Parasites as biological tags in marine fisheries research: European Atlantic waters.

Science.gov (United States)

Mackenzie, K; Hemmingsen, W

2015-01-01

Studies of the use of parasites as biological tags for stock identification and to follow migrations of marine fish, mammals and invertebrates in European Atlantic waters are critically reviewed and evaluated. The region covered includes the North, Baltic, Barents and White Seas plus Icelandic waters, but excludes the Mediterranean and Black Seas. Each fish species or ecological group of species is treated separately. More parasite tag studies have been carried out on Atlantic herring Clupea harengus than on any other species, while cod Gadus morhua have also been the subject of many studies. Other species that have been the subjects of more than one study are: blue whiting Micromesistius poutassou, whiting Merlangius merlangus, haddock Melanogrammus aeglefinus, Norway pout Trisopterus esmarkii, horse mackerel Trachurus trachurus and mackerel Scomber scombrus. Other species are dealt with under the general headings redfishes, flatfish, tunas, anadromous fish, elasmobranchs, marine mammals and invertebrates. A final section highlights how parasites can be, and have been, misused as biological tags, and how this can be avoided. It also reviews recent developments in methodology and parasite genetics, considers the potential effects of climate change on the distributions of both hosts and parasites, and suggests host-parasite systems that should reward further research.

Preparation and biological efficacy of haddock bone calcium tablets

Science.gov (United States)

Huo, Jiancong; Deng, Shanggui; Xie, Chao; Tong, Guozhong

2010-03-01

To investigate the possible use of waste products obtained after processing haddock, the present study prepared haddock bone calcium powder by NaOH and ethanol soaking (alkalinealcohol method) and prepared haddock bone calcium tablets using the powder in combination with appropriate excipients. The biological efficacy of the haddock bone calcium tablets was investigated using Wistar rats as an experiment model. Results show that the optimal parameters for the alkalinealcohol method are: NaOH concentration 1 mol/L, immersion time 30 h; ethanol concentration 60%, immersion time 15 h. A mixture of 2% polyvinylpyrrolidone in ethanol was used as an excipient at a ratio of 1:2 to full-cream milk powder, without the use of a disintegrating agent. This process provided satisfactory tablets in terms of rigidity and taste. Animal studies showed that the haddock bone calcium tablets at a dose of 2 g·kg-1·d-1 or 5g·kg-1·d-1 significantly increased blood calcium and phosphorus levels and bone calcium content in rats. Therefore, these tablets could be used for calcium supplementation and prevent osteoporosis. Although the reasons of high absorption in the rats fed with haddock bone calcium tablets are unclear, it is suggested that there are some factors, such as treatment with method of alkaline-alcohol or the added milk, may play positive roles in increasing absorption ratio.

Shipboard-irradiation of haddock

International Nuclear Information System (INIS)

Ehlermann, D.; Reinacher, E.; Antonacopoulos, N.

1977-01-01

Haddock caught during the 183rd and 185th voyage of the RV 'Anton Dohrn' off Faeroeer was gutted, washed and packed under vacuum in polyethylene pouches. The samples were irradiated with the onboard X-ray source. During one series of experiments a minimum dose of 65 krad and a maximum dose of 130 krad was used. During further series the minimal dose was set to 100 krad, resulting in maximum values of 140 krad and 180 krad. As judged by taste panel evaluation of steam-cooked, unseasoned filets, quality preservation of all samples during the first 16 days of iced storage did not depend on irradiation. After that period the fish had lost prime quality. At this time, irradiated samples were rated slightly better than unirradiated ones. Base on our results, the shipboard-irradiation of prepacked haddock cannot be recommended. This does not exclude that under different conditions (e.g. fishfilets in retail packages) beneficial effects of irradiation may be observed. (orig.) [de

Shipboard-irradiation of haddock

International Nuclear Information System (INIS)

Ehlermann, D.; Reinacher, E.; Antonacopoulos, N.

1977-01-01

Haddock caught during the 183rd and 185th voyage of the RV 'Anton Dohrn' off Faeroer was gutted, washed and packed under vacuum in polythylene pouches. The samples were irradiated with the onboard X-ray source. During one series of experiments a minimum dose of 65 krad and a maximum dose of 130 krad was used. During further series the minimal dose was set to 100 krad, resulting in maximum values of 140 krad and 180 krad. As judged by taste panel evalution of steam-cooked, unseasoned filets, quality preservation of all samples during the first 16 days of iced storage did not depend on irradiation. After that period the fish had lost prime quality. At this time, irradiated samples were rated slightly better than unirradiated ones. On the basis of these results, the shipboard-irradiation of prepacked haddock cannot be recommended. This does not exclude that under different conditions (e.g. fishfilets in retail packages) beneficial effects of irradiation may be observed. (orig.) [de

Landscape effects on demersal fish revealed by field observations and predictive seabed modelling.

Science.gov (United States)

Elliott, Sophie A M; Sabatino, Alessandro D; Heath, Michael R; Turrell, William R; Bailey, David M

2017-01-01

Nature conservation and fisheries management often focus on particular seabed features that are considered vulnerable or important to commercial species. As a result, individual seabed types are protected in isolation, without any understanding of what effect the mixture of seabed types within the landscape has on ecosystem functions. Here we undertook predictive seabed modelling within a coastal marine protected area using observations from underwater stereo-video camera deployments and environmental information (depth, wave fetch, maximum tidal speeds, distance from coast and underlying geology). The effect of the predicted substratum type, extent and heterogeneity or the diversity of substrata, within a radius of 1500 m around each camera deployment of juvenile gadoid relative abundance was analysed. The predicted substratum model performed well with wave fetch and depth being the most influential predictor variables. Gadus morhua (Atlantic cod) were associated with relatively more rugose substrata (Algal-gravel-pebble and seagrass) and heterogeneous landscapes, than Melanogrammus aeglefinus (haddock) or Merlangius merlangus (whiting) (sand and mud). An increase in M. merlangus relative abundance was observed with increasing substratum extent. These results reveal that landscape effects should be considered when protecting the seabed for fish and not just individual seabed types. The landscape approach used in this study therefore has important implications for marine protected area, fisheries management and monitoring advice concerning demersal fish populations.

Derived concentration factors for caesium-137 in edible species of North Sea fish

International Nuclear Information System (INIS)

Steele, A.K.

1990-01-01

Concentration factor (CF=Bq kg -1 fillet/Bg kg -1 filtered sea water) values for 137 Cs in fillets of cod (Gadus morhua), haddock (Merlanogrammus aeglefinus), plaice (Pleuronectes platessa) and whiting (Merlangius merlangius), were derived from fish and filtered seawater concentrations. Samples were collected in twelve sampling boxes in the North Sea over an eight-year period - 1978-1985. The range of results with species, between species, and between surveys are discussed. Mean CF values of 92, 58, 39 and 150 were found in cod, haddock, plaice and whiting respectively. These support the International Atomic Energy Authority recommended CF value of 100 for fish in generalised dose assessments. (author)

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.

Science.gov (United States)

van Zundert, G C P; Rodrigues, J P G L M; Trellet, M; Schmitz, C; Kastritis, P L; Karaca, E; Melquiond, A S J; van Dijk, M; de Vries, S J; Bonvin, A M J J

2016-02-22

The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Biomarkers in natural fish populations indicate adverse biological effects of offshore oil production.

Directory of Open Access Journals (Sweden)

Lennart Balk

Full Text Available Despite the growing awareness of the necessity of a sustainable development, the global economy continues to depend largely on the consumption of non-renewable energy resources. One such energy resource is fossil oil extracted from the seabed at offshore oil platforms. This type of oil production causes continuous environmental pollution from drilling waste, discharge of large amounts of produced water, and accidental spills.Samples from natural populations of haddock (Melanogrammus aeglefinus and Atlantic cod (Gadus morhua in two North Sea areas with extensive oil production were investigated. Exposure to and uptake of polycyclic aromatic hydrocarbons (PAHs were demonstrated, and biomarker analyses revealed adverse biological effects, including induction of biotransformation enzymes, oxidative stress, altered fatty acid composition, and genotoxicity. Genotoxicity was reflected by a hepatic DNA adduct pattern typical for exposure to a mixture of PAHs. Control material was collected from a North Sea area without oil production and from remote Icelandic waters. The difference between the two control areas indicates significant background pollution in the North Sea.It is most remarkable to obtain biomarker responses in natural fish populations in the open sea that are similar to the biomarker responses in fish from highly polluted areas close to a point source. Risk assessment of various threats to the marine fish populations in the North Sea, such as overfishing, global warming, and eutrophication, should also take into account the ecologically relevant impact of offshore oil production.

Characterization of Atlantic cod spawning habitat and behavior in Icelandic coastal waters.

Directory of Open Access Journals (Sweden)

Timothy B Grabowski

Full Text Available The physical habitat used during spawning may potentially be an important factor affecting reproductive output of broadcast spawning marine fishes, particularly for species with complex, substrate-oriented mating systems and behaviors, such as Atlantic cod Gadus morhua. We characterized the habitat use and behavior of spawning Atlantic cod at two locations off the coast of southwestern Iceland during a 2-d research cruise (15-16 April 2009. We simultaneously operated two different active hydroacoustic gear types, a split beam echosounder and a dual frequency imaging sonar (DIDSON, as well as a remotely operated underwater vehicle (ROV. A total of five fish species were identified through ROV surveys: including cusk Brosme brosme, Atlantic cod, haddock Melanogrammus aeglefinus, lemon sole Microstomus kitt, and Atlantic redfish Sebastes spp. Of the three habitats identified in the acoustic surveys, the transitional habitat between boulder/lava field and sand habitats was characterized by greater fish density and acoustic target strength compared to that of sand or boulder/lava field habitats independently. Atlantic cod were observed behaving in a manner consistent with published descriptions of spawning. Individuals were observed ascending 1-5 m into the water column from the bottom at an average vertical swimming speed of 0.20-0.25 m s(-1 and maintained an average spacing of 1.0-1.4 m between individuals. Our results suggest that cod do not choose spawning locations indiscriminately despite the fact that it is a broadcast spawning fish with planktonic eggs that are released well above the seafloor.

Characterization of Atlantic cod spawning habitat and behavior in Icelandic coastal waters

Science.gov (United States)

Grabowski, Timothy B.; Boswell, Kevin M.; McAdam, Bruce J.; Wells, R. J. David; Marteinsdóttir, Gudrún

2012-01-01

The physical habitat used during spawning may potentially be an important factor affecting reproductive output of broadcast spawning marine fishes, particularly for species with complex, substrate-oriented mating systems and behaviors, such as Atlantic cod Gadus morhua. We characterized the habitat use and behavior of spawning Atlantic cod at two locations off the coast of southwestern Iceland during a 2-d research cruise (15–16 April 2009). We simultaneously operated two different active hydroacoustic gear types, a split beam echosounder and a dual frequency imaging sonar (DIDSON), as well as a remotely operated underwater vehicle (ROV). A total of five fish species were identified through ROV surveys: including cusk Brosme brosme, Atlantic cod, haddock Melanogrammus aeglefinus, lemon sole Microstomus kitt, and Atlantic redfish Sebastes spp. Of the three habitats identified in the acoustic surveys, the transitional habitat between boulder/lava field and sand habitats was characterized by greater fish density and acoustic target strength compared to that of sand or boulder/lava field habitats independently. Atlantic cod were observed behaving in a manner consistent with published descriptions of spawning. Individuals were observed ascending 1–5 m into the water column from the bottom at an average vertical swimming speed of 0.20–0.25 m s−1 and maintained an average spacing of 1.0–1.4 m between individuals. Our results suggest that cod do not choose spawning locations indiscriminately despite the fact that it is a broadcast spawning fish with planktonic eggs that are released well above the seafloor.

Screening for viral hemorrhagic septicemia virus in marine fish along the Norwegian coastal line.

Directory of Open Access Journals (Sweden)

Nina Sandlund

Full Text Available Viral hemorrhagic septicemia virus (VHSV infects a wide range of marine fish species. To study the occurrence of VHSV in wild marine fish populations in Norwegian coastal waters and fjord systems a total of 1927 fish from 39 different species were sampled through 5 research cruises conducted in 2009 to 2011. In total, VHSV was detected by rRT-PCR in twelve samples originating from Atlantic herring (Clupea harengus, haddock (Melanogrammus aeglefinus, whiting (Merlangius merlangus and silvery pout (Gadiculus argenteus. All fish tested positive in gills while four herring and one silvery pout also tested positive in internal organs. Successful virus isolation in cell culture was only obtained from one pooled Atlantic herring sample which shows that today's PCR methodology have a much higher sensitivity than cell culture for detection of VHSV. Sequencing revealed that the positive samples belonged to VHSV genotype Ib and phylogenetic analysis shows that the isolate from Atlantic herring and silvery pout are closely related. All positive fish were sampled in the same area in the northern county of Finnmark. This is the first detection of VHSV in Atlantic herring this far north, and to our knowledge the first detection of VHSV in silvery pout. However, low prevalence of VHSV genotype Ib in Atlantic herring and other wild marine fish are well known in other parts of Europe. Earlier there have been a few reports of disease outbreaks in farmed rainbow trout with VHSV of genotype Ib, and our results show that there is a possibility of transfer of VHSV from wild to farmed fish along the Norwegian coast line. The impact of VHSV on wild fish is not well documented.

Fish product mislabelling: failings of traceability in the production chain and implications for illegal, unreported and unregulated (IUU) fishing.

Science.gov (United States)

Helyar, Sarah J; Lloyd, Hywel Ap D; de Bruyn, Mark; Leake, Jonathan; Bennett, Niall; Carvalho, Gary R

2014-01-01

Increasing consumer demand for seafood, combined with concern over the health of our oceans, has led to many initiatives aimed at tackling destructive fishing practices and promoting the sustainability of fisheries. An important global threat to sustainable fisheries is Illegal, Unreported and Unregulated (IUU) fishing, and there is now an increased emphasis on the use of trade measures to prevent IUU-sourced fish and fish products from entering the international market. Initiatives encompass new legislation in the European Union requiring the inclusion of species names on catch labels throughout the distribution chain. Such certification measures do not, however, guarantee accuracy of species designation. Using two DNA-based methods to compare species descriptions with molecular ID, we examined 386 samples of white fish, or products labelled as primarily containing white fish, from major UK supermarket chains. Species specific real-time PCR probes were used for cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) to provide a highly sensitive and species-specific test for the major species of white fish sold in the UK. Additionally, fish-specific primers were used to sequence the forensically validated barcoding gene, mitochondrial cytochrome oxidase I (COI). Overall levels of congruence between product label and genetic species identification were high, with 94.34% of samples correctly labelled, though a significant proportion in terms of potential volume, were mislabelled. Substitution was usually for a cheaper alternative and, in one case, extended to a tropical species. To our knowledge, this is the first published study encompassing a large-scale assessment of UK retailers, and if representative, indicates a potentially significant incidence of incorrect product designation.

