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Vertical egg distributions are needed knowledge for understanding exposure to physical forcing, predation pressure, and modelling initial transport from the spawning areas. Egg density and size are the biotic factors determining vertical distributions while the ambient salinity and turbulent mixing are the physical factors contributing to their vertical distributions. Egg buoyancies and densities of Atlantic cod (Gadus morhua) have been extensively studied, while limited information on haddock (Melanogrammus aeglefinus) egg density is available. This is the first comprehensive study on haddock egg densities in Norwegian waters. Eggs were collected from pairs of spawning fish caught at the coast of western Norway and inserted into a density gradient column where density was measured. The haddock eggs were neutrally buoyant at salinities ranging from 28.5 to 31. The density changed during egg development, and the results from the measurements were used to model the vertical distribution of the eggs. The simulations showed that the changes in buoyancy substantially affected vertical distributions. A comparison to previously published data on cod eggs showed that haddock eggs are considerably more buoyant than the cod eggs and are—particularly during calm wind conditions—confined to the surface layer to a larger extent than the cod eggs. The more buoyant attribute of the haddock eggs, together with the lipophilic surface of the egg membrane, is suggested to make haddock eggs more vulnerable to buoyant pollutants, like hydrocarbons. [ABSTRACT FROM AUTHOR]

The Northeast Arctic stock of haddock (Melanogrammus aeglefinus) is the most northerly stock of the species. It is one of the largest haddock stocks but not the most studied. Similar to the more extensively studied sympatric cod (Gadus morhua) and herring (Clupea harengus) stocks, it relies on Atlantic currents for egg and larvae transportation from spawning grounds to nursery areas in the Barents Sea. The exact locations of the spawning grounds have not been known and the maps that have been published differ substantially. Here, we present results from the first survey dedicated to exploring the spawning habitat of Northeast Arctic (NEA) haddock, and a particle drift and larvae growth model with physical forcing from a high‐resolution ocean model. Gadoid eggs, later identified as haddock by DNA analyses, as well as spawning individuals were sampled at the survey. Spawning haddock was found in Atlantic water in temperatures 3.6–6.2°C and depths of 240–560 m. Sampled eggs were mostly in early development stages, suggesting that they were largely spawned in the surveyed area. Using the drift model, we found that most of the modelled particles released as eggs at our surveyed area ended up in the nursery area in the Barents Sea. A crude estimate of the spawning stock biomass based on the survey suggests that the most updated spawning ground map of NEA haddock might be too restricted in its extent. Particle drift and growth with physical forcing for the years 2012–2022 indicated small interannual variation in aberrant drift, and that growth driven by ambient temperature could be important in explaining interannual variation in haddock recruitment. [ABSTRACT FROM AUTHOR]

Abstract The novel coronavirus SARS-CoV-2 resulted in a significant worldwide health emergency known as the COVID-19 pandemic. This crisis has been marked by the widespread of various variants, with certain ones causing notable apprehension. In this study, we harnessed computational techniques to scrutinize these Variants of Concern (VOCs), including various Omicron subvariants. Our approach involved the use of protein structure prediction algorithms and molecular docking techniques, we have investigated the effects of mutations within the Receptor Binding Domain (RBD) of SARS-CoV-2 and how these mutations influence its interactions with the human angiotensin-converting enzyme 2 (hACE-2) receptor. Further we have predicted the structural alterations in the RBD of naturally occurring SARS-CoV-2 variants using the tr-Rosetta algorithm. Subsequent docking and binding analysis employing HADDOCK and PRODIGY illuminated crucial interactions occurring at the Receptor-Binding Motif (RBM). Our findings revealed a hierarchy of increased binding affinity between the human ACE2 receptor and the various RBDs, in the order of wild type (Wuhan-strain)

