activity in vitro than the reference drugs. By fluorescent and transmission electron microscopy analyses, we found that this AIA localizes in DNA-enriched compartments and induces considerable damage to the mitochondria. DB766 effectively reduces the parasite load in the blood and cardiac tissue and presents efficacy similar to that of benznidazole in mouse models of T. cruzi infection employing the Y and Colombian strains, using oral and intraperitoneal doses of up to 100 mg/kg/day that were given after the establishment of parasite infection. This AIA ameliorates electrocardiographic alterations, reduces hepatic and heart lesions induced by the infection, and provides 90 to 100% protection against mortality, which is similar to that provided by benznidazole. Our data clearly show the trypanocidal efficacy of DB766, suggesting that this AIA may represent a new lead compound candidate to Chagas' disease treatment. PMID:20457822

  19. Obesity promotes PhIP-induced small intestinal carcinogenesis in hCYP1A-db/db mice: involvement of mutations and DNA hypermethylation of Apc.

    Science.gov (United States)

    Wang, Hong; Liu, Anna; Kuo, Yingyi; Chi, Eric; Yang, Xu; Zhang, Lanjing; Yang, Chung S

    2016-07-01

    Obesity is associated with an increased risk of cancer. To study the promotion of dietary carcinogen-induced gastrointestinal cancer by obesity, we employed 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) to induce intestinal tumorigenesis in CYP1A-humanized (hCYP1A) mice, in which mouse Cyp1a1/1a2 was replaced with human CYP1A1/1A2 Obesity was introduced in hCYP1A mice by breeding with Lepr(db/+) mice to establish the genetically induced obese hCYP1A-Lepr(db/db) mice or by feeding hCYP1A mice a high-fat diet. PhIP induced the formation of small intestinal tumors at the ages of weeks 28-40 in obese hCYP1A mice, but not in lean hCYP1A mice. No tumors were found in colon and other gastrointestinal organs in the lean or obese mice. Using immunohistochemistry (IHC), we found strong positive staining of NF-κB p65, pSTAT3 and COX2 as well as elevated levels of nuclear β-catenin (Ctnnb1) in small intestinal tumors, but not in normal tissues. By sequencing Apc and Ctnnb1 genes, we found that most PhIP-induced small intestinal tumors in obese mice carried only a single heterozygous mutation in Apc By bisulfite-sequencing of CpG islands of Apc, we found DNA hypermethylation in a CpG cluster located in its transcription initiation site, which most likely caused the inactivation of the wild-type Apc allele. Our findings demonstrate that PhIP-induced small intestinal carcinogenesis in hCYP1A-db/db mice is promoted by obesity and involves Apc mutation and inactivation by DNA hypermethylation. This experimental result is consistent with the association of obesity and the increased incidence of small intestinal cancer in humans in recent decades. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  20. Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB

    Directory of Open Access Journals (Sweden)

    Antoni Hermoso

    2007-01-01

    Full Text Available Loops represent an important part of protein structures. The study of loop is critical for two main reasons: First, loops are often involved in protein function, stability and folding. Second, despite improvements in experimental and computational structure prediction methods, modeling the conformation of loops remains problematic. Here, we present a structural classification of loops, ArchDB, a mine of information with application in both mentioned fields: loop structure prediction and function prediction. ArchDB (http://sbi.imim.es/archdb is a database of classified protein loop motifs. The current database provides four different classification sets tailored for different purposes. ArchDB-40, a loop classification derived from SCOP40, well suited for modeling common loop motifs. Since features relevant to loop structure or function can be more easily determined on well-populated clusters, we have developed ArchDB-95, a loop classification derived from SCOP95. This new classification set shows a ∼40% increase in the number of subclasses, and a large 7-fold increase in the number of putative structure/function-related subclasses. We also present ArchDB-EC, a classification of loop motifs from enzymes, and ArchDB-KI, a manually annotated classification of loop motifs from kinases. Information about ligand contacts and PDB sites has been included in all classification sets. Improvements in our classification scheme are described, as well as several new database features, such as the ability to query by conserved annotations, sequence similarity, or uploading 3D coordinates of a protein. The lengths of classified loops range between 0 and 36 residues long. ArchDB offers an exhaustive sampling of loop structures. Functional information about loops and links with related biological databases are also provided. All this information and the possibility to browse/query the database through a web-server outline an useful tool with application in the

  1. Scalable Earth-observation Analytics for Geoscientists: Spacetime Extensions to the Array Database SciDB

    Science.gov (United States)

    Appel, Marius; Lahn, Florian; Pebesma, Edzer; Buytaert, Wouter; Moulds, Simon

    2016-04-01

    Today's amount of freely available data requires scientists to spend large parts of their work on data management. This is especially true in environmental sciences when working with large remote sensing datasets, such as obtained from earth-observation satellites like the Sentinel fleet. Many frameworks like SpatialHadoop or Apache Spark address the scalability but target programmers rather than data analysts, and are not dedicated to imagery or array data. In this work, we use the open-source data management and analytics system SciDB to bring large earth-observation datasets closer to analysts. Its underlying data representation as multidimensional arrays fits naturally to earth-observation datasets, distributes storage and computational load over multiple instances by multidimensional chunking, and also enables efficient time-series based analyses, which is usually difficult using file- or tile-based approaches. Existing interfaces to R and Python furthermore allow for scalable analytics with relatively little learning effort. However, interfacing SciDB and file-based earth-observation datasets that come as tiled temporal snapshots requires a lot of manual bookkeeping during ingestion, and SciDB natively only supports loading data from CSV-like and custom binary formatted files, which currently limits its practical use in earth-observation analytics. To make it easier to work with large multi-temporal datasets in SciDB, we developed software tools that enrich SciDB with earth observation metadata and allow working with commonly used file formats: (i) the SciDB extension library scidb4geo simplifies working with spatiotemporal arrays by adding relevant metadata to the database and (ii) the Geospatial Data Abstraction Library (GDAL) driver implementation scidb4gdal allows to ingest and export remote sensing imagery from and to a large number of file formats. Using added metadata on temporal resolution and coverage, the GDAL driver supports time-based ingestion of

  2. TR32DB - Management of Research Data in a Collaborative, Interdisciplinary Research Project

    Science.gov (United States)

    Curdt, Constanze; Hoffmeister, Dirk; Waldhoff, Guido; Lang, Ulrich; Bareth, Georg

    2015-04-01

    The management of research data in a well-structured and documented manner is essential in the context of collaborative, interdisciplinary research environments (e.g. across various institutions). Consequently, set-up and use of a research data management (RDM) system like a data repository or project database is necessary. These systems should accompany and support scientists during the entire research life cycle (e.g. data collection, documentation, storage, archiving, sharing, publishing) and operate cross-disciplinary in interdisciplinary research projects. Challenges and problems of RDM are well-know. Consequently, the set-up of a user-friendly, well-documented, sustainable RDM system is essential, as well as user support and further assistance. In the framework of the Transregio Collaborative Research Centre 32 'Patterns in Soil-Vegetation-Atmosphere Systems: Monitoring, Modelling, and Data Assimilation' (CRC/TR32), funded by the German Research Foundation (DFG), a RDM system was self-designed and implemented. The CRC/TR32 project database (TR32DB, www.tr32db.de) is operating online since early 2008. The TR32DB handles all data, which are created by the involved project participants from several institutions (e.g. Universities of Cologne, Bonn, Aachen, and the Research Centre Jülich) and research fields (e.g. soil and plant sciences, hydrology, geography, geophysics, meteorology, remote sensing). Very heterogeneous research data are considered, which are resulting from field measurement campaigns, meteorological monitoring, remote sensing, laboratory studies and modelling approaches. Furthermore, outcomes like publications, conference contributions, PhD reports and corresponding images are regarded. The TR32DB project database is set-up in cooperation with the Regional Computing Centre of the University of Cologne (RRZK) and also located in this hardware environment. The TR32DB system architecture is composed of three main components: (i) a file-based data

  3. RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration.

    Science.gov (United States)

    Alves, Gelio; Ogurtsov, Aleksey Y; Yu, Yi-Kuo

    2008-10-27

    Existing scientific literature is a rich source of biological information such as disease markers. Integration of this information with data analysis may help researchers to identify possible controversies and to form useful hypotheses for further validations. In the context of proteomics studies, individualized proteomics era may be approached through consideration of amino acid substitutions/modifications as well as information from disease studies. Integration of such information with peptide searches facilitates speedy, dynamic information retrieval that may significantly benefit clinical laboratory studies. We have integrated from various sources annotated single amino acid polymorphisms, post-translational modifications, and their documented disease associations (if they exist) into one enhanced database per organism. We have also augmented our peptide identification software RAId_DbS to take into account this information while analyzing a tandem mass spectrum. In principle, one may choose to respect or ignore the correlation of amino acid polymorphisms/modifications within each protein. The former leads to targeted searches and avoids scoring of unnecessary polymorphism/modification combinations; the latter explores possible polymorphisms in a controlled fashion. To facilitate new discoveries, RAId_DbS also allows users to conduct searches permitting novel polymorphisms as well as to search a knowledge database created by the users. We have finished constructing enhanced databases for 17 organisms. The web link to RAId_DbS and the enhanced databases is http://www.ncbi.nlm.nih.gov/CBBResearch/qmbp/RAId_DbS/index.html. The relevant databases and binaries of RAId_DbS for Linux, Windows, and Mac OS X are available for download from the same web page.

  4. HIVsirDB: a database of HIV inhibiting siRNAs.

    Directory of Open Access Journals (Sweden)

    Atul Tyagi

    Full Text Available BACKGROUND: Human immunodeficiency virus (HIV is responsible for millions of deaths every year. The current treatment involves the use of multiple antiretroviral agents that may harm patients due to their toxic nature. RNA interference (RNAi is a potent candidate for the future treatment of HIV, uses short interfering RNA (siRNA/shRNA for silencing HIV genes. In this study, attempts have been made to create a database HIVsirDB of siRNAs responsible for silencing HIV genes. DESCRIPTIONS: HIVsirDB is a manually curated database of HIV inhibiting siRNAs that provides comprehensive information about each siRNA or shRNA. Information was collected and compiled from literature and public resources. This database contains around 750 siRNAs that includes 75 partially complementary siRNAs differing by one or more bases with the target sites and over 100 escape mutant sequences. HIVsirDB structure contains sixteen fields including siRNA sequence, HIV strain, targeted genome region, efficacy and conservation of target sequences. In order to facilitate user, many tools have been integrated in this database that includes; i siRNAmap for mapping siRNAs on target sequence, ii HIVsirblast for BLAST search against database, iii siRNAalign for aligning siRNAs. CONCLUSION: HIVsirDB is a freely accessible database of siRNAs which can silence or degrade HIV genes. It covers 26 types of HIV strains and 28 cell types. This database will be very useful for developing models for predicting efficacy of HIV inhibiting siRNAs. In summary this is a useful resource for researchers working in the field of siRNA based HIV therapy. HIVsirDB database is accessible at http://crdd.osdd.net/raghava/hivsir/.

  5. CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources

    Directory of Open Access Journals (Sweden)

    Lucchetti-Miganeh Céline

    2010-03-01

    Full Text Available Abstract Background The functions of proteins are strongly related to their localization in cell compartments (for example the cytoplasm or membranes but the experimental determination of the sub-cellular localization of proteomes is laborious and expensive. A fast and low-cost alternative approach is in silico prediction, based on features of the protein primary sequences. However, biologists are confronted with a very large number of computational tools that use different methods that address various localization features with diverse specificities and sensitivities. As a result, exploiting these computer resources to predict protein localization accurately involves querying all tools and comparing every prediction output; this is a painstaking task. Therefore, we developed a comprehensive database, called CoBaltDB, that gathers all prediction outputs concerning complete prokaryotic proteomes. Description The current version of CoBaltDB integrates the results of 43 localization predictors for 784 complete bacterial and archaeal proteomes (2.548.292 proteins in total. CoBaltDB supplies a simple user-friendly interface for retrieving and exploring relevant information about predicted features (such as signal peptide cleavage sites and transmembrane segments. Data are organized into three work-sets ("specialized tools", "meta-tools" and "additional tools". The database can be queried using the organism name, a locus tag or a list of locus tags and may be browsed using numerous graphical and text displays. Conclusions With its new functionalities, CoBaltDB is a novel powerful platform that provides easy access to the results of multiple localization tools and support for predicting prokaryotic protein localizations with higher confidence than previously possible. CoBaltDB is available at http://www.umr6026.univ-rennes1.fr/english/home/research/basic/software/cobalten.

  6. RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration

    Directory of Open Access Journals (Sweden)

    Ogurtsov Aleksey Y

    2008-10-01

    Full Text Available Abstract Background Existing scientific literature is a rich source of biological information such as disease markers. Integration of this information with data analysis may help researchers to identify possible controversies and to form useful hypotheses for further validations. In the context of proteomics studies, individualized proteomics era may be approached through consideration of amino acid substitutions/modifications as well as information from disease studies. Integration of such information with peptide searches facilitates speedy, dynamic information retrieval that may significantly benefit clinical laboratory studies. Description We have integrated from various sources annotated single amino acid polymorphisms, post-translational modifications, and their documented disease associations (if they exist into one enhanced database per organism. We have also augmented our peptide identification software RAId_DbS to take into account this information while analyzing a tandem mass spectrum. In principle, one may choose to respect or ignore the correlation of amino acid polymorphisms/modifications within each protein. The former leads to targeted searches and avoids scoring of unnecessary polymorphism/modification combinations; the latter explores possible polymorphisms in a controlled fashion. To facilitate new discoveries, RAId_DbS also allows users to conduct searches permitting novel polymorphisms as well as to search a knowledge database created by the users. Conclusion We have finished constructing enhanced databases for 17 organisms. The web link to RAId_DbS and the enhanced databases is http://www.ncbi.nlm.nih.gov/CBBResearch/qmbp/RAId_DbS/index.html. The relevant databases and binaries of RAId_DbS for Linux, Windows, and Mac OS X are available for download from the same web page.