Fish product mislabelling: failings of traceability in the production chain and implications for illegal, unreported and unregulated (IUU fishing.

Directory of Open Access Journals (Sweden)

Sarah J Helyar

Full Text Available Increasing consumer demand for seafood, combined with concern over the health of our oceans, has led to many initiatives aimed at tackling destructive fishing practices and promoting the sustainability of fisheries. An important global threat to sustainable fisheries is Illegal, Unreported and Unregulated (IUU fishing, and there is now an increased emphasis on the use of trade measures to prevent IUU-sourced fish and fish products from entering the international market. Initiatives encompass new legislation in the European Union requiring the inclusion of species names on catch labels throughout the distribution chain. Such certification measures do not, however, guarantee accuracy of species designation. Using two DNA-based methods to compare species descriptions with molecular ID, we examined 386 samples of white fish, or products labelled as primarily containing white fish, from major UK supermarket chains. Species specific real-time PCR probes were used for cod (Gadus morhua and haddock (Melanogrammus aeglefinus to provide a highly sensitive and species-specific test for the major species of white fish sold in the UK. Additionally, fish-specific primers were used to sequence the forensically validated barcoding gene, mitochondrial cytochrome oxidase I (COI. Overall levels of congruence between product label and genetic species identification were high, with 94.34% of samples correctly labelled, though a significant proportion in terms of potential volume, were mislabelled. Substitution was usually for a cheaper alternative and, in one case, extended to a tropical species. To our knowledge, this is the first published study encompassing a large-scale assessment of UK retailers, and if representative, indicates a potentially significant incidence of incorrect product designation.

Eco-Labeling and Retailer Pricing Strategies: The U.K. Haddock Market

OpenAIRE

Dengjun Zhang; Geir Sogn-Grundvåg; Frank Asche; James A. Young

2018-01-01

In attempts to differentiate their store imagery, grocery retailers frequently introduce new products, which are often rich in extrinsic attributes such as claims regarding healthiness and environmental sustainability. This paper explores retailers’ pricing strategies for product attributes of haddock in the United Kingdom. The results show that retailers’ pricing strategies vary, in particular for extrinsic product attributes such as eco-labels and country-of-origin. The high pri...

North Sea Scyphomedusae; summer distribution, estimated biomass and significance particularly for 0-group Gadoid fish

Science.gov (United States)

Hay, S. J.; Hislop, J. R. G.; Shanks, A. M.

Data on the by-catch of Scyphomedusae from pelagic trawls was collected during the routine ICES International 0-group Gadoid Surveys of the North Sea, in June and July of the years 1971-1986 (except 1984). These data are used to describe the distributions, abundances and biomasses of three common North Sea Scyphomedusae: Aurelia aurita (L.), Cyanea capillata (L.) and C. lamarckii (Péron & Lesuer). Information is also presented on inter-annual variability, size (umbrella diameter) frequencies and, for the Cyanea species, umbrella diameter: wet weight relationships. The general role and ecological significance of Scyphomedusae is discussed and, given the well known 'shelter' relationships between Scyphomedusae and certain 0-group fish, whiting ( Merlangius merlangus) and haddock ( Melanogrammus aeglefinus), in particular. The data were examined for evidence of such relationships. Aurelia aurita, although fairly widespread in the northern North Sea was virtually absent from the central North Sea but very abundant in coastal waters. This species was particularly abundant off the Scottish east coast and especially in the Moray Firth. Cyanea lamerckii was most abundant in the southern and eastern North Sea. More widespread than Aurelia, this species was also most abundant in coastal regions, particularly off the Danish west coast. Cyanea capillata, with a more northern distribution was also more widely distributed and abundant offshore. This species was most abundant in the area between the Orkney/Shetland Isles and the Norwegian Deep and in shelf waters of the north west approaches to the North Sea. As with C. lamarckii it was also, in some years, abundant off the Scottish east coast and west of Denmark. The abundance and the size frequency of the jellyfish show considerable inter-annual variability, and variability between regions of the North Sea. It is considered that hydrographic variability and differences in food supply to both medusae and to their sessile

Solvated protein–DNA docking using HADDOCK

International Nuclear Information System (INIS)

Dijk, Marc van; Visscher, Koen M.; Kastritis, Panagiotis L.; Bonvin, Alexandre M. J. J.

2013-01-01

Interfacial water molecules play an important role in many aspects of protein–DNA specificity and recognition. Yet they have been mostly neglected in the computational modeling of these complexes. We present here a solvated docking protocol that allows explicit inclusion of water molecules in the docking of protein–DNA complexes and demonstrate its feasibility on a benchmark of 30 high-resolution protein–DNA complexes containing crystallographically-determined water molecules at their interfaces. Our protocol is capable of reproducing the solvation pattern at the interface and recovers hydrogen-bonded water-mediated contacts in many of the benchmark cases. Solvated docking leads to an overall improvement in the quality of the generated protein–DNA models for cases with limited conformational change of the partners upon complex formation. The applicability of this approach is demonstrated on real cases by docking a representative set of 6 complexes using unbound protein coordinates, model-built DNA and knowledge-based restraints. As HADDOCK supports the inclusion of a variety of NMR restraints, solvated docking is also applicable for NMR-based structure calculations of protein–DNA complexes.

Solvated protein-DNA docking using HADDOCK

Energy Technology Data Exchange (ETDEWEB)

Dijk, Marc van; Visscher, Koen M.; Kastritis, Panagiotis L.; Bonvin, Alexandre M. J. J., E-mail: a.m.j.j.bonvin@uu.nl [Utrecht University, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands)

2013-05-15

Interfacial water molecules play an important role in many aspects of protein-DNA specificity and recognition. Yet they have been mostly neglected in the computational modeling of these complexes. We present here a solvated docking protocol that allows explicit inclusion of water molecules in the docking of protein-DNA complexes and demonstrate its feasibility on a benchmark of 30 high-resolution protein-DNA complexes containing crystallographically-determined water molecules at their interfaces. Our protocol is capable of reproducing the solvation pattern at the interface and recovers hydrogen-bonded water-mediated contacts in many of the benchmark cases. Solvated docking leads to an overall improvement in the quality of the generated protein-DNA models for cases with limited conformational change of the partners upon complex formation. The applicability of this approach is demonstrated on real cases by docking a representative set of 6 complexes using unbound protein coordinates, model-built DNA and knowledge-based restraints. As HADDOCK supports the inclusion of a variety of NMR restraints, solvated docking is also applicable for NMR-based structure calculations of protein-DNA complexes.

Temporal trends in age and size at maturation of four North Sea gadid populations: cod, haddock, whiting, and Norway pout

DEFF Research Database (Denmark)

Marty, Lise; Rochet, Marie-Joëlle; Ernande, Bruno

2014-01-01

, phenotypic plasticity, and evolution to these trends were assessed. First, maturation trends were extricated from demographic effects and growth-dependent plasticity by estimating probabilistic maturation reaction norms (PMRNs). PMRN midpoints have significantly shifted downwards at most ages for cod......, haddock, and whiting, but not for Norway pout. Second, increased temperature and food abundance, loosened trophic competition, and relaxed social pressure may also trigger growth-independent plasticity in maturation. Principal component regression of PMRN midpoints on annual estimates of relevant...... environmental variables exhibiting a temporal trend suggest that, despite some evidence of environmental effects, PMRN trends were mostly independent of growth-independent plasticity in haddock, whiting, and male cod, but not in female cod. According to these findings, evolution of maturation, potentially...

Eco-Labeling and Retailer Pricing Strategies: The U.K. Haddock Market

Directory of Open Access Journals (Sweden)

Dengjun Zhang

2018-05-01

Full Text Available In attempts to differentiate their store imagery, grocery retailers frequently introduce new products, which are often rich in extrinsic attributes such as claims regarding healthiness and environmental sustainability. This paper explores retailers’ pricing strategies for product attributes of haddock in the United Kingdom. The results show that retailers’ pricing strategies vary, in particular for extrinsic product attributes such as eco-labels and country-of-origin. The high price premium generated from the most advocated eco-labels and an emphasis upon promotion strategies appear to play a role in the success of high-end retailers, and may have implications for any heightened competitive responses by larger retail chains in the future.

78 FR 48420 - New England Fishery Management Council; Public Meeting

Science.gov (United States)

2013-08-08

... and develop ABC recommendations for Georges Bank yellowtail flounder for fishing year 2014; review... of Maine haddock ABC may be adjusted in response to possible movement of Georges Bank haddock into... accessible to people with disabilities. Requests for sign language interpretation or other auxiliary aids...

76 FR 56985 - Magnuson-Stevens Fishery Conservation and Management Act Provisions; Fisheries of the...

Science.gov (United States)

2011-09-15

... to estimate total haddock catch by the herring midwater trawl fleet in these herring management areas.... 110627355-1539-02] RIN 0648-BB08 Magnuson-Stevens Fishery Conservation and Management Act Provisions... the NE Multispecies Fishery Management Plan (FMP), which increases the haddock incidental catch cap...

Growth changes in plaice, cod, haddock and saithe in the North Sea: a comparison of (post-)medieval and present-day growth rates based on otolith measurements

Science.gov (United States)

Bolle, Loes J.; Rijnsdorp, Adriaan D.; van Neer, Wim; Millner, Richard S.; van Leeuwen, Piet I.; Ervynck, Anton; Ayers, Richard; Ongenae, Ellen

2004-05-01

Fishing effort has strongly increased in the North Sea since the mid-19th century, causing a substantial reduction in the population size of exploited fish stocks. As fisheries research has developed simultaneously with the industrialisation of the fisheries, our knowledge of population dynamics at low levels of exploitations is limited. Otoliths retrieved from archaeological excavations offer a unique opportunity to study growth rates in the past. This study compares historical and present-day growth rates for four commercially important demersal fish species. A total of 2532 modern otoliths (AD 1984-1999) and 1286 historical otoliths (AD 1200-1925) obtained from archaeological excavations in Belgium and Scotland were analysed. Comparison of the growth patterns between eras revealed a major increase in growth rate of haddock, whereas growth changes were not observed in saithe and only in the smaller size classes of plaice and cod. Comparison of our results with literature data indicates that the observed growth rate changes in plaice and cod occurred within the 20th century. Apparently the onset of industrialised fisheries has not greatly affected the growth of plaice, cod and saithe populations in the North Sea. This result contradicts the expectation of density-dependent limitation of growth during the era of pre-industrialised fishing, but is in agreement with the concentration hypothesis of Beverton (Neth. J. Sea Res. 34 (1995) 1) stating that species which concentrate spatially into nursery grounds during their early life-history may 'saturate' the carrying capacity of the juvenile habitat even though the adult part of the population is not limited by the adult habitat.

Evaluation of three levels of selective devices relevant to management of the Danish Kattegat-Skagerrak Nephrops fishery

DEFF Research Database (Denmark)

Frandsen, Rikke; Holst, René; Madsen, Niels

2009-01-01

This study illuminates a range of technological options relevant to present legislation for regulating fish by-catch in a small-meshed Nephrops fishery. The selection of cod, haddock, hake, lemon sole, Nephrops, plaice, saithe, witch, and whiting were evaluated using the twin-trawl technique for...... parameters by species and confidence bands to compare the selective properties of different gear types. For cod, haddock, hake, Nephrops, plaice, and whiting we obtained estimates for all three gear variants, whereas we obtained estimates for lemon sole and witch only with the standard and the SMP codends...

Combination of Ambiguous and Unambiguous Data in the Restraint-driven Docking of Flexible Peptides with HADDOCK: The Binding of the Spider Toxin PcTx1 to the Acid Sensing Ion Channel (ASIC) 1a.

Science.gov (United States)

Deplazes, Evelyne; Davies, Josephine; Bonvin, Alexandre M J J; King, Glenn F; Mark, Alan E

2016-01-25

Peptides that bind to ion channels have attracted much interest as potential lead molecules for the development of new drugs and insecticides. However, the structure determination of large peptide-channel complexes using experimental methods is challenging. Thus structural models are often derived from combining experimental information with restraint-driven docking approaches. Using the complex formed by the venom peptide PcTx1 and the acid sensing ion channel (ASIC) 1a as a case study, we have examined the effect of different combinations of restraints and input structures on the statistical likelihood of (a) correctly predicting the structure of the binding interface and (b) the ability to predict which residues are involved in specific pairwise peptide-channel interactions. For this, we have analyzed over 200,000 water-refined docked structures obtained with various amounts and types of restraints of the peptide-channel complex predicted using the docking program HADDOCK. We found that increasing the number of restraints or even the use of pairwise interaction data resulted in only a modest improvement in the likelihood of finding a structure within a given accuracy. This suggests that shape complementarity and the force field make a large contribution to the accuracy of the predicted structure. The results also showed that there are large variations in the accuracy of the predicted structure depending on the precise combination of residues used as restraints. Finally, we reflect on the limitations of relying on geometric criteria such as root-mean square deviations to assess the accuracy of docking procedures. We propose that in addition to currently used measures, the likelihood of finding a structure within a given level of accuracy should be also used to evaluate docking methods.

Determination of alpha radionuclides in fish

International Nuclear Information System (INIS)

Pernicka, L.; Matel, L.; Rosskopfova, O.

2002-01-01

The specific activity of alpha radionuclides was determined in biological samples. The biological samples were chosen in kinds of fish, concretely mackerels, herrings and haddocks. Experimental data were presented on the poster

Solvated protein-DNA docking using HADDOCK

NARCIS (Netherlands)

van Dijk, Marc; Visscher, Koen M; Bonvin, Alexandre M.J.J; Kastritis, Panagiotis L.