Abstract Background The novel coronavirus disease of 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Data from the COVID-19 clinical control case studies showed that this disease could also manifest in patients with underlying microbial infections such as aspergillosis. The current study aimed to determine if the Aspergillus (A.) fumigatus culture media (i.e., supernatant) possessed protease activity that was sufficient to activate the SARS-CoV-2 spike protein. Methods The supernatant was first analysed for protease activity. Thereafter, it was assessed to determine if it possessed proteolytic activity to cleave a fluorogenic mimetic peptide of the SARS-CoV-2 spike protein that contained the S1/S2 site and a full-length spike protein contained in a SARS-CoV-2 pseudovirion. To complement this, a computer-based tool, HADDOCK, was used to predict if A. fumigatus alkaline protease 1 could bind to the SARS-CoV-2 spike protein. Results We show that the supernatant possessed proteolytic activity, and analyses of the molecular docking parameters revealed that A. fumigatus alkaline protease 1 could bind to the spike protein. To confirm the in silico data, it was imperative to provide experimental evidence for enzymatic activity. Here, it was noted that the A. fumigatus supernatant cleaved the mimetic peptide as well as transduced the HEK-293T cells with SARS-CoV-2 pseudovirions. Conclusion These results suggest that A. fumigatus secretes a protease(s) that activates the SARS-CoV-2 spike protein. Importantly, should these two infectious agents co-occur, there is the potential for A. fumigatus to activate the SARS-CoV-2 spike protein, thus aggravating COVID-19 development.

Temperature fluctuations impact the distribution of various marine fish species and typically result in distributional changes, seeing either a geographical expansion or, possibly, a retraction. Survival and fitness in the new habitat depend, however, on the species' adaptability capacity. Here, we describe changes in geographical distribution of Icelandic haddock (Melanogrammus aeglefinus) based on annual survey data for a 38-year period, 1985–2022. Most of the stock is in the warm waters off the south and west coasts of Iceland (south area), but a small proportion in colder water masses off the north and east coasts (north area). Due to high recruitment, density increased greatly in both areas in the years 2001–2005. Haddock density was usually higher in the south area in 1985–2004, in the north area in 2005–2014, but similar in both areas in 2015–2022. Haddock condition was found to be influenced by both temperature and haddock density. Density-dependent factors influenced haddock mean weight, which dropped considerable during times of high haddock density. Capelin was of great importance as a diet, especially in the south, where stomach fullness decreased considerably when capelin was not a part of the diet. Food availability seems to be highly variable between the two areas but more stable in the north, where fluctuations in capelin fullness were small. Even though favourable environmental conditions may result in increased haddock density in the colder waters in the north, lower condition indicates that the northern area may be less suitable for this species. [ABSTRACT FROM AUTHOR]

Background: The novel coronavirus disease of 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Data from the COVID-19 clinical control case studies showed that this disease could also manifest in patients with underlying microbial infections such as aspergillosis. The current study aimed to determine if the Aspergillus (A.) fumigatus culture media (i.e., supernatant) possessed protease activity that was sufficient to activate the SARS-CoV-2 spike protein. Methods: The supernatant was first analysed for protease activity. Thereafter, it was assessed to determine if it possessed proteolytic activity to cleave a fluorogenic mimetic peptide of the SARS-CoV-2 spike protein that contained the S1/S2 site and a full-length spike protein contained in a SARS-CoV-2 pseudovirion. To complement this, a computer-based tool, HADDOCK, was used to predict if A. fumigatus alkaline protease 1 could bind to the SARS-CoV-2 spike protein. Results: We show that the supernatant possessed proteolytic activity, and analyses of the molecular docking parameters revealed that A. fumigatus alkaline protease 1 could bind to the spike protein. To confirm the in silico data, it was imperative to provide experimental evidence for enzymatic activity. Here, it was noted that the A. fumigatus supernatant cleaved the mimetic peptide as well as transduced the HEK-293T cells with SARS-CoV-2 pseudovirions. Conclusion: These results suggest that A. fumigatus secretes a protease(s) that activates the SARS-CoV-2 spike protein. Importantly, should these two infectious agents co-occur, there is the potential for A. fumigatus to activate the SARS-CoV-2 spike protein, thus aggravating COVID-19 development. [ABSTRACT FROM AUTHOR]

