Dissection of class III major histocompatibility complex haplotypes associated with rheumatoid arthritis

Objective. We have previously identified a single-nucleotide polymorphism (SNP) haplotype involving the lymphotoxin α (LTA) and tumor necrosis factor (TNF) loci (termed haplotype LTA-TNF2) on chromosome 6 that shows differential association with rheumatoid arthritis (RA) on HLA-DRB1*0404 and *0401 haplotypes, suggesting the presence of additional non-HLA-DRB1 RA susceptibility genes on these haplotypes. To refine this association, we performed a case-control association study using both SNPs and microsatellite markers in haplotypes matched either for HLA-DRB1*0404 or for HLA-DRB1*0401. Methods. Fourteen SNPs lying between HLA-DRB1 and LTA were genotyped in 87 DRB1*04-positive families. High-density microsatellite typing was performed using 24 markers spanning 2,500 kb centered around the TNF gene in 305 DRB1*0401 or *0404 cases and 400 DRB1*0401 or *0404 controls. Single-marker, 2-marker, and 3-marker minihaplotypes were constructed and their frequencies compared between the DRB1*0401 and DRB1*0404 matched case and control haplotypes. Results. Marked preservation of major histocompatibility complex haplotypes was seen, with chromosomes carrying LTA-TNF2 and either DRB1*0401 or DRB1*0404 both carrying an identical SNP haplotype across the 1-Mb region between TNF and HLA-DRB1. Using microsatellite markers, we observed two 3-marker minihaplotypes that were significantly overrepresented in the DRB1*0404 case haplotypes (P = 0.00024 and P = 0.00097). Conclusion. The presence of a single extended SNP haplotype between LTA-TNF2 and both DRB1*0401 and DRB1*0404 is evidence against this region harboring the genetic effects in linkage disequillbrium with LTA-TNF2. Two RA-associated haplotypes on the background of DRB1*0404 were identified in a 126-kb region surrounding and centromeric to the TNF locus.

Importance of amino-terminus in maintenance of oligomeric structure of cytosolic serine hydroxymethyltransferase

The role of the amino and carboxyl-terminal regions of cytosolic serine hydroxymethyltransferase (SHMT) in subunit assembly and catalysis was studied using six amino-terminal (lacking the first 6, 14, 30, 49, 58, and 75 residues) and two carboxyl-terminal (lacking the last 49 and 185 residues) deletion mutants. These mutants were constructed from a full length cDNA clone using restriction enzyme/PCR-based methods and overexpressed in Escherichia coli. The overexpressed proteins, des-(A1-K6)-SHMT and des-(A1- W14)-SHMT were present in the soluble fraction and they were purified to homogeneity. The deletion clones, for des-(A1–V30)-SHMT and des-(A1–L49)-SHMT were expressed at very low levels, whereas des-(A1–R58)-SHMT, des-(A1–G75)-SHMT, des-(Q435–F483)-SHMT and des-(L299-F483)-SHMT mutant proteins were not soluble and formed inclusion bodies. Des-(A1–K6)-SHMT and des-(A1–W14)-SHMT catalyzed both the tetrahydrofolate-dependent and tetrahydrofolate-independent reactions, generating characteristic spectral intermediates with glycine and tetrahydrofolate. The two mutants had similar kinetic parameters to that of the recombinant SHMT (rSHMT). However, at 55 °C, the des-(A1–W14)-SHMT lost almost all the activity within 5 min, while at the same temperature rSHMT and des-(A1–K6)-SHMT retained 85% and 70% activity, respectively. Thermal denaturation studies showed that des-(A1–W14)-SHMT had a lower apparent melting temperature (52°C) compared to rSHMT (56°C) and des-(A1–K6)-SHMT (55 °C), suggesting that N-terminal deletion had resulted in a decrease in the thermal stability of the enzyme. Further, urea induced inactivation of the enzymes revealed that 50% inactivation occurred at a lower urea concentration (1.2 ± 0.1 M) in the case of des-(A1–W14)-SHMT compared to rSHMT (1.8 ±0.1 M) and des-(A1–K6)-SHMT (1.7 ±0.1 M). The apoenzyme of des-(A1- W14)-SHMT was present predominantly in the dimer form, whereas the apoenzymes of rSHMT and des-(A1–K6)-SHMT were a mixture of tetramers (≈75% and ≈65%, respectively) and dimers. While, rSHMT and des-(A1–K6)-SHMT apoenzymes could be reconstituted upon the addition of pyridoxal-5'-phosphate to 96% and 94% enzyme activity, respectively, des-(A1–W14)-SHMT apoenzyme could be reconstituted only upto 22%. The percentage activity regained correlated with the appearance of visible CD at 425 nm and with the amount of enzyme present in the tetrameric form upon reconstitution as monitored by gel filtration. These results demonstrate that, in addition to the cofactor, the N-terminal arm plays an important role in stabilizing the tetrameric structure of SHMT.

