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Bent Herrmann - One of the best experts on this subject based on the ideXlab platform.
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improving release efficiency of cod gadus morhua and Haddock melanogrammus aeglefinus in the barents sea demersal trawl fishery by stimulating escape behaviour
Canadian Journal of Fisheries and Aquatic Sciences, 2018Co-Authors: Eduardo Grimaldo, Roger B Larsen, Bent Herrmann, Manu Berrondo Sistiaga, Jesse Brinkhof, Ivan TatoneAbstract:We tested the ability of stimulators to improve the release efficiency of cod (Gadus morhua) and Haddock (Melanogrammus aeglefinus) through the meshes of a square mesh section installed in a trawl....
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size selective performance of two flexible sorting grid designs in the northeast arctic cod gadus morhua and Haddock melanogrammus aeglefinus fishery
Fisheries Research, 2016Co-Authors: Manu Berrondo Sistiaga, Eduardo Grimaldo, Bent Herrmann, Jesse Brinkhof, Lise Langard, Dagfinn LillengAbstract:The flexigrid is a flexible double grid design and is one of the mandatory selection devices used in the Northeast Arctic cod (Gadus morhua) and Haddock (Melanogrammus aeglefinus) fishery. Traditionally the flexigrid is mounted in a two-panel extension section of a trawl just ahead of the codend, but this design has performance limitations, especially during high volume catch situations. The aim of this study was to investigate the size selective properties of a new four-panel section design for the flexigrid and compare them to those of the traditional two-panel section. Specifically, we wanted to determine if this new design would increase the probability for undersized fish to make contact with the grid and subsequently escape through at least one of the two grids in the section. We quantified the parameter “grid contact” for both grids independently and combined for both the mandatory two-panel and the new four-panel designs. We directly compared the two designs using a single trawl with a three compartment experimental design which enabled estimation of the contribution of each of the grids to the combined selectivity of the flexigrid section. The results based on 51 hauls with 108,518 cod and Haddock length measurements indicate that the four-panel flexigrid design was better able to release undersized fish than the two-panel design. While the mean values of “grid contact” estimated for both grid designs were similar, the four-panel section had lower risk of clogging in situations of high fish entry rates. Underwater video recordings revealed that the cause for this difference between designs may be related to the difference in shape of the two sections while fishing. The results showed that undersized cod escape mostly through the lower grid of the flexigrid section, whereas Haddock generally utilize the upper grid. This finding is in good agreement with the behavioral differences previously described for these two species. Due to the favourable results obtained from this study, the four-panel flexigrid section is now legalized in the Northeast Arctic cod and Haddock fishery.
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size selection of Haddock melanogrammus aeglefinus in square mesh codends a study based on assessment of decisive morphology for mesh penetration
Fisheries Research, 2011Co-Authors: Ludvig Ahm Krag, Niels Madsen, Bent Herrmann, Rikke FrandsenAbstract:Abstract In the past, experimental fishing with square mesh codends was conducted with the expectation that this would lead to a better defined size selection indicated by a smaller selection range (SR) of Haddock ( Melanogrammus aeglefinus ) and other gadoid species compared to that provided by traditional diamond mesh codends. However, experimental results demonstrated considerable between-haul variations in the selection parameters (L50 and SR). It was speculated that these results could be linked to differences in morphology of individual Haddock of the same length. In the present study we assessed which measures of Haddock morphology are important for size selection through meshes. We quantified between-individual variation in morphology and used simulation techniques to estimate that this variation can account for less than 28% (range 15–28%) of the SR values found during experimental fishing. By including a realistic range of mesh openings when simulating the fishing process of a square mesh codend, we were able to explain most of the experimental results. Additionally, we used our method to better understand the seasonal variation in size selectivity reported in the literature and to predict the basic selective properties for Haddock for other mesh shapes. Finally, we found that the conditions of our model, which describes mesh penetration for Haddock based on assessment of morphology, is very similar to the conditions previously applied in the literature to study size selection of Haddock in diamond mesh codends.
Eduardo Grimaldo - One of the best experts on this subject based on the ideXlab platform.