Developing and diversifying market opportunities for lesser known yet abundant seafood species has been a successful strategy for seafood businesses in the Northeast United States. Since climate change and other stressors are currently threatening the economic vitality of New England's seafood industry, it is important to identify if there are lesser-known species that could simultaneously support additional market opportunities and remain resilient in a warming climate. We developed a quantitative definition for the term "underutilized species'' based on five criteria derived from science-based sustainable fishing metrics. Using this definition, we evaluated 47 stocks in the Northeast United States during the initial time period of 2013-2017 to identify seven underutilized finfish species that could be considered for new market opportunities as part of a climate-smart approach: 1) Acadian redfish (Sebastes fasciatus), 2) Atlantic pollock (Pollachius virens), 3) butterfish (Peprilus triacanthus), 4) haddock (Melanogrammus aeglefinus), 5) scup (Stenotomus chrysops), 6) silver hake (Merluccius bilinearis), and 7) white hake (Urophycis tenuis). The climate resiliency of these resulting seven species was then evaluated using a framework consisting of species-specific metrics on climate sensitivity, directionality (of responses to climate impacts) and future habitat availability under warming scenarios. Our results show that assessing underutilized species on a regular basis and evaluating their ongoing responses to climate change can be a part of a climate-smart approach towards building more diversified and adaptive markets. [ABSTRACT FROM AUTHOR]

Zika virus infections lead to neurological complications such as congenital Zika syndrome and Guillain–Barré syndrome. Rising Zika infections in newborns and adults have triggered the need for vaccine development. In the current study, the precursor membrane (prM) protein of the Zika virus is explored for its functional importance and design of epitopes enriched conserved peptides with the usage of different immunoinformatics approach. Phylogenetic and mutational analyses inferred that the prM protein is highly conserved. Three conserved peptides containing multiple T and B cell epitopes were designed by employing different epitope prediction algorithms. IEDB population coverage analysis of selected peptides in six different continents has shown the population coverage of 60–99.8% (class I HLA) and 80–100% (class II HLA). Molecular docking of selected peptides/epitopes was carried out with each of class I and II HLA alleles using HADDOCK. A majority of peptide–HLA complex (pHLA) have HADDOCK scores found to be comparable and more than native–HLA complex representing the good binding interaction of peptides to HLA. Molecular dynamics simulation with best docked pHLA complexes revealed that pHLA complexes are stable with RMSD <5.5Å. Current work highlights the importance of prM as a strong antigenic protein and selected peptides have the potential to elicit humoral and cell-mediated immune responses. [ABSTRACT FROM AUTHOR]

The steep rise in protein sequences and structures has paved the way for bioinformatics approaches to predict residue–residue interactions in protein complexes. Multiple sequence alignments are commonly used in contact predictions to identify co‐evolving residues. These contacts, however, often include false positives (FPs), which may impair their use to predict three dimensional structures of biomolecular complexes and affect the accuracy of the generated models. Previously, we have developed DisVis to identify FP in mass spectrometry cross‐linking data. DisVis allows to assess the accessible interaction space between two proteins consistent with a set of distance restraints. Here, we investigate if a similar approach could be applied to co‐evolution predicted contacts in order to improve their precision prior to using them for modeling. We analyze co‐evolution contact predictions with DisVis for a set of 26 protein–protein complexes. The DisVis‐reranked and the original co‐evolution contacts are then used to model the complexes with our integrative docking software HADDOCK using different filtering scenarios. Our results show that HADDOCK is robust with respect to the precision of the predicted contacts due to the 50% random contact removal during docking and can enhance the quality of docking predictions when combined with DisVis filtering for low precision contact data. DisVis can thus have a beneficial effect on low quality data, but overall HADDOCK can accommodate FP restraints without negatively impacting the quality of the resulting models. Other more precision‐sensitive docking protocols might, however, benefit from the increased precision of the predicted contacts after DisVis filtering. [ABSTRACT FROM AUTHOR]