PICES Press, Vol. 14, No. 2, July 2006

The 2006 inter-sessional Science Board and Governing Council meeting: A note from the Chairman (pdf, 0.1 Mb) Future Integrative Science Program – Progress report (pdf, 0.2 Mb) Big-picture synthesis requires understanding the small and "in-between" stuff - A summary of the CCCC Synthesis Symposium (pdf, 0.4 Mb) PICES Calendar (pdf, 0.4 Mb) Integration of ecological indicators for the North Pacific with emphasis on the Bering Sea (pdf, 0.2 Mb) Time series of the Northeast Pacific: A symposium to mark the 50th anniversary of Line-P (pdf, 0.1 Mb) PICES hosts an ESSAS workshop in St. Petersberg, Russia (pdf, 0.2 Mb) Professor Mikhail N. Koshlyakov (pdf, 0.5 Mb) The state of the western North Pacific in the second half of 2005 (pdf, 0.8 Mb) Recent trends in waters of the subarctic NE Pacific (pdf, 0.2 Mb) Unusual invertebrates and fish observed in the Gulf of Alaska, 2004-2005 (pdf, 0.1 Mb) The Bering Sea: Current status and recent events (pdf, 0.2 Mb) The Year of the Euphausiid (pdf, 0.01 Mb) Michio J. Kishi awarded 2005 Uda Prize by the Japan Society of Fisheries Oceanography (pdf, 0.03 Mb)

Annual report 2005 - North Pacific Marine Science Organization (PICES). Fourteenth meeting, Vladivostok, Russia, September 29-October 9, 2005

Report of Opening Session (pdf 0.07 Mb) Report of Governing Council (pdf 0.2 Mb) Report of the Finance and Administration Committee (pdf 0.07 Mb) Reports of Science Board and Committees Science Board inter-sessional meeting (pdf 0.07 Mb) Science Board (pdf 0.1 Mb) Biological Oceanography Committee (pdf 0.2 Mb) Fishery Science Committee (pdf 0.04 Mb) Marine Environmental Quality Committee (pdf 0.06 Mb) MONITOR Technical Committee (pdf 0.05 Mb) Physical Oceanography and Climate Committee (pdf 0.06 Mb) Technical Committee on Data Exchange (pdf 0.04 Mb) Reports of Sections, Working and Study Groups Section on Ecology of harmful algal blooms in the North Pacific (pdf 0.03 Mb) Section on Carbon and Climate Working Group 18 on Mariculture in the 21st century - The intersection between ecology, socio-economics and production (pdf 0.06 Mb) Working Group 19 on Ecosystem-based management science and its application to the North Pacific (pdf 0.03 Mb) Reports of the Climate Change and Carrying Capacity Program Implementation Panel on the CCCC Program (pdf 0.04 Mb) CFAME Task Team (pdf 0.04 Mb) MODEL Task Team (pdf 0.04 Mb) Reports of Advisory Panels Advisory Panel on Iron Fertilization Experiment in the Subarctic Pacific Ocean (pdf 0.04 Mb) Advisory Panel on Marine Birds and Mammals (pdf 0.03 Mb) Advisory Panel on Micronekton Sampling Inter-Calibration experiment (pdf 0.05 Mb) Summary of Scientific Sessions and Workshops (pdf 0.2 Mb) Membership List (pdf 0.07 Mb) List of Participants (pdf 0.07 Mb) List of Acronyms (pdf 0.03 Mb)

Annual report 2004 - North Pacific Marine Science Organization (PICES). Thirteenth meeting, Honolulu, Hawaii, U.S.A., October 14-24, 2004

Report of Opening Session (pdf 0.07 Mb) Report of Governing Council (pdf 0.2 Mb) Report of the Finance and Administration Committee (pdf 0.08 Mb) Reports of Science Board and Committees Science Board inter-sessional meeting (pdf 0.05 Mb) Science Board (pdf 0.1 Mb) Biological Oceanography Committee (pdf 0.1 Mb) Fishery Science Committee (pdf 0.04 Mb) Marine Environmental Quality Committee (pdf 0.04 Mb) Physical Oceanography and Climate Committee (pdf 0.04 Mb) Technical Committee on Data Exchange (pdf 0.04 Mb) Reports of Sections, Working and Study Groups Harmful Algal Blooms Section (pdf 0.03 Mb) Working Group 17 on Biogeochemical data integration and synthesis (pdf 0.03 Mb) Working Group 18 on Mariculture in the 21st century - The intersection between ecology, socio-economics and production (pdf 0.06 Mb) Study Group on Ecosystem-based management science and its application to the North Pacific (pdf 0.04 Mb) Reports of the Climate Change and Carrying Capacity Program Implementation Panel on the CCCC Program (pdf 0.04 Mb) BASS Task Team (pdf 0.04 Mb) CFAME Task Team (pdf 0.04 Mb) MODEL Task Team (pdf 0.04 Mb) MONITOR Task Team (pdf 0.03 Mb) REX Task Team (pdf 0.04 Mb) Reports of Advisory Panels Advisory Panel on Continuous Plankton Recorder Survey in the North Pacific (pdf 0.4 Mb) Advisory Panel on Iron Fertilization Experiment in the Subarctic Pacific Ocean (pdf 0.03 Mb) Advisory Panel on Marine Birds and Mammals (pdf 0.04 Mb) Advisory Panel on Micronekton Sampling Inter-Calibration experiment (pdf 0.04 Mb) Summary of Scientific Sessions and Workshops (pdf 0.2 Mb) Membership List (pdf 0.07 Mb) List of Participants (pdf 0.09 Mb) List of Acronyms (pdf 0.03 Mb)

Report of the 2004 Workshop on In Situ Iron Enrichment Experiments in the Eastern and Western Subarctic Pacific