  7. Effects of Qing-Hua Granule on Bitter Taste Receptors in Ileum of db/db Diabetes Mice%清化颗粒对db/db糖尿病小鼠肠道苦味受体的影响

    Institute of Scientific and Technical Information of China (English)

    李俊燕; 王静懿; 徐杰; 陆灏; 陶枫

    2016-01-01

    目的:探讨清化颗粒对db/db糖尿病小鼠肠道苦味受体(taste receptor type 2,TAS2Rs)的影响.方法:将db/db糖尿病小鼠随机分为模型对照组及清化颗粒低、中、高剂量组,db/m小鼠为空白对照组.清化颗粒低、中、高剂量组分别灌胃给药(3.77、7.54、15.08 g·kg-1·d-1),模型对照组和空白对照组灌胃等体积的生理盐水,均干预4周.干预结束后,腹腔注射葡萄糖耐量试验(IPGTT)观察每组小鼠血糖水平变化;ELISA法分析小鼠血清胰高血糖素样肽-1(GLP-1)浓度;qRT-PCR测定每组小鼠肠道苦味受体(TAS2R7、TAS2R9和TAS2R38)的mRNA水平;Western blot检测小鼠肠道苦味信号通路因子磷酸二酯酶1A(PDE1A)的蛋白水平.结果:清化颗粒各剂量组的空腹血糖水平均较模型对照组显著降低(P<0.01),血清GLP-1浓度显著高于模型对照组(P<0.01);清化颗粒中、高剂量组的TAS2R7、TAS2R9和TAS2R38的mRNA水平较模型对照组显著增加(P<0.01);清化颗粒各剂量组的PDE1A的蛋白水平较模型对照组显著增加(P<0.01),呈剂量依赖效应.结论:清化颗粒能够降低db/db糖尿病小鼠的空腹血糖水平,其机制可能与促进肠道GLP-1分泌的苦味信号通路有关.

  8. A 1.1 mW 87 dB dynamic range {Delta} {sigma} modulator for audio applications

    Energy Technology Data Exchange (ETDEWEB)

    Liu Liyuan; Wang Zhihua; Wei Shaojun [Institute of Microelectronics, Tsinghua University, Beijing 100084 (China); Chen Liangdong; Li Dongmei, E-mail: lidmei@tsinghua.edu.c [Department of Electronic Engineering, Tsinghua University, Beijing 100084 (China)

    2010-05-15

    This paper presents a 1.1 mW 87 dB dynamic range third order {Delta} {sigma} modulator implemented in 0.18 {mu}m CMOS technology for audio applications. By adopting a feed-forward multi-bit topology, the signal swing at the output of the first integrator can be suppressed. A simple current mirror single stage OTA with 34 dB DC gain working under 1 V power supply is used in the first integrator. The prototype modulator achieves 87 dB DR and 83.8 dB peak SNDR across the bandwidth from 100 Hz to 24 kHz with 3 kHz input signal. (semiconductor integrated circuits)

  9. The definitive guide to MongoDB the noSQL database for cloud and desktop computing

    CERN Document Server

    Plugge, Eelco; Hawkins, Tim

    2010-01-01

    MongoDB, a cross-platform NoSQL database, is the fastest-growing new database in the world. MongoDB provides a rich document orientated structure with dynamic queries that you'll recognize from RDMBS offerings such as MySQL. In other words, this is a book about a NoSQL database that does not require the SQL crowd to re-learn how the database world works! MongoDB has reached 1.0 and already boasts 50,000+ users. The community is strong and vibrant and MongoDB is improving at a fast rate. With scalable and fast databases becoming critical for today's applications, this book shows you how to inst

  10. Plant extracts of winter savory, purple coneflower, buckwheat and black elder activate PPAR-γ in COS-1 cells but do not lower blood glucose in Db/db mice in vivo.

    Science.gov (United States)

    Schrader, Eva; Wein, Silvia; Kristiansen, Karsten; Christensen, Lars P; Rimbach, Gerald; Wolffram, Siegfried

    2012-12-01

    The aim of this study was to investigate possible blood glucose-lowering effects of plant extracts in vivo for which prior to this a peroxisome proliferator-activated receptor-γ activity in vitro was observed. The ability of extracts of winter savory, purple coneflower, buckwheat and black elder to dose-dependently activate peroxisome proliferator-activated receptor-γ was determined in a reporter gene assay in COS-1 cells. For evaluation of glucose-lowering effects in vivo, db/db mice were fed a diet containing either rosiglitazone (0.02 g/kg diet, positive control) or one of the plant extracts (0.1 and 1 g/kg diet) for four weeks. Apart from glucose, insulin, triacylglycerols, non-esterified fatty acids, cholesterol and adiponectin were determined in plasma. All plant extracts showed a dose-dependent peroxisome proliferator-activated receptor-γ-activating effect in vitro. In db/db mice none of the plant extracts exerted glucose-lowering effects at the used dosages compared to rosiglitazone. Non-esterified fatty acids, triacylglycerols, cholesterol, insulin and adiponectin in plasma were not altered by the plant extracts as well. Although dose-dependent peroxisome proliferator-activated receptor-γ activity could be shown in COS-1 cells, the experiments in db/db mice lacked to confirm any anti-diabetic effect of the plant extracts in vivo and emphasizes the importance of verifying cell culture data using an appropriate in vivo model.

  11. Index of /data/mouse-b6n-bac-clone-db/20120215 [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Index of /data/mouse-b6n-bac-clone-db/20120215 Name Last modified Size Description ...Parent Directory - README.html 02-Apr-2014 10:25 8.1K mouse_b6n_bac_clone.zip 15-Feb-2012 13:33 64M Index of /data/mouse-b6n-bac-clone-db/20120215 ...

  12. Safety, pharmacokinetic, and efficacy studies of oral DB868 in a first stage vervet monkey model of human African trypanosomiasis.

    Directory of Open Access Journals (Sweden)

    John K Thuita

    Full Text Available There are no oral drugs for human African trypanosomiasis (HAT, sleeping sickness. A successful oral drug would have the potential to reduce or eliminate the need for patient hospitalization, thus reducing healthcare costs of HAT. The development of oral medications is a key objective of the Consortium for Parasitic Drug Development (CPDD. In this study, we investigated the safety, pharmacokinetics, and efficacy of a new orally administered CPDD diamidine prodrug, 2,5-bis[5-(N-methoxyamidino-2-pyridyl]furan (DB868; CPD-007-10, in the vervet monkey model of first stage HAT. DB868 was well tolerated at a dose up to 30 mg/kg/day for 10 days, a cumulative dose of 300 mg/kg. Mean plasma levels of biomarkers indicative of liver injury (alanine aminotransferase, aspartate aminotransferase were not significantly altered by drug administration. In addition, no kidney-mediated alterations in creatinine and urea concentrations were detected. Pharmacokinetic analysis of plasma confirmed that DB868 was orally available and was converted to the active compound DB829 in both uninfected and infected monkeys. Treatment of infected monkeys with DB868 began 7 days post-infection. In the infected monkeys, DB829 attained a median C(max (dosing regimen that was 12-fold (3 mg/kg/day for 7 days, 15-fold (10 mg/kg/day for 7 days, and 31-fold (20 mg/kg/day for 5 days greater than the IC50 (14 nmol/L against T. b. rhodesiense STIB900. DB868 cured all infected monkeys, even at the lowest dose tested. In conclusion, oral DB868 cured monkeys with first stage HAT at a cumulative dose 14-fold lower than the maximum tolerated dose and should be considered a lead preclinical candidate in efforts to develop a safe, short course (5-7 days, oral regimen for first stage HAT.

  13. VentDB: A Global Online Synthesis Database of Seafloor Hydrothermal Spring Geochemistry

    Science.gov (United States)

    Mottl, M. J.; Lehnert, K. A.; Johansson, A. K.; Hsu, L.

    2011-12-01

    Chemical data for seafloor hydrothermal springs are fundamental to the study of mid-ocean ridge and seafloor processes, ocean water chemistry, and global geochemical cycles, as well as vent ecosystems and the sub-seafloor biosphere. So far, these data have been accessible only in the scientific literature or in online data catalogs where they are widely dispersed in individual data tables, and are often insufficiently documented for re-use. We have developed VentDB as an online data system for geochemical data for hydrothermal springs that will facilitate access and analysis of these data. VentDB uses the concept and architecture of the popular PetDB database for seafloor igneous and metamorphic rock geochemistry (www.petdb.org) to provide easy and fast access to a global synthesis of seafloor hydrothermal spring geochemical data. The VentDB database contains concentrations of major and trace species, dissolved gases, and radiogenic and isotopic ratios for hydrothermal vents on the seafloor. Further chemical or physical properties of hydrothermal springs can be included in the future if desired. The database comprises both the calculated hydrothermal end-member solution compositions as estimated by extrapolation of the concentrations of individual chemical species to a Mg concentration of zero, and the raw data for hydrothermal solution samples as collected, where available. Data quality is documented by including information for the raw analytical data about the analytical method, precision, and reference material measurements, and quality control parameters for end-member compositions including the lowest Mg measured in any sample, the number of samples and correlation coefficient of the linear regression, and the charge balance for the extrapolated zero-Mg composition. The database also includes information about the sampled locations (geospatial coordinates, vent or vent field names, names of other physiographic features), temperature, flow and vent type

  14. Angiotensin Ⅱ receptor blocker provides pancreatic β-cell protection independent of blood pressure lowering in diabetic db/db mice

    Institute of Scientific and Technical Information of China (English)

    Jia-qing SHAO; Noseki IWASHITA; Hong DU; Yang-tian WANG; Yan-yan WANG; Ming ZHAO; Jian WANG; Hirotaka WATADA; Ryuzo KAWAMORI

    2007-01-01

    Aim: Several epidemiological studies have suggested that treatment with angiotensin Ⅱ type 1 receptor blocker provided a risk reduction of developing type 2 diabetes. The aim of this study was to investigate whether and how chronic candesartan treatment can attenuate the deleterious influence of the hyperactive local intra-islet renin-angiotensin system in the diabetes state. Methods: Eight-week-old db/db mice were randomized to candesartan 1 mg/kg, candesartan 10mg/kg, manidipine 10 mg/kg, or placebo via gavage for 6 weeks. Their age-matched nondiabetic littermates db/m mice were treated with placebo and acted as nondia-betic controls. After 6 weeks' treatment, an intraperitoneal glucose tolerance test, immunohistochemical staining of oxidative stress markers, insulin, CD31, azan staining and an electron microscopy observation were performed. Results: Chronic candesartan treatment provided an improvement of glucose tolerance, and greatly rescued islet β-cell mass. Candesartan treatment also notably decreased staining intensity of oxidative stress markers, as well as attenuating intra-islet fibrosis and improving blood supply in the islet. In the electron microscopy observation, candesartan-treated animals exhibited improved granulation and less remarkable endoplasmic reticulum and Golgi bodies; furthermore, candesartan treatment greatly relieved the swelling of mitochondria to nearly normal. Both the benefits of reducing oxidative stress and ultra structure protection were in a dose-dependent and blood pressure-independent manner. Conclusion: After diabetes was initiated, candesartan treatment could not reverse the state of diabetes, but it effectively improved glucose tolerance and protected β-cell function by attenuating oxidative stress, islet fibrosis, sparsity of blood supply and ultrastructure disruption in a dose-dependent and blood pressure-independent manner.

  15. R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops

    Science.gov (United States)

    Jenjaroenpun, Piroon; Wongsurawat, Thidathip; Sutheeworapong, Sawannee; Kuznetsov, Vladimir A.

    2017-01-01

    R-loopDB (http://rloop.bii.a-star.edu.sg) was originally constructed as a collection of computationally predicted R-loop forming sequences (RLFSs) in the human genic regions. The renewed R-loopDB provides updates, improvements and new options, including access to recent experimental data. It includes genome-scale prediction of RLFSs for humans, six other animals and yeast. Using the extended quantitative model of RLFSs (QmRLFS), we significantly increased the number of RLFSs predicted in the human genes and identified RLFSs in other organism genomes. R-loopDB allows searching of RLFSs in the genes and in the 2 kb upstream and downstream flanking sequences of any gene. R-loopDB exploits the Ensembl gene annotation system, providing users with chromosome coordinates, sequences, gene and genomic data of the 1 565 795 RLFSs distributed in 121 056 genic or proximal gene regions of the covered organisms. It provides a comprehensive annotation of Ensembl RLFS-positive genes including 93 454 protein coding genes, 12 480 long non-coding RNA and 7 568 small non-coding RNA genes and 7 554 pseudogenes. Using new interface and genome viewers of R-loopDB, users can search the gene(s) in multiple species with keywords in a single query. R-loopDB provides tools to carry out comparative evolution and genome-scale analyses in R-loop biology. PMID:27899586

  16. 2型糖尿病模型db/db小鼠内侧隔核-斜角带核NOS阳性神经元变化%The study of the changes of nitric oxide synthase (NOS) positive cells in septum medialis-diagonal band of genetically obese diabetic db/db mice

    Institute of Scientific and Technical Information of China (English)

    张松筠; 张庆九; 郝咏梅; 杨天祝; 刘文淑

    2001-01-01

    目的:观察人类2型糖尿病模型——C57BL/KsJ db/db(db/db)小鼠内侧隔核-斜角带核NOS阳性神经元变化. 方法: 糖尿病组: 6周龄57CBL/KsJ(db+/db+)小鼠5只, 尾静脉空腹血糖高于11.1mmol/L且肥胖. 对照组: 非糖尿病小鼠C57BL/KsJ(?/+)5只, 尾静脉空腹血糖低于6.0mmol/L 体重正常. 于30周龄(成模第6月末)时, 灌注固定取脑, 以NADPH-d组化法显示内侧隔核-斜角带核NOS阳性神经元. 结果: 与正常对照组相比, 糖尿病小鼠内侧隔核-斜角带核NOS阳性神经元密度显著减少(P<0.01). 结论: 以上改变可能是导致糖尿病中枢神经系统功能障碍的形态基础.