SARS-CoV-2, responsible for the COVID-19 pandemic, invades host cells via its spike protein, which includes critical binding regions, such as the receptor-binding domain (RBD), the S1/S2 cleavage site, the S2 cleavage site, and heptad-repeat (HR) sections. Peptides targeting the RBD and HR1 inhibit binding to host ACE2 receptors and the formation of the fusion core. Other peptides target proteases, such as TMPRSS2 and cathepsin L, to prevent the cleavage of the S protein. However, research has largely ignored peptides targeting the S1/S2 cleavage site. In this study, bioinformatics was used to investigate the binding of the S1/S2 cleavage site to host proteases, including furin, trypsin, TMPRSS2, matriptase, cathepsin B, and cathepsin L. Peptides targeting the S1/S2 site were designed by identifying binding residues. Peptides were docked to the S1/S2 site using HADDOCK (High-Ambiguity-Driven protein–protein DOCKing). Nine peptides with the lowest HADDOCK scores and strong binding affinities were selected, which was followed by molecular dynamics simulations (MDSs) for further investigation. Among these peptides, BR582 and BR599 stand out. They exhibited relatively high interaction energies with the S protein at −1004.769 ± 21.2 kJ/mol and −1040.334 ± 24.1 kJ/mol, respectively. It is noteworthy that the binding of these peptides to the S protein remained stable during the MDSs. In conclusion, this research highlights the potential of peptides targeting the S1/S2 cleavage site as a means to prevent SARS-CoV-2 from entering cells, and contributes to the development of therapeutic interventions against COVID-19. [ABSTRACT FROM AUTHOR]

Lipocalin‐type prostaglandin D synthase (L‐PGDS) is a secretory lipid‐transporter protein that was shown to bind a wide variety of hydrophobic ligands in vitro. Exploiting this function, we previously examined the feasibility of using L‐PGDS as a novel delivery vehicle for poorly water‐soluble drugs. However, the mechanism by which human L‐PGDS binds to poorly water‐soluble drugs is unclear. In this study, we determined the solution structure of human L‐PGDS and investigated the mechanism of L‐PGDS binding to 6‐nitro‐7‐sulfamoyl‐benzo[f]quinoxalin‐2,3‐dione (NBQX), an α‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazole‐propionic acid receptor antagonist. NMR experiments showed that human L‐PGDS has an eight‐stranded antiparallel β‐barrel structure that forms a central cavity, a short 310‐helix and two α‐helices. Titration with NBQX was monitored using 1H‐15N HSQC spectroscopy. At higher NBQX concentrations, some cross‐peaks of the protein exhibited fast‐exchanging shifts with a curvature, indicating at least two binding sites. These residues were located in the upper portion of the cavity. Singular value decomposition analysis revealed that human L‐PGDS has two NBQX binding sites. Large chemical shift changes were observed in the H2‐helix and A‐, B‐, C‐, D‐, H‐ and I‐strands and H2‐helix upon NBQX binding. Calorimetric experiments revealed that human L‐PGDS binds two NBQX molecules with dissociation constants of 46.7 μm for primary binding and 185.0 μm for secondary binding. Molecular docking simulations indicated that these NBQX binding sites are located within the β‐barrel. These results provide new insights into the interaction between poorly water‐soluble drugs and human L‐PGDS as a drug carrier. [ABSTRACT FROM AUTHOR]

As the climate warms, boreal fish species are expected to expand into the Arctic domain. Though water temperature is an important factor driving expansion of aquatic species, other variables may play a critical role in restricting those movements. Continuous darkness during the Arctic polar night has been suggested to impair foraging in visually searching boreal fish and may thus limit their northward expansion. We discuss feeding and diet composition of co-existing polar cod (Boreogadus saida), Atlantic cod (Gadus morhua), and haddock (Melanogrammus aeglefinus) during the polar night. The data presented cover January sampling during five consecutive years (2012–2016) in Svalbard fjords (78–80°N). Across species, more than 70% of individuals were feeding. Few stomachs were well filled, suggesting an overall moderate foraging activity or success. The endemic polar cod had the highest frequency of empty stomachs (40%), while Atlantic cod (25% empty) and haddock (21% empty) had fed most extensively. Diet composition indicated opportunistic feeding, with extensive diet overlap of the most abundant prey species (krill, Thysanoessa spp.) during years of highly abundant krill (2014–2015) but reverting to more distinct diets in a year (2016) with lower krill abundance. For all three species, presence of prey items in advanced degrees of digestion indicated feeding activity prior to each annual trawl sampling. The stomach fullness and diet overlap suggest that coexisting and similar sized gadoids feed on the same available prey resources during polar night. [ABSTRACT FROM AUTHOR]