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improving release efficiency of cod gadus morhua and Haddock melanogrammus aeglefinus in the barents sea demersal trawl fishery by stimulating escape behaviour
Canadian Journal of Fisheries and Aquatic Sciences, 2018Co-Authors: Eduardo Grimaldo, Roger B Larsen, Bent Herrmann, Manu Berrondo Sistiaga, Jesse Brinkhof, Ivan TatoneAbstract:We tested the ability of stimulators to improve the release efficiency of cod (Gadus morhua) and Haddock (Melanogrammus aeglefinus) through the meshes of a square mesh section installed in a trawl....
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size selective performance of two flexible sorting grid designs in the northeast arctic cod gadus morhua and Haddock melanogrammus aeglefinus fishery
Fisheries Research, 2016Co-Authors: Manu Berrondo Sistiaga, Eduardo Grimaldo, Bent Herrmann, Jesse Brinkhof, Lise Langard, Dagfinn LillengAbstract:The flexigrid is a flexible double grid design and is one of the mandatory selection devices used in the Northeast Arctic cod (Gadus morhua) and Haddock (Melanogrammus aeglefinus) fishery. Traditionally the flexigrid is mounted in a two-panel extension section of a trawl just ahead of the codend, but this design has performance limitations, especially during high volume catch situations. The aim of this study was to investigate the size selective properties of a new four-panel section design for the flexigrid and compare them to those of the traditional two-panel section. Specifically, we wanted to determine if this new design would increase the probability for undersized fish to make contact with the grid and subsequently escape through at least one of the two grids in the section. We quantified the parameter “grid contact” for both grids independently and combined for both the mandatory two-panel and the new four-panel designs. We directly compared the two designs using a single trawl with a three compartment experimental design which enabled estimation of the contribution of each of the grids to the combined selectivity of the flexigrid section. The results based on 51 hauls with 108,518 cod and Haddock length measurements indicate that the four-panel flexigrid design was better able to release undersized fish than the two-panel design. While the mean values of “grid contact” estimated for both grid designs were similar, the four-panel section had lower risk of clogging in situations of high fish entry rates. Underwater video recordings revealed that the cause for this difference between designs may be related to the difference in shape of the two sections while fishing. The results showed that undersized cod escape mostly through the lower grid of the flexigrid section, whereas Haddock generally utilize the upper grid. This finding is in good agreement with the behavioral differences previously described for these two species. Due to the favourable results obtained from this study, the four-panel flexigrid section is now legalized in the Northeast Arctic cod and Haddock fishery.
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exit windows as an alternative selective system for the barents sea demersal fishery for cod and Haddock
Fisheries Research, 2007Co-Authors: Eduardo Grimaldo, Roger B Larsen, Rene HolstAbstract:Abstract During a 4-year research period, trouser trawl experiments were performed to assess the cod and Haddock selection capacity of a codend fitted with two 130 mm exit windows. These windows, which were 10 meshes high and 45 meshes long, were inserted in the rearmost part of the codend. The results showed that this codend was very efficient in releasing large amounts of undersized fish and the 50% retention length (l50) was far above the minimum landing size (MLS) for both the analysed species (the MLS for cod is 47 cm, 44 cm for Haddock). For cod, the mean l50 values varied between 53.6 and 57.3 cm and the mean selection range (SR) values from 6.8 to 9.3 cm. Haddock was measured during two trials with the mean l50 at 50.5 and 50.6 cm; and the mean SR values at 6.3 and 6.0 cm. Total catch weights varied between 0.7 and 6.6 metric tonnes. In some cases an important effect of catch weights upon the l50 could be detected.
Alexandre M J J Bonvin - One of the best experts on this subject based on the ideXlab platform.