Foreword 1. BACKGROUND AND OBJECTIVES (pdf, 0.1 Mb) 2. 2004 WORKSHOP SUMMARY (pdf, < 0.1 Mb) 2.1. What have we learned from the enrichment experiments? 2.2 What are the outstanding questions? 2.3 Recommendations for SEEDS-II 3. EXTENDED ABSTRACTS OF THE 2004 WORKSHOP 3.1 Synthesis of the Iron Enrichment Experiments: SEEDS and SERIES (pdf, 0.5 Mb) Iron fertilization experiment in the western subarctic Pacific (SEEDS) by Atsushi Tsuda The response of N and Si to iron enrichment in the Northeast Pacific Ocean: Results from SERIES by David Timothy, C.S. Wong, Yukihiro Nojiri, Frank A. Whitney, W. Keith Johnson and Janet Barwell-Clarke 3.2 Biological and Physiological Responses (pdf, 0.2 Mb) Zooplankton responses during SEEDS by Hiroaki Saito Phytoplankton community response to iron and temperature gradient in the NW and NE subarctic Pacific Ocean by Isao Kudo, Yoshifumi Noiri, Jun Nishioka, Hiroshi Kiyosawa and Atsushi Tsuda SERIES: Copepod grazing on diatoms by Frank A. Whitney, Moira Galbraith, Janet Barwell-Clarke and Akash Sastri The Southern Ocean Iron Enrichment Experiment: The nitrogen uptake response by William P. Cochlan and Raphael M. Kudela 3.3 Biogeochemical Responses (pdf, 0.5 Mb) What have we learned regarding iron biogeochemistry from iron enrichment experiments? by Jun Nishioka, Shigenobu Takeda and W. Keith Johnson Iron dynamics and temporal changes of iron speciation in SERIES by W. Keith Johnson, C.S. Wong, Nes Sutherland and Jun Nishioka Dissolved organic matter dynamics during SEEDS and SERIES experiments by Takeshi Yoshimura and Hiroshi Ogawa Formation of transparent exopolymer particles during the in-situ iron enrichment experiment in the western subarctic Pacific (SEEDS) by Shigenobu Takeda, Neelam Ramaiah, Ken Furuya and Takeshi Yoshimura Atmospheric measurement by Mitsuo Uematsu 3.4 Prediction from Models (pdf, 0.3 Mb) Modelling iron limitation in the North Pacific by Kenneth L. Denman and M. Angelica Peña A proposed model of the SERIES iron fertilization patch by Debby Ianson, Christoph Voelker and Kenneth L. Denman 4. LIST OF PARTICIPANTS FOR THE 2004 WORKSHOP (pdf, < 0.1 Mb) APPENDIX 1 Report of the 2000 Planning Workshop on Designing the Iron Fertilization Experiment in the Subarctic Pacific (pdf, 1 Mb) APPENDIX 2 Terms of Reference for the Advisory Panel on Iron fertilization experiment in the subarctic Pacific Ocean (pdf, < 0.1 Mb) APPENDIX 3 Historical List of Advisory Panel Members on Iron fertilization experiment in the subarctic Pacific Ocean (pdf, < 0.1 Mb) APPENDIX 4 IFEP-AP Annual Reports (pdf, 0.1 Mb) APPENDIX 5 PICES Press Articles (pdf, 0.6 Mb) (194 page document)

PICES-GLOBEC International Program on Climate Change and Carrying Capacity

Introduction [pdf, 0.27 MB] Methods [pdf, 0.15 MB] Results and discussion [pdf, 2.1 MB] Conclusions [pdf, 0.12 MB] Appendix A: Data gathering review, results and balancing [pdf, 0.3 MB] Appendix B: Data tables [pdf, 0.35 MB] Appendix C: BASS Workshop on the "Development of a conceptual model of the subarctic Pacific Basin ecosystems" [pdf, 0.16 MB] Appendix D: BASS/MODEL Workshop on "Higher trohic level modeling" [pdf, 0.24 MB] Appendix E: BASS/MODEL Workshop to review ecosystem models for the subarctic Pacific gyres [pdf, 4.39 MB] Appendix F: BASS/MODEL Workshop on "Perturbation analysis" on subarctic Pacific gyre ecosystem models using ECOPATH/ECOSIM" [pdf, 0.37 MB] Appendix G: Proposal for a BASS Workshop on "Linkages between open and coastal systems" [pdf, 0.15 MB] References [pdf, 0.14 MB] (97 page document)

C02 in the North Pacific Ocean.

Executive Summary [pdf, 0.01 MB] Introduction [pdf, 0.01 MB] Synthesis of the WOCE/JGOFS global CO2 survey data in the North Pacific [pdf, 0.3 MB] Air-sea CO2 fluxes [pdf, 0.1 MB] DIC, TAlk and anthropogenic CO2 distributions in the North Pacific [pdf, 3 MB] Biogeochemical and global implications [pdf, 0.1 MB] Recommendations for the future of carbon studies within PICES [pdf, 0.1 MB] References [pdf, 0.1 MB] Appendix A. Summary of PICES Working Group 13 activities (1998-2001) [pdf, 0.1 MB] Appendix B. Results of Working Group 13 method inter-comparison studies [pdf, 0.6 MB] Appendix C. Results of Working Group 13 data integration workshops [pdf, 0.5 MB] (57 page document)