With its fast-paced mutagenesis, the SARS-CoV-2 Omicron variant has threatened many societies worldwide. Strategies for predicting mutagenesis such as the computational prediction of SARS-CoV-2 structural diversity and its interaction with the human receptor will greatly benefit our understanding of the virus and help develop therapeutics against it. We aim to use protein structure prediction algorithms along with molecular docking to study the effects of various mutations in the Receptor Binding Domain (RBD) of the SARS-CoV-2 and its key interactions with the angiotensin-converting enzyme 2 (ACE-2) receptor. The RBD structures of the naturally occurring variants of SARS-CoV-2 were generated from the WUHAN-Hu-1 using the trRosetta algorithm. Docking (HADDOCK) and binding analysis (PRODIGY) between the predicted RBD sequences and ACE-2 highlighted key interactions at the Receptor-Binding Motif (RBM). Further mutagenesis at conserved residues in the Original, Delta, and Omicron variants (P499S and T500R) demonstrated stronger binding and interactions with the ACE-2 receptor. The predicted T500R mutation underwent some preliminary tests in vitro for its binding and transmissibility in cells; the results correlate with the in-silico analysis. In summary, we suggest conserved residues P499 and T500 as potential mutation sites that could increase the binding affinity and yet do not exist in nature. This work demonstrates the use of the trRosetta algorithm to predict protein structure and future mutations at the RBM of SARS-CoV-2, followed by experimental testing for further efficacy verification. It is important to understand the protein structure and folding to help develop potential therapeutics. [ABSTRACT FROM AUTHOR]

SARS-CoV-2, responsible for the COVID-19 pandemic, invades host cells via its spike protein, which includes critical binding regions, such as the receptor-binding domain (RBD), the S1/S2 cleavage site, the S2 cleavage site, and heptad-repeat (HR) sections. Peptides targeting the RBD and HR1 inhibit binding to host ACE2 receptors and the formation of the fusion core. Other peptides target proteases, such as TMPRSS2 and cathepsin L, to prevent the cleavage of the S protein. However, research has largely ignored peptides targeting the S1/S2 cleavage site. In this study, bioinformatics was used to investigate the binding of the S1/S2 cleavage site to host proteases, including furin, trypsin, TMPRSS2, matriptase, cathepsin B, and cathepsin L. Peptides targeting the S1/S2 site were designed by identifying binding residues. Peptides were docked to the S1/S2 site using HADDOCK (High-Ambiguity-Driven protein–protein DOCKing). Nine peptides with the lowest HADDOCK scores and strong binding affinities were selected, which was followed by molecular dynamics simulations (MDSs) for further investigation. Among these peptides, BR582 and BR599 stand out. They exhibited relatively high interaction energies with the S protein at −1004.769 ± 21.2 kJ/mol and −1040.334 ± 24.1 kJ/mol, respectively. It is noteworthy that the binding of these peptides to the S protein remained stable during the MDSs. In conclusion, this research highlights the potential of peptides targeting the S1/S2 cleavage site as a means to prevent SARS-CoV-2 from entering cells, and contributes to the development of therapeutic interventions against COVID-19.

The less virulent human (h) coronaviruses (CoVs) 229E, NL63, OC43, and HKU1 cause mild, self-limiting respiratory tract infections, while the more virulent SARS-CoV-1, MERS-CoV, and SARS-CoV-2 have caused severe outbreaks. The CoV envelope (E) protein, an important contributor to the pathogenesis of severe hCoV infections, may provide insight into this disparate severity of the disease. We, therefore, generated full-length E protein models for SARS-CoV-1 and -2, MERS-CoV, HCoV-229E, and HCoV-NL63 and docked C-terminal peptides of each model to the PDZ domain of the human PALS1 protein. The PDZ-binding motif (PBM) of the SARS-CoV-1 and -2 and MERS-CoV models adopted a more flexible, extended coil, while the HCoV-229E and HCoV-NL63 models adopted a less flexible alpha helix. All the E peptides docked to PALS1 occupied the same binding site and the more virulent hCoV E peptides generally interacted more stably with PALS1 than the less virulent ones. We hypothesize that the increased flexibility of the PBM in the more virulent hCoVs facilitates more stable binding to various host proteins, thereby contributing to more severe disease. This is the first paper to model full-length 3D structures for both the more virulent and less virulent hCoV E proteins, providing novel insights for possible drug and/or vaccine development. [ABSTRACT FROM AUTHOR]