  17. SolDB: A Database of Solanum lycopersicum and Solanum tuberosum Primers

    Directory of Open Access Journals (Sweden)

    Hassan Tariq

    2010-12-01

    Full Text Available SolDB is the Database of Solanaceae Family. It is an interactive, free online specialized database for Solanaceae family. Currently, it spans complete nucleotide sequences of expressed genes of Solanum lycopersicum and Solanum tuberosum along with their annotation. We have designed PCR oligonucleotide primer sequences for each gene, with their features and conditions given. This feature alone greatly facilitates researchers in PCR amplification of genes sequences, especially in cloning experiments. We also provided chloroplast genome section which gives access to fully sequenced plastid genomes and their annotations. Flexible database design, easy expandability, and easy retrieval of information are the main features of SolDB. The Database is publicly available at www.soldb.pakbiz.org.

  18. Skewon-Axion Medium and Soft-and-Hard/DB Boundary Condition

    CERN Document Server

    Lindell, Ismo V

    2012-01-01

    The class of skewon-axion media can be defined in a simple and natural manner applying four-dimensional differential-form representation of electromagnetic fields and media. It has been recently shown that an interface of a uniaxial skewon-axion medium acts as a DB boundary requiring vanishing normal components of the D and B vectors. In the present paper a more general skewon-axion medium is considered. It is shown that a planar interface of such a medium acts as a boundary generalizing both soft-and-hard (SH) and DB boundary conditions to SHDB conditions. Reflection of a plane wave from a planar SHDB boundary is studied. It is shown that for the two eigenpolarizations the boundary can be replaced by equivalent PEC or PMC boundaries. The theory is tested with a numerical example.

  19. A CMOS image-rejection mixer with 58-dB IRR for DTV receivers

    Institute of Scientific and Technical Information of China (English)

    Yuan Shuai; Li Zhiqun; Huang Jing; Wang Zhigong

    2009-01-01

    The design, implementation, and characterization of an image-rejection double quadrature conversion mixer based on RC asymmetric polyphase filters (PPF) are presented. The mixer consists of three sets of PPFs and a mixer core for quadrature down conversion. Two sets of PPFs are used for the quadrature generation and the other one is used for the IF signal selection to reject the unwanted image band. Realized in 0.18-μm CMOS technology as a part of the DVB-T receiver chip, the mixer exhibits a high image rejection ratio (IRR) of 58 dB, a power consumption of 11 mW, and a 1-dB gain compression point of -15 dBm.

  20. Writing and querying MapReduce views in CouchDB

    CERN Document Server

    Holt, Bradley

    2011-01-01

    If you want to use CouchDB to support real-world applications, you'll need to create MapReduce views that let you query this document-oriented database for meaningful data. With this short and concise ebook, you'll learn how to create a variety of MapReduce views to help you query and aggregate data in CouchDB's large, distributed datasets. You'll get step-by-step instructions and lots of sample code to create and explore several MapReduce views through the course of the book, using an example database you construct. To work with these different views, you'll learn how to use the Futon web a

  1. SEMICONDUCTOR INTEGRATED CIRCUITS: An undersampling 14-bit cyclic ADC with over 100-dB SFDR

    Science.gov (United States)

    Weitao, Li; Fule, Li; Dandan, Guo; Chun, Zhang; Zhihua, Wang

    2010-02-01

    A high linearity, undersampling 14-bit 357 kSps cyclic analog-to-digital convert (ADC) is designed for a radio frequency identification transceiver system. The passive capacitor error-average (PCEA) technique is adopted for high accuracy. An improved PCEA sampling network, capable of eliminating the crosstalk path of two pipelined stages, is employed. Opamp sharing and the removal of the front-end sample and hold amplifier are utilized for low power dissipation and small chip area. An additional digital calibration block is added to compensate for the error due to defective layout design. The presented ADC is fabricated in a 180 nm CMOS process, occupying 0.65 × 1.6 mm2. The input of the undersampling ADC achieves 15.5 MHz with more than 90 dB spurious free dynamic range (SFDR), and the peak SFDR is as high as 106.4 dB with 2.431 MHz input.

  2. TaDb: A time-aware diffusion-based recommender algorithm

    Science.gov (United States)

    Li, Wen-Jun; Xu, Yuan-Yuan; Dong, Qiang; Zhou, Jun-Lin; Fu, Yan

    2015-02-01

    Traditional recommender algorithms usually employ the early and recent records indiscriminately, which overlooks the change of user interests over time. In this paper, we show that the interests of a user remain stable in a short-term interval and drift during a long-term period. Based on this observation, we propose a time-aware diffusion-based (TaDb) recommender algorithm, which assigns different temporal weights to the leading links existing before the target user's collection and the following links appearing after that in the diffusion process. Experiments on four real datasets, Netflix, MovieLens, FriendFeed and Delicious show that TaDb algorithm significantly improves the prediction accuracy compared with the algorithms not considering temporal effects.

  3. DB&A: An Open Source Web Service for Meter Data Management

    DEFF Research Database (Denmark)

    Mikkelsen, Søren Aagaard; Jacobsen, Rune Hylsberg; Terkelsen, Anders Franz

    2016-01-01

    that is instantiated as a web service. Its design is based on a set of design goals, an explicitly addressed data latency scope and five real-world scenarios. We present an abstract model of the metering hierarchy that allows MDM systems to be used as compositional services, forming a service tree. Moreover, we...... provide implementation details about analytic functions to support the service tree. The DB&A is evaluated on a cloud and embedded platform using a subset of data constructed from a case study that includes 8 months of real data. The results show that the DB&A complies with the boundaries of the defined......With the increasing number of initiatives dealing with storing meter data, systems that perform Meter Data Management (MDM) constitute a critical component for realising the potential benefits of the smart grid. However, most of the MDM systems designed today are generalised to such an extent...

  4. Indexing Bibliographic Database Content Using MariaDB and Sphinx Search Server

    Directory of Open Access Journals (Sweden)

    Arie Nugraha

    2014-07-01

    Full Text Available Fast retrieval of digital content has become mandatory for library and archive information systems. Many software applications have emerged to handle the indexing of digital content, from low-level ones such Apache Lucene, to more RESTful and web-services-ready ones such Apache Solr and ElasticSearch. Solr’s popularity among library software developers makes it the “de-facto” standard software for indexing digital content. For content (full-text content or bibliographic description already stored inside a relational DBMS such as MariaDB (a fork of MySQL or PostgreSQL, Sphinx Search Server (Sphinx is a suitable alternative. This article will cover an introduction on how to use Sphinx with MariaDB databases to index database content as well as some examples of Sphinx API usage.

  5. Animal model integration to AutDB, a genetic database for autism

    Directory of Open Access Journals (Sweden)

    Kollu Ravi

    2011-01-01

    Full Text Available Abstract Background In the post-genomic era, multi-faceted research on complex disorders such as autism has generated diverse types of molecular information related to its pathogenesis. The rapid accumulation of putative candidate genes/loci for Autism Spectrum Disorders (ASD and ASD-related animal models poses a major challenge for systematic analysis of their content. We previously created the Autism Database (AutDB to provide a publicly available web portal for ongoing collection, manual annotation, and visualization of genes linked to ASD. Here, we describe the design, development, and integration of a new module within AutDB for ongoing collection and comprehensive cataloguing of ASD-related animal models. Description As with the original AutDB, all data is extracted from published, peer-reviewed scientific literature. Animal models are annotated with a new standardized vocabulary of phenotypic terms developed by our researchers which is designed to reflect the diverse clinical manifestations of ASD. The new Animal Model module is seamlessly integrated to AutDB for dissemination of diverse information related to ASD. Animal model entries within the new module are linked to corresponding candidate genes in the original "Human Gene" module of the resource, thereby allowing for cross-modal navigation between gene models and human gene studies. Although the current release of the Animal Model module is restricted to mouse models, it was designed with an expandable framework which can easily incorporate additional species and non-genetic etiological models of autism in the future. Conclusions Importantly, this modular ASD database provides a platform from which data mining, bioinformatics, and/or computational biology strategies may be adopted to develop predictive disease models that may offer further insights into the molecular underpinnings of this disorder. It also serves as a general model for disease-driven databases curating phenotypic

  6. ProtRepeatsDB: a database of amino acid repeats in genomes

    Directory of Open Access Journals (Sweden)

    Chauhan Virander S

    2006-07-01

    Full Text Available Abstract Background Genome wide and cross species comparisons of amino acid repeats is an intriguing problem in biology mainly due to the highly polymorphic nature and diverse functions of amino acid repeats. Innate protein repeats constitute vital functional and structural regions in proteins. Repeats are of great consequence in evolution of proteins, as evident from analysis of repeats in different organisms. In the post genomic era, availability of protein sequences encoded in different genomes provides a unique opportunity to perform large scale comparative studies of amino acid repeats. ProtRepeatsDB http://bioinfo.icgeb.res.in/repeats/ is a relational database of perfect and mismatch repeats, access to which is designed as a resource and collection of tools for detection and cross species comparisons of different types of amino acid repeats. Description ProtRepeatsDB (v1.2 consists of perfect as well as mismatch amino acid repeats in the protein sequences of 141 organisms, the genomes of which are now available. The web interface of ProtRepeatsDB consists of different tools to perform repeat s; based on protein IDs, organism name, repeat sequences, and keywords as in FASTA headers, size, frequency, gene ontology (GO annotation IDs and regular expressions (REGEXP describing repeats. These tools also allow formulation of a variety of simple, complex and logical queries to facilitate mining and large-scale cross-species comparisons of amino acid repeats. In addition to this, the database also contains sequence analysis tools to determine repeats in user input sequences. Conclusion ProtRepeatsDB is a multi-organism database of different types of amino acid repeats present in proteins. It integrates useful tools to perform genome wide queries for rapid screening and identification of amino acid repeats and facilitates comparative and evolutionary studies of the repeats. The database is useful for identification of species or organism specific

  7. MIPS PlantsDB: a database framework for comparative plant genome research.

    Science.gov (United States)

    Nussbaumer, Thomas; Martis, Mihaela M; Roessner, Stephan K; Pfeifer, Matthias; Bader, Kai C; Sharma, Sapna; Gundlach, Heidrun; Spannagl, Manuel

    2013-01-01

    The rapidly increasing amount of plant genome (sequence) data enables powerful comparative analyses and integrative approaches and also requires structured and comprehensive information resources. Databases are needed for both model and crop plant organisms and both intuitive search/browse views and comparative genomics tools should communicate the data to researchers and help them interpret it. MIPS PlantsDB (http://mips.helmholtz-muenchen.de/plant/genomes.jsp) was initially described in NAR in 2007 [Spannagl,M., Noubibou,O., Haase,D., Yang,L., Gundlach,H., Hindemitt, T., Klee,K., Haberer,G., Schoof,H. and Mayer,K.F. (2007) MIPSPlantsDB-plant database resource for integrative and comparative plant genome research. Nucleic Acids Res., 35, D834-D840] and was set up from the start to provide data and information resources for individual plant species as well as a framework for integrative and comparative plant genome research. PlantsDB comprises database instances for tomato, Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat. Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB.

  8. NCBI - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...2 10.18908/lsdba.nbdc01181-009.V002 Update History V1 - Description of data contents The RDF data of several...ports in NCBI Assembly. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us NCBI - MicrobeDB.jp | LSDB Archive ...

  9. Ortholog - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...ersion V2 10.18908/lsdba.nbdc01181-010.V002 Update History V1 - Description of data contents Microbial ortho...814 triples - About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Ortholog - MicrobeDB.jp | LSDB Archive ...

  10. BRC - MicrobeDB.jp | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...10.18908/lsdba.nbdc01181-001.V002 Update History V1 10.18908/lsdba.nbdc01181-001.V001 - Description of data ...rains in JCM. About This Database Database Description Download License Update History of This Database Site Policy | Contact Us BRC - MicrobeDB.jp | LSDB Archive ...

  11. The relation between the generalised Eshelby integral and the generalised BCS and DB models

    Institute of Scientific and Technical Information of China (English)

    Fan Tian-You; Fan Lei

    2011-01-01

    The generalised BCS dislocation group model and the generalised DB atomic cohesive force zone model have obtained the same results on nonlinear fracture study of some one-, two-and three-dimensional quasicrystals. This work reveals some inherent connection between the two models, and finds that their common basis is the generalised Eshelby integral based on the generalised Eshelby energy-momentum tensor for quasicrystals. Further applications of the theory in solving nonlinear fracture problems of the materials are also discussed.

