Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks

Background: Thermophilic proteins sustain themselves and function at higher temperatures. Despite their structural and functional similarities with their mesophilic homologues, they show enhanced stability. Various comparative studies at genomic, protein sequence and structure levels, and experimental works highlight the different factors and dominant interacting forces contributing to this increased stability. Methods: In this comparative structure based study, we have used interaction energies between amino acids, to generate structure networks called as Protein Energy Networks (PENs). These PENs are used to compute network, sub-graph, and node specific parameters. These parameters are then compared between the thermophile-mesophile homologues. Results: The results show an increased number of clusters and low energy cliques in thermophiles as the main contributing factors for their enhanced stability. Further more, we see an increase in the number of hubs in thermophiles. We also observe no community of electrostatic cliques forming in PENs. Conclusion: In this study we were able to take an energy based network approach, to identify the factors responsible for enhanced stability of thermophiles, by comparative analysis. We were able to point out that the sub-graph parameters are the prominent contributing factors. The thermophiles have a better-packed hydrophobic core. We have also discussed how thermophiles, although increasing stability through higher connectivity retains conformational flexibility, from a cliques and communities perspective.

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)

1979 Ecological study of fishes and the water quality characteristics of Florida Bay, Everglades National Park, Florida

Fish collections under varying ecological conditions were made by trawling and seining, monthly and quarterly in depths of <1 m to depths of 3 m of the Florida Bay portion of Everglades National Park, Florida. From May 1973 through September 1976, a total of 182,530 fishes representing 128 species and 50 families were taken at 27 stations. An additional 21 species were identified from sportfish-creel surveys and supplemental observations. Most of the species collected were juveniles of species that occur as adults in the Florida Bay creel census survey, or were small species that were seasonal residents. Marked temporal and spatial abundance of the catches was observed. The greatest numbers and biomass of the fishes occurred in the wet season (summer/fall), whereas lowest numbers and biomass appeared during the dry season (winter/spring) The greatest abundance and diversity of fishes was found in western Florida Bay followed by eastern and central Bay regions respectively. Overall, five species comprised 75% of the numerical total while eleven species made up 75% of the total biomass. Collections were dominated numerically by anchovies (Engraulidae), especially Anchoa mitchilli, in western Florida Bay. Mojarras (Gerridae), mostly silver jenny Eucinostomus gula, and porgies (Sparidae), especially pinfish Lagodon rhomboides, dominated numerically in central and eastern portions of the Bay, respectively. Except for salinity, other measured physico-chemical parameters (water temperature, pH, dissolved oxygen, and turbidity) showed no variation beyond ranges considered normal for shallow, tropical marine environments. Salinity varied from 0 to 66 ppt near the mainland. Nearshore hypersaline conditions (>45 ppt) persisted for nearly 2 years during the 1974 - 1975 severe drought period. Significant reductions in fish abundance/diversity were observed in relation to hypersaline conditions. Bay-wide macrobenthic communities were mapped (presence/absence) and were primarily comprised of turtle grass (Thalassia), shoalgrass [(Diplanthera = (Halodule)], and/or green algae Penicillus. Seasonal dieoff of seagrasses was observed in north-central Florida Bay. (PDF contains 107 pages)

Impact of fertlizers and pesticides on soil and water quality

[ES]En la presente tesis se ha estudiado el impacto de diferentes fertilizantes y pesticidas utilizados en la Zona Vulnerable de Vitoria-Gasteiz en la calidad del suelo y las aguas de dicha zona. Se ha podido constatar que hoy en día siguen lixiviándose cantidades significativas de nitratos y pesticidas (e.g., etofumesato y difenoconazol) a las aguas de la Zona Vulnerable, durante el cultivo de remolacha azucarera (Beta vulgaris L.), muy característico de la zona de estudio. Se comprobó que el alto contenido en nitratos de las aguas subterráneas en la Zona Vulnerable es mitigado, al menos en parte, por la acción de la actividad microbiana desnitrificante que alberga la zona riparia del humedal de Salburua. Dicho proceso, sin embargo, supone la emisión a la atmósfera de importantes cantidades de gases de efecto invernadero (CO2 y N2O), y puede verse afectado negativamente por la presencia de pesticidas (e.g., deltametrina) en el medio.Por otra parte, hemos observado que diversos pesticidas (deltametrina, etofumesato, difenoconazol) aplicados en concentraciones similares a las dosis de aplicación en campo inducen cambios, de carácter limitado y transitorio, en las comunidades microbianas edáficas, siendo más significativos en el caso del fungicida difenoconazol. El efecto de los pesticidas fue más acusado a medida que aumentaba su concentración en el medio. Finalmente, encontramos que la aplicación de abonos orgánicos (avicompost), en lugar de los fertilizantes sintéticos tradicionales (NPK), además de mejorar la degradación de los pesticidas y disminuir el impacto de éstos sobre la calidad del suelo, podría ayudar a reducir las pérdidas de nitratos por lixiviación.