2013-01-01

Interfacial water molecules play an important role in many aspects of protein-DNA specificity and recognition. Yet they have been mostly neglected in the computational modeling of these complexes. We present here a solvated docking protocol that allows explicit inclusion of water molecules in the

76 FR 44577 - New England Fishery Management Council; Public meeting

Science.gov (United States)

2011-07-26

... Georges Bank yellowtail flounder, Eastern Georges Bank cod, and Eastern Georges Bank haddock. The Committee will identify alternatives for modifying the Georges Bank yellowtail flounder rebuilding strategy... Accommodations This meeting is physically accessible to people with disabilities. Requests for sign language...

77 FR 14351 - New England Fishery Management Council; Public Meeting

Science.gov (United States)

2012-03-09

... assessments and develop ABC recommendations for the Council for redfish, Georges Bank haddock, Gulf of Maine/Georges Bank windowpane flounder, Southern New England/Mid-Atlantic windowpane flounder, ocean pout... address the emergency. Special Accommodations This meeting is physically accessible to people with...

Visualisation of animal anatomy using MRI and CT

DEFF Research Database (Denmark)

Lauridsen, Henrik; Hansen, Kasper; Pedersen, Michael

imaging (MRI) and CT. Various species (tarantula, horseshoe crab, carp, haddock, lungfish, axolotl) were subjected to multi-slice MRI and CT protocols to produce 2D images of body slices, followed by volume rendering producing 3D digital models of animal anatomy with applications for visualising specific...

Status and trends of the major roundfish, flatfish, and pelagic fish stocks in the North Sea: thirty- year overview

NARCIS (Netherlands)

Serchuk, F.M.; Kirkegaard, E.; Daan, N.

1996-01-01

Changes in the status of the major roundfish, flatfish, and pelagic stocks in the North Sea over the past 30 years are reviewed. Synopses are presented on trends in catches, fishing mortality, spawning-stock biomass, and recruitment for eight stocks (cod, haddock, whitting, saithe, plaice, sole,

Solvated protein-protein docking using Kyte-Doolittle-based water preferences

NARCIS (Netherlands)

Kastritis, P.; Visscher, K.M.; van Dijk, A.D.J.; Bonvin, A.M.J.J.

2013-01-01

HADDOCK is one of the few docking programs that can explicitly account for water molecules in the docking process. Its solvated docking protocol starts from hydrated molecules and a fraction of the resulting interfacial waters is subsequently removed in a biased Monte Carlo procedure based on

Solvated protein-protein docking using Kyte-Doolittle-based water preferences

NARCIS (Netherlands)

Kastritis, Panagiotis L.; Visscher, Koen M.; van Dijk, Aalt D.J.; Bonvin, Alexandre M.J.J.

HADDOCK is one of the few docking programs that can explicitly account for water molecules in the docking process. Its solvated docking protocol starts from hydrated molecules and a fraction of the resulting interfacial waters is subsequently removed in a biased Monte Carlo procedure based on

77 FR 53868 - New England Fishery Management Council; Public Meeting

Science.gov (United States)

2012-09-04

... modifications to the sector program, such as creating areas for fishing on Georges Bank (GB) that are not... catch advice developed for Eastern Georges Bank cod and haddock, and Georges Bank yellowtail flounder.... Special Accommodations This meeting is physically accessible to people with disabilities. Requests for...

Selectivity in a trawl codend during haul-back operation: An overlooked phenomenon

DEFF Research Database (Denmark)

Madsen, Niels; Skeide, R.; Breen, M.

2008-01-01

), whiting (Merlangius merlangus) and Norway lobster (Nephrops norvegicus), respectively, the mean percentages escaping at the surface were 16, 12 and 38% of the total escape while 17, 8 and 28% escaped during the haul-up phase. Compared to towing, the escape rate (no./min) increased for haddock by a factor...... 2.7 during haul-up and by a factor 1.7 at the surface, whereas the escape rates of whiting were similar for the three phases. The escape rate of Norway lobster increased by a factor of approximately 7 for both the haul-up and surface phases, compared to the towing phase. The selectivity parameters L......50 (50% retention length) and SR (selection rangeá=áL75-L25) were estimated and compared for the three different phases and for the whole haul for haddock, whiting and Norway lobster. For all three species there was no significant (Pá>á0.05) difference in L50 between the three phases of the haul...

On Contextuality.

Science.gov (United States)

Thayer-Bacon, Barbara J.

This exploration of what feminism has to contribute to pragmatism, and vice versa, considers the idea of contextuality through an examination of the role of current pragmatists, such as Cornel West and Richard Rorty, and current feminists, including Charlene Haddock Siegfried, Maxine Greene, and Seyla Benhabib. To set the stage historically for…

Main Directions of Increasing Efficiency of Foreign Trade Activities of the Fishing Industry of the European North

Directory of Open Access Journals (Sweden)

Anatolii Mikhailovich Vasil’ev

2015-09-01

Full Text Available Analysis of the List of Orders of the Russian Federation President Vladimir Putin has shown that many priority challenges of the fishing industry development, including promotion of fish production with a high degree of processing and its exports have not been solved. Analysis of exports of cod, haddock and saithe from Russia (Murmansk Oblast and Norway proves that there is a wider range of products from Norway with high added value. The unit cost of the same products from Norway is also significantly higher. The consequence of these factors is the low unit cost of Russian exports, compared to Norwegian. For 2009–2013 the average unit cost of cod is lower by 2.66 US dollars (47.9%, of haddock – by 0.23 US dollars (10.6%. The article estimates foreign currency revenues, which were not fully received due to the reasons mentioned above. The author points out key directions of increase of economic efficiency of Russian exports of cod, haddock and saithe: 1. Change in the access of economic agents to marketable resources by stimulating the obtainment of larger quotas of biological resources at the expense of profit ratio. 2. Establishment of an organization for the export of fish products. The purpose of the organization is to study international markets, to regulate foreign trade activities and perform other functions as set forth above, in accordance with the Russian legislation. 3. Exclusion of intermediaries in the sales of fish products by organizing electronic auctions. 4. Prohibition of using fishery products for the payment of loans obtained from foreign banks. 5. Use of trawlers that are not able to produce products with added value, to provide fish processing enterprises of Russia with fish resources

Some conclusions of studies on irradiation of whole fish aboard fishing vessels

International Nuclear Information System (INIS)

Reinacher, E.; Ehlermann, D.A.E.

1978-01-01

Studies were conducted on irradiation of whole redfish and haddock (at 100 krad) and subsequent storage of the irradiated fish for up to approx. 30 days in ice. The fish were organoleptically evaluated at intervals during storage. The results show no significant difference in organoleptic quality between irradiated and non-irradiated samples during storage for [de

A vida ea obra de Zaíra Cintra Vidal

Directory of Open Access Journals (Sweden)

Gertrudes Teixeira Lopes

2001-06-01

Full Text Available Estudo histórico social, cujo objetivo é descrever a trajetória de Zaira Cintra Vidal, sua inserção na Escola de Enfermeiras Rachel Haddock Lobo e sua participação na Associação Brasileira de Enfermagem (ABEn. O estudo fundamenta-se nos conceitos de poder simbólico, habitus e luta simbólica de Pierre Bourdieu. As fontes primárias foram documentos existentes no Centro de Documentação da EEAN/UFRJ e no Centro de Memória da FENF/UERJ. Os dados foram obtidos no período de agosto de 2000 a abril de 2001 mediante um roteiro de análise documental. Os resultados evidenciaram que Zaira Cintra Vidal, nasceu em 05 de maio de 1903, graduou-se pela Escola de Enfermeiras do Departamento Nacional de Saúde Pública, em 1926; pós-graduou-se nos EUA de 1927 a 1929, retornando em 1943. Criou a Escola de Enfermeiras Rachel Haddock Lobo, sendo a primeira diretora por nove anos e participou na diretoria da ABEn e na redação da Revista Anais de Enfermagem.

Gentamicin binds to the megalin receptor as a competitive inhibitor using the common ligand binding motif of complement type repeats

DEFF Research Database (Denmark)

Dagil, Robert; O'Shea, Charlotte; Nykjær, Anders

2013-01-01

megalin and investigated its interaction with gentamicin. Using NMR titration data in HADDOCK, we have generated a three-dimensional model describing the complex between megalin and gentamicin. Gentamicin binds to megalin with low affinity and exploits the common ligand binding motif previously described...... to megalin is highly similar to gentamicin binding to calreticulin. We discuss the impact of this novel insight for the future structure-based design of gentamicin antagonists....

Spectral Irradiance Calibration in the Infrared. XVI. Improved Accuracy in the Infrared Spectra of the Secondary and Tertiary Standard Calibration Stars

Science.gov (United States)

2006-10-01

resolution ( AlA ). -, 400) spectroscopy obtained on infrared standard stars by the Short Wavelength Spectrometer on the Infrared Space Observatory with high...1995): 2.1-2.4 pm Strecker et al. (1979): 1.22-2.4 pm 6 See http://vizier.hia.nrc.ca/viz-bin/VizieR. REFERENCES Alonso, A., Salaris, M., Arribas , S...Haddock, D. J., Arribas , S., Leggett, S. K., & Mountain, C. M. 1988, A&AS, 74, 127

The HADDOCK web server for data-driven biomolecular docking

NARCIS (Netherlands)

de Vries, S.J.|info:eu-repo/dai/nl/304837717; van Dijk, M.|info:eu-repo/dai/nl/325811113; Bonvin, A.M.J.J.|info:eu-repo/dai/nl/113691238

2010-01-01

Computational docking is the prediction or modeling of the three-dimensional structure of a biomolecular complex, starting from the structures of the individual molecules in their free, unbound form. HADDOC K is a popular docking program that takes a datadriven approach to docking, with support for

[The life and work of Zaíra Cintra Vidal].

Science.gov (United States)

Lopes, G T; Caldas, N P; Lima, T C; Martingil, I C

2001-01-01

This is a social-historical study that aims at describing the trajectory of Zaíra Cintra Vidal, her participation in the Nursing School Rachel Haddock Lobo and in the Brazilian Association of Nursing (ABEn). The study is based on the concepts of symbolic power, habitus and symbolic struggle of Pierre Bourdieu. The primary sources are documents which were collected in the Documentation Center of Escola de Enfermagem Ana Neri (EEAN--Ana Neri School of Nursing) in the Federeal University of Rio de Janeiro (UFRJ) and at the Memory Center of the Faculty of Nursing (FENF) in the State University of Rio de Janeiro (UERJ). The data was collected between August 2000 and April 2001 by means of document analysis script. The outcomes showed that Zaíra Cintra Vidal was born on 5 May 1903; graduated from the Nursing School of the National Public Health Department in 1926; studied and post-graduated in the United States from 1927 until 1929 and returned to Brazil in 1943. Zaíra Cintra Vidal was the founder of the Nursing School Rachel Haddock Lobo and was its first director for nine years. She also and took part in ABEn's Direction Board and in the Revista Anais de Enfermagem (Nursing Magazine).

What are the needs for sufficient protection of fisheries

International Nuclear Information System (INIS)

Misund, Ole Arve

2006-01-01

The presentation discusses various aspects of the fisheries in the Northern hemisphere and focuses on key fish species such as cod, haddock, herring and whiting particularly in the North Sea, North Atlantic and the Barents Sea. Effects of seismic exploration, pollution from offshore oil production and oil spills both in short and long term, are of particular interest. Various indicators are measured and the biological effects of alkylated phenols are discussed (tk)

A Study to Develop a Methodology to Enable Direct Cost UCA (Uniform Chart of Accounts) Data to Be Expressed in Terms of Cost per Admission for Specific Diagnosis Related Groups

Science.gov (United States)

1985-07-01

Medical Center, Tuskegee, Alabama, interview conducted during visit to his office, 11 April 1985. 5. Turner, Jeff R , "The Inadequacies of the Medical... bedridden soldier, not only because of his adverse effect on the mission of the unit, but also because of the unit’s inability to provide proper assistance...Fye, S. P.; Bigelow, R . E.; Haddock, W. D.; and Ward, R . F. "The Relationship Between Inpatient Service Cost and Case- Complexity at Wilford Hall

Some conclusions from shipboard experiments on the radurization of whole fish in the Federal Republic of Germany

International Nuclear Information System (INIS)

Ehlermann, D.A.E.; Reinacher, E.

1978-01-01

Redfish and haddock were radurized (100krad) with the X-ray facility onboard the research vessel ''Anton Dohrn''. The whole fish were stored under crushed ice. In addition whole haddock packaged in plastic pouches under vacuum were studied. In general, during the first 16 days of storage no marked difference in the sensory quality between irradiated and unirradiated samples was observed. Bacteriological and chemical analyses proved the effectiveness of radurization to reduce the microbial flora usually responsible for spoilage. When compared with the results from other shipboard experiments and laboratory studies, the results of sensory evaluation are also in general accordance - if the same criterion for the judgement of final quality is used. After a storage period longer than 16 days occasionally the irradiated samples were scored higher than the unirradiated ones, but then the quality was no longer acceptable. If a lower criterion for shelf-life extension is used, it may be stated that a considerable shelf-life extension results from irradiation. By the standards used in our experiments, it is not possible to preserve an acceptable quality and to extend the shelf-life of ocean fish under the conditions prevailing in practical fishing. Taking into account the many factors that influence the results of such studies, it is not excluded that under other conditions the beneficial effects of radiation processing may be observed. (author)

Jargonial-Obfuscation(J-O) DISambiguation Elimination via Siegel-Baez Cognition Category-Semantics(C-S) in Siegel FUZZYICS=CATEGORYICS (Son of TRIZ)/(F=C) Tabular List-Format Dichotomy Truth-Table Matrix Analytics

Science.gov (United States)

Siegel, Carl Ludwig; Siegel, Edward Carl-Ludwig

2011-03-01

NOT "philosophy" per se but raising serious salient Arnol'd [Huygens and Barrow, Newton and Hooke(96)] questions begged is Rota empiricism Husserl VS. Frege maths-objects Dichotomy controversy: Hill-Haddock[Husserl or Frege?(00)]as manifestly-demonstrated by Hintikka[B.U.]-Critchey[Derrida Deconstruction Ethics(78)] deconstruction; Altshuler TRIZ; Siegel F=C/C-S; Siegel-Baez(UCR) Cognition C-S = "Category-theory ``+'' Cognitive-Semantics[Wierzbica-Langacker-Lakoff-Nunez[Where Maths Comes From(00)]-Fauconnier-Turner[Blending(98)]-Coulson[Semantic-Leaps (00)

Status and trends of the major roundfish, flatfish, and pelagic fish stocks in the North Sea : Thirty-year overview

DEFF Research Database (Denmark)

Serchuk, F.M.; Kirkegaard, Eskild; Daan, N.