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shape restrained modelling of protein small molecule complexes with Haddock
bioRxiv, 2021Co-Authors: Panos Koukos, Manon Reau, Alexandre M J J BonvinAbstract:Small molecule docking remains one of the most valuable computational techniques for the structure prediction of protein-small molecule complexes. It allows us to study the interactions between compounds and the protein receptors they target at atomic detail, in a timely and efficient manner. Here we present a new protocol in Haddock, our integrative modelling platform, which incorporates homology information for both receptor and compounds. It makes use of Haddocks unique ability to integrate information in the simulation to drive it toward conformations which agree with the provided data. The focal point is the use of shape restraints derived from homologous compounds bound to the target receptors. We have developed two protocols: In the first, the shape is composed of fake atom beads based on the position of the heavy atoms of the homologous template compound, whereas in the second the shape is additionally annotated with pharmacophore data, for some or all beads. For both protocols, ambiguous distance restraints are subsequently defined between those beads and the heavy atoms of the ligand to be docked. We have benchmarked the performance of these protocols with a fully unbound version of the widely used DUD-E dataset. In this unbound docking scenario, our template/shape-based docking protocol reaches an overall success rate of 81% on 99 complexes, which is close to the best results reported for bound docking on the DUD-E dataset. Table of contents graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/447890v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1bede28org.highwire.dtl.DTLVardef@1eb1e38org.highwire.dtl.DTLVardef@10d1ba0org.highwire.dtl.DTLVardef@190ac11_HPS_FORMAT_FIGEXP M_FIG C_FIG
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understanding docking complexes of macromolecules using Haddock the synergy between experimental data and computations
Bio-protocol, 2020Co-Authors: A.c. Saponaro, Alexandre M J J Bonvin, V. Maione, F. CantiniAbstract:This protocol illustrates the modelling of a protein-peptide complex using the synergic combination of in silico analysis and experimental results. To this end, we use the integrative modelling software Haddock, which possesses the powerful ability to incorporate experimental data, such as NMR Chemical Shift Perturbations and biochemical protein-peptide interaction data, as restraints to guide the docking process. Based on the modelling results, a rational mutagenesis approach is used to validate the generated models. The experimental results allow to select a final structural model best representing the bona fide protein-peptide complex. The described protocol can also be applied to model protein-protein complexes. There is no size limit for the macromolecular complexes that can be characterized by Haddock as long as the 3D structures of the individual components are available.
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dmm pbsa a new Haddock scoring function for protein peptide docking
Frontiers in Molecular Biosciences, 2016Co-Authors: Dimitrios Spiliotopoulos, Alexandre M J J Bonvin, Panagiotis L Kastritis, Adrien S J Melquiond, Giovanna Musco, Walter Rocchia, Andrea SpitaleriAbstract:Molecular-docking programs coupled with suitable scoring functions are now established and very useful tools enabling computational chemists to rapidly screen large chemical databases and thereby to identify promising candidate compounds for further experimental processing. In a broader scenario, predicting binding affinity is one of the most critical and challenging components of computer-aided structure-based drug design. The development of a molecular docking scoring function which in principle could combine both features, namely ranking putative poses and predicting complex affinity, would be of paramount importance. Here, we systematically investigated the performance of the MM-PBSA approach, using two different Poisson-Boltzmann solvers (APBS and DelPhi), in the currently rising field of protein-peptide interactions (PPIs), identifying the correct binding conformations of 19 different protein-peptide complexes and predicting their binding free energies. First, we scored the decoy structures from Haddock calculation via the MM-PBSA approach in order to assess the capability of retrieving near-native poses in the best-scoring clusters and of evaluating the corresponding free energies of binding. MM-PBSA behaves well in finding the poses corresponding to the lowest binding free energy, however the built-in Haddock score shows a better performance. In order to improve the MM-PBSA-based scoring function, we dampened the MM-PBSA solvation and coulombic terms by 0.2, as proposed in the Haddock score and LIE approaches. The new dampened MM-PBSA (dMM-PBSA) outperforms the original MM-PBSA and ranks the decoys structures as the Haddock score does. Second, we found a good correlation between the dMM-PBSA and Haddock scores for the near-native clusters of each system and the experimental binding energies, respectively. Therefore, we propose a new scoring function, dMM-PBSA, to be used together with the built-in Haddock score in the context of protein-peptide docking simulations.
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Haddock 2p2i a biophysical model for predicting the binding affinity of protein protein interaction inhibitors
Journal of Chemical Information and Modeling, 2014Co-Authors: Panagiotis L Kastritis, Joao P G L M Rodrigues, Alexandre M J J BonvinAbstract:The Haddock score, a scoring function for both protein-protein and protein-nucleic acid modeling, has been successful in selecting near-native docking poses in a variety of cases, including those of the CAPRI blind prediction experiment. However, it has yet to be optimized for small molecules, and in particular inhibitors of protein-protein interactions, that constitute an "unmined gold reserve" for drug design ventures. We describe here Haddock(2P2I), a biophysical model capable of predicting the binding affinity of protein-protein complex inhibitors close to experimental error (~2-fold larger). The algorithm was trained and 4-fold cross-validated against experimental data for 27 inhibitors targeting 7 protein-protein complexes of various functions and tested on an independent set of 24 different inhibitors for which K(d)/IC50 data are available. In addition, two popular ligand topology generation and parametrization methods (ACPYPE and PRODRG) were assessed. The resulting Haddock(2P2I) model, derived from the original Haddock score, provides insights into inhibition determinants: while the role of electrostatics and desolvation energies is case-dependent, the interface area plays a more critical role compared to protein-protein interactions.