Harmful algal blooms in the PICES region of the North Pacific

Foreword Background and objectives [pdf, 0.84 MB] Country reviews and status reports Section I. Western North Pacific Japan Yasuwo Fukuyo, Ichiro Imai, Masaaki Kodama and Kyoichi Tamai Red tides and harmful algal blooms in Japan [pdf, 0.7 MB] People's Republic of China Tian Yan, Ming-Jiang Zhou and Jing-Zhong Zou A national report of HABs in China [pdf, 0.24 MB] Republic of Korea Sam Geun Lee, Hak Gyoon Kim, Eon Seob Cho and Chang Kyu Lee Harmful algal blooms (red tides): Management and mitigation in Korea [pdf, 0.27 MB] Russia Tatiana Y. Orlova, Galina V. Konovalova, Inna V. Stonik, Tatiana V. Morozova and Olga G. Shevchenko Harmful algal blooms on the eastern coast of Russia [pdf, 1.4 MB] Section II. Eastern North Pacific Canada F.J.R. "Max" Taylor and Paul J. Harrison Harmful marine algal blooms in western Canada [pdf, 0.87 MB] United States of America Vera L. Trainer Harmful algal blooms on the U.S. west coast [pdf, 0.5 MB] Mexico Jose L. Ochoa, S. Lluch-Cota, B.O. Arredondo-Vega, E. Nuñes-Vázquez, A. Heredia-Tapia, J. Pérez-Linares and R. Alonso-Rodriguez Marine Biotoxins and harmful algal blooms in Mexico's Pacific littora [pdf, 0.2 MB] Summary and conclusions [pdf, 0.6 MB] Appendices A. Members of the Working Group [pdf, 0.1 MB] B. Original terms of reference (Vladivostok, 1999) [pdf, 0.08 MB] C. Annual reports of WG 15 [pdf, 0.15 MB] D. Workshop report on taxonomy and identification of HAB species and data management [pdf, 0.15 MB] (Document pdf contains 156 pages)

Proceedings of the Workshop on the Okhotsk Sea and Adjacent Areas [Vladivostok, June 1995]