1996-01-01

Changes in the status of the major roundfish, flatfish, and pelagic stocks in the North Sea over the past 30 years are reviewed. Synopses are presented on trends in catches, fishing mortality, spawning-stock biomass, and recruitment for eight stocks (cod, haddock, whiting, saithe, plaice, sole......, herring, and mackerel), together with an evaluation of the current state of these resources and the most resent management advice provided by the ICES Advisory, Committee on Fishery Management. (C) 1996 International Council for the Exploration of the Sea...

ADULT CADDISFLY (TRICHOPTERA) PHENOLOGY AT THE HANFORD REACH NATIONAL MONUMENT, WASHINGTON STATE

International Nuclear Information System (INIS)

Zack, Richard S.; Ruiter, David E.; Strenge, Dennis L.; Landolt, Peter J.

2006-01-01

Adult caddisflies were sampled on the Wahluke Wildlife Area and Saddle Mountain National Wildlife Refuge subunits of the newly created (2000) Hanford Reach National Monument using 15-watt ''black lights'' from April 2002 through April 2003. A diverse fauna consisting of nine families, 21 genera, and 33 species were collected. Protoptila Coloma Ross, Agraylea multipunctata Curtis, Hydroptila xera Ross, Ceraclea alagma (Ross), Nectopsych Iahontanensis Haddock Oecetis cinerascens (Hagen), and Ylodes reuteri (MacLachlan) represent new records for Washington State. Species composition and phenology are presented in tabular form

The importance of α-CT and Salt bridges in the Formation of Insulin and its Receptor Complex by Computational Simulation.

Science.gov (United States)

Dehghan-Shasaltaneh, Marzieh; Lanjanian, Hossein; Riazi, Gholam Hossein; Masoudi-Nejad, Ali

2018-01-01

Insulin hormone is an important part of the endocrine system. It contains two polypeptide chains and plays a pivotal role in regulating carbohydrate metabolism. Insulin receptors (IR) located on cell surface interacts with insulin to control the intake of glucose. Although several studies have tried to clarify the interaction between insulin and its receptor, the mechanism of this interaction remains elusive because of the receptor's structural complexity and structural changes during the interaction. In this work, we tried to fractionate the interactions. Therefore, sequential docking method utilization of HADDOCK was used to achieve the mentioned goal, so the following processes were done: the first, two pdb files of IR i.e., 3LOH and 3W11 were concatenated using modeller. The second, flexible regions of IR were predicted by HingeProt. Output files resulting from HingeProt were uploaded into HADDOCK. Our results predict new salt bridges in the complex and emphasize on the role of salt bridges to maintain an inverted V structure of IR. Having an inverted V structure leads to activate intracellular signaling pathway. In addition to presence salt bridges to form a convenient structure of IR, the importance of α-chain of carboxyl terminal (α-CT) to interact with insulin was surveyed and also foretokened new insulin/IR contacts, particularly at site 2 (rigid parts 2 and 3). Finally, several conformational changes in residues Asn711-Val715 of α-CT were occurred, we suggest that α-CT is a suitable situation relative to insulin due to these conformational alterations.

Interaction between S100P and the anti-allergy drug cromolyn

International Nuclear Information System (INIS)

Penumutchu, Srinivasa R.; Chou, Ruey-Hwang; Yu, Chin

2014-01-01

Highlights: • The interaction between S100P–cromolyn was investigated by fluorescence spectroscopy. • The interfacial residues on S100P and cromolyn contact surface were mapped by 1 H- 15 N HSQC experiments. • S100P–cromolyn complex model was generated from NMR restraints using HADDOCK program. • The stability of the S100P–cromolyn complex was studied using molecular dynamics simulations. - Abstract: The S100P protein has been known to mediate cell proliferation by binding the receptor for advanced glycation end products (RAGE) to activate signaling pathways, such as the extracellular regulated kinase (ERK) and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathways. S100P/RAGE signaling is involved in a variety of diseases, such as cancer, metastasis, and diabetes. Cromolyn is an anti-allergy drug that binds S100P to block the interaction between S100P and RAGE. In the present study, we characterized the properties of the binding between cromolyn and calcium-bound S100P using various biophysical techniques. The binding affinity for S100P and cromolyn was measured to be in the millimolar range by fluorescence spectroscopy. NMR-HSQC titration experiments and HADDOCK modeling was employed to determine the spatial structure of the proposed heterotetramer model of the S100P–cromolyn complex. Additional MD simulation results revealed the important properties in the complex stability and conformational flexibility of the S100P–cromolyn complex. This proposed model has provided an understanding of the molecular level interactions of S100P–cromolyn complex

Shape and Texture Based Classification of Fish Species

DEFF Research Database (Denmark)

Larsen, Rasmus; Ólafsdóttir, Hildur; Ersbøll, Bjarne Kjær

2009-01-01

In this paper we conduct a case study of ¯sh species classi- fication based on shape and texture. We consider three fish species: cod, haddock, and whiting. We derive shape and texture features from an appearance model of a set of training data. The fish in the training images were manual outlined......, and a few features including the eye and backbone contour were also annotated. From these annotations an optimal MDL curve correspondence and a subsequent image registration were derived. We have analyzed a series of shape and texture and combined shape and texture modes of variation for their ability...

Understanding and predicting size selection in diamond-mesh cod ends for danish seining: A study based on sea trials and computer simulations

DEFF Research Database (Denmark)

Herrmann, Bent; Krag, Ludvig Ahm; Feekings, Jordan P.

2016-01-01

described by a double logistic selection curve, implying that two different size selection processes occur in the cod end. The double selection process could be explained by an additional selection process occurring through slack meshes. The results imply that the escapement of 46% and 34% of the larger...... Atlantic Cod and Haddock (those above 48 cm), respectively, would be through wide-open or slack meshes. Since these mesh states are only likely to be present in the latest stage of the fishing process (e.g., when the cod end is near the surface), a large fraction of the bigger fish probably escaped near...

Effects of industrial processing on the immunogenicity of commonly ingested fish species.

Science.gov (United States)

Sletten, Gaynour; Van Do, Thien; Lindvik, Helene; Egaas, Eliann; Florvaag, Erik

2010-01-01

Food-processing techniques may induce changes in fish protein immunogenicity. Allergens from >100 fish species have been identified, but little is known on the effects of processing on fish protein immunogenicity. IgE binding of sera of patients allergic to fresh and processed (smoked, salted/sugar-cured, canned, lye-treated and fermented) cod, haddock, salmon, trout, tuna, mackerel and herring and of hydrolysates based on salmon and whiting was investigated using immunoblot and inhibition ELISA. Parvalbumin oligomers were identified using monoclonal and polyclonal antibodies. IgE binding was seen in most sera at 12-14 kDa (parvalbumin), and at 17-60 kDa for all fish except tuna. Changes in IgE binding appeared to reflect altered parvalbumin monomers and oligomers. Smoked haddock, salmon and mackerel had increased IgE binding and novel bands at 30 kDa. Chemically processed cod, salmon, trout and pickled herring had reduced or abolished IgE binding. The serum of 1 subject, however, had increased IgE binding to these products and also inhibition of binding by both fish hydrolysates to their constituent fish species. Process-induced changes in fish protein immunogenicity were more dependent on process rather than species, although individual responses varied. Changes in the allergenicity of a product may depend on the net effect of processing on parvalbumin oligomerization patterns, which may also vary in different species. Chemical processes generally caused loss in IgE-binding activity, though sensitization may occur to modified or degraded rather than intact peptides as shown by increased binding by chemically processed fish and hydrolysates in 1 subject. The clinical significance of these findings remains to be established.

Interaction between S100P and the anti-allergy drug cromolyn

Energy Technology Data Exchange (ETDEWEB)

Penumutchu, Srinivasa R. [Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan (China); Chou, Ruey-Hwang [Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan (China); Department of Biotechnology, Asia University, Taichung 413, Taiwan (China); Yu, Chin, E-mail: cyu.nthu@gmail.com [Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan (China); The Key Laboratory for Chemical Biology of Fujian Province, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005 (China)

2014-11-21

Highlights: • The interaction between S100P–cromolyn was investigated by fluorescence spectroscopy. • The interfacial residues on S100P and cromolyn contact surface were mapped by {sup 1}H-{sup 15}N HSQC experiments. • S100P–cromolyn complex model was generated from NMR restraints using HADDOCK program. • The stability of the S100P–cromolyn complex was studied using molecular dynamics simulations. - Abstract: The S100P protein has been known to mediate cell proliferation by binding the receptor for advanced glycation end products (RAGE) to activate signaling pathways, such as the extracellular regulated kinase (ERK) and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathways. S100P/RAGE signaling is involved in a variety of diseases, such as cancer, metastasis, and diabetes. Cromolyn is an anti-allergy drug that binds S100P to block the interaction between S100P and RAGE. In the present study, we characterized the properties of the binding between cromolyn and calcium-bound S100P using various biophysical techniques. The binding affinity for S100P and cromolyn was measured to be in the millimolar range by fluorescence spectroscopy. NMR-HSQC titration experiments and HADDOCK modeling was employed to determine the spatial structure of the proposed heterotetramer model of the S100P–cromolyn complex. Additional MD simulation results revealed the important properties in the complex stability and conformational flexibility of the S100P–cromolyn complex. This proposed model has provided an understanding of the molecular level interactions of S100P–cromolyn complex.

Variability in growth rates of larval haddock in the northern North Sea

DEFF Research Database (Denmark)

Gallego, A.; Heath, M.R.; Basford, D.J.

1999-01-01

of the spring plankton production bloom, and a likely explanation for the absence of environmental effects on larval growth was high food availability and larval feeding rates. Nevertheless, differences in growth were observed between cohorts, with larvae hatched later in the spring displaying higher growth...... at age than those hatched earlier. Particle-tracking modelling suggested that differences in temperature history between cohorts, on their own or compounded by a potential interaction between temperature and the development of plankton production, may explain the higher growth rate of the larvae hatched...

Who Needs Religion When You Have The Desert?

DEFF Research Database (Denmark)

Sørensen, Bent

In my paper I propose to read so-called ‘post-ironic’ texts by authors associated with the Blank Generation and Generation X (including Bret Easton Ellis and Douglas Coupland, as well as less well-known authors such as K.S. Haddock) and examine their use of the desert as a trope for identity...... testing and summation. Perhaps surprisingly, one finds in novels such as Ellis’ Less Than Zero (1984) and Coupland’s Generation X (1991) a reliance on desert locations to provide an alternative to the numerous non-places (in Marc Augé’s sense of the term) that otherwise make up the setting of these works....

SQUEEZE-E: The Optimal Solution for Molecular Simulations with Periodic Boundary Conditions.

Science.gov (United States)

Wassenaar, Tsjerk A; de Vries, Sjoerd; Bonvin, Alexandre M J J; Bekker, Henk

2012-10-09

In molecular simulations of macromolecules, it is desirable to limit the amount of solvent in the system to avoid spending computational resources on uninteresting solvent-solvent interactions. As a consequence, periodic boundary conditions are commonly used, with a simulation box chosen as small as possible, for a given minimal distance between images. Here, we describe how such a simulation cell can be set up for ensembles, taking into account a priori available or estimable information regarding conformational flexibility. Doing so ensures that any conformation present in the input ensemble will satisfy the distance criterion during the simulation. This helps avoid periodicity artifacts due to conformational changes. The method introduces three new approaches in computational geometry: (1) The first is the derivation of an optimal packing of ensembles, for which the mathematical framework is described. (2) A new method for approximating the α-hull and the contact body for single bodies and ensembles is presented, which is orders of magnitude faster than existing routines, allowing the calculation of packings of large ensembles and/or large bodies. 3. A routine is described for searching a combination of three vectors on a discretized contact body forming a reduced base for a lattice with minimal cell volume. The new algorithms reduce the time required to calculate packings of single bodies from minutes or hours to seconds. The use and efficacy of the method is demonstrated for ensembles obtained from NMR, MD simulations, and elastic network modeling. An implementation of the method has been made available online at http://haddock.chem.uu.nl/services/SQUEEZE/ and has been made available as an option for running simulations through the weNMR GRID MD server at http://haddock.science.uu.nl/enmr/services/GROMACS/main.php .

Advances on the molecular characterization, clinical relevance, and detection methods of Gadiform parvalbumin allergens.

Science.gov (United States)

Fernandes, Telmo J R; Costa, Joana; Carrapatoso, Isabel; Oliveira, Maria Beatriz P P; Mafra, Isabel

2017-10-13

Gadiform order includes several fish families, from which Gadidae and Merlucciidae are part of, comprising the most commercially important and highly appreciated fish species, such as cod, pollock, haddock, and hake. Parvalbumins, classified as calcium-binding proteins, are considered the main components involved in the majority of fish allergies. Nine and thirteen parvalbumins were identified in different fish species from Gadidae and Merlucciidae families, respectively. This review intends to describe their molecular characterization and the clinical relevance, as well as the prevalence of fish allergy. In addition, the main protein- and DNA-based methods to detect fish allergens are fully reviewed owing to their importance in the safeguard of sensitized/allergic individuals.