The Zanzibar Workshop Proceedings: Asserting Rights, Defining Responsibilities:Perspectives from Small-scale Fishing Communities on Coastal and Fisheries Management in Eastern and Southern Africa

The Zanzibar Workshop Proceedings consists of the report and the Statement of the Workshop and provides a rich understanding of the dynamics of traditional, indigenous, small-scale and artisanal fisheries and fishing communities in the Eastern and Southern African (ESA) context. The issues covered include: the saga of rights denied to coastal lands, fishing, and threats to livelihood arising from lack of recognition of traditional rights and the livelihood needs of people in the region; the aspirations of coastal and inland communities to maintain or improve their livelihoods; and a bottom-up perspective on access rights to fishing, post-harvest rights and economic and social rights. This report will be a valuable source of information for community organizers, trade union leaders, government officials and the donor community, including multilateral organizations, researchers and for all those who are interested in the well-being of ESA fishing communities.

Improving reporting of uncertainties in sea level rise assessments

Sea level rise (SLR) assessments are commonly used to identify the extent that coastal populations are at risk to flooding. However, the data and assumptions used to develop these assessments contain numerous sources and types of uncertainty, which limit confidence in the accuracy of modeled results. This study illustrates how the intersection of uncertainty in digital elevation models (DEMs) and SLR lead to a wide range of modeled outcomes. SLR assessments are then reviewed to identify the extent that uncertainty is documented in peer-reviewed articles. The paper concludes by discussing priorities needed to further understand SLR impacts. (PDF contains 4 pages)

Comparison of resident and tourist preferences for public beach access

As coastal destinations continue to grow, due to tourism and residential expansion, the demand for public beach access and related amenities will also increase. As a resultagencies that provide beach access and related amenities face challenges when considering both residents and visitors use beaches and likely possess different needs, as well as different preferences for management decisions. Being a resident of a coastal county provides more opportunity to use local beaches, but coastal tourism is an important and growing economic engine in coastal communities (Kriesel, Landry, & Keeler, 2005; Pogue & Lee, 1999). Therefore, providing agencies with a comprehensive assessment of the differences between these two groups will increase the likelihood of effective management programs and policies for the provision of public beach access and related amenities. The purpose of this paper was to use a stated preference choice method (SPCM) to identify the extent of both residents’ and visitors’ preferences for public beach management options. (PDF contains 4 pages)

Poverty alleviation among fishermen within the floodplains of Kaduna River: implication for introducing commercial fish farming at village level in Doko local government area of Niger State, Nigeria

A diagnostic survey was conducted among the fishermen in six selected villages in Doko Local Government Area of Niger State. One hundred and fifty fishermen were randomly selected and interviewed to find out whether or not they had interest in commercial fish farming aimed at improving their livelihood. The dwindling fish catches in the natural flood plain ponds and Ex-bow Lakes continue to have a serious negative effect on the socio-economic well being of the village communities in question. A break on natural regular annual flooding of the plains had resulted into very low natural fish recruitment. Data analysis using simple descriptive statistics revealed that land tenure system, educational status, inadequate infrastructural facilities, religious taboos, existing fish species among others were found to be favourable indices for commercial fish farming. However, serious conflicts among the fishermen concerning the ownership status of these natural fish ponds are found to be major obstacles to commercial fish farming despite that the traditional ownership of the ponds were vested in the lands of individuals and village communities. Extensive fish farming and small-scale fish farming in the ponds and Ex-bow Lake with improved management practices are considered to be profitable venture. Despite the fact that fish seeds supply and extension effort are still inadequate, the fish farmers have indicated willingness to adopt commercial fish farming in the Ex-bow Lakes and flood plains in order to restore abundant fish production thereby providing for their food security and also increasing the daily income

Climate Change and Knowledge Communities

19 p.