  12. Le nuove specifiche di contenuto del DB25K per derivazione dei DBT regionali

    Directory of Open Access Journals (Sweden)

    Leonardo Donnaloia

    2013-06-01

    Full Text Available In applicazione della direttiva INSPIRE ed in linea con la necessità della PA di creare database geotopografici multiscala omogenei a livello nazionale, il CPSG del CISIS sta svolgendo un’attività finalizzata alla normalizzazione dei DB25k (database geotopografici scala 1:25.000. Tale attività, partendo dal presupposto di derivare, in maniera controllata, i DB25K da DBT a scale maggiori (realizzati in conformità alla specifica introdotta dal DM 10 novembre 2011 si pone come obbiettivo la produzione di una specifica tecnica di riferimento da formalizzare, come previstodall’art. 59 del CAD, secondo l’iter legislativo stabilito.In accordance with the INSPIRE Directive and in line with theneeds of the Italian Public Sector to create geo-topographicdatabases at different scales and homogeneous at the national level, the CISIS Committee for the Geographic Systems is carrying out an activity aimed at the normalization of the DB25k (the geo-topographic database at the scale 1:25000.This activity, based on the assumption to derive, in a controlled manner, the DB25K by the DBT at larger scales (implemented in conformance with the specifications introduced by the Ministerial Decree 10 November 2011 has as its objective the production of a reference technical specification that will be formalized, as stated by the art. 59 of the Digital Administration Code, according to the established legislative iter. 

  13. AH-DB: collecting protein structure pairs before and after binding

    OpenAIRE

    2011-01-01

    This work presents the Apo–Holo DataBase (AH-DB, http://ahdb.ee.ncku.edu.tw/ and http://ahdb.csbb.ntu.edu.tw/), which provides corresponding pairs of protein structures before and after binding. Conformational transitions are commonly observed in various protein interactions that are involved in important biological functions. For example, copper–zinc superoxide dismutase (SOD1), which destroys free superoxide radicals in the body, undergoes a large conformational transition from an ‘open’ st...

  14. LitDB - Keeping Track of Research Papers From Your Institute Made Simple.

    Science.gov (United States)

    Bethune, Jörn; Kraemer, Lars; Thomsen, Ingo; Keller, Andreas; Ellinghaus, David; Franke, Andre

    2017-01-01

    In science peer-reviewed publications serve as an important indicator of scientific excellence and productivity. Therefore, every scientist and institution must carefully maintain and update records of their scientific publications. However, in most institutions and universities articles are often managed in a redundant file-based and non-central way. Whereas excellent reference management software packages such as Zotero, Endnote or Mendeley exist to manage bibliographies and references when writing scientific articles, we are not aware of any open source database solution keeping track of publication records from large scientific groups, entire institutions and/or universities. We here describe LitDB, a novel open source literature database solution for easy maintenance of publication lists assigned to various topics. In the last 2 years more than 50 users have been using LitDB at our research institute. The LitDB system is accessed via a web browser. Publications can be uploaded through direct exports from reference manager libraries or by entering PubMed IDs. Single users or user groups can track their citation counts, h-index and impact factor statistics and gain insights into the publication records of other users. It offers various visualization functions like coauthor networks and provides ways to organize publications from dedicated projects and user groups. The latter is in particular beneficial to manage publication lists of large research groups and research initiatives through a "crowd-sourcing" effort. Keeping track of papers authored and published by a research group, institute or university is an important and non-trivial task. By using a centralized web-based platform for publication management such as LitDB the compilation of project- and group-related publication lists becomes easily manageable and it is less likely that papers are forgotten along the way.

  15. Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.

    Science.gov (United States)

    Sakai, Hiroaki; Lee, Sung Shin; Tanaka, Tsuyoshi; Numa, Hisataka; Kim, Jungsok; Kawahara, Yoshihiro; Wakimoto, Hironobu; Yang, Ching-chia; Iwamoto, Masao; Abe, Takashi; Yamada, Yuko; Muto, Akira; Inokuchi, Hachiro; Ikemura, Toshimichi; Matsumoto, Takashi; Sasaki, Takuji; Itoh, Takeshi

    2013-02-01

    The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare. Since the first release in 2005, RAP-DB has been updated several times along with the genome assembly updates. Here, we present our newest RAP-DB based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), which was released in 2011. We detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species. To provide plant researchers with highly reliable and up to date rice gene annotations, we have been incorporating literature-based manually curated data, and 1,626 loci currently incorporate literature-based annotation data, including commonly used gene names or gene symbols. Transcriptional activities are shown at the nucleotide level by mapping RNA-Seq reads derived from 27 samples. We also mapped the Illumina reads of a Japanese leading japonica cultivar, Koshihikari, and a Chinese indica cultivar, Guangluai-4, to the genome and show alignments together with the single nucleotide polymorphisms (SNPs) and gene functional annotations through a newly developed browser, Short-Read Assembly Browser (S-RAB). We have developed two satellite databases, Plant Gene Family Database (PGFD) and Integrative Database of Cereal Gene Phylogeny (IDCGP), which display gene family and homologous gene relationships among diverse plant species. RAP-DB and the satellite databases offer simple and user-friendly web interfaces, enabling plant and genome researchers to access the data easily and facilitating a broad range of plant research topics.

  16. SciDB versus Spark: A Preliminary Comparison Based on an Earth Science Use Case

    Science.gov (United States)

    Clune, T.; Kuo, K. S.; Doan, K.; Oloso, A.

    2015-12-01

    We compare two Big Data technologies, SciDB and Spark, for performance, usability, and extensibility, when applied to a representative Earth science use case. SciDB is a new-generation parallel distributed database management system (DBMS) based on the array data model that is capable of handling multidimensional arrays efficiently but requires lengthy data ingest prior to analysis, whereas Spark is a fast and general engine for large scale data processing that can immediately process raw data files and thereby avoid the ingest process. Once data have been ingested, SciDB is very efficient in database operations such as subsetting. Spark, on the other hand, provides greater flexibility by supporting a wide variety of high-level tools including DBMS's. For the performance aspect of this preliminary comparison, we configure Spark to operate directly on text or binary data files and thereby limit the need for additional tools. Arguably, a more appropriate comparison would involve exploring other configurations of Spark which exploit supported high-level tools, but that is beyond our current resources. To make the comparison as "fair" as possible, we export the arrays produced by SciDB into text files (or converting them to binary files) for the intake by Spark and thereby avoid any additional file processing penalties. The Earth science use case selected for this comparison is the identification and tracking of snowstorms in the NASA Modern Era Retrospective-analysis for Research and Applications (MERRA) reanalysis data. The identification portion of the use case is to flag all grid cells of the MERRA high-resolution hourly data that satisfies our criteria for snowstorm, whereas the tracking portion connects flagged cells adjacent in time and space to form a snowstorm episode. We will report the results of our comparisons at this presentation.

  17. CerealsDB 2.0: an integrated resource for plant breeders and scientists

    Directory of Open Access Journals (Sweden)

    Wilkinson Paul A

    2012-09-01

    Full Text Available Abstract Background Food security is an issue that has come under renewed scrutiny amidst concerns that substantial yield increases in cereal crops are required to feed the world’s booming population. Wheat is of fundamental importance in this regard being one of the three most important crops for both human consumption and livestock feed; however, increase in crop yields have not kept pace with the demands of a growing world population. In order to address this issue, plant breeders require new molecular tools to help them identify genes for important agronomic traits that can be introduced into elite varieties. Studies of the genome using next-generation sequencing enable the identification of molecular markers such as single nucleotide polymorphisms that may be used by breeders to identify and follow genes when breeding new varieties. The development and application of next-generation sequencing technologies has made the characterisation of SNP markers in wheat relatively cheap and straightforward. There is a growing need for the widespread dissemination of this information to plant breeders. Description CerealsDB is an online resource containing a range of genomic datasets for wheat (Triticum aestivum that will assist plant breeders and scientists to select the most appropriate markers for marker assisted selection. CerealsDB includes a database which currently contains in excess of 100,000 putative varietal SNPs, of which several thousand have been experimentally validated. In addition, CerealsDB contains databases for DArT markers and EST sequences, and links to a draft genome sequence for the wheat variety Chinese Spring. Conclusion CerealsDB is an open access website that is rapidly becoming an invaluable resource within the wheat research and plant breeding communities.

  18. PHYMYCO-DB: a curated database for analyses of fungal diversity and evolution.

    Directory of Open Access Journals (Sweden)

    Stéphane Mahé

    Full Text Available BACKGROUND: In environmental sequencing studies, fungi can be identified based on nucleic acid sequences, using either highly variable sequences as species barcodes or conserved sequences containing a high-quality phylogenetic signal. For the latter, identification relies on phylogenetic analyses and the adoption of the phylogenetic species concept. Such analysis requires that the reference sequences are well identified and deposited in public-access databases. However, many entries in the public sequence databases are problematic in terms of quality and reliability and these data require screening to ensure correct phylogenetic interpretation. METHODS AND PRINCIPAL FINDINGS: To facilitate phylogenetic inferences and phylogenetic assignment, we introduce a fungal sequence database. The database PHYMYCO-DB comprises fungal sequences from GenBank that have been filtered to satisfy stringent sequence quality criteria. For the first release, two widely used molecular taxonomic markers were chosen: the nuclear SSU rRNA and EF1-α gene sequences. Following the automatic extraction and filtration, a manual curation is performed to remove problematic sequences while preserving relevant sequences useful for phylogenetic studies. As a result of curation, ~20% of the automatically filtered sequences have been removed from the database. To demonstrate how PHYMYCO-DB can be employed, we test a set of environmental Chytridiomycota sequences obtained from deep sea samples. CONCLUSION: PHYMYCO-DB offers the tools necessary to: (i extract high quality fungal sequences for each of the 5 fungal phyla, at all taxonomic levels, (ii extract already performed alignments, to act as 'reference alignments', (iii launch alignments of personal sequences along with stored data. A total of 9120 SSU rRNA and 672 EF1-α high-quality fungal sequences are now available. The PHYMYCO-DB is accessible through the URL http://phymycodb.genouest.org/.

  19. PHYMYCO-DB: A Curated Database for Analyses of Fungal Diversity and Evolution

    Science.gov (United States)

    Mahé, Stéphane; Duhamel, Marie; Le Calvez, Thomas; Guillot, Laetitia; Sarbu, Ludmila; Bretaudeau, Anthony; Collin, Olivier; Dufresne, Alexis; Kiers, E. Toby; Vandenkoornhuyse, Philippe

    2012-01-01

    Background In environmental sequencing studies, fungi can be identified based on nucleic acid sequences, using either highly variable sequences as species barcodes or conserved sequences containing a high-quality phylogenetic signal. For the latter, identification relies on phylogenetic analyses and the adoption of the phylogenetic species concept. Such analysis requires that the reference sequences are well identified and deposited in public-access databases. However, many entries in the public sequence databases are problematic in terms of quality and reliability and these data require screening to ensure correct phylogenetic interpretation. Methods and Principal Findings To facilitate phylogenetic inferences and phylogenetic assignment, we introduce a fungal sequence database. The database PHYMYCO-DB comprises fungal sequences from GenBank that have been filtered to satisfy stringent sequence quality criteria. For the first release, two widely used molecular taxonomic markers were chosen: the nuclear SSU rRNA and EF1-α gene sequences. Following the automatic extraction and filtration, a manual curation is performed to remove problematic sequences while preserving relevant sequences useful for phylogenetic studies. As a result of curation, ∼20% of the automatically filtered sequences have been removed from the database. To demonstrate how PHYMYCO-DB can be employed, we test a set of environmental Chytridiomycota sequences obtained from deep sea samples. Conclusion PHYMYCO-DB offers the tools necessary to: (i) extract high quality fungal sequences for each of the 5 fungal phyla, at all taxonomic levels, (ii) extract already performed alignments, to act as ‘reference alignments’, (iii) launch alignments of personal sequences along with stored data. A total of 9120 SSU rRNA and 672 EF1-α high-quality fungal sequences are now available. The PHYMYCO-DB is accessible through the URL http://phymycodb.genouest.org/. PMID:23028445

  20. Programming Amazon Web Services S3, EC2, SQS, FPS, and SimpleDB

    CERN Document Server

    Murty, James

    2009-01-01

    With this book, you'll learn how companies can take advantage of Amazon Web Services (AWS) to rent" computing power, data storage and bandwidth on Amazon's vast network infrastructure. Programming Amazon Web Services gives developers the background and technical detail they need for using Amazon's subscription-based Simple Storage Service (S3), Elastic Compute Cloud (EC2), Simple Queue Service (SQS), Flexible Payments Service (FPS), and SimpleDB to build web-scale business applications. "

  1. dbPSHP: a database of recent positive selection across human populations

    OpenAIRE

    Li, Mulin Jun; Wang, Lily Yan; Xia, Zhengyuan; Wong, Maria P.; Sham, Pak Chung; WANG, JUNWEN

    2013-01-01

    The dbPSHP database (http://jjwanglab.org/dbpshp) aims to help researchers to efficiently identify, validate and visualize putative positively selected loci in human evolution and further discover the mechanism governing these natural selections. Recent evolution of human populations at the genomic level reflects the adaptations to the living environments, including climate change and availability and stability of nutrients. Many genetic regions under positive selection have been identified, ...