Regulation by Phloroglucinol of Nrf2/Maf-Mediated Expression of Antioxidant Enzymes and Inhibition of Osteoclastogenesis via the RANKL/RANK Signaling Pathway: In Silico study

Science.gov (United States)

Rahim, Agus Hadian; Setiawan, Bambang; Dewi, Firli Rahmah Primula; Noor, Zairin

2015-01-01

Introduction: Phloroglucinol is an antioxidant compound with many positive effects on health. The purpose of this study was to determine the role of phloroglucinol in osteoclastogenesis via the RANKL/RANK signaling pathway and the activity of the transcription factor Nrf2. Material and methods: Analysis was performed in silico using the primary method of docking by the use of Hex 8.0 software and Haddock web server. Analysis of interactions was then performed to determine interactions between the ligand and its receptors by using the software LigPlus and LigandScout 3.1. Results: Results indicated that phloroglucinol compound was thought to inhibit osteoclastogenesis via three mechanisms: inhibiting RANKL−RANK interaction, sustaining the RANKL−OPG bond, and increasing the activity of the transcription factor Nrf2. PMID:26483597

Social sustainability of cod and haddock fisheries in the northeast Atlantic: what issues are important?

NARCIS (Netherlands)

Veldhuizen, L.J.L.; Berentsen, P.; Bokkers, E.A.M.; Boer, de I.J.M.

2015-01-01

Research on the sustainability of capture fisheries has focused more on environmental and economic sustainability than on social sustainability. To assess social sustainability, first relevant and important social sustainability issues need to be identified. The objective of this study was to

Selected anthropogenic and natural radioisotopes in the Barents Sea and off the western coast of Svalbard

International Nuclear Information System (INIS)

Leppänen, Ari-Pekka; Kasatkina, Nadezhda; Vaaramaa, Kaisa; Matishov, Gennady G.; Solatie, Dina

2013-01-01

137 Cs concentrations found in cod and in haddock were compared with studies done in the early 1990's an effective half-life of 137 Cs in cod and in haddock was deduced. For cod the estimated effective half-life of 137 Cs was between 5.8 and 7.5 years and for haddock between 5.3 and 9.5 years. Similarly, the concentrations of naturally occurring 210 Po and 210 Pb were from 0.1 to 0.3 Bq/kg w.w. The 210 Po/ 210 Pb ratio varied from 1.8 to 30 indicating a more efficient bioaccumulation of 210 Po than its precursor 210 Pb. The dose to humans eating Barents Sea fish was estimated. Even for people consuming large quantities of Barents Sea fish the annual dose was found to be below 20 μSv. The effective dose from anthropogenic 137 Cs was found to be less than 1% compared to the dose caused naturally occurring 210 Po and 210 Pb. -- Highlights: • Levels of anthropogenic radionuclides were found to be low in all studied media. • No spatial variation was found in the 90 Sr and 137 Cs concentrations in sea water. • Spatial variation was found in anthropogenic and natural radionuclide concentrations in sediment. • In fish 210 Po was found to accumulate better than it's precursor 210 Pb

Theoretical study of the influence of twine thickness on haddock selectivity in diamond mesh cod-ends

DEFF Research Database (Denmark)

Herrmann, Bent; O'Neill, F.G.

2006-01-01

Using the cod-end simulation model PRESEMO, the influence of twine thickness on cod-end selectivity is investigated. The reduction of lateral mesh opening that arises as a result of both twine bending stiffness and the physical presence of the twine is considered. While it is shown that this lead...

The structure of myristoylated Mason-Pfizer monkey virus matrix protein and the role of phosphatidylinositol-(4,5)-bisphosphate in its membrane binding.

Science.gov (United States)

Prchal, Jan; Srb, Pavel; Hunter, Eric; Ruml, Tomáš; Hrabal, Richard

2012-10-26

We determined the solution structure of myristoylated Mason-Pfizer monkey virus matrix protein by NMR spectroscopy. The myristoyl group is buried inside the protein and causes a slight reorientation of the helices. This reorientation leads to the creation of a binding site for phosphatidylinositols. The interaction between the matrix protein and phosphatidylinositols carrying C(8) fatty acid chains was monitored by observation of concentration-dependent chemical shift changes of the affected amino acid residues, a saturation transfer difference experiment and changes in (31)P chemical shifts. No differences in the binding mode or affinity were observed with differently phosphorylated phosphatidylinositols. The structure of the matrix protein-phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P(2)] complex was then calculated with HADDOCK software based on the intermolecular nuclear Overhauser enhancement contacts between the ligand and the matrix protein obtained from a (13)C-filtered/(13)C-edited nuclear Overhauser enhancement spectroscopy experiment. PI(4,5)P(2) binding was not strong enough for triggering of the myristoyl-switch. The structural changes of the myristoylated matrix protein were also found to result in a drop in the oligomerization capacity of the protein. Copyright © 2012. Published by Elsevier Ltd.

A description of two new species of the genus Erenna (Siphonophora: Physonectae: Erennidae), with notes on recently collected specimens of other Erenna species.

Science.gov (United States)

Pugh, P R; Haddock, S H D

2016-11-10

Two new Erenna species, E. insidiator sp. nov. and E. sirena sp. nov., are described from specimens collected in the vicinity of Monterey Bay, California, and also, for E. sirena at the southern end of the Gulf of California, Mexico. Further information on the three extant Erenna species is given, based on specimens collected in the same areas. These have enabled, for instance, the identification of three types of tentilla on the tentacles of E. cornuta Pugh, 2001, rather than the two noted on the single previously known specimen. The genus is remarkable for the presence of bioluminescent lures on the tentilla of all five species. In E. sirena sp. nov. the tentilla are also covered by a red-fluorescent layer, which was briefly described by Haddock et al. (2005), and further details are given herein. Another extraordinary feature of the colonies E. sirena sp. nov. is that the main part of the tentacle, with its tentilla, can be extended away from the siphosomal stem on a long peduncle. This phenomenon also appears to occur in E. laciniata Pugh, 2001, and has not been observed before for other physonect species.

Temperature and Ca2+-dependence of the sarcoplasmic reticulum Ca2(+)-ATPase in haddock, salmon, rainbow trout and zebra cichlid

DEFF Research Database (Denmark)

Godiksen, Helene; Jessen, Flemming

2002-01-01

Temperature dependence of Ca2+-ATPase from the sarcoplasmic reticulum (SR) in rabbit muscle has been widely studied, and it is generally accepted that a break point in Arrhenius plot exist at approximately 20 degreesC. Whether the break point arises as a result of temperature dependent changes......+- ATPase activity. The temperature range of the plateau was 14-21 and 18-25 degreesC in salmon and rainbow trout, respectively. Ca2+-dependence in the four different fish species investigated was very similar with half maximal activation (K-0.5) between 0.2 and 0.6 muM and half maximal inhibition (I-0.......5) between 60 and 250 muM. Results indicated that interaction between SR Ca2+-ATPase and its lipid environment may play an important role for the different Arrhenius plot of the different types of fish species investigated. (C) 2002 Elsevier Science Inc. All rights reserved....

HPEPDOCK: a web server for blind peptide-protein docking based on a hierarchical algorithm.

Science.gov (United States)

Zhou, Pei; Jin, Bowen; Li, Hao; Huang, Sheng-You

2018-05-09

Protein-peptide interactions are crucial in many cellular functions. Therefore, determining the structure of protein-peptide complexes is important for understanding the molecular mechanism of related biological processes and developing peptide drugs. HPEPDOCK is a novel web server for blind protein-peptide docking through a hierarchical algorithm. Instead of running lengthy simulations to refine peptide conformations, HPEPDOCK considers the peptide flexibility through an ensemble of peptide conformations generated by our MODPEP program. For blind global peptide docking, HPEPDOCK obtained a success rate of 33.3% in binding mode prediction on a benchmark of 57 unbound cases when the top 10 models were considered, compared to 21.1% for pepATTRACT server. HPEPDOCK also performed well in docking against homology models and obtained a success rate of 29.8% within top 10 predictions. For local peptide docking, HPEPDOCK achieved a high success rate of 72.6% on a benchmark of 62 unbound cases within top 10 predictions, compared to 45.2% for HADDOCK peptide protocol. Our HPEPDOCK server is computationally efficient and consumed an average of 29.8 mins for a global peptide docking job and 14.2 mins for a local peptide docking job. The HPEPDOCK web server is available at http://huanglab.phys.hust.edu.cn/hpepdock/.

In silico analysis, mapping of regulatory elements and corresponding dna-protein interaction in polyphenol oxidase gene promoter from different rice varieties

International Nuclear Information System (INIS)

Mahmood, T.; Rehman, M.; Aziz, E.

2015-01-01

Polyphenol oxidase (PPO) is an important enzyme that has positive impact regarding plant resistance against different biotic and abiotic stresses. In the present study PPO promoter from six different rice varieties was amplified and then analyzed for cis- and trans-acting elements. The study revealed a total of 79 different cis-acting regulatory elements including 11 elements restricted to only one or other variety. Among six varieties Pakhal-Basmati had highest number (5) of these elements, whereas C-622 and Rachna-Basmati have no such sequences. Rachna-Basmati, IR-36-Basmati and Kashmir- Basmati had 1, 2 and 3 unique elements, respectively. Different elementsrelated to pathogen, salt and water stresses were found, which may be helpful in controlling PPO activity according to changing environment. Moreover, HADDOCK was used to understand molecular mechanism of PPO regulation and it was found that DNA-protein interactions are stabilized by many potential hydrogen bonds. Adenine and arginine were the most reactive residues in DNA and proteins respectively.Structural comparison of different protein-DNA complexes show that even a highly conserved transcriptional factor can adopt different conformations when they contact a different DNA binding sequence, however their stable interactions depend on the number of hydrogen bonds formed and distance. (author)

DEVELOPMENT OF TECHNOLOGY FOR FISH CANNED PATE'S COD-FISH SPECIES

Directory of Open Access Journals (Sweden)

A. A. Efremova

2014-01-01

Full Text Available Summary. Fish and seafood play an important role in a balanced diet. The most reliable method of preservation is the production of canned fish. Cod fishery considered traditional objects of the North Basin, which catches in recent years stored at a consistently high level. They are represented, mainly cod, haddock, pollack, whiting. Lately there has been a tendency to increase yield loaves (polar bib. The aim of this work - the development of technology - canned pate's cod fish species with the addition of plant materials. We used the adopted research microbiological, chemical and physical methods. The weight proportion of water, lipids, protein, mineral raw determined according to State standard 7636-85. Developed a technology - canned pate's cod fish species with the addition of plant materials. Optimized formulation is set to sterilization. Experimentally determined parameters of quality canned and given comprehensive assessment nutritional value of new products, organoleptic, physico-chemical, biochemical and microbiological tests showed that canned pates of Gadidae species of fish with vegetables, meet all safety requirements and are characterized, along with excellent consumer properties, high nutritional value. Based on the results of the research complex developed technical documentation for production of canned vegetables, pates of Gadidae species.

Structural analysis of poly-SUMO chain recognition by the RNF4-SIMs domain.

Science.gov (United States)

Kung, Camy C-H; Naik, Mandar T; Wang, Szu-Huan; Shih, Hsiu-Ming; Chang, Che-Chang; Lin, Li-Ying; Chen, Chia-Lin; Ma, Che; Chang, Chi-Fon; Huang, Tai-Huang

2014-08-15

The E3 ubiquitin ligase RNF4 (RING finger protein 4) contains four tandem SIM [SUMO (small ubiquitin-like modifier)-interaction motif] repeats for selective interaction with poly-SUMO-modified proteins, which it targets for degradation. We employed a multi-faceted approach to characterize the structure of the RNF4-SIMs domain and the tetra-SUMO2 chain to elucidate the interaction between them. In solution, the SIM domain was intrinsically disordered and the linkers of the tetra-SUMO2 were highly flexible. Individual SIMs of the RNF4-SIMs domains bind to SUMO2 in the groove between the β2-strand and the α1-helix parallel to the β2-strand. SIM2 and SIM3 bound to SUMO with a high affinity and together constituted the recognition module necessary for SUMO binding. SIM4 alone bound to SUMO with low affinity; however, its contribution to tetra-SUMO2 binding avidity is comparable with that of SIM3 when in the RNF4-SIMs domain. The SAXS data of the tetra-SUMO2-RNF4-SIMs domain complex indicate that it exists as an ordered structure. The HADDOCK model showed that the tandem RNF4-SIMs domain bound antiparallel to the tetra-SUMO2 chain orientation and wrapped around the SUMO protamers in a superhelical turn without imposing steric hindrance on either molecule.

The fish and fisheries of Jones Bank and the wider Celtic Sea

Science.gov (United States)

Martinez, I.; Ellis, J. R.; Scott, B.; Tidd, A.

2013-10-01

information on the ichthyofauna of the Jones Bank. Further site-specific data for bank and off-bank habitats were collected during dedicated surveys on the Jones Bank in 2008 using commercial trawlers and baited camera deployments. Twenty-three species were recorded on the top of the bank, where horse mackerel, haddock and boarfish were the most abundant species; 18 species were found along the slope of the bank (with blue whiting, poor cod, hake and horse mackerel predominant) and 18 species observed off the bank (where catches were dominated by blue whiting, poor cod and hake). The differences between camera and trawls were important with cameras only picking up 28% of the species seen in the trawls. However both camera and trawl results suggest that some species are very habitat specific, with species such as haddock only observed on the top of the bank, whilst Nephrops norvegicus was abundant on the flat areas off the bank but was infrequent on the top of the bank. These results suggest that future surveys of offshore sandbank habitats should stratify sampling more specifically to deal with smaller scale features that may play an important role in providing a greater range of habitats than just their relative size would suggest.

Structural insights into a high affinity nanobody:antigen complex by homology modelling.

Science.gov (United States)

Skottrup, Peter Durand

2017-09-01

Porphyromonas gingivalis is a major periodontitis-causing pathogens. P. gingivalis secrete a cysteine protease termed RgpB, which is specific for Arg-Xaa bonds in substrates. Recently, a nanobody-based assay was used to demonstrate that RgpB could represent a novel diagnostic target, thereby simplifying. P. gingivalis detection. The nanobody, VHH7, had a high binding affinity and was specific for RgpB, when tested towards the highly identical RgpA. In this study a homology model of VHH7 was build. The complementarity determining regions (CDR) comprising the paratope residues responsible for RgpB binding were identified and used as input to the docking. Furthermore, residues likely involved in the RgpB epitope was identified based upon RgpB:RgpA alignment and analysis of residue surface accessibility. CDR residues and putitative RgpB epitope residues were used as input to an information-driven flexible docking approach using the HADDOCK server. Analysis of the VHH7:RgpB model demonstrated that the epitope was found in the immunoglobulin-like domain and residue pairs located at the molecular paratope:epitope interface important for complex stability was identified. Collectively, the VHH7 homology model and VHH7:RgpB docking supplies knowledge of the residues involved in the high affinity interaction. This information could prove valuable in the design of an antibody-drug conjugate for specific RgpB targeting. Copyright © 2017 Elsevier Inc. All rights reserved.