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modeling protein protein complexes using the Haddock webserver modeling protein complexes with Haddock
Methods of Molecular Biology, 2014Co-Authors: Gydo C P Van Zundert, Alexandre M J J BonvinAbstract:Protein-protein interactions lie at the heart of most cellular processes. Determining their high-resolution structures by experimental methods is a nontrivial task, which is why complementary computational approaches have been developed over the years. To gain structural and dynamical insight on an atomic scale in these interactions, computational modeling must often be complemented by low-resolution experimental information. For this purpose, we developed the user-friendly Haddock webserver, the interface to our biomolecular docking program, which can make use of a variety of low-resolution data to drive the docking process. In this chapter, we explain the use of the Haddock webserver based on the real-life Lys48-linked di-ubiquitin case, which led to the 2BGF PDB model. We demonstrate the use of chemical shift perturbation data in combination with residual dipolar couplings and further highlight a few other cases where our software was successfully used. The Haddock webserver is available to the science community for free at Haddock.science.uu.nl/services/Haddock.
Manu Berrondo Sistiaga - One of the best experts on this subject based on the ideXlab platform.
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improving release efficiency of cod gadus morhua and Haddock melanogrammus aeglefinus in the barents sea demersal trawl fishery by stimulating escape behaviour
Canadian Journal of Fisheries and Aquatic Sciences, 2018Co-Authors: Eduardo Grimaldo, Roger B Larsen, Bent Herrmann, Manu Berrondo Sistiaga, Jesse Brinkhof, Ivan TatoneAbstract:We tested the ability of stimulators to improve the release efficiency of cod (Gadus morhua) and Haddock (Melanogrammus aeglefinus) through the meshes of a square mesh section installed in a trawl....
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size selective performance of two flexible sorting grid designs in the northeast arctic cod gadus morhua and Haddock melanogrammus aeglefinus fishery
Fisheries Research, 2016Co-Authors: Manu Berrondo Sistiaga, Eduardo Grimaldo, Bent Herrmann, Jesse Brinkhof, Lise Langard, Dagfinn LillengAbstract:The flexigrid is a flexible double grid design and is one of the mandatory selection devices used in the Northeast Arctic cod (Gadus morhua) and Haddock (Melanogrammus aeglefinus) fishery. Traditionally the flexigrid is mounted in a two-panel extension section of a trawl just ahead of the codend, but this design has performance limitations, especially during high volume catch situations. The aim of this study was to investigate the size selective properties of a new four-panel section design for the flexigrid and compare them to those of the traditional two-panel section. Specifically, we wanted to determine if this new design would increase the probability for undersized fish to make contact with the grid and subsequently escape through at least one of the two grids in the section. We quantified the parameter “grid contact” for both grids independently and combined for both the mandatory two-panel and the new four-panel designs. We directly compared the two designs using a single trawl with a three compartment experimental design which enabled estimation of the contribution of each of the grids to the combined selectivity of the flexigrid section. The results based on 51 hauls with 108,518 cod and Haddock length measurements indicate that the four-panel flexigrid design was better able to release undersized fish than the two-panel design. While the mean values of “grid contact” estimated for both grid designs were similar, the four-panel section had lower risk of clogging in situations of high fish entry rates. Underwater video recordings revealed that the cause for this difference between designs may be related to the difference in shape of the two sections while fishing. The results showed that undersized cod escape mostly through the lower grid of the flexigrid section, whereas Haddock generally utilize the upper grid. This finding is in good agreement with the behavioral differences previously described for these two species. Due to the favourable results obtained from this study, the four-panel flexigrid section is now legalized in the Northeast Arctic cod and Haddock fishery.
Elaine M Caldarone - One of the best experts on this subject based on the ideXlab platform.