I REPORT OF THE PICES WORKSHOP ON THE OKHOTSK SEA AND ADJACENT AREAS (pdf, 0.1 Mb) 1. Outline of the workshop 2. Summary reports from sessions 3. Recommendations of the workshop 4. Acknowledgments II SCIENTIFIC PAPERS SUBMITTED FROM SESSIONS 1. Physical Oceanography Sessions (pdf, 4 Mb) A. Circulation and water mass structure of the Okhotsk Sea and Northwestern Pacific Valentina D. Budaeva & Vyacheslav G. Makarov Seasonal variability of the pycnocline in La Perouse Strait and Aniva Gulf Valentina D. Budaeva & Vyacheslav G. Makarov Modeling of the typical water circulations in the La Perouse Strait and Aniva Gulf region Nina A. Dashko, Sergey M. Varlamov, Young-Ho Han & Young-Seup Kim Anticyclogenesis over the Okhotsk Sea and its influence on weather Boris S. Dyakov, Alexander A. Nikitin & Vadim P. Pavlychev Research of water structure and dynamics in the Okhotsk Sea and adjacent Pacific Howard J. Freeland, Alexander S. Bychkov, C.S. Wong, Frank A. Whitney & Gennady I. Yurasov The Ohkotsk Sea component of Pacific Intermediate Water Emil E. Herbeck, Anatoly I. Alexanin, Igor A. Gontcharenko, Igor I. Gorin, Yury V. Naumkin & Yury G. Proshjants Some experience of the satellite environmental support of marine expeditions at the Far East Seas Alexander A. Karnaukhov The tidal influence on the Sakhalin shelf hydrology Yasuhiro Kawasaki On the formation process of the subsurface mixed water around the Central Kuril Islands Lloyd D. Keigwin Northwest Pacific paleohydrography Talgat R. Kilmatov Physical mechanisms for the North Pacific Intermediate Water formation Vladimir A. Luchin Water masses in the Okhotsk Sea Andrey V. Martynov, Elena N. Golubeva & Victor I. Kuzin Numerical experiments with finite element model of the Okhotsk Sea circulation Nikolay A. Maximenko, Anatoly I. Kharlamov & Raissa I. Gouskina Structure of Intermediate Water layer in the Northwest Pacific Nikolay A. Maximenko & Andrey Yu. Shcherbina Fine-structure of the North Pacific Intermediate Water layer Renat D. Medjitov & Boris I. Reznikov An experimental study of water transport through the Straits of Okhotsk Sea by electromagnetic method Valentina V. Moroz Oceanological zoning of the Kuril Islands area in the spring-summer period Yutaka Nagata Note on the salinity balance in the Okhotsk Sea Alexander D. Nelezin Variability of the Kuroshio Front in 1965-1991 Vladimir I. Ponomarev, Evgeny P. Varlaty & Mikhail Yu. Cheranyev An experimental study of currents in the near-Kuril region of the Pacific Ocean and in the Okhotsk Sea Stephen C. Riser, Gennady I. Yurasov & Mark J. Warner Hydrographic and tracer measurements of the water mass structure and transport in the Okhotsk Sea in early spring Konstantin A. Rogachev & Andrey V. Verkhunov Circulation and water mass structure in the southern Okhotsk Sea, as observed in summer, 1994 Lynne D. Talley North Pacific Intermediate Water formation and the role of the Okhotsk Sea Anatoly S. Vasiliev & Fedor F. Khrapchenkov Seasonal variability of integral water circulation in the Okhotsk Sea B. Sea ice and its relation to circulation and climate V.P. Gavrilo, G.A. Lebedev & A.P. Polyakov Acoustic methods in sea ice dynamics studies Nina M. Pestereva & Larisa A. Starodubtseva The role of the Far-East atmospheric circulation in the formation of the ice cover in the Okhotsk Sea Yoshihiko Sekine Anomalous Oyashio intrusion and its teleconnection with Subarctic North Pacific circulation, sea ice of the Okhotsk Sea and air temperature of the northern Asian continent C. Waves and tides Vladimir A. Luchin Characteristics of the tidal motions in the Kuril Straits George V. Shevtchenko On seasonal variability of tidal constants in the northwestern part of the Okhotsk Sea D. Physical oceanography of the Japan Sea/East Sea Mikhail A. Danchenkov, Kuh Kim, Igor A. Goncharenko & Young-Gyu Kim A “chimney” of cold salt waters near Vladivostok Christopher N.K. Mooers & Hee Sook Kang Preliminary results from a numerical circulation model of the Japan Sea Lev P. Yakunin Influence of ice production on the deep water formation in the Japan Sea 2. Fisheries and Biology Sessions (pdf, 2.8 Mb) A. Communities of the Okhotsk Sea and adjacent waters: composition, structure and dynamics Lubov A. Balkonskaya Exogenous succession of the southwestern Sakhalin algal communities Tatyana A. Belan, Yelena V. Oleynik, Alexander V. Tkalin & Tat’yana S. Lishavskaya Characteristics of pelagic and benthic communities on the North Sakhalin Island shelf Lev N. Bocharov & Vladimir K. Ozyorin Fishery and oceanographic database of Okhotsk Sea Victor V. Lapko Interannual dynamics of the epipelagic ichthyocen structure in the Okhotsk Sea Valentina I. Lapshina Quantitative seasonal and year-to-year changes of phytoplankton in the Okhotsk Sea and off Kuril area of the Pacific Lyudmila N. Luchsheva Biological productivity in anomalous mercury conditions (northern part of Okhotsk Sea) Inna A. Nemirovskaya Origin of hydrocarbons in the ecosystems of coastal region of the Okhotsk Sea Tatyana A. Shatilina Elements of the Pacific South Kuril area ecosystem Vyacheslav P. Shuntov & Yelena P. Dulepova Biota of the Okhotsk Sea: Structure of communities, the interannual dynamics and current status B. Abundance, distribution, dynamics of the common fishes of the Okhotsk Sea Yuri P. Diakov Influence of some abiotic factors on spatial population dynamics of the West Kamchatka flounders (Pleuronectidae) Gordon A. McFarlane, Richard J. Beamish & Larisa M. Zverkova An examination of age estimates of walleye pollock (Theragra chalcogramma) from the Sea of Okhotsk using the burnt otolith method and implications for stock assessment and management Larisa P. Nikolenko Migration of Greenland turbot (Reinhardtius hippoglossoides) in the Okhotsk Sea Galina M. Pushnikova Fisheries impact on the Sakhalin-Hokkaido herring population Vidar G. Wespestad Is pollock overfished? C. Salmon of the Okhotsk Sea: biology, abundance and stock identification Vladimir A. Belyaev, Alexander Yu. Zhigalin Epipelagic Far Eastern sardine of the Okhotsk Sea Yuri E. Bregman, Victor V. Pushnikov, Lyudmila G. Sedova & Vladimir Ph. Ivanov A preliminary report on stock status and productive capacity of horsehair crab Erimacrus isenbeckii (Brandt) in the South Kuril Strait Natalia T. Dolganova Mezoplankton distribution in the West Japan Sea Vladimir V. Efremov, Richard L. Wilmot, Christine M. Kondzela, Natalia V. Varnavskaya, Sharon L. Hawkins & Maria E. Malinina Application of pink and chum salmon genetic baseline to fishery management Vyacheslav N. Ivankov & Valentina V. Andreyeva Strategy for culture, breeding and numerous dynamics of Sakhalin salmon populations Alla M. Kovalevskaya, Natalia I. Savelyeva & Dmitry M. Polyakov Primary production in Sakhalin shelf waters Tatyana N. Krupnova Some reasons for resource reduction of Laminaria japonica (Primorye region) Lyudmila N. Luchsheva & Anatoliy I. Botsul Mercury in bottom sediments of the northeastern Okhotsk Sea Pavel A. Luk’yanov, Natalia I. Belogortseva, Alexander A. Bulgakov, Alexander A. Kurika & Olga D. Novikova Lectins and glycosidases from marine macro and micro-organisms of Japan and Okhotsk Seas Boris A. Malyarchuk, Olga A. Radchenko, Miroslava V. Derenko, Andrey G. Lapinski & Leonid L. Solovenchuk PCR-fingerprinting of mitochondrial genome of chum salmon, Oncorhynchus keta Alexander A. Mikheev Chaos and relaxation in dynamics of the pink salmon (Oncorhynchus gorbuscha) returns for two regions Yuri A. Mitrofanov & Larisa N. Lesnikova Fish-culture of Pacific Salmons increases the number of heredity defects Larisa P. Nikolenko Abundance of young halibut along the West Kamchatka shelf in 1982-1992 Sergey A. Nizyaev Living conditions of golden king crab Lithodes aequispina in the Okhotsk Sea and near the Kuril Islands Ludmila A. Pozdnyakova & Alla V. Silina Settlements of Japanese scallop in Reid Pallada Bay (Sea of Japan) Galina M. Pushnikova Features of the Southwest Okhotsk Sea herring Vladimir I. Radchenko & Igor I. Glebov Present state of the Okhotsk herring stock and fisheries outlook Alla V. Silina & Ida I. Ovsyannikova Distribution of the barnacle Balanus rostratus eurostratus near the coasts of Primorye (Sea of Japan) Galina I. Victorovskaya Dependence of urchin Strongylocentrotus intermedius reproduction on water temperature Anatoly F. Volkov, Alexander Y. Efimkin & Valery I. Chuchukalo Feeding habits of Pacific salmon in the Sea of Okhotsk and in the Pacific waters of Kuril Islands in summer 1993 Larisa M. Zverkova & Georgy A. Oktyabrsky Okhotsk Sea walleye pollock stock status Tatyana N. Zvyagintseva, Elena V. Sundukova, Natalia M. Shevchenko & Ludmila A. Elyakova Water soluble polysaccharides of some Far-Eastern seaweeds 3. Biodiversity Program (pdf, 0.2 Mb) A. Biodiversity of island ecosystems and seasides of the North Pacific Larissa A. Gayko Productivity of Japanese scallop Patinopecten yessoensis (IAY) culture in Posieta Bay (Sea of Japan) III APPENDICES 1. List of acronyms 2. List of participants (Document pdf contains 431 pages)