  2. DbMDR: a relational database for multidrug resistance genes as potential drug targets.

    Science.gov (United States)

    Gupta, Sanchita; Mishra, Manoj; Sen, Naresh; Parihar, Rashi; Dwivedi, Gaurav Raj; Khan, Feroz; Sharma, Ashok

    2011-10-01

    DbMDR is non-redundant reference database of multidrug resistance (MDR) genes and their orthologs acting as potential drug targets. Drug resistance is a common phenomenon of pathogens, creating a serious problem of inactivation of drugs and antibiotics resulting in occurrence of diseases. Apart from other factors, the MDR genes present in pathogens are shown to be responsible for multidrug resistance. Much of the unorganized information on MDR genes is scattered across the literature and other web resources. Thus, consolidation of such knowledge about MDR genes into one database will make the drug discovery research more efficient. Mining of text for MDR genes has resulted into a large number of publications but in scattered and unorganized form. This information was compiled into a database, which enables a user not only to look at a particular MDR gene but also to find out putative homologs based on sequence similarity, conserved domains, and motifs in proteins encoded by MDR genes more efficiently. At present, DbMDR database contains 2843 MDR genes characterized experimentally as well as functionally annotated with cross-referencing search support. The DbMDR database (http://203.190.147.116/dbmdr/) is a comprehensive resource for comparative study focused on MDR genes and metabolic pathway efflux pumps and intended to provide a platform for researchers for further research in drug resistance.

  3. MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics.

    Science.gov (United States)

    Schoof, Heiko; Ernst, Rebecca; Nazarov, Vladimir; Pfeifer, Lukas; Mewes, Hans-Werner; Mayer, Klaus F X

    2004-01-01

    Arabidopsis thaliana is the most widely studied model plant. Functional genomics is intensively underway in many laboratories worldwide. Beyond the basic annotation of the primary sequence data, the annotated genetic elements of Arabidopsis must be linked to diverse biological data and higher order information such as metabolic or regulatory pathways. The MIPS Arabidopsis thaliana database MAtDB aims to provide a comprehensive resource for Arabidopsis as a genome model that serves as a primary reference for research in plants and is suitable for transfer of knowledge to other plants, especially crops. The genome sequence as a common backbone serves as a scaffold for the integration of data, while, in a complementary effort, these data are enhanced through the application of state-of-the-art bioinformatics tools. This information is visualized on a genome-wide and a gene-by-gene basis with access both for web users and applications. This report updates the information given in a previous report and provides an outlook on further developments. The MAtDB web interface can be accessed at http://mips.gsf.de/proj/thal/db.

  4. XML related data exchange from the test machine to a web-enabled MAT-DB

    Directory of Open Access Journals (Sweden)

    M Nagy

    2006-01-01

    Full Text Available One of the JRC Petten tasks is to support European Research and Development (R&D projects in the material and energy related areas with the management and dissemination of research results. By using XML technology test data can be entered directly from the test machines into the Web-enabled 'Materials Database' (Mat-DB, which is an integral part of the On-line Data Information Network (ODIN On-line Data Information Network, 2004 that has been developed at JRC Petten. Test data, which are kept in XML format and sent by R&D project partners via the World Wide Web to the Petten Server are stored within the Mat-DB XML module. There they can be checked and updated on-line before they are uploaded into the database. After validation by the source administrator they can immediately be retrieved and evaluated by all project partners. A pilot test with the new XML related data exchange module from test machine into Mat-DB has currently been started within the European TMF Standard R&D project.

  5. MediaDB: a database of microbial growth conditions in defined media.

    Science.gov (United States)

    Richards, Matthew A; Cassen, Victor; Heavner, Benjamin D; Ajami, Nassim E; Herrmann, Andrea; Simeonidis, Evangelos; Price, Nathan D

    2014-01-01

    Isolating pure microbial cultures and cultivating them in the laboratory on defined media is used to more fully characterize the metabolism and physiology of organisms. However, identifying an appropriate growth medium for a novel isolate remains a challenging task. Even organisms with sequenced and annotated genomes can be difficult to grow, despite our ability to build genome-scale metabolic networks that connect genomic data with metabolic function. The scientific literature is scattered with information about defined growth media used successfully for cultivating a wide variety of organisms, but to date there exists no centralized repository to inform efforts to cultivate less characterized organisms by bridging the gap between genomic data and compound composition for growth media. Here we present MediaDB, a manually curated database of defined media that have been used for cultivating organisms with sequenced genomes, with an emphasis on organisms with metabolic network models. The database is accessible online, can be queried by keyword searches or downloaded in its entirety, and can generate exportable individual media formulation files. The data assembled in MediaDB facilitate comparative studies of organism growth media, serve as a starting point for formulating novel growth media, and contribute to formulating media for in silico investigation of metabolic networks. MediaDB is freely available for public use at https://mediadb.systemsbiology.net.

  6. The DB gap and a new class of pulsating white dwarfs

    Directory of Open Access Journals (Sweden)

    Shibahashi H.

    2013-03-01

    Full Text Available The recent systematic surveys providing enormously massive datasets of white dwarfs show that there is still a deficit of a factor of 2.5 in the DA/non-DA ratio within the temperature range of 30 000 K < Teff < 45 000 K, which has been regarded as the “DB gap” meaning a range with almost no helium atmosphere white dwarfs. Since all white dwarfs have to evolve through this temperature range along almost the identical sequence on the color-magnitude diagram, this implies that most of the helium atmosphere DO stars once evolve into hydrogen atmosphere hot DA stars in the temperature range of the DB gap and then back to helium atmosphere DB stars. Possible scenarios for this chameleon-like disguises of white dwarfs with helium dominant atmospheres are described and a new class of pulsating white dwarfs, named the hot-DAV stars, is predicted from these scenarios. One pulsating DA white dwarf, being consistent with the prediction, has been discovered indeed.

  7. PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome

    Science.gov (United States)

    Schlüter, Agatha; Real-Chicharro, Alejandro; Gabaldón, Toni; Sánchez-Jiménez, Francisca; Pujol, Aurora

    2010-01-01

    Peroxisomes are essential organelles that play a key role in redox signalling and lipid homeostasis. They contain a highly diverse enzymatic network among different species, mirroring the varied metabolic needs of the organisms. The previous PeroxisomeDB version organized the peroxisomal proteome of humans and Saccharomyces cerevisiae based on genetic and functional information into metabolic categories with a special focus on peroxisomal disease. The new release (http://www.peroxisomeDB.org) adds peroxisomal proteins from 35 newly sequenced eukaryotic genomes including fungi, yeasts, plants and lower eukaryotes. We searched these genomes for a core ensemble of 139 peroxisomal protein families and identified 2706 putative peroxisomal protein homologs. Approximately 37% of the identified homologs contained putative peroxisome targeting signals (PTS). To help develop understanding of the evolutionary relationships among peroxisomal proteins, the new database includes phylogenetic trees for 2386 of the peroxisomal proteins. Additional new features are provided, such as a tool to capture kinetic information from Brenda, CheBI and Sabio-RK databases and more than 1400 selected bibliographic references. PeroxisomeDB 2.0 is a freely available, highly interactive functional genomics platform that offers an extensive view on the peroxisomal metabolome across lineages, thus facilitating comparative genomics and systems analysis of the organelle. PMID:19892824

  8. Deformed Potential Energy of 263Db in a Generalized Liquid Drop Model

    Institute of Scientific and Technical Information of China (English)

    陈宝秋; 马中玉; 赵耀林

    2003-01-01

    The macroscopic deformed potential energy for super-heavy nuclei 263 Db,which governs the entrance and alpha decay channels,is determined within a generalized liquid drop model(GLDM).A quasi-molecular shape is as sumed in the GLDM,which includes volume-,surface-,and Coulomb-energies,proximity effects,mass asymmetry,and an accurate nuclear radius.The microscopic single particle energies are derived from a shell model in an axially deformed Woods-Saxon potential with a quasi-molecular shape.The shell correction is calculated by the Strutinsky method.The total deformed potential energy of a nucleus can be calculated by the macro-microscopic method as the summation of the liquid-drop energy and the Strutinsky shell correction.The theory is applied to predict the deformed potential energy of the experiment 22Ne + 241Am → 263Db* → 259Db + 4n,which was performed on the Heavy Ion Accelerator in Lanzhou.It is found that the neck in the quasi-molecular shape is responsible for the deep valley of the fusion barrier due to the shell corrections.In the cold fusion path,the double-hump fusion barrier is predicted by the shell correction and complete fusion events may occur.

  9. dbPPT: a comprehensive database of protein phosphorylation in plants.

    Science.gov (United States)

    Cheng, Han; Deng, Wankun; Wang, Yongbo; Ren, Jian; Liu, Zexian; Xue, Yu

    2014-01-01

    As one of the most important protein post-translational modifications, the reversible phosphorylation is critical for plants in regulating a variety of biological processes such as cellular metabolism, signal transduction and responses to environmental stress. Numerous efforts especially large-scale phosphoproteome profiling studies have been contributed to dissect the phosphorylation signaling in various plants, while a large number of phosphorylation events were identified. To provide an integrated data resource for further investigations, here we present a comprehensive database of dbPPT (database of Phosphorylation site in PlanTs, at http://dbppt.biocuckoo.org), which contains experimentally identified phosphorylation sites in proteins from plants. The phosphorylation sites in dbPPT were manually curated from the literatures, whereas datasets in other public databases were also integrated. In total, there were 82,175 phosphorylation sites in 31,012 proteins from 20 plant organisms in dbPPT, presenting a larger quantity of phosphorylation sites and a higher coverage of plant species in comparison with other databases. The proportions of residue types including serine, threonine and tyrosine were 77.99, 17.81 and 4.20%, respectively. All the phosphoproteins and phosphorylation sites in the database were critically annotated. Since the phosphorylation signaling in plants attracted great attention recently, such a comprehensive resource of plant protein phosphorylation can be useful for the research community. Database URL: http://dbppt.biocuckoo.or

  10. AIMS D2DB simulation for DUV and EUV mask inspection

    Science.gov (United States)

    Peng, Danping; Li, Ying; Satake, Masaki; Hu, Peter; Chen, Jerry; Hsu, S. C.; Lai, Rick; Lin, C. S.; Tuo, Laurent C. C.

    2012-02-01

    AIMS™ Die-to-Die (D2D) is widely used in checking the wafer printability of mask defects for DUV lithography. Two AIMS images, a reference and a defect image, are captured and compared with differences larger than certain tolerances identified as real defects. Since two AIMS images are needed, and since AIMS system time is precious, it is desirable to save image search and capture time by simulating reference images from the OPC mask pattern and AIMS optics. This approach is called Die-to-Database (D2DB). Another reason that D2DB is desirable is in single die mask, where the reference image from another die does not exist. This paper presents our approach to simulate AIMS optics and mask 3D effects. Unlike OPC model, whose major concern is predicting printed CD, AIMS D2DB model must produce simulated images that match measured images across the image field. This requires a careful modeling of all effects that impact the final image quality. We present a vector-diffraction theory that is based on solid theoretical foundations and a general formulation of mask model that are applicable to both rigorous Maxwell solver and empirical model that can capture the mask 3D-effects. We demonstrated the validity of our approach by comparing our simulated image with AIMS machine measured images. We also briefly discuss the necessary changes needed to model EUV optics. Simulation is particularly useful while the industry waits for an actinic EUV-AIMS tool.

  11. The rice proteogenomics database OryzaPG-DB: development, expansion and new features

    Directory of Open Access Journals (Sweden)

    Mohamed eHelmy

    2012-04-01

    Full Text Available Proteogenomics is the utilization of large-scale proteome data in genome annotation refinement. Our recently developed rice proteogenomics database (OryzaPG-DB is the first sustainable resource for rice shotgun-based proteogenomics, providing information on peptides identified in rice protein digested peptides measured by means of liquid chromatography-tandem mass spectrometry (LC-MS/MS, and mapping of the peptides to their genomic origins and the genomic novelty of each peptide. The sequences of the peptides, proteins, cDNAs and genes, and the gene annotations are available for download in FASTA and GFF3 formats, respectively. Further, an annotated visualization of the gene models, corresponding peptides and genomic novelty is available for each gene, and MS/MS spectra are available for each peptide. In this article, we discuss the utilization of OryzaPG-DB and report on its development, recent content expansions and newly added features in the current version (OryzaPG-DB v1.1.

  12. RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures

    Science.gov (United States)

    Paladin, Lisanna; Hirsh, Layla; Piovesan, Damiano; Andrade-Navarro, Miguel A.; Kajava, Andrey V.; Tosatto, Silvio C.E.