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estimating growth in Haddock larvae melanogrammus aeglefinus from rna dna ratios and water temperature
Marine Ecology Progress Series, 2005Co-Authors: Elaine M CaldaroneAbstract:Five biochemically based variables (RNA, DNA, protein content, RNA:DNA [R:D] ratio, protein:DNA [pro:DNA] ratio) were evaluated as potential indirect measures of growth in larval Haddock Melanogrammus aeglefinus. Larvae were reared in the laboratory from hatch to 47 d post-hatch under temperature (T)-controlled conditions (6, 8, and 10°C) and, to produce a variety of growth rates, were starved or reared at 1 of 3 prey levels. The nucleic acid content of the larvae was measured with a spectrofluorometric microplate assay, and the protein-specific growth rate (SGR,% d -1 ) was estimated from the difference in mean protein content between consecutive sampling intervals. Larval Haddock growth rate was best described by R:D or pro:DNA ratios. The growth models developed were: SGR=4.61R:D+ 1.18T- 17.31 (R 2 = 0.52) and SGR = 0.92 pro:DNA + 1.10T- 24.97 (R 2 = 0.52). These models can be used to estimate recent growth of larval Haddock collected from both the laboratory and field. A combined Haddock/Atlantic cod Gadus morhua growth model was calculated as: SGR = 4.67R:D + 0.96T- 15.30 (R 2 = 0.45). This model will be used to estimate recent growth of Haddock and cod larvae collected during a multi-year field sampling effort on Georges Bank.
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optimum temperature and food limited growth of larval atlantic cod gadus morhua and Haddock melanogrammus aeglefinus on georges bank
Fisheries Oceanography, 2004Co-Authors: Lawrence J Buckley, Elaine M Caldarone, Gregory R LoughAbstract:We estimated recent growth of Atlantic cod (Gadus morhua) and Haddock (Melanogrammus aeglefinus) larvae collected on the southern flank of Georges Bank in May 1992–94 from the ratio of RNA to DNA (R/D) and water temperature. Growth of both species increased with water temperature to about 7°C and then decreased. The highest growth rates were observed in May 1993 at water temperatures around 7°C. These data confirm an earlier observation of comparable temperature optima for growth of Atlantic cod and Haddock larvae in the north-west Atlantic. Comparisons of field growth rates and temperature optima with data for larvae cultured at high temperatures and prey densities in the laboratory suggest that growth may have been food-limited at higher temperatures on Georges Bank. Given that 7°C is the long-term mean water temperature on the southern flank in May and that climate models predict a possible 2–4°C rise in water temperatures for the western North Atlantic, our findings point to a possible adverse effect of global warming on Atlantic cod and Haddock.
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effects of food consumption and temperature on growth rate and biochemical based indicators of growth in early juvenile atlantic cod gadus morhua and Haddock melanogrammus aeglefinus
Marine Ecology Progress Series, 2003Co-Authors: Myron A Peck, Lawrence J Buckley, Elaine M Caldarone, David A BengtsonAbstract:The relationship between the somatic growth rate (G) and feeding level (unfed, inter- mediate, and maximum rations) of age-0 juvenile cod Gadus morhua and Haddock Melanogrammus aeglefinus was quantified at different temperatures. Laboratory trials were conducted using 2 size- classes of cod (3.6 to 5.6 cm standard length (SL), and 8.1 to 12.4 cm SL) at 5, 8, 12, and 15°C, and 1 size-class of Haddock (6.0 to 9.6 cm SL) at 8 and 12°C. The shape of the growth-feeding relationship was well described by a 3-parameter asymptotic function for cod and by a linear function for Haddock (R 2 range = 0.837 to 0.966). The growth rate and scope for growth were maximum at 12°C, whereas growth efficiency was greatest (26.0 to 32.2%) at temperatures between 5 and 8°C. Juvenile cod held at 15°C exhibited reduced rates and efficiencies of somatic growth compared to fish at other temper- atures. Biochemical-based growth indicators for age-0 juveniles were calibrated from measurements of the amounts of RNA, DNA, and protein in white muscle samples. A multiple linear regression using RNA:DNA and temperature as independent variables explained a significant portion of the variability observed in G of juvenile cod (R 2 = 0.716) and Haddock (R 2 = 0.637). This relationship may be useful in estimating recent growth of age-0 juvenile cod and Haddock in the field.