Marine ecosystems of the North Pacific

Key Messages [pdf, 2.5 Mb] Climate Information Gaps Ocean Productivity Information gaps Living Marine Resources Information gaps Climate [pdf, 1.8 Mb] Productivity [pdf, 5.2 Mb] Nutrients Phytoplankton Zooplankton Living Resources [pdf, 10 Mb] Subarctic coastal systems Central oceanic gyres Temperate coastal and oceanic systems Marine mammals The Human Population [pdf, 5 Mb] Contaminants and Habitat Modifications Aquaculture Knowledge Gaps Glossary Ocean and Climate Changes [pdf, 4.1Mb] Highlights Introduction Atmospheric Indices Change in 1998/99 Comparison of Atmospheric Indices Authorship Yellow Sea / East China Sea [pdf, 2.3 Mb] Highlights Background Status and Trends Hydrography Chemistry Plankton Benthos Fish and invertebrates Marine birds and mammals Issues Critical factors causing change Authorship Japan/East Sea [pdf, 3.3 Mb] Highlights Background Status and Trends Hydrography Chemistry Plankton Fish and Invertebrates Marine Birds and Mammals Critical factors causing change Issues Authorship Okhotsk Sea [pdf, 1.7 Mb] Background Status and Trends Climate Hydrography Chemistry Plankton Fish and Invertebrates Marine Birds and Mammals Issues Critical factors causing change Authorship Oyashio / Kuroshio [pdf, 4.5 Mb] Highlights Background Status and Trends Hydrography Plankton Fish and Invertebrates Marine Birds and Mammals Issues Authorship Western Subarctic Gyre [pdf, 4.5 Mb] Highlights Background Status and Trends Hydrography Chemistry Plankton Fish and Invertebrates Marine Birds and Mammals Issues Authorship Bering Sea [pdf, 2.2 Mb] Highlights Background Status and Trends Hydrography Chemistry Plankton Fish and Invertebrates Marine Birds and Mammals Critical Factors Causing Change Issues Authorship Gulf of Alaska [pdf, 2.6 Mb] Highlights Background Status and trends Hydrography Chemistry Plankton Fish and Invertebrates Marine birds and mammals Critical factors causing change Issues Authorship California Current [pdf, 2.7 Mb] Highlights Background Status and Trends Hydrography Chemistry Plankton Fish and Invertebrates Marine Birds and Mammals Critical Factors Causing Change Issues Authorship Gulf of California [pdf, 1.7 Mb] Highlights Background Status and Trends Hydrography Chemistry Plankton Fisheries Marine Birds and Mammals Critical Factors Causing Change Issues Authorship Transition Zone [pdf, 2.5 Mb] Background Status and Trends Hydrography Chemistry Plankton Fish and Invertebrates Marine Birds and Mammals Issues Authorship Tuna [pdf, 1.5 Mb] Highlights Background Pacific bluefin tuna Albacore tuna Status and trends Ecosystem model and climate forcing Authorship Pacific halibut [pdf, 1.1 Mb] Background The Fishery Climate Influences Authorship Pacific salmon [Updated, pdf, 0.4 Mb] Background Status and Trends Washington, Oregon, and California British Columbia Southeast Alaska Central Alaska Western Alaska Russia Japan Authorship References [pdf, 0.5 Mb]