Structural insights into calcium-bound S100P and the V domain of the RAGE complex.

Directory of Open Access Journals (Sweden)

Srinivasa R Penumutchu

Full Text Available The S100P protein is a member of the S100 family of calcium-binding proteins and possesses both intracellular and extracellular functions. Extracellular S100P binds to the cell surface receptor for advanced glycation end products (RAGE and activates its downstream signaling cascade to meditate tumor growth, drug resistance and metastasis. Preventing the formation of this S100P-RAGE complex is an effective strategy to treat various disease conditions. Despite its importance, the detailed structural characterization of the S100P-RAGE complex has not yet been reported. In this study, we report that S100P preferentially binds to the V domain of RAGE. Furthermore, we characterized the interactions between the RAGE V domain and Ca(2+-bound S100P using various biophysical techniques, including isothermal titration calorimetry (ITC, fluorescence spectroscopy, multidimensional NMR spectroscopy, functional assays and site-directed mutagenesis. The entropy-driven binding between the V domain of RAGE and Ca(+2-bound S100P was found to lie in the micromolar range (Kd of ∼ 6 µM. NMR data-driven HADDOCK modeling revealed the putative sites that interact to yield a proposed heterotetrameric model of the S100P-RAGE V domain complex. Our study on the spatial structural information of the proposed protein-protein complex has pharmaceutical relevance and will significantly contribute toward drug development for the prevention of RAGE-related multifarious diseases.

Irradiated food: validity of extrapolating wholesomeness data

International Nuclear Information System (INIS)

Taub, I.A.; Angelini, P.; Merritt, C. Jr.

1976-01-01

Criteria are considered for validly extrapolating the conclusions reached on the wholesomeness of an irradiated food receiving high doses to the same food receiving a lower dose. A consideration first is made of the possible chemical mechanisms that could give rise to different functional dependences of radiolytic products on dose. It is shown that such products should increase linearly with dose and the ratio of products should be constant throughout the dose range considered. The assumption, generally accepted in pharmacology, then is made that if any adverse effects related to the food are discerned in the test animals, then the intensity of these effects would increase with the concentration of radiolytic products in the food. Lastly, the need to compare data from animal studies with foods irradiated to several doses against chemical evidence obtained over a comparable dose range is considered. It is concluded that if the products depend linearly on dose and if feeding studies indicate no adverse effects, then an extrapolation to lower doses is clearly valid. This approach is illustrated for irradiated codfish. The formation of selected volatile products in samples receiving between 0.1 and 3 Mrads was examined, and their concentrations were found to increase linearly at least up to 1 Mrad. These data were compared with results from animal feeding studies establishing the wholesomeness of codfish and haddock irradiated to 0.2, 0.6 and 2.8 Mrads. It is stated, therefore, that if ocean fish, currently under consideration for onboard processing, were irradiated to 0.1 Mrad, it would be correspondingly wholesome

Climate-driven changes in functional biogeography of Arctic marine fish communities.

Science.gov (United States)

Frainer, André; Primicerio, Raul; Kortsch, Susanne; Aune, Magnus; Dolgov, Andrey V; Fossheim, Maria; Aschan, Michaela M

2017-11-14

Climate change triggers poleward shifts in species distribution leading to changes in biogeography. In the marine environment, fish respond quickly to warming, causing community-wide reorganizations, which result in profound changes in ecosystem functioning. Functional biogeography provides a framework to address how ecosystem functioning may be affected by climate change over large spatial scales. However, there are few studies on functional biogeography in the marine environment, and none in the Arctic, where climate-driven changes are most rapid and extensive. We investigated the impact of climate warming on the functional biogeography of the Barents Sea, which is characterized by a sharp zoogeographic divide separating boreal from Arctic species. Our unique dataset covered 52 fish species, 15 functional traits, and 3,660 stations sampled during the recent warming period. We found that the functional traits characterizing Arctic fish communities, mainly composed of small-sized bottom-dwelling benthivores, are being rapidly replaced by traits of incoming boreal species, particularly the larger, longer lived, and more piscivorous species. The changes in functional traits detected in the Arctic can be predicted based on the characteristics of species expected to undergo quick poleward shifts in response to warming. These are the large, generalist, motile species, such as cod and haddock. We show how functional biogeography can provide important insights into the relationship between species composition, diversity, ecosystem functioning, and environmental drivers. This represents invaluable knowledge in a period when communities and ecosystems experience rapid climate-driven changes across biogeographical regions. Copyright © 2017 the Author(s). Published by PNAS.

Growth changes in plaice, cod, haddock and saithe in the North Sea: a comparison of (post-)medieval and present-day growth rates based on otolith measurements

NARCIS (Netherlands)

Bolle, L.J.; Rijnsdorp, A.D.; Neer, van W.; Millner, R.S.; Leeuwen, van P.I.; Ervynck, A.

2004-01-01

Fishing effort has strongly increased in the North Sea since the mid-19th century, causing a substantial reduction in the population size of exploited fish stocks. As fisheries research has developed simultaneously with the industrialisation of the fisheries, our knowledge of population dynamics at

Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex

International Nuclear Information System (INIS)

Hennig, Janosch; Wang, Iren; Sonntag, Miriam; Gabel, Frank; Sattler, Michael

2013-01-01

Many processes in the regulation of gene expression and signaling involve the formation of protein complexes involving multi-domain proteins. Individual domains that mediate protein-protein and protein-nucleic acid interactions are typically connected by flexible linkers, which contribute to conformational dynamics and enable the formation of complexes with distinct binding partners. Solution techniques are therefore required for structural analysis and to characterize potential conformational dynamics. Nuclear magnetic resonance spectroscopy (NMR) provides such information but often only sparse data are obtained with increasing molecular weight of the complexes. It is therefore beneficial to combine NMR data with additional structural restraints from complementary solution techniques. Small angle X-ray/neutron scattering (SAXS/SANS) data can be efficiently combined with NMR-derived information, either for validation or by providing additional restraints for structural analysis. Here, we show that the combination of SAXS and SANS data can help to refine structural models obtained from data-driven docking using HADDOCK based on sparse NMR data. The approach is demonstrated with the ternary protein-protein-RNA complex involving two RNA recognition motif (RRM) domains of Sex-lethal, the N-terminal cold shock domain of Upstream-to-N-Ras, and msl-2 mRNA. Based on chemical shift perturbations we have mapped protein-protein and protein-RNA interfaces and complemented this NMR-derived information with SAXS data, as well as SANS measurements on subunit-selectively deuterated samples of the ternary complex. Our results show that, while the use of SAXS data is beneficial, the additional combination with contrast variation in SANS data resolves remaining ambiguities and improves the docking based on chemical shift perturbations of the ternary protein-RNA complex.

Structural modelling and molecular dynamics of a multi-stress responsive WRKY TF-DNA complex towards elucidating its role in stress signalling mechanisms in chickpea.

Science.gov (United States)

Konda, Aravind Kumar; Farmer, Rohit; Soren, Khela Ram; P S, Shanmugavadivel; Setti, Aravind

2017-07-28

Chickpea is a premier food legume crop with high nutritional quality and attains prime importance in the current era of 795 million people being undernourished worldwide. Chickpea production encounters setbacks due to various stresses and understanding the role of key transcription factors (TFs) involved in multiple stresses becomes inevitable. We have recently identified a multi-stress responsive WRKY TF in chickpea. The present study was conducted to predict the structure of WRKY TF to identify the DNA-interacting residues and decipher DNA-protein interactions. Comparative modelling approach produced 3D model of the WRKY TF with good stereochemistry, local/global quality and further revealed W19, R20, K21, and Y22 motifs within a vicinity of 5 Å to the DNA amongst R18, G23, Q24, K25, Y36, Y37, R38 and K47 and these positions were equivalent to the 2LEX WRKY domain of Arabidopsis. Molecular simulations analysis of reference protein -PDB ID 2LEX, along with Car-WRKY TF modelled structure with the DNA coordinates derived from PDB ID 2LEX and docked using HADDOCK were executed. Root Mean Square (RMS) Deviation and RMS Fluctuation values yielded consistently stable trajectories over 50 ns simulation. Strengthening the obtained results, neither radius of gyration, distance and total energy showed any signs of DNA-WRKY complex falling apart nor any significant dissociation event over 50 ns run. Therefore, the study provides first insights into the structural properties of multi-stress responsive WRKY TF-DNA complex in chickpea, enabling genome wide identification of TF binding sites and thereby deciphers their gene regulatory networks.

Revista Brasileira de Enfermagem: uma história de resistência

Directory of Open Access Journals (Sweden)

Iraci dos Santos

1998-06-01

Full Text Available Parte das conquistas da ANEDB, atual ABEn, desde 1920 a REBEn se inseriu na luta dos protissionais pela difusão dos feitos da enfermagem. Deve-se a Edith Magalhães Fraenkel e Rachel Haddock Lobo a inspiração e iniciativa para criação, desde 1929, com a participação no I Congresso Quadrienal do ICN, em Montreal onde se discutiu facilidades, dificuldades e avanços dos periódicos de enfermagem. Os ANNAES de Enfermagem, editado pelo Jornal do Brasil - RJ, em 1932, foi o precursor da REBEn. Com sua existência, leitores, estudantes e profissionais ávidos por ampliar seus conhecimentos específicos, construtores da documentação histórica e do saber da profissão, responsáveis pelo desenvolvimento científico e tecnológico e pela emissão de conceitos de diferentes épocas da enfermagem brasileira, aprenderam a aproveitar seus benefícios. Com mais de 50 volumes e 200 números editados, a REBEn adquiriu "status" de referência nas áreas de saúde e das ciências humanas nacional e internacional. Já consolidada, dissemina resultados de dissertações, teses e trabalhos apresentados nos Congressos Brasileiros de Enfermagem. É o periódico mais consultado como fonte e campo de investigação científica. Propicia o crescimento de leitores, organizadores no processo de editoração e formação de conselheiros "ad hoc" através da avaliação e crítica permanentes.

Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex

Energy Technology Data Exchange (ETDEWEB)

Hennig, Janosch; Wang, Iren; Sonntag, Miriam [Institute of Structural Biology, Helmholtz Zentrum Muenchen (Germany); Gabel, Frank [Extremophiles and Large Molecular Assemblies Group (ELMA), Institut de Biologie Structurale (IBS) CEA-CNRS-UJF (France); Sattler, Michael, E-mail: sattler@helmholtz-muenchen.de [Institute of Structural Biology, Helmholtz Zentrum Muenchen (Germany)

2013-05-15

Many processes in the regulation of gene expression and signaling involve the formation of protein complexes involving multi-domain proteins. Individual domains that mediate protein-protein and protein-nucleic acid interactions are typically connected by flexible linkers, which contribute to conformational dynamics and enable the formation of complexes with distinct binding partners. Solution techniques are therefore required for structural analysis and to characterize potential conformational dynamics. Nuclear magnetic resonance spectroscopy (NMR) provides such information but often only sparse data are obtained with increasing molecular weight of the complexes. It is therefore beneficial to combine NMR data with additional structural restraints from complementary solution techniques. Small angle X-ray/neutron scattering (SAXS/SANS) data can be efficiently combined with NMR-derived information, either for validation or by providing additional restraints for structural analysis. Here, we show that the combination of SAXS and SANS data can help to refine structural models obtained from data-driven docking using HADDOCK based on sparse NMR data. The approach is demonstrated with the ternary protein-protein-RNA complex involving two RNA recognition motif (RRM) domains of Sex-lethal, the N-terminal cold shock domain of Upstream-to-N-Ras, and msl-2 mRNA. Based on chemical shift perturbations we have mapped protein-protein and protein-RNA interfaces and complemented this NMR-derived information with SAXS data, as well as SANS measurements on subunit-selectively deuterated samples of the ternary complex. Our results show that, while the use of SAXS data is beneficial, the additional combination with contrast variation in SANS data resolves remaining ambiguities and improves the docking based on chemical shift perturbations of the ternary protein-RNA complex.

A unified conformational selection and induced fit approach to protein-peptide docking.

Directory of Open Access Journals (Sweden)

Mikael Trellet

Full Text Available Protein-peptide interactions are vital for the cell. They mediate, inhibit or serve as structural components in nearly 40% of all macromolecular interactions, and are often associated with diseases, making them interesting leads for protein drug design. In recent years, large-scale technologies have enabled exhaustive studies on the peptide recognition preferences for a number of peptide-binding domain families. Yet, the paucity of data regarding their molecular binding mechanisms together with their inherent flexibility makes the structural prediction of protein-peptide interactions very challenging. This leaves flexible docking as one of the few amenable computational techniques to model these complexes. We present here an ensemble, flexible protein-peptide docking protocol that combines conformational selection and induced fit mechanisms. Starting from an ensemble of three peptide conformations (extended, a-helix, polyproline-II, flexible docking with HADDOCK generates 79.4% of high quality models for bound/unbound and 69.4% for unbound/unbound docking when tested against the largest protein-peptide complexes benchmark dataset available to date. Conformational selection at the rigid-body docking stage successfully recovers the most relevant conformation for a given protein-peptide complex and the subsequent flexible refinement further improves the interface by up to 4.5 Å interface RMSD. Cluster-based scoring of the models results in a selection of near-native solutions in the top three for ∼75% of the successfully predicted cases. This unified conformational selection and induced fit approach to protein-peptide docking should open the route to the modeling of challenging systems such as disorder-order transitions taking place upon binding, significantly expanding the applicability limit of biomolecular interaction modeling by docking.