    2017-01-01

    RepeatsDB 2.0 (URL: http://repeatsdb.bio.unipd.it/) is an update of the database of annotated tandem repeat protein structures. Repeat proteins are a widespread class of non-globular proteins carrying heterogeneous functions involved in several diseases. Here we provide a new version of RepeatsDB with an improved classification schema including high quality annotations for ∼5400 protein structures. RepeatsDB 2.0 features information on start and end positions for the repeat regions and units for all entries. The extensive growth of repeat unit characterization was possible by applying the novel ReUPred annotation method over the entire Protein Data Bank, with data quality is guaranteed by an extensive manual validation for >60% of the entries. The updated web interface includes a new search engine for complex queries and a fully re-designed entry page for a better overview of structural data. It is now possible to compare unit positions, together with secondary structure, fold information and Pfam domains. Moreover, a new classification level has been introduced on top of the existing scheme as an independent layer for sequence similarity relationships at 40%, 60% and 90% identity. PMID:27899671

  13. Comparing NetCDF and SciDB on managing and querying 5D hydrologic dataset

    Science.gov (United States)

    Liu, Haicheng; Xiao, Xiao

    2016-11-01

    Efficiently extracting information from high dimensional hydro-meteorological modelling datasets requires smart solutions. Traditional methods are mostly based on files, which can be edited and accessed handily. But they have problems of efficiency due to contiguous storage structure. Others propose databases as an alternative for advantages such as native functionalities for manipulating multidimensional (MD) arrays, smart caching strategy and scalability. In this research, NetCDF file based solutions and the multidimensional array database management system (DBMS) SciDB applying chunked storage structure are benchmarked to determine the best solution for storing and querying 5D large hydrologic modelling dataset. The effect of data storage configurations including chunk size, dimension order and compression on query performance is explored. Results indicate that dimension order to organize storage of 5D data has significant influence on query performance if chunk size is very large. But the effect becomes insignificant when chunk size is properly set. Compression of SciDB mostly has negative influence on query performance. Caching is an advantage but may be influenced by execution of different query processes. On the whole, NetCDF solution without compression is in general more efficient than the SciDB DBMS.

  14. pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins

    Science.gov (United States)

    Varadi, Mihaly; Kosol, Simone; Lebrun, Pierre; Valentini, Erica; Blackledge, Martin; Dunker, A. Keith; Felli, Isabella C.; Forman-Kay, Julie D.; Kriwacki, Richard W.; Pierattelli, Roberta; Sussman, Joel; Svergun, Dmitri I.; Uversky, Vladimir N.; Vendruscolo, Michele; Wishart, David; Wright, Peter E.; Tompa, Peter

    2014-01-01

    The goal of pE-DB (http://pedb.vib.be) is to serve as an openly accessible database for the deposition of structural ensembles of intrinsically disordered proteins (IDPs) and of denatured proteins based on nuclear magnetic resonance spectroscopy, small-angle X-ray scattering and other data measured in solution. Owing to the inherent flexibility of IDPs, solution techniques are particularly appropriate for characterizing their biophysical properties, and structural ensembles in agreement with these data provide a convenient tool for describing the underlying conformational sampling. Database entries consist of (i) primary experimental data with descriptions of the acquisition methods and algorithms used for the ensemble calculations, and (ii) the structural ensembles consistent with these data, provided as a set of models in a Protein Data Bank format. PE-DB is open for submissions from the community, and is intended as a forum for disseminating the structural ensembles and the methodologies used to generate them. While the need to represent the IDP structures is clear, methods for determining and evaluating the structural ensembles are still evolving. The availability of the pE-DB database is expected to promote the development of new modeling methods and leads to a better understanding of how function arises from disordered states. PMID:24174539

  15. 70 dB long-pass filter on a nanophotonic chip.

    Science.gov (United States)

    Guo, Xiang; Zou, Chang-Ling; Tang, Hong X

    2016-09-01

    Integrated quantum photonic chips are promising for scalable, photonic based quantum information processing. Although on-chip quantum photon sources and single photon detectors have been demostrated separately, the full integration of these components on single chip is hindered by the background photons from the strong classical pump light. Here we design and fabricate an on-chip long-pass filter which can provide 70 dB attenuation for visible light near 775 nm with less than 3 dB insertion loss for light in the telecom C-band near 1550 nm. The adiabatic design makes this device broadband and robust against fabrication errors as well as working conditions. Combined with the previously demonstrated non-classical on-chip source based on spontaneous parametric down conversion on the same material system, this platform could enable 100 dB suppression of pump light and holds promise in realizing fully integrated quantum photonic chips where the sources, filters and detectors are monolithically integrated.

  16. iPPI-DB: an online database of modulators of protein-protein interactions.

    Science.gov (United States)

    Labbé, Céline M; Kuenemann, Mélaine A; Zarzycka, Barbara; Vriend, Gert; Nicolaes, Gerry A F; Lagorce, David; Miteva, Maria A; Villoutreix, Bruno O; Sperandio, Olivier

    2016-01-01

    In order to boost the identification of low-molecular-weight drugs on protein-protein interactions (PPI), it is essential to properly collect and annotate experimental data about successful examples. This provides the scientific community with the necessary information to derive trends about privileged physicochemical properties and chemotypes that maximize the likelihood of promoting a given chemical probe to the most advanced stages of development. To this end we have developed iPPI-DB (freely accessible at http://www.ippidb.cdithem.fr), a database that contains the structure, some physicochemical characteristics, the pharmacological data and the profile of the PPI targets of several hundreds modulators of protein-protein interactions. iPPI-DB is accessible through a web application and can be queried according to two general approaches: using physicochemical/pharmacological criteria; or by chemical similarity to a user-defined structure input. In both cases the results are displayed as a sortable and exportable datasheet with links to external databases such as Uniprot, PubMed. Furthermore each compound in the table has a link to an individual ID card that contains its physicochemical and pharmacological profile derived from iPPI-DB data. This includes information about its binding data, ligand and lipophilic efficiencies, location in the PPI chemical space, and importantly similarity with known drugs, and links to external databases like PubChem, and ChEMBL.

  17. Tree shrew database (TreeshrewDB): a genomic knowledge base for the Chinese tree shrew.

    Science.gov (United States)

    Fan, Yu; Yu, Dandan; Yao, Yong-Gang

    2014-11-21

    The tree shrew (Tupaia belangeri) is a small mammal with a close relationship to primates and it has been proposed as an alternative experimental animal to primates in biomedical research. The recent release of a high-quality Chinese tree shrew genome enables more researchers to use this species as the model animal in their studies. With the aim to making the access to an extensively annotated genome database straightforward and easy, we have created the Tree shrew Database (TreeshrewDB). This is a web-based platform that integrates the currently available data from the tree shrew genome, including an updated gene set, with a systematic functional annotation and a mRNA expression pattern. In addition, to assist with automatic gene sequence analysis, we have integrated the common programs Blast, Muscle, GBrowse, GeneWise and codeml, into TreeshrewDB. We have also developed a pipeline for the analysis of positive selection. The user-friendly interface of TreeshrewDB, which is available at http://www.treeshrewdb.org, will undoubtedly help in many areas of biological research into the tree shrew.

  18. ChemDB update--full-text search and virtual chemical space.

    Science.gov (United States)

    Chen, Jonathan H; Linstead, Erik; Swamidass, S Joshua; Wang, Dennis; Baldi, Pierre

    2007-09-01

    ChemDB is a chemical database containing nearly 5M commercially available small molecules, important for use as synthetic building blocks, probes in systems biology and as leads for the discovery of drugs and other useful compounds. The data is publicly available over the web for download and for targeted searches using a variety of powerful methods. The chemical data includes predicted or experimentally determined physicochemical properties, such as 3D structure, melting temperature and solubility. Recent developments include optimization of chemical structure (and substructure) retrieval algorithms, enabling full database searches in less than a second. A text-based search engine allows efficient searching of compounds based on over 65M annotations from over 150 vendors. When searching for chemicals by name, fuzzy text matching capabilities yield productive results even when the correct spelling of a chemical name is unknown, taking advantage of both systematic and common names. Finally, built in reaction models enable searches through virtual chemical space, consisting of hypothetical products readily synthesizable from the building blocks in ChemDB. ChemDB and Supplementary Materials are available at http://cdb.ics.uci.edu. Supplementary data are available at Bioinformatics online.

  19. High-throughput screening for GPR119 modulators identifies a novel compound with anti-diabetic efficacy in db/db mice.

    Directory of Open Access Journals (Sweden)

    Meng Zhang

    Full Text Available G protein-coupled receptor 119 (GPR119 is highly expressed in pancreatic β cells and enteroendocrine cells. It is involved in glucose-stimulated insulin secretion and glucagon-like peptide-1 (GLP-1 release, thereby representing a promising target for the treatment of type 2 diabetes. Although a number of GPR119 agonists were developed, no positive allosteric modulator (PAM to this receptor has been reported. Here we describe a high-throughput assay for screening GPR119 PAMs and agonists simultaneously. Following screening of a small molecule compound library containing 312,000 synthetic and natural product-derived samples, one potent GPR119 agonist with novel chemical structure, MW1219, was identified. Exposure of MIN6 and GLUTag cells to MW1219 enhanced glucose-stimulated insulin secretion and GLP-1 release; once-daily oral dosing of MW1219 for 6 weeks in diabetic db/db mice reduced hemoglobin A1c (HbA1c and improved plasma glucose, insulin and GLP-1 levels; it also increased glucose tolerance. The results demonstrate that MW1219 is capable of effectively controlling blood glucose level and may have the potential to be developed as a new class of anti-diabetic agents.

  20. X-3, a mangiferin derivative, stimulates AMP-activated protein kinase and reduces hyperglycemia and obesity in db/db mice.

    Science.gov (United States)

    Han, Jun; Yi, Jia; Liang, Fengying; Jiang, Bo; Xiao, Ying; Gao, Shouhong; Yang, Na; Hu, Honggang; Xie, Wei-Fen; Chen, Wansheng

    2015-04-15

    Diabetes mellitus is a major health concern, affecting nearly 10% of the population. Here we describe a potential novel therapeutic agent for this disease, X-3, a derivative of mangiferin. Therapeutic administration of X-3 significantly and dose-dependently reduced plasma glucose and triglycerides in db/db mice following 8 week-treatments. Treatment with X-3 dose-dependently increased the number of insulin-positive β-cell mass. Importantly, X-3 did not cause any death or signs of toxicity in acute toxicity studies. Study of mechanism of action revealed that X-3 increased glucose uptake in parallel with increased phosphorylation of AMP-activated protein kinase (AMPK) in 3T3-L1 cells. It activates AMPK in both LKB1-dependent and -independent manner. Furthermore, administration of X-3 resulted in activation of AMPK and its downstream target, acetyl-CoA carboxylase (ACC) in the hypothalamus, liver, muscle and adipose tissues of C57BL/6 mice. An 80 mg/kg X-3 was more potent than metformin at 500 mg/kg in the hypothalamus, and interscapular fat tissues, potent than MF at the same dose in the liver. Thus, we conclude that X-3 is a promising new class of AMPK activating drug, and can potentially be used in the treatment of type 2 diabetes.

  1. Delayed wound healing in diabetic (db/db) mice with Pseudomonas aeruginosa biofilm challenge: a model for the study of chronic wounds.

    Science.gov (United States)

    Zhao, Ge; Hochwalt, Phillip C; Usui, Marcia L; Underwood, Robert A; Singh, Pradeep K; James, Garth A; Stewart, Philip S; Fleckman, Philip; Olerud, John E

    2010-01-01

    Chronic wounds are a major clinical problem that lead to considerable morbidity and mortality. We hypothesized that an important factor in the failure of chronic wounds to heal was the presence of microbial biofilm resistant to antibiotics and protected from host defenses. A major difficulty in studying chronic wounds is the absence of suitable animal models. The goal of this study was to create a reproducible chronic wound model in diabetic mice by the application of bacterial biofilm. Six-millimeter punch biopsy wounds were created on the dorsal surface of diabetic (db/db) mice, subsequently challenged with Pseudomonas aeruginosa (PAO1) biofilms 2 days postwounding, and covered with semiocclusive dressings for 2 weeks. Most of the control wounds were epithelialized by 28 days postwounding. In contrast, none of biofilm-challenged wounds were closed. Histological analysis showed extensive inflammatory cell infiltration, tissue necrosis, and epidermal hyperplasia adjacent to challenged wounds-all indicators of an inflammatory nonhealing wound. Quantitative cultures and transmission electron microscopy demonstrated that the majority of bacteria were in the scab above the wound bed rather than in the wound tissue. The model was reproducible, allowed localized cutaneous wound infections without high mortality, and demonstrated delayed wound healing following a biofilm challenge. This model may provide an approach to study the role of microbial biofilms in chronic wounds as well as the effect of specific biofilm therapy on wound healing.

  2. Once daily administration of the SGLT2 inhibitor, empagliflozin, attenuates markers of renal fibrosis without improving albuminuria in diabetic db/db mice.

    Science.gov (United States)

    Gallo, Linda A; Ward, Micheal S; Fotheringham, Amelia K; Zhuang, Aowen; Borg, Danielle J; Flemming, Nicole B; Harvie, Ben M; Kinneally, Toni L; Yeh, Shang-Ming; McCarthy, Domenica A; Koepsell, Hermann; Vallon, Volker; Pollock, Carol; Panchapakesan, Usha; Forbes, Josephine M

    2016-05-26

    Blood glucose control is the primary strategy to prevent complications in diabetes. At the onset of kidney disease, therapies that inhibit components of the renin angiotensin system (RAS) are also indicated, but these approaches are not wholly effective. Here, we show that once daily administration of the novel glucose lowering agent, empagliflozin, an SGLT2 inhibitor which targets the kidney to block glucose reabsorption, has the potential to improve kidney disease in type 2 diabetes. In male db/db mice, a 10-week treatment with empagliflozin attenuated the diabetes-induced upregulation of profibrotic gene markers, fibronectin and transforming-growth-factor-beta. Other molecular (collagen IV and connective tissue growth factor) and histological (tubulointerstitial total collagen and glomerular collagen IV accumulation) benefits were seen upon dual therapy with metformin. Albuminuria, urinary markers of tubule damage (kidney injury molecule-1, KIM-1 and neutrophil gelatinase-associated lipocalin, NGAL), kidney growth, and glomerulosclerosis, however, were not improved with empagliflozin or metformin, and plasma and intra-renal renin activity was enhanced with empagliflozin. In this model, blood glucose lowering with empagliflozin attenuated some molecular and histological markers of fibrosis but, as per treatment with metformin, did not provide complete renoprotection. Further research to refine the treatment regimen in type 2 diabetes and nephropathy is warranted.