Different patterns of uptake and depuration of cadmium by periphyton community and a grazer species (Physa sp.): A mesocosm evalution

Widespread pollution by heavy metals generated by various industries has serious adverse effects on human health and the environment. Cadmium is a heavy metal recognised as one of the most hazardous environmental pollutants. It is a non-essential and non-beneficial element to organisms, causing toxicity and other deleterious effects on various components of the aquatic environment. The ability of algal periphyton to concentrate cadmium from fresh water is well known. Moreover, periphyton communities are able to accumulate large amounts of cadmium despite its low concentration in fresh water. Many researchers use algal periphyton as an indicator of water quality in aquatic environments. In the present study, the authors ask two basic questions: Does cadmium accumulate along a food chain consisting of the periphyton community and a grazer species (Physa sp.) under semi-natural conditions provided by artificial streams? If not, which one can better indicate the water quality?

Comparison of permanent and temporary streams of calcareous Provence [Translation from: Annales de Limnologie 9(3) 273-292, 1973]

The rainfall regime and the karstic nature of the subsoil determines the alternation of a period of flow and a period of drought for a large number of Mediterranean streams. Amongst this type of stream it is possible to distinguish temporary streams, characterised by a period of flow for several months permitting the establishment of the principal groups of aquatic insects; and ephemeral streams whose very brief period of flow permits the establishment of a community reduced to a few species of Diptera. This paper aims to study the structure of the communities which colonise this particular type of stream and the ecology of the principal species which constitute these communities. Four French temporary streams were examined and temperature regimes, dissolved oxygen, calcium and magnesium measured. Samples of fauna were taken regularly and the biotic composition established. The analysis of similarities between the three permanent streams are discussed and compared with permanent streams.

From social to political. New forms of mobilization and democratization. Conference proceedings

In the recent evolution of contemporary social movements three phases can be identified. The first phase is marked by the labour movement and the systemic importance attributed to the labour conflict in industrial societies. This conflict has been interpreted as a consequence of the shortcoming of social integration mechanisms by Emile Durkheim, as a rational conflict by entrepreneurs’ and workers’ interests by Max Wener, and as a central class struggle for the transformation of society by Karl Marx. The second phase in this development was led by the new social movements of the post-industrial society of the 1960s and 1970s’ students, women and environmentalist movements. Two new analytical perspectives have explained these movements’ meaning and actions. Resource mobilization theory (McAdam and Tilly) has focuses on rational attitudes and conflicts. Actionalist sociology, in turn, has identified the new protagonists of social conflicts that replaced the labour movement in postindustrial societies. The third phase emerges in a world characterized by the ascendance of markets, the increasingly prominent role of financial capital flows, the closure of communities, and fundamentalism. In this context, human rights and pro-democratization movements constitute alternatives to global domination and the systemic conditioning of individual and groups.

Sumilon Island reserve: 20 years of hopes and frustrations

Over 20 years, successive openings and closures of the Sumilon Island marine reserve to fishers have provided unique opportunities to examine the effects of marine reserves on populations and communities of fishes and upon local fisheries. The history of the reserve also highlights the problems and frustrations of educating and convincing people of the need for rational management of renewable marine resources. Yet, it is a symbol of hope in that it has provided a unique example of the potential benefits of marine reserves in fisheries management, particularly in the developing world.

NMFS Cooperative SharkTagging Program, 1962-93: An Atlas of SharkTag and Recapture Data

The National Marine Fisheries Service (NMFS) Cooperative Shark Tagging Program (CSTP) is part of continuing research directed to the study of the biology of large Atlantic sharks. The CSTP was initiated in 1962 at the Sandy Hook Laboratory in New Jersey under the Department of Interior's U.S. Fish and Wildlife Service (USFWS). During the late 1950's and early 1960's, sharks were considered a liability to the economy of resort communities, of little or no commercial value, and a detriment to fishermen in areas where sharks might damage expensive fishing gear or reduce catches of more commercially valuable species.