Examination of the Fish Price Offered for Sale During 2012-2013 Fishing Season in Sinop, Turkey

Directory of Open Access Journals (Sweden)

Şennan Yücel

2017-10-01

Full Text Available The aim of the study was to determine the monthly price distribution of the offered fish species for sale within the scope of information received from the centers engaged in the sale of retail fish during 2012-2013 fishing season in Sinop, Turkey. The enterprises were grouped as I (the most, II (middle and III (the least according to the sales volume and fish species. Each group was represented by two different fish enterprise and so a total of six separate enterprises were determined by purpose sampling method. During the study, sale prices and fish species were obtained twice every month at the same time of day. It was determined that anchovy (Engraulis encrasicolus ponticus, horse mackerel (Trachurus trachurus, bluefish (Pomatomus saltatrix, atlantic bonito (Sarda sarda, twait shad (Alosa fallax nilotica, needlefish (Belone belone, mullet (Mugil cephalus, shi drum (Umbrina cirrosa, brown meagre (Sciana umbra, common two-banded seabream (Diplodus vulgaris, annular bream (Diplodus annularis, tub gurnard (Trigla lucerna, picarel (Maena smaris, turbot (Psetta maxima, red mullet (Mullus barbatus, whiting (Merlangus merlangus, scorpion fish (Scorpaena porcus, goby (Gobius niger were offered for sale in fish markets. While the prices of higher economic valued fish species like anchovy, bluefish, atlantic bonito and turbot prices were different between the enterprises, the prices of horse mackerel, red mullet and whiting species were not different. When considering the fish prices based on years, the prices of horse mackerel, bluefish, atlantic bonito, red mullet and haddock during 2012-2013 years were close to the average price of 2008-2012 years and the prices of anchovy and turbot during 2012-2013 years were higher than the average price of 2008-2012 years in Sinop.

Suramin blocks interaction between human FGF1 and FGFR2 D2 domain and reduces downstream signaling activity

Energy Technology Data Exchange (ETDEWEB)

Wu, Zong-Sian, E-mail: gary810426@hotmail.com [Department of Chemistry, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan (China); Liu, Che Fu, E-mail: s9823002@m98.nthu.edu.tw [Department of Chemistry, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan (China); Fu, Brian, E-mail: brianfu9@gmail.com [Northwood High School, Irvine, CA (United States); Chou, Ruey-Hwang, E-mail: rhchou@mail.cmu.edu.tw [Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, No.91, Hsueh-Shih Road, Taichung 40402, Taiwan (China); Department of Biotechnology, Asia University, Taiwan (China); Yu, Chin, E-mail: cyu.nthu@gmail.com [Department of Chemistry, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan (China)

2016-09-02

The extracellular portion of the human fibroblast growth factor receptor2 D2 domain (FGFR2 D2) interacts with human fibroblast growth factor 1 (hFGF1) to activate a downstream signaling cascade that ultimately affects mitosis and differentiation. Suramin is an antiparasiticdrug and a potent inhibitor of FGF-induced angiogenesis. Suramin has been shown to bind to hFGF1, and might block the interaction between hFGF1 and FGFR2 D2. Here, we titrated hFGF1 with FGFR2 D2 and suramin to elucidate their interactions using the detection of NMR. The docking results of both hFGF1-FGFR2 D2 domain and hFGF1-suramin complex were superimposed. The results indicate that suramin blocks the interaction between hFGF1 and FGFR2 D2. We used the PyMOL software to show the hydrophobic interaction of hFGF1-suramin. In addition, we used a Water-soluble Tetrazolium salts assay (WST1) to assess hFGF1 bioactivity. The results will be useful for the development of new antimitogenic activity drugs. - Highlights: • The interfacial residues on hFGF1-FGFR2 D2 and hFGF1-Suramin contact surface were mapped by {sup 1}H-{sup 15}N HSQC experiments. • hFGF1-FGFR2 D2 and hFGF1-Suramin complex models were generated from NMR restraints by using HADDOCK program. • We analyzed hFGF1-Suramin complex models and found the interaction between hFGF1-Suramin is hydrophobic. • The bioactivity of the hFGF1-FGFR2 D2 and hFGF1-Suramin complex was studied by using WST1 assay.

A method to assess social sustainability of capture fisheries: An application to a Norwegian trawler

Energy Technology Data Exchange (ETDEWEB)

Veldhuizen, L.J.L., E-mail: linda.veldhuizen@wur.nl [Animal Production Systems group, Wageningen University, P.O. Box 338, 6700 AH Wageningen (Netherlands); Berentsen, P.B.M. [Business Economics group, Wageningen University, P.O. Box 8130, 6700 EW Wageningen (Netherlands); Bokkers, E.A.M.; Boer, I.J.M. de [Animal Production Systems group, Wageningen University, P.O. Box 338, 6700 AH Wageningen (Netherlands)

2015-07-15

Social sustainability assessment of capture fisheries is, both in terms of method development and measurement, not well developed. The objective of this study, therefore, was to develop a method consisting of indicators and rubrics (i.e. categories that articulate levels of performance) to assess social sustainability of capture fisheries. This method was applied to a Norwegian trawler that targets cod and haddock in the northeast Atlantic. Based on previous research, 13 social sustainability issues were selected. To measure the state of these issues, 17 process and outcome indicators were determined. To interpret indicator values, rubrics were developed for each indicator, using standards set by international conventions or data retrieved from national statistics, industry agreements or scientific publications that explore rubric scales. The indicators and rubrics were subsequently used in a social sustainability assessment of a Norwegian trawler. This assessment indicated that overall, social sustainability of this trawler is relatively high, with high rubric scores, for example, for worker safety, provisions aboard for the crew and companies' salary levels. The assessment also indicated that the trawler could improve on healthy working environment, product freshness and fish welfare during capture. This application demonstrated that our method provides insight into social sustainability at the level of the vessel and can be used to identify potential room for improvement. This method is also promising for social sustainability assessment of other capture fisheries. - Highlights: • A method was developed for social sustainability assessment of capture fisheries. • This method entailed determining outcome and process indicators for important issues. • To interpret indicator values, a rubric was developed for each indicator. • Use of this method gives insight into social sustainability and improvement options. • This method is promising for social

A method to assess social sustainability of capture fisheries: An application to a Norwegian trawler

International Nuclear Information System (INIS)

Veldhuizen, L.J.L.; Berentsen, P.B.M.; Bokkers, E.A.M.; Boer, I.J.M. de

2015-01-01

Social sustainability assessment of capture fisheries is, both in terms of method development and measurement, not well developed. The objective of this study, therefore, was to develop a method consisting of indicators and rubrics (i.e. categories that articulate levels of performance) to assess social sustainability of capture fisheries. This method was applied to a Norwegian trawler that targets cod and haddock in the northeast Atlantic. Based on previous research, 13 social sustainability issues were selected. To measure the state of these issues, 17 process and outcome indicators were determined. To interpret indicator values, rubrics were developed for each indicator, using standards set by international conventions or data retrieved from national statistics, industry agreements or scientific publications that explore rubric scales. The indicators and rubrics were subsequently used in a social sustainability assessment of a Norwegian trawler. This assessment indicated that overall, social sustainability of this trawler is relatively high, with high rubric scores, for example, for worker safety, provisions aboard for the crew and companies' salary levels. The assessment also indicated that the trawler could improve on healthy working environment, product freshness and fish welfare during capture. This application demonstrated that our method provides insight into social sustainability at the level of the vessel and can be used to identify potential room for improvement. This method is also promising for social sustainability assessment of other capture fisheries. - Highlights: • A method was developed for social sustainability assessment of capture fisheries. • This method entailed determining outcome and process indicators for important issues. • To interpret indicator values, a rubric was developed for each indicator. • Use of this method gives insight into social sustainability and improvement options. • This method is promising for social

Suramin blocks interaction between human FGF1 and FGFR2 D2 domain and reduces downstream signaling activity

International Nuclear Information System (INIS)

Wu, Zong-Sian; Liu, Che Fu; Fu, Brian; Chou, Ruey-Hwang; Yu, Chin

2016-01-01

The extracellular portion of the human fibroblast growth factor receptor2 D2 domain (FGFR2 D2) interacts with human fibroblast growth factor 1 (hFGF1) to activate a downstream signaling cascade that ultimately affects mitosis and differentiation. Suramin is an antiparasiticdrug and a potent inhibitor of FGF-induced angiogenesis. Suramin has been shown to bind to hFGF1, and might block the interaction between hFGF1 and FGFR2 D2. Here, we titrated hFGF1 with FGFR2 D2 and suramin to elucidate their interactions using the detection of NMR. The docking results of both hFGF1-FGFR2 D2 domain and hFGF1-suramin complex were superimposed. The results indicate that suramin blocks the interaction between hFGF1 and FGFR2 D2. We used the PyMOL software to show the hydrophobic interaction of hFGF1-suramin. In addition, we used a Water-soluble Tetrazolium salts assay (WST1) to assess hFGF1 bioactivity. The results will be useful for the development of new antimitogenic activity drugs. - Highlights: • The interfacial residues on hFGF1-FGFR2 D2 and hFGF1-Suramin contact surface were mapped by "1H-"1"5N HSQC experiments. • hFGF1-FGFR2 D2 and hFGF1-Suramin complex models were generated from NMR restraints by using HADDOCK program. • We analyzed hFGF1-Suramin complex models and found the interaction between hFGF1-Suramin is hydrophobic. • The bioactivity of the hFGF1-FGFR2 D2 and hFGF1-Suramin complex was studied by using WST1 assay.

Understanding Aggregation and Estimating Seasonal Abundance of Chrysaora quinquecirrha Medusae from a Fixed-station Time Series in the Choptank River, Chesapeake Bay

Science.gov (United States)

Tay, J.; Hood, R. R.

2016-02-01

Although jellyfish exert strong control over marine plankton dynamics (Richardson et al. 2009, Robison et al. 2014) and negatively impact human commercial and recreational activities (Purcell et al. 2007, Purcell 2012), jellyfish biomass is not well quantified due primarily to sampling difficulties with plankton nets or fisheries trawls (Haddock 2004). As a result, some of the longest records of jellyfish are visual shore-based surveys, such as the fixed-station time series of Chrysaora quinquecirrha that began in 1960 in the Patuxent River in Chesapeake Bay, USA (Cargo and King 1990). Time series counts from fixed-station surveys capture two signals: 1) demographic change at timescales on the order of reproductive processes and 2) spatial patchiness at shorter timescales as different parcels of water move in and out of the survey area by tidal and estuarine advection and turbulent mixing (Lee and McAlice 1979). In this study, our goal was to separate these two signals using a 4-year time series of C. quinquecirrha medusa counts from a fixed-station in the Choptank River, Chesapeake Bay. Idealized modeling of tidal and estuarine advection was used to conceptualize the sampling scheme. Change point and time series analysis was used to detect demographic changes. Indices of aggregation (Negative Binomial coefficient, Taylor's Power Law coefficient, and Morisita's Index) were calculated to describe the spatial patchiness of the medusae. Abundance estimates revealed a bloom cycle that differed in duration and magnitude for each of the study years. Indices of aggregation indicated that medusae were aggregated and that patches grew in the number of individuals, and likely in size, as abundance increased. Further inference from the conceptual modeling suggested that medusae patch structure was generally homogenous over the tidal extent. This study highlights the benefits of using fixed-station shore-based surveys for understanding the biology and ecology of jellyfish.

Productivity patterns and abundance-area relationships in 3 marine fish species (cod,herring and haddock); meta-analyses on the effects of temperature, life-history andhabitat size across the N Atlantic

DEFF Research Database (Denmark)

Mantzouni, Irene; MacKenzie, Brian

Stock status evaluation and recovery policies in fisheries management rely largely onreference points derived from spawner-recruit (SR) models. The key-parameters of thesemodels, representing productivity and carrying capacity, have been shown to be sensitive toenvironmental forcing and to depend...

Pentamidine blocks the interaction between mutant S100A5 and RAGE V domain and inhibits the RAGE signaling pathway

Energy Technology Data Exchange (ETDEWEB)

Cho, Ching Chang, E-mail: ccjwo@yahoo.com.tw [Department of Chemistry, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan (China); Chou, Ruey Hwang, E-mail: rhchou@mail.cmu.edu.tw [Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, No.91, Hsueh-Shih Road, Taichung 40402, Taiwan (China); Yu, Chin, E-mail: cyu.nthu@gmail.com [Department of Chemistry, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan (China)

2016-08-19

The human S100 protein family contains small, dimeric and acidic proteins that contain two EF-hand motifs and bind calcium. When S100A5 binds calcium, its conformation changes and promotes interaction with the target protein. The extracellular domain of RAGE (Receptor of Advanced Glycation End products) contain three domains: C1, C2 and V. The RAGE V domain is the target protein of S100A5 that promotes cell survival, growth and differentiation by activating several signaling pathways. Pentamidine is an apoptotic and antiparasitic drug that is used to treat or prevent pneumonia. Here, we found that pentamidine interacts with S100A5 using HSQC titration. We elucidated the interactions of S100A5 with RAGE V domain and pentamidine using fluorescence and NMR spectroscopy. We generated two binary models—the S100A5-RAGE V domain and S100A5-Pentamidine complex—and then observed that the pentamidine and RAGE V domain share a similar binding region in mS100A5. We also used the WST-1 assay to investigate the bioactivity of S100A5, RAGE V domain and pentamidine. These results indicated that pentamidine blocks the binding between S100A5 and RAGE V domain. This finding is useful for the development of new anti-proliferation drugs. - Highlights: • The interaction between mS100A5–RAGE V was investigated by fluorescence spectroscopy. • The interfacial residues on mS100A5–RAGE V and mS100A5–pentamidine contact surface were mapped by {sup 1}H-{sup 15}N HSQC experiments. • mS100A5–RAGE V and mS100A5–pentamidine complex models were generated from NMR restraints using HADDOCK program. • The bioactivity of the mS100A5–RAGE V and mS100A5–pentamidine complex was studied using WST-1 assay.