  3. Delayed Wound Healing in Diabetic (db/db) Mice with Pseudomonas aeruginosa Biofilm Challenge – A Model for the Study of Chronic Wounds

    Science.gov (United States)

    Zhao, Ge; Hochwalt, Phillip C.; Usui, Marcia L.; Underwood, Robert A.; Singh, Pradeep K.; James, Garth A.; Stewart, Philip S.; Fleckman, Philip; Olerud, John E.

    2010-01-01

    Chronic wounds are a major clinical problem that leads to considerable morbidity and mortality. We hypothesized that an important factor in the failure of chronic wounds to heal was the presence of microbial biofilm resistant to antibiotics and protected from host defenses. A major difficulty in studying chronic wounds is the absence of suitable animal models. The goal of this study was to create a reproducible chronic wound model in diabetic mice by application of bacterial biofilm. Six millimeter punch biopsy wounds were created on the dorsal surface of diabetic (db/db) mice, subsequently challenged with Pseudomonas aeruginosa (PAO1) biofilms two days post-wounding, and covered with semi-occlusive dressings for two weeks. Most of the control wounds were epithelialized by 28 days post-wounding. In contrast, none of biofilm challenged wounds were closed. Histological analysis showed extensive inflammatory cell infiltration, tissue necrosis and epidermal hyperplasia adjacent to challenged wounds- all indicators of an inflammatory non-healing wound. Quantitative cultures and transmission electron microscopy demonstrated that the majority of bacteria were in the scab above the wound bed rather than in the wound tissue. The model was reproducible, allowed localized cutaneous wound infections without high mortality and demonstrated delayed wound healing following biofilm challenge. This model may provide an approach to study the role of microbial biofilms in chronic wounds as well as the effect of specific biofilm therapy on wound healing. PMID:20731798

  4. Anti-Diabetic Activities of Jiaotaiwan in db/db Mice by Augmentation of AMPK Protein Activity and Upregulation of GLUT4 Expression

    Directory of Open Access Journals (Sweden)

    Na Hu

    2013-01-01

    Full Text Available Jiaotaiwan (JTW, which is composed of Coptis chinensis (CC and cinnamon (CIN, is one of the most well-known traditional Chinese medicines. In this study, we investigated the antidiabetic effects and mechanism of JTW in db/db mice. Results showed that JTW significantly decreased the level of fasting blood glucose and improved glucose and insulin tolerance better than CC or CIN alone. JTW also effectively protected the pancreatic islet shape, augmented the activation of AMP-activated protein kinase (AMPK in the liver, and increased the expression of glucose transporter 4 (GLUT4 protein in skeletal muscle and white fat. AMPK and GLUT4 contributed to glucose metabolism regulation and had an essential function in the development of diabetes mellitus (DM. Therefore, the mechanisms of JTW may be related to suppressing gluconeogenesis by activating AMPK in the liver and affecting glucose uptake in surrounding tissues through the upregulation of GLUT4 protein expression. These findings provided a new insight into the antidiabetic clinical applications of JTW and demonstrated the potential of JTW as a new drug candidate for DM treatment.

  5. The Beneficial Effects of Combined Grape Pomace and Omija Fruit Extracts on Hyperglycemia, Adiposity and Hepatic Steatosis in db/db Mice: A Comparison with Major Index Compounds

    Directory of Open Access Journals (Sweden)

    Su-Jung Cho

    2014-09-01

    Full Text Available This study investigated the effects of combined grape pomace and omija fruit extracts (GO on diabetes-related metabolic changes in type 2 diabetic db/db mice. The effects of GO were compared with those of a resveratrol and schizandrin mixture (RS, which is a mixture of major components of GO. Mice were fed a normal diet with RS (0.005% resveratrol and 0.02% schizandrin in diet, w/w or GO (0.3% grape pomace ethanol extract and 0.05% omija fruit ethanol extract in diet, w/w for seven weeks. RS and GO not only lowered the levels of blood and plasma glucose, HbA1c, insulin and homeostasis model assessment of insulin resistance (HOMA-IR with a simultaneous decrease in hepatic gluconeogenic enzymes activities and adiposity, but also improved preservation of the pancreatic β-cells. Plasma leptin and resistin levels were lower while the plasma adiponectin level was higher in the RS and GO groups than in the control group. Especially, GO increased hepatic glucokinase activity and gene expression and improved hepatic steatosis by elevating fatty acid oxidation compared to RS. These findings suggest that GO ameliorates hyperglycemia, adiposity and hepatic steatosis in type 2 diabetic mice.

  6. Informatics in radiology: use of CouchDB for document-based storage of DICOM objects.

    Science.gov (United States)

    Rascovsky, Simón J; Delgado, Jorge A; Sanz, Alexander; Calvo, Víctor D; Castrillón, Gabriel

    2012-01-01

    Picture archiving and communication systems traditionally have depended on schema-based Structured Query Language (SQL) databases for imaging data management. To optimize database size and performance, many such systems store a reduced set of Digital Imaging and Communications in Medicine (DICOM) metadata, discarding informational content that might be needed in the future. As an alternative to traditional database systems, document-based key-value stores recently have gained popularity. These systems store documents containing key-value pairs that facilitate data searches without predefined schemas. Document-based key-value stores are especially suited to archive DICOM objects because DICOM metadata are highly heterogeneous collections of tag-value pairs conveying specific information about imaging modalities, acquisition protocols, and vendor-supported postprocessing options. The authors used an open-source document-based database management system (Apache CouchDB) to create and test two such databases; CouchDB was selected for its overall ease of use, capability for managing attachments, and reliance on HTTP and Representational State Transfer standards for accessing and retrieving data. A large database was created first in which the DICOM metadata from 5880 anonymized magnetic resonance imaging studies (1,949,753 images) were loaded by using a Ruby script. To provide the usual DICOM query functionality, several predefined "views" (standard queries) were created by using JavaScript. For performance comparison, the same queries were executed in both the CouchDB database and a SQL-based DICOM archive. The capabilities of CouchDB for attachment management and database replication were separately assessed in tests of a similar, smaller database. Results showed that CouchDB allowed efficient storage and interrogation of all DICOM objects; with the use of information retrieval algorithms such as map-reduce, all the DICOM metadata stored in the large database were

  7. TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life.

    Science.gov (United States)

    Elbourne, Liam D H; Tetu, Sasha G; Hassan, Karl A; Paulsen, Ian T

    2017-01-04

    All cellular life contains an extensive array of membrane transport proteins. The vast majority of these transporters have not been experimentally characterized. We have developed a bioinformatic pipeline to identify and annotate complete sets of transporters in any sequenced genome. This pipeline is now fully automated enabling it to better keep pace with the accelerating rate of genome sequencing. This manuscript describes TransportDB 2.0 (http://www.membranetransport.org/transportDB2/), a completely updated version of TransportDB, which provides access to the large volumes of data generated by our automated transporter annotation pipeline. The TransportDB 2.0 web portal has been rebuilt to utilize contemporary JavaScript libraries, providing a highly interactive interface to the annotation information, and incorporates analysis tools that enable users to query the database on a number of levels. For example, TransportDB 2.0 includes tools that allow users to select annotated genomes of interest from the thousands of species held in the database and compare their complete transporter complements.

  8. Observational Assessment of Preschool Disruptive Behavior, Part I: reliability of the Disruptive Behavior Diagnostic Observation Schedule (DB-DOS).

    Science.gov (United States)

    Wakschlag, Lauren S; Hill, Carri; Carter, Alice S; Danis, Barbara; Egger, Helen L; Keenan, Kate; Leventhal, Bennett L; Cicchetti, Domenic; Maskowitz, Katie; Burns, James; Briggs-Gowan, Margaret J

    2008-06-01

    To examine the reliability of the Disruptive Behavior Diagnostic Observation Schedule (DB-DOS), a new observational method for assessing preschool disruptive behavior. The DB-DOS is a structured clinic-based assessment designed to elicit clinically salient behaviors relevant to the diagnosis of disruptive behavior in preschoolers. Child behavior is assessed in three interactional contexts that vary by partner (parent versus examiner) and level of support provided. Twenty-one disruptive behaviors are coded within two domains: problems in Behavioral Regulation and problems in Anger Modulation. A total of 364 referred and nonreferred preschoolers participated: interrater reliability and internal consistency were assessed on a primary sample (n = 335) and test-retest reliability was assessed in a separate sample (n = 29). The DB-DOS demonstrated good interrater and test-retest reliability. Confirmatory factor analysis demonstrated an excellent fit of the DB-DOS multidomain model of disruptive behavior. The DB-DOS is a reliable observational tool for clinic-based assessment of preschool disruptive behavior. This standardized assessment method holds promise for advancing developmentally sensitive characterization of preschool psychopathology.

  9. TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life

    Science.gov (United States)

    Elbourne, Liam D. H.; Tetu, Sasha G.; Hassan, Karl A.; Paulsen, Ian T.

    2017-01-01

    All cellular life contains an extensive array of membrane transport proteins. The vast majority of these transporters have not been experimentally characterized. We have developed a bioinformatic pipeline to identify and annotate complete sets of transporters in any sequenced genome. This pipeline is now fully automated enabling it to better keep pace with the accelerating rate of genome sequencing. This manuscript describes TransportDB 2.0 (http://www.membranetransport.org/transportDB2/), a completely updated version of TransportDB, which provides access to the large volumes of data generated by our automated transporter annotation pipeline. The TransportDB 2.0 web portal has been rebuilt to utilize contemporary JavaScript libraries, providing a highly interactive interface to the annotation information, and incorporates analysis tools that enable users to query the database on a number of levels. For example, TransportDB 2.0 includes tools that allow users to select annotated genomes of interest from the thousands of species held in the database and compare their complete transporter complements. PMID:27899676

  10. An Analysis of Station Blackout Sequences Using MELCOR1.8.5 Code for the Severe Accident Analysis DB

    Energy Technology Data Exchange (ETDEWEB)

    Song, Y. M.; Ahn, K. I. [KAERI, Daejeon (Korea, Republic of)

    2010-12-15

    The Korea Atomic Energy Research Institute (KAERI) has been constructing severe accident analysis database (DB) under a National Nuclear R and D Program. Especially, MAAP (commercial code being widely used for industries) DB for many scenarios including station blackout (SBO) has been completed up to now. This report shows the analysis results for SBO scenarios using MELCOR code. These results will be used for the degree of completion after being compared with MAAP results. The developing strategy of MELCOR code is the same with that of MAAP DB. For the generation of data set, the Korean standard nuclear power plant (KSNP) has been selected as a reference plant and the eight SBO scenarios are chosen to be analyzed based on the PSA results (these eight scenarios accounted for 99 percent of occurrence frequency of total 197 SBO scenarios). Both thermal hydraulics (T/H) and source term analysis have been performed using MELCOR version 1.8.5 for the chosen scenarios. But only major T/H variables treated in the MAAP report are listed among the generated data set, which shows the characteristics of each scenario. These SBO results together with those of the other initiating events (to be analyzed in the future) will be used as inputs for DB construction and special value will be found in the comparing and complimentary process with MAAP DB

  11. Contig sequences and their annotation (amino acid sequence and results of homology search), and expression profile - Dicty_cDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Dicty_cDB Contig sequences and their annotation (amino acid sequence and results of homology search), and express...s of homology search), and expression profile Description of data contents Contig...o acid sequence and results of homology search), and expression profile - Dicty_cDB | LSDB Archive ...

  12. 2型糖尿病模型db/db小鼠海马NOS阳性神经元变化%The Changes of Nitric Oxide Synthase(NOS) Positive Cells in the Hippocampus of Genetically Obese Diabetic db/db mice

    Institute of Scientific and Technical Information of China (English)

    张松筠; 杨天祝; 马常开; 张庆九; 刘文淑

    2002-01-01

    目的观察人类2型糖尿病模型--C57BL/KsJdb/db(db/db)小鼠海马NOS阳性神经元变化.方法糖尿病组:6周龄C57BL/KsJ(db+db+)小鼠5只,尾静脉空腹血糖高于11.1 mmol/L且肥胖.对照组:非糖尿病小鼠C57B/KsJ(?+)5只,尾静脉空腹血糖低于6.0 mmol/L体重正常,于30周龄(成模第6月末)时,灌注固定取脑,以NADPH-d组化法显示海马NOS阳性神经元.结果与正常对照组相比,糖尿病组小鼠海马齿状回NOS阳性神经元密度显著减少(P<0.01).结论糖尿病时NOS阳性神经元数量减少,NO的合成降低表明NO可能参与糖尿病中枢神经系统功能障碍.

  13. The novel GLP-1-gastrin dual agonist ZP3022 improves glucose homeostasis and increases β-cell mass without affecting islet number in db/db mice.