Metadata Federation of PICES Member Countries

(Document pdf contains 193 pages) Executive Summary (pdf, < 0.1 Mb) 1. Introduction (pdf, 0.2 Mb) 1.1 Data sharing, international boundaries and large marine ecosystems 2. Objectives (pdf, 0.3 Mb) 3. Background (pdf, < 0.1 Mb) 3.1 North Pacific Ecosystem Metadatabase 3.2 First federation effort: NPEM and the Korea Oceanographic Data Center 3.2 Continuing effort: Adding Japan’s Marine Information Research Center 4. Metadata Standards (pdf, < 0.1 Mb) 4.1 Directory Interchange Format 4.2 Ecological Metadata Language 4.3 Dublin Core 4.3.1. Elements of DC 4.4 Federal Geographic Data Committee 4.5 The ISO 19115 Metadata Standard 4.6 Metadata stylesheets 4.7 Crosswalks 4.8 Tools for creating metadata 5. Communication Protocols (pdf, < 0.1 Mb) 5.1 Z39.50 5.1.1. What does Z39.50 do? 5.1.2. Isite 6. Clearinghouses (pdf, < 0.1 Mb) 7. Methodology (pdf, 0.2 Mb) 7.1 FGDC metadata 7.1.1. Main sections 7.1.2. Supporting sections 7.1.3. Metadata validation 7.2 Getting a copy of Isite 7.3 NSDI Clearinghouse 8. Server Configuration and Technical Issues (pdf, 0.4 Mb) 8.1 Hardware recommendations 8.2 Operating system – Red Hat Linux Fedora 8.3 Web services – Apache HTTP Server version 2.2.3 8.4 Create and validate FGDC-compliant Metadata in XML format 8.5 Obtaining, installing and configuring Isite for UNIX/Linux 8.5.1. Download the appropriate Isite software 8.5.2. Untar the file 8.5.3. Name your database 8.5.4. The zserver.ini file 8.5.5. The sapi.ini file 8.5.6. Indexing metadata 8.5.7. Start the Clearinghouse Server process 8.5.8. Testing the zserver installation 8.6 Registering with NSDI Clearinghouse 8.7 Security issues 9. Search Tutorial and Examples (pdf, 1 Mb) 9.1 Legacy NSDI Clearinghouse search interface 9.2 New GeoNetwork search interface 10. Challenges (pdf, < 0.1 Mb) 11. Emerging Standards (pdf, < 0.1 Mb) 12. Future Activity (pdf, < 0.1 Mb) 13. Acknowledgments (pdf, < 0.1 Mb) 14. References (pdf, < 0.1 Mb) 15. Acronyms (pdf, < 0.1 Mb) 16. Appendices 16.1. KODC-NPEM meeting agendas and minutes (pdf, < 0.1 Mb) 16.1.1. Seattle meeting agenda, August 22–23, 2005 16.1.2. Seattle meeting minutes, August 22–23, 2005 16.1.3. Busan meeting agenda, October 10–11, 2005 16.1.4. Busan meeting minutes, October 10–11, 2005 16.2. MIRC-NPEM meeting agendas and minutes (pdf, < 0.1 Mb) 16.2.1. Seattle Meeting agenda, August 14-15, 2006 16.2.2. Seattle meeting minutes, August 14–15, 2006 16.2.3. Tokyo meeting agenda, October 19–20, 2006 16.2.4. Tokyo, meeting minutes, October 19–20, 2006 16.3. XML stylesheet conversion crosswalks (pdf, < 0.1 Mb) 16.3.1. FGDCI to DIF stylesheet converter 16.3.2. DIF to FGDCI stylesheet converter 16.3.3. String-modified stylesheet 16.4. FGDC Metadata Standard (pdf, 0.1 Mb) 16.4.1. Overall structure 16.4.2. Section 1: Identification information 16.4.3. Section 2: Data quality information 16.4.4. Section 3: Spatial data organization information 16.4.5. Section 4: Spatial reference information 16.4.6. Section 5: Entity and attribute information 16.4.7. Section 6: Distribution information 16.4.8. Section 7: Metadata reference information 16.4.9. Sections 8, 9 and 10: Citation information, time period information, and contact information 16.5. Images of the Isite server directory structure and the files contained in each subdirectory after Isite installation (pdf, 0.2 Mb) 16.6 Listing of NPEM’s Isite configuration files (pdf, < 0.1 Mb) 16.6.1. zserver.ini 16.6.2. sapi.ini 16.7 Java program to extract records from the NPEM metadatabase and write one XML file for each record (pdf, < 0.1 Mb) 16.8 Java program to execute the metadata extraction program (pdf, < 0.1 Mb) A1 Addendum 1: Instructions for Isite for Windows (pdf, 0.6 Mb) A2 Addendum 2: Instructions for Isite for Windows ADHOST (pdf, 0.3 Mb)

Forecasting Climate Impacts on Future Production of Commercially Exploited Fish and Shellfish