Targeted Molecular Dynamics to determine Focal Adhesion Targeting Domain Folding Intermediates

Directory of Open Access Journals (Sweden)

Pallavi Mohanty

2017-10-01

Full Text Available The Focal adhesion kinase (FAT domain of Focal Adhesion Kinase is a four helical bundle known for conformational plasticity. FAT adopts two distinctly different conformations i.e., close (cFAT and arm-exchanged (aeFAT states under native conditions [1]. The slow transition from cFAT to aeFAT is likely to proceed through an open intermediate state that allows YENV motif to attain β-turn conformation and phosphorylation of Y925 by Src kinases [2]. The two end states of FAT are known to interact with Paxillin and are responsible for maintaining steady state in Heart while intermediate conformation interacts with Grb2-SH2 leading to Pathological Cardiac Hypertrophy (PAH [2]. 10ns Targeted Molecular Dynamics (TMD was done between c- and aeFAT in order to explore the conformational transition and to capture pathologically relevant oFAT. Cluster and dynamic cross correlation analysis (DCCA of TMD generated trajectory was done and the selected FAT intermediate was docked with Grb2-SH2 using HADDOCK v2.2 docking followed by molecular dynamics. Conservation analysis of FAT-Grb2 binding site was done using CONSURF [3]. A Pharmacophore FAT-Grb2 complex was generated using SPARKv1.2 and submitted for Virtual screening using BLAZE v4. Drug likeliness and ADMET properties were calculated using MOLINSPIRATION tool. TMD reveals six clusters and DCCA showed positively and negatively correlated region along the transition pathway. Intermediates with competence for Grb2 interaction were docked with Grb2 and best binding complex was further refined. MMPBSA binding energy calculations revealed the best binding pose where the phosphorylated YENV motif of Human FAT interacted with a charged and hydrophobic pocket of Grb2. The conservation analysis showed that the charged pocket was more conserved in comparison with the hydrophobic pocket, hence providing useful insights on binding and specificity determining residues in Grb2. Virtual screening using the pharmacophore

Development of technology for gourmet smoked products from cod species using enzyme preparation from hepatopancreas of snow crab Chionoecetes opilio

Directory of Open Access Journals (Sweden)

E. B. Shkuratova

2017-01-01

Full Text Available At the Food Production Department of Murmansk State Technical University (MSTU was developed a technology of production of smoked fish products with the use of air-flue mixture, produced in an infrared smoke generator under conditions of low-temperature pyrolysis of wood chips with an initial moisture content of 40 to 60% and a bulk density of from 104 to 154 kg/m3. A method of producing smoke and its hardware design enabled to securely control the temperature of the smoke receiving smoking environment, which guarantees a minimum content of threat to human health of polycyclic aromatic hydrocarbons (РАНs. The developed technology involves short cycle smoked salted semi – fish fillets and allows to obtain finished products with excellent organoleptic properties. The content of РАНs in finished products less than 0.0002 microgram/kg, which is significantly below the maximum permissible concentrations (MPC according to the requirements of SаnРiN 2.3.2.1078 (less than 0.001 mg/kg product and according to the requirements of TR CU 021/2011 (0.005 mg/kg product. This technology successfully implemented in production at fish processing plants in Murmansk region. However, marketing research has shown that the market for smoked fish in the Murmansk region is characterized by a narrow range, which affects consumer demand and reduces the competitiveness of the regional enterprises-manufacturers of smoked products. To solve this problem it is offered to expand the range of smoked fish products due to use of non-traditional Smoking techniques raw materials – fillet of cod fish (saithe, haddock, cod. To improve consumer properties of products, in particular, to improve the indicator of “consistency: and "juiciness" of the proposed use on the stage of the salting of prefabricated enzyme preparation from hepatopancreas of snow crab (Chionoecetes opilio, added to brine with density of 1.18 to 1.2 g/сm3 at a dosage of 0.04%, the curing time of

Preclinical Biodistribution and Safety Evaluation of a pbi-shRNA STMN1 Lipoplex after Subcutaneous Delivery.

Science.gov (United States)

Wang, Zhaohui; Jay, Christopher M; Evans, Courtney; Kumar, Padmasini; Phalon, Connor; Rao, Donald D; Senzer, Neil; Nemunaitis, John

2017-02-01

Stathmin-1 (STMN1) is a microtubule-destabilizing protein which is overexpressed in cancer. Its overexpression is associated with poor prognosis and also serves as a predictive marker to taxane therapy. We have developed a proprietary bi-functional shRNA (bi-shRNA) platform to execute RNA interference (RNAi)-mediated gene silencing and a liposome-carrier complex to systemically deliver the pbi-shRNA plasmids. In vitro and in vivo testing demonstrated efficacy and specificity of pbi-shRNA plasmid in targeting STMN1 (Phadke, A. P., Jay, C. M., Wang, Z., Chen, S., Liu, S., Haddock, C., Kumar, P., Pappen, B. O., Rao, D. D., Templeton, N. S., et al. (2011). In vivo safety and antitumor efficacy of bifunctional small hairpin RNAs specific for the human Stathmin 1 oncoprotein. DNA Cell Biol. 30, 715-726.). Biodistribution and toxicology studies in bio-relevant Sprague Dawley rats with pbi-shRNA STMN1 lipoplex revealed that the plasmid DNA was delivered to a broad distribution of organs after a single subcutaneous injection. Specifically, plasmid was detected within the first week using QPCR (threshold 50 copies plasmid/1 µg genomic DNA) at the injection site, lung, spleen, blood, skin, ovary (limited), lymph nodes, and liver. It was not detected in the heart, testis or bone marrow. No plasmid was detected from any organ 30 days after injection. Treatment was well tolerated. Minimal inflammation/erythema was observed at the injection site. Circulating cytokine response was also examined by ELISA. The IL-6 levels were induced within 6 h then declined to the vehicle control level 72 h after the injection. TNFα induction was transiently observed 4 days after the DNA lipoplex treatment. In summary, the pbi-shRNA STMN1 lipoplex was well tolerated and displayed broad distribution after a single subcutaneous injection. The pre-clinical data has been filed to FDA and the pbi-shRNA STMN1 lipoplex is being investigated in a phase I clinical study. © The Author 2016. Published

Obituary: Cornell H. Mayer, 1921-2005

Science.gov (United States)

Radhakrishnan, Venkataraman

2006-12-01

Cornell (Connie) H. Mayer, a pioneer of radio astronomy, died on 19 November 2005 of congestive heart failure at his home in Mt. Vernon, Virginia. He was eighty-three. Cornell Mayer was born in Ossian, Iowa on 10 December 1921. After graduating from the University of Iowa in 1943, he joined the Navy during World War II and was stationed at the Naval Research Laboratory (NRL) in Washington, DC. There he assisted Fred T. Haddock in the development of the first radar antenna inside a submarine periscope. This device has been credited with shortening the war in the Pacific because of the number of Japanese ships that were sunk with its aid. With Haddock, Connie also discovered centimeter-wave radio bursts from the sun coincident with solar flares. They made the first detection of thermal radio emission from the Orion nebula and other galactic HII regions. They also detected extragalactic objects and thus initiated the important field of centimeter-wave astronomy. Their observations were made with a 50-foot parabolic reflector on a gun mount located on the roof of one of the NRL buildings. This telescope had the world's highest radio resolving power for many years. With Haddock's departure to the University of Michigan in 1956 to create a new radio observatory there, Connie became head of a group in the Radio Astronomy Branch at NRL, where he remained until his retirement in 1980. Much of his work involved the measurement of planetary temperatures by analysis of radio emissions. By making technical innovations in instrumentation--such as replacing disc choppers with a ferrite switch to compare the sky and reference load, or using argon gas tubes for calibration--Connie greatly improved the performance of his equipment. This resulted in the discovery of an astonishing, 600oC surface temperature of Venus, which contradicted the widespread notion that Venus was similar to the Earth and potentially habitable. In spite of the extraordinarily careful and systematic way that

Present Status and Future Prospects of Irradiation Preservation for Fish; Etat Actuel et Perspectives de la Radioconservation du Poisson; Nastoyashchee polozhenie i perspektivy na budushchee v sterilizatsii ryby putem oblucheniya; Estado Actual y Perspectivas de la Conservacion de Pescado por Irradiacion

Energy Technology Data Exchange (ETDEWEB)

Shewan, J. M. [Torry Research Station, Aberdeen, Scotland (United Kingdom)

1966-11-15

All the present evidence seems to.show that radiation sterilization of almost all kinds of sea foods is not a practical proposition owing to the production of undesirable organoleptic changes, mainly in flavour and odour, of the cooked product. On the other hand, a variety of sea foods (including about 30 species of fish and shellfish) can withstand pasteurizing doses of from 0.3 to 0.5. Mrad without any such organoleptic changes being detectable. Moreover, the shelf life of such irradiated products, in terms of good commercial quality, can be extended by factors of approximately 1 Vulgar-Fraction-One-Half and 2 times at storage temperatures of 40 and 32 Degree-Sign F respectively. Thus, newly-caught cod and haddock which remain of good quality for a shelf life of 9 and 12 days at 40 and 32 Degree-Sign F can, after irradiation at 0.3 Mrad, still have similar qualities after storage at these temperatures for approximately 14 and 24 days, respectively. To obtain the maximum extension of storage life, irradiation on board the fishing vessel would be the most appropriate, but the technical difficulties of such a task are formidable. Most of the white fish, such as cod arid haddock, are not landed immediately after catching but may be anything from a few hours old up to the limit of edibility, viz. about 17 days for well-iced cod at 32 Degree-Sign F at landing. Accordingly, the longer the fish have been stored in the fishing vessel before landing the shorter the remaining life on shore. Taking the storage limit of good commercial quality cod and haddock as being 9 and 12 days at 40 and 32 Degree-Sign F respectively, experiment has shown that the remaining shelf life of such species on landing can be extended by factors of approximately 1 1/2 and 2 at 40 and 32 Degree-Sign F. Thus, cod or haddock stored for six days at 32 Degree-Sign F before landing would have their subsequent storage life of six days at landing extended to twelve if irradiated. Feasibility studies in

Winter distribution of euphausiids ( Euphausiacea) in the Barents Sea (2000-2005)

Science.gov (United States)

Zhukova, Natalia G.; Nesterova, Valentina N.; Prokopchuk, Irina P.; Rudneva, Galina B.

2009-10-01

disappearing in 1970-1990s. The peak of this species' occurrence (18-26%) took place in the beginning of warm period (1999-2000) after a succession of cold years. The subsequent reduction of the relative abundance of M. norvegica to 7% might have been mostly caused by fish predation during a period of low population densities of capelin. This high predation pressure may therefore have been mediated both by other pelagic fishes (i.e. herring, blue whiting, polar cod) but also by demersal fishes such as cod and haddock. Similar sharp fluctuations in the capelin stock (the major consumer of euphausiids) created marked perturbations in the food web in the Barents Sea in the middle 1980s and the early 1990s.

Collection, pre-treatment and analyses of Cs-137 and Tc-99 in marine samples at the Institute of Marine Research (IMR), Norway

International Nuclear Information System (INIS)

Heldal, H.E.

2010-01-01

Full text: The Institute of Marine Research (IMR) is an important contributor to the Norwegian marine monitoring programme RAME (Radioactivity in the Marine Environment). RAME is funded by the Ministry of the Environment and coordinated by the Norwegian Radiation Protection Authority (NRPA). Sample collection is performed from IMRs research vessels in the open sea areas of the North-, Norwegian- and Barents Seas and in Norwegian fjords. The samples consist of biota (fish and other marine organisms), sediments and seawater. Biota samples are frozen onboard the ship and transported to IMR where the samples are subsequently ground up, freeze dried, homogenized and aliquoted into polyethylene counting boxes of appropriate size prior to analysis. Attempts are made to collect filets from 25 fish for each sample of large fish such as cod, haddock, saithe, red-fish and Greenland halibut. For smaller fish (e.g. blue whiting, polar cod, capelin and Atlantic herring) and other organisms such as amphipods, krill, and deep-sea shrimps, a sample of 2-3 kg of each species is taken. These samples are ground up whole. Sediment samples are collected using a Smoegen boxcorer, from where both surface samples and cores are taken. The samples are frozen onboard the ship. While half-frozen, the cores are cut into slices of 1 or 2 cm thickness on board the ship, then frozen again and transported to IMR where they are treated as described above for the biota samples. Large volumes (typically 50-200 L) of seawater are needed in order to get enough material for analysis. Pre-treatment of the samples in the field is therefore an advantage. Surface samples (5 m) of seawater are collected from a shipboard pump, while a CTD-rosette multi-bottle sampler with 12 10 L samplers is used to collect seawater from depths below 5 meters. For the analysis of Cs-137, Cu 2 [Fe(CN) 6 ]-impregnated cotton filters are used for the pre-concentration. One pre-filter without impregnation, two Cu 2 [Fe(CN) 6

Obituary: Michael John Klein, 1940-2005

Science.gov (United States)

Gulkis, Samuel

2006-12-01

Michael John Klein died on 14 May 2005 at home in South Pasadena, California. The cause of death was tongue cancer that metastasized to the lungs. He was a non-smoker. Mike was a passionate radio astronomer, a trusted astronomical observer, an educator and a family man. Mike was born on 19 January 1940 in Ames, Iowa, the son of Florence Marie (Graf) and Fred Michael Klein. His mother was a homemaker, and his father was a banker. Mike had two older sisters, Lois Jean (Klein) Flauher and Marilyn June (Klein) Griffin. In 1962, Mike married his high school sweetheart Barbara Dahlberg, who survives him along with their three children, Kristin Marie (Klein) Shields, Michael John Klein Jr., Timothy Joel Klein, and six grandchildren. Mike developed a love for astronomy early in his life, and credited an early morning, newspaper-delivery route that he had at age twelve, which took him outside well before sunrise. He told family members that as he walked along his route, he stared into the sky and wondered what everything was. He studied sky charts, located stars, and began to understand how the planets shifted their positions relative to the stars each day. Another big influence in Mike's life was his brother in-law, Jim Griffin. Jim helped Mike understand that his passion for science did not have to remain a hobby, but could and should become a career. Jim's encouragement led Mike to attend Iowa State University in Ames, where he earned a BS in electrical engineering in 1962. Mike then started graduate school in electrical engineering at Michigan State, but after one semester transferred to the University of Michigan, Ann Arbor, where he earned an MS (1966) and PhD (1968) in astronomy. His doctoral dissertation, under the direction of Professor Fred Haddock, was based on extensive observations of the planets and examined the physical and thermal properties of planetary atmospheres and surfaces. Mike was awarded a Resident Research Associate position at JPL by the National