    Science.gov (United States)

    Dalbøge, Louise S; Almholt, Dorthe L C; Neerup, Trine S R; Vrang, Niels; Jelsing, Jacob; Fosgerau, Keld

    2014-08-01

    Antidiabetic treatments aiming to preserve or even to increase β-cell mass are currently gaining increased interest. Here we investigated the effect of chronic treatment with the novel glucagon-like peptide-1 (GLP-1)-gastrin dual agonist ZP3022 (HGEGTFTSDLSKQMEEEAVRLFIEWLKN-8Ado-8Ado-YGWLDF-NH2) on glycemic control, β-cell mass and proliferation, and islet number. Male db/db mice were treated with ZP3022, liraglutide, or vehicle for 2, 4, or 8 weeks, with terminal assessment of hemoglobin A1c, basal blood glucose, and plasma insulin concentrations. Pancreata were removed for immunohistochemical staining and stereological quantification of β-cell mass, islet numbers, proliferation, and apoptosis. Treatment with ZP3022 or liraglutide led to a significant improvement in glycemic control. ZP3022 treatment resulted in a sustained increase in β-cell mass after 4 and 8 weeks of treatment, whereas the effect of liraglutide was transient. The expansion in β-cell mass observed in the ZP3022-treated mice appeared to be driven by increased β-cell proliferation in existing islets rather than by formation of new islets, as mean islet mass increased but the number of islets remained constant. Our data demonstrate that the GLP-1-gastrin dual agonist ZP3022 causes a sustained improvement in glycemic control accompanied by an increase in β-cell mass, increased proliferation, and increased mean islet mass. The results highlight that the GLP-1-gastrin dual agonist increases β-cell mass more than liraglutide and that dual agonists could potentially be developed into a new class of antidiabetic treatments.

  14. HPN, a Synthetic Analogue of Bromophenol from Red Alga Rhodomela confervoides: Synthesis and Anti-Diabetic Effects in C57BL/KsJ-db/db Mice

    Science.gov (United States)

    Shi, Dayong; Guo, Shuju; Jiang, Bo; Guo, Chao; Wang, Tao; Zhang, Luyong; Li, Jingya

    2013-01-01

    3,4-dibromo-5-(2-bromo-3,4-dihydroxy-6-(isopropoxymethyl)benzyl)benzene-1,2-diol (HPN) is a synthetic analogue of 3,4-dibromo-5-(2-bromo-3,4-dihydroxy-6-(ethoxymethyl)benzyl)benzene-1,2-diol (BPN), which is isolated from marine red alga Rhodomela confervoides with potent protein tyrosine phosphatase 1B (PTP1B) inhibition (IC50 = 0.84 μmol/L). The in vitro assay showed that HPN exhibited enhanced inhibitory activity against PTP1B with IC50 0.63 μmol/L and high selectivity against other PTPs (T cell protein tyrosine phosphatase (TCPTP), leucocyte antigen-related tyrosine phosphatase (LAR), Src homology 2-containing protein tyrosine phosphatase-1 (SHP-1) and SHP-2). The results of antihyperglycemic activity using db/db mouse model demonstrated that HPN significantly decreased plasma glucose (P < 0.01) after eight weeks treatment period. HPN lowered serum triglycerides and total cholesterol concentration in a dose-dependent manner. Besides, both of the high and medium dose groups of HPN remarkably decreased HbA1c levels (P < 0.05). HPN in the high dose group markedly lowered the insulin level compared to the model group (P < 0.05), whereas the effects were less potent than the positive drug rosiglitazone. Western blotting results showed that HPN decreased PTP1B levels in pancreatic tissue. Last but not least, the results of an intraperitoneal glucose tolerance test in Sprague–Dawley rats indicate that HPN have a similar antihyperglycemic activity as rosiglitazone. HPN therefore have potential for development as treatments for Type 2 diabetes. PMID:23364683

  15. 16.7 Hz traction power supply and automated reporting in the main system control centre of DB Energie; 16,7-Hz-Traktionsenergieversorgung und automatisiertes Berichtswesen in der Hauptschaltleitung der DB Energie

    Energy Technology Data Exchange (ETDEWEB)

    Schaarschmidt, J. [DB Energie GmbH, I.EBV 1, Frankfurt am Main (Germany); Nestler, S. [Teleteam Concepts GmbH, Simmozheim (Germany)

    2008-07-01

    It is of great importance in a centralized network to provide an optimum supply of 16.7 Hz traction power through the systematic use of the power and control stations. The methods used by DB Energie to ensure this goal have been working successfully since almost ten years. The process data collected in the DataWareHouse must be automated and made available directly for reporting. Furthermore, the information must be transmitted and received reliably and without delay. DB Energie makes use of powerful software tools for this purpose. (orig.)

  16. CNX-012-570, a direct AMPK activator provides strong glycemic and lipid control along with significant reduction in body weight; studies from both diet-induced obese mice and db/db mice models.

    Science.gov (United States)

    Anil, Tharappel M; Harish, Chandrashekaran; Lakshmi, Mudigere N; Harsha, Krishnareddy; Onkaramurthy, Mallappa; Sathish Kumar, Venkatesh; Shree, Nitya; Geetha, Venkatachalaiah; Balamurali, Gundalmandikal V; Gopala, Aralakuppe S; Madhusudhan Reddy, Bobbili; Govind, Madabosse K; Anup, Mammen O; Moolemath, Yoganand; Venkataranganna, Marikunte V; Jagannath, Madanahalli R; Somesh, Baggavalli P

    2014-01-25

    AMP activated protein kinase (AMPK) regulates the coordination of anabolic and catabolic processes and is an attractive therapeutic target for T2DM, obesity and metabolic syndrome. We report the anti-hyperglycemic and anti-hyperlipidemic effects of CNX-012-570 is an orally bioavailable small molecule (molecular weight of 530 Daltons) that directly activates AMPK in DIO and db/db animal models of diabetes. Activity and efficacy of the compound was tested in cell based as well as cell free systems in vitro. Male C57BL/6 mice fed with high fat diet (HFD) were assigned to either vehicle or CNX-012-570 (3 mg/kg, orally once a day) for 8 weeks (n = 8). Genetically diabetic db/db mice on chow diet were dosed with vehicle control or CNX-012-570 (2.5 mg/kg, orally once a day) for 6 weeks (n = 8). CNX-012-570 is a highly potent and orally bioavailable compound activating AMPK in both cell and cell free systems. It inhibits lipolysis (33%) and gluconeogenesis (28%) in 3T3L1 cells and rat primary hepatocytes respectively. The efficacy of the molecule was translated to both DIO and db/db animal models of diabetes. CNX-012-570 has reduced fasting blood glucose levels by 14%, body weight by 24% and fasting serum triglycerides (TG) by 24%. CNX-012-570 showed a 22% reduction in fed serum cholesterol levels and 19% increase in HDL levels.In db/db mice model, CNX-012-570 has shown 18% decrease in fed glucose and 32% decrease in fasting glucose with a 2.57% reduction in absolute HbA1c. Decrease in serum insulin and glucose AUC indicates the increased insulin sensitivity. Body weight was reduced by 13% with increased browning of adipose tissue and decreased inguinal and mesenteric fat mass. There was significant reduction in liver TG and liver total cholesterol. CNX-012-570 has the potential to control hyperglycemia and hyperlipidemia. It also reduces body weight gain with an additional benefit of minimizing cardiovascular risks in diabetics.

  17. Asteroid 2015 DB216: a recurring co-orbital companion to Uranus

    Science.gov (United States)

    de la Fuente Marcos, C.; de la Fuente Marcos, R.

    2015-10-01

    Minor bodies trapped in 1:1 co-orbital resonances with a host planet could be relevant to explain the origin of captured satellites. Among the giant planets, Uranus has one of the smallest known populations of co-orbitals, three objects, and all of them are short-lived. Asteroid 2015 DB216 has an orbital period that matches well that of Uranus, and here we investigate its dynamical state. Direct N-body calculations are used to assess the current status of this object, reconstruct its immediate dynamical past, and explore its future orbital evolution. A covariance matrix-based Monte Carlo scheme is presented and applied to study its short-term stability. We find that 2015 DB216 is trapped in a temporary co-orbital resonance with Uranus, the fourth known minor body to do so. A detailed analysis of its dynamical evolution shows that it is an unstable but recurring co-orbital companion to Uranus. It currently follows an asymmetric horseshoe trajectory that will last for at least 10 kyr, but it may remain inside Uranus' co-orbital zone for millions of years. As in the case of other transient Uranian co-orbitals, complex multibody ephemeral mean motion resonances trigger the switching between the various resonant co-orbital states. The new Uranian co-orbital exhibits a secular behaviour markedly different from that of the other known Uranian co-orbitals because of its higher inclination, nearly 38°. Given its rather unusual discovery circumstances, the presence of 2015 DB216 hints at the existence of a relatively large population of objects moving in similar orbits.

  18. SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets.

    Science.gov (United States)

    Guo, Jing; Liu, Hui; Zheng, Jie

    2016-01-04

    Synthetic lethality (SL) is a type of genetic interaction between two genes such that simultaneous perturbations of the two genes result in cell death or a dramatic decrease of cell viability, while a perturbation of either gene alone is not lethal. SL reflects the biologically endogenous difference between cancer cells and normal cells, and thus the inhibition of SL partners of genes with cancer-specific mutations could selectively kill cancer cells but spare normal cells. Therefore, SL is emerging as a promising anticancer strategy that could potentially overcome the drawbacks of traditional chemotherapies by reducing severe side effects. Researchers have developed experimental technologies and computational prediction methods to identify SL gene pairs on human and a few model species. However, there has not been a comprehensive database dedicated to collecting SL pairs and related knowledge. In this paper, we propose a comprehensive database, SynLethDB (http://histone.sce.ntu.edu.sg/SynLethDB/), which contains SL pairs collected from biochemical assays, other related databases, computational predictions and text mining results on human and four model species, i.e. mouse, fruit fly, worm and yeast. For each SL pair, a confidence score was calculated by integrating individual scores derived from different evidence sources. We also developed a statistical analysis module to estimate the druggability and sensitivity of cancer cells upon drug treatments targeting human SL partners, based on large-scale genomic data, gene expression profiles and drug sensitivity profiles on more than 1000 cancer cell lines. To help users access and mine the wealth of the data, we developed other practical functionalities, such as search and filtering, orthology search, gene set enrichment analysis. Furthermore, a user-friendly web interface has been implemented to facilitate data analysis and interpretation. With the integrated data sets and analytics functionalities, SynLethDB would

  19. HBVRegDB: Annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequences

    Directory of Open Access Journals (Sweden)

    Firth Andrew E

    2007-12-01

    Full Text Available Abstract Background The many Hepadnaviridae sequences available have widely varied functional annotation. The genomes are very compact (~3.2 kb but contain multiple layers of functional regulatory elements in addition to coding regions. Key regions are subject to purifying selection, as mutations in these regions will produce non-functional viruses. Results These genomic sequences have been organized into a structured database to facilitate research at the molecular level. HBVRegDB is a comparative genomic analysis tool with an integrated underlying sequence database. The database contains genomic sequence data from representative viruses. In addition to INSDC and RefSeq annotation, HBVRegDB also contains expert and systematically calculated annotations (e.g. promoters and comparative genome analysis results (e.g. blastn, tblastx. It also contains analyses based on curated HBV alignments. Information about conserved regions – including primary conservation (e.g. CDS-Plotcon and RNA secondary structure predictions (e.g. Alidot – is integrated into the database. A large amount of data is graphically presented using the GBrowse (Generic Genome Browser adapted for analysis of viral genomes. Flexible query access is provided based on any annotated genomic feature. Novel regulatory motifs can be found by analysing the annotated sequences. Conclusion HBVRegDB serves as a knowledge database and as a comparative genomic analysis tool for molecular biologists investigating HBV. It is publicly available and complementary to other viral and HBV focused datasets and tools http://hbvregdb.otago.ac.nz. The availability of multiple and highly annotated sequences of viral genomes in one database combined with comparative analysis tools facilitates detection of novel genomic elements.

  20. PHENOPSIS DB: an Information System for Arabidopsis thaliana phenotypic data in an environmental context

    Directory of Open Access Journals (Sweden)

    Massonnet Catherine

    2011-05-01

    Full Text Available Abstract Background Renewed interest in plant × environment interactions has risen in the post-genomic era. In this context, high-throughput phenotyping platforms have been developed to create reproducible environmental scenarios in which the phenotypic responses of multiple genotypes can be analysed in a reproducible way. These platforms benefit hugely from the development of suitable databases for storage, sharing and analysis of the large amount of data collected. In the model plant Arabidopsis thaliana, most databases available to the scientific community contain data related to genetic and molecular biology and are characterised by an inadequacy in the description of plant developmental stages and experimental metadata such as environmental conditions. Our goal was to develop a comprehensive information system for sharing of the data collected in PHENOPSIS, an automated platform for Arabidopsis thaliana phenotyping, with the scientific community. Description PHENOPSIS DB is a publicly available (URL: http://bioweb.supagro.inra.fr/phenopsis/ information system developed for storage, browsing and sharing of online data generated by the PHENOPSIS platform and offline data collected by experimenters and experimental metadata. It provides modules coupled to a Web interface for (i the visualisation of environmental data of an experiment, (ii the visualisation and statistical analysis of phenotypic data, and (iii the analysis of Arabidopsis thaliana plant images. Conclusions Firstly, data stored in the PHENOPSIS DB are of interest to the Arabidopsis thaliana community, particularly in allowing phenotypic meta-analyses directly linked to environmental conditions on which publications are still scarce. Secondly, data or image analysis modules can be downloaded from the Web interface for direct usage or as the basis for modifications according to new requirements. Finally, the structure of PHENOPSIS DB provides a useful template for the development