Foreword [pdf, < 0.1 MB] Acknowledgements PHASE 1 [pdf, 0.2 MB] Summary of the PICES/NPRB Workshop on Forecasting Climate Impacts on Future Production of Commercially Exploited Fish and Shellfish (July 19–20, 2007, Seattle, U.S.A.) Background Links to Other Programs Workshop Format Session I. Status of climate change scenarios in the PICES region Session II. What are the expected impacts of climate change on regional oceanography and what are some scenarios for these drivers for the next 10 years? Session III. Recruitment forecasting Session IV. What models are out there? How is climate linked to the model? Session V. Assumptions regarding future fishing scenarios and enhancement activities Session VI Where do we go from here? References Appendix 1.1 List of Participants PHASE 2 [pdf, 0.7 MB] Summary of the PICES/NPRB Workshop on Forecasting Climate Impacts on Future Production of Commercially Exploited Fish and Shellfish (October 30, 2007, Victoria, Canada) Background Workshop Agenda Forecast Feasibility Format of Information Modeling Approaches Coupled bio-physical models Stock assessment projection models Comparative approaches Similarities in Data Requests Opportunities for Coordination with Other PICES Groups and International Efforts BACKGROUND REPORTS PREPARED FOR THE PHASE 2 WORKSHOP Northern California Current (U.S.) groundfish production by Melissa Haltuch Changes in sablefish (Anoplopoma fimbria) recruitment in relation to oceanographic conditions by Michael J. Schirripa Northern California Current (British Columbia) Pacific cod (Gadus macrocephalus) production by Caihong Fu and Richard Beamish Northern California Current (British Columbia) sablefish (Anoplopoma fimbria) production by Richard Beamish Northern California Current (British Columbia) pink (Oncorhynchus gorbuscha) and chum (O. keta) salmon production by Richard Beamish Northern California Current (British Columbia) ocean shrimp (Pandalus jordani) production by Caihong Fu Alaska salmon production by Anne Hollowed U.S. walleye pollock (Theragra chalcogramma) production in the eastern Bering Sea and Gulf of Alaska by Kevin Bailey and Anne Hollowed U.S. groundfish production in the eastern Bering Sea by Tom Wilderbuer U.S. crab production in the eastern Bering Sea by Gordon H. Kruse Forecasting Japanese commercially exploited species by Shin-ichi Ito, Kazuaki Tadokoro and Yasuhiro Yamanka Russian fish production in the Japan/East Sea by Yury Zuenko, Vladimir Nuzhdin and Natalia Dolganova Chum salmon (Oncorhynchus keta) production in Korea by Sukyung Kang, Suam Kim and Hyunju Seo Jack mackerel (Trachurus japonicus) production in Korea by Jae Bong Lee and Chang-Ik Zhang Chub mackerel (Scomber japonicus) production in Korea by Jae Bong Lee, Sukyung Kang, Suam Kim, Chang-Ik Zhang and Jin Yeong Kim References Appendix 2.1 List of Participants PHASE 3 [pdf, < 0.1 MB] Summary of the PICES Workshop on Linking Global Climate Model Output to (a) Trends in Commercial Species Productivity and (b) Changes in Broader Biological Communities in the World’s Oceans (May 18, 2008, Gijón, Spain) Appendix 3.1 List of Participants Appendix 3.2 Workshop Agenda (Document contains 101 pages)

PICES Press, Vol. 16, No. 2, July 2008

The 2008 Inter-Sessional Science Board Meeting (pp.1-2, pdf, 0.1 Mb) FUTURE – From Science Plan to Implementation Plan (pp. 3-4, pdf, 0.1 Mb) CFAME Task Team Workshop – Linking and Visualising (p. 5, pdf, 0.1 Mb) PICES WG 21 Meets in Busan, Korea: The Database Meeting (pp. 6-7, pdf, 0.1 Mb) ICES-PICES-IOC Symposium on Climate Change (pp. 8-12, pdf, 1.2 Mb) Zooplankton and Climate: Response Modes and Linkages (pp. 13-15, pdf, 0.2 Mb) PICES Fishery Science Committee Workshop in Gijón (pp. 16-18, pdf, 0.1 Mb) The North Pacific Continuous Plankton Recorder Survey (pp. 19-21, pdf, 0.4 Mb) PICES Ecosystem Status Report Wins Design Award (p. 21, pdf, 0.4 Mb) Canada’s Three Oceans (C3O): A Canadian Contribution to the International Polar Year (pp. 22-25, pdf, 0.8 Mb) New Surface Mooring at Station Papa Monitors Climate (pp. 26-27, pdf, 0.2 Mb) The State of the Western North Pacific in the Second Half of 2007 (pp. 28-29, pdf, 0.4 Mb) The Bering Sea: Current Status and Recent Events (pp. 30-31, pdf, 0.4 Mb) Recent Trends in Waters of the Subarctic NE Pacific (pp.32-33, pdf, 0.3 Mb) 2009 Vintage of Fraser River Sockeye Salmon: A Complex Full Bodied Redd with Mysterious Bouquet (p. 34, pdf, 0.1 Mb) Pacific Biological Station Celebrates Centennial Anniversary, 1908–2008 (p. 35, pdf, 0.3 Mb) Marine and Coastal Fisheries: American Fisheries Society Open Access E-journal (p. 36, pdf, 0.1 Mb) Latest and Upcoming PICES Publications (p. 36, pdf, 0.1 Mb)

PICES Press, Vol. 17, No. 2, July 2009

Major Outcomes from the 2009 PICES Annual Meeting: A Note from the Chairman (pdf, 0.1 Mb) The FUTURE is Here (pdf, 0.1 Mb) PICES Harmful Algal Bloom International Seafood Safety Project (pdf, 0.3 Mb) PICES at the 2009 GLOBEC Open Science Meeting (pdf, 0.4 Mb) Modeling Ecosystems and Ocean Processes Workshop (pdf, 0.1 Mb) Krill Biology and Ecology Workshop (pdf, 0.1 Mb) Polar and Sub-Polar Marine Ecosystems Workshop (pdf, 0.4 Mb) Biogeochemistry of the Oceans in a Changing Climate Workshop (pdf, 0.1 Mb) Continuous Plankton Recorder Surveys of the Global Oceans (pdf, 0.4 Mb) Plankton Phenology Workshop (pdf, 0.2 Mb) Workshop on “Climate Impact on Ecosystem Dynamics of Marginal Seas” (pdf, 0.1 Mb) Erratum (pdf, 0.4 Mb) The State of the Western North Pacific in the Second Half of 2008 (pdf, 0.2 Mb) State of the Northeast Pacific into early 2009 (pdf, 0.1 Mb) Current Status of the Bering Sea Ecosystem (pdf, 0.1 Mb) 2009 Salmon Forecasting Forum (pdf, 0.3 Mb) The Third Argo Science Workshop: “The Future of Argo” (pdf, 0.1 Mb) 2009 ESSAS Annual Science Meeting (pdf, 0.1 Mb) A Visit Fit for an Emperor and Empress of Japan (pdf, 0.9 Mb)