Motivation: Antibody-antigen complex modelling is an important step in computational workflows for therapeutic antibody design. While experimentally determined structures of both antibody and the cognate antigen are often not available, recent advances in machine learning-driven protein modelling have enabled accurate prediction of both antibody and antigen structures. Here, we analyse the ability of protein-protein docking tools to use machine learning generated input structures for information-driven docking., Results: In an information-driven scenario, we find that HADDOCK can generate accurate models of antibody-antigen complexes using an ensemble of antibody structures generated by machine learning tools and AlphaFold2 predicted antigen structures. Targeted docking using knowledge of the complementary determining regions on the antibody and some information about the targeted epitope allows the generation of high quality models of the complex with reduced sampling, resulting in a computationally cheap protocol that outperforms the ZDOCK baseline., Availability: The source code of HADDOCK3 is freely available at github.com/haddocking/haddock3. The code to generate and analyse the data is available at github.com/haddocking/ai-antibodies. The full runs, including docking models from all modules of a workflow have been deposited in our lab collection (data.sbgrid.org/labs/32/1139) at the SBGRID data repository., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2024. Published by Oxford University Press.)

The present study tracked oocyte development over 9 months and noted incidences of 'skipping', i.e., adults terminating their upcoming reproductive cycle, in field‐caught north‐east Arctic (NEA) haddock (Melanogrammus aeglefinus), currently the largest stock of this species. Applications of advanced image and histological techniques revealed the presence of cortical alveoli oocytes (CAO), which prevailed as the most advanced oocyte phase for 4–5 months. This new finding of an extended and early appearance of CAOs in this gadoid was supported by that vitellogenesis first started to appear 3 months later. The subsequent oocyte growth trajectories indicated that larger individuals [total length (TL) = 70 cm] typically spawn in the order of 3 weeks earlier than the smaller ones (TL = 40 cm). The spawning season appeared stretched over about 3 months. The majority of skipping females arrested oocyte growth at the CAO phase followed by atretic reabsorption. Compared to those individuals maturing for the spawning season, 'skippers' generally exhibited lower body condition, characterized also by relatively lower liver sizes at the time of the main spawning season. This study demonstrated well‐developed skipping dynamics, but also that the CAO period, i.e., when skipping takes place, may be exceedingly long in this commercially valuable gadoid and that its reproductive cycle in many ways deviates from that of the data‐rich, sympatric NEA cod (Gadus morhua). [ABSTRACT FROM AUTHOR]

BAF250b and its paralog BAF250a are the DNA‐binding central hub proteins present in BAF‐B and BAF‐A classes of SWI/SNF chromatin‐remodeling complexes. BAF250b contains an AT‐rich interaction domain (ARID) and C‐terminal BAF250_C domain, and it is found mutated in several cancers. ARID is a conserved helix‐turn‐helix motif‐containing DNA‐binding domain present in several eukaryotic proteins. The ARID of BAF250b has been proposed to play roles in recruiting SWI/SNF to the target gene promoters for their activation. BAF250b ARID structures had been deposited in the protein data bank by a structural genomics consortium. However, it is not well‐studied for its DNA‐binding and solution dynamic properties. Here, we report complete backbone NMR resonance assignments of human BAF250b ARID. NMR chemical shifts and the backbone dynamics showed that the solution structure of the protein matched the reported crystal structures. The structure and chemical shift indexing revealed the presence of a short β‐sheet in the DNA‐binding region of BAF250b ARID that was absent in the structure of its paralog BAF250a ARID. NMR chemical shift perturbations identified DNA‐binding residues and revealed the DNA‐binding interface on BAF250b ARID. NMR data‐driven HADDOCK models of BAF250b ARID – DNA complexes revealed its plausible mode of DNA‐binding. Isothermal titration calorimetry experiments showed that BAF250b ARID interacts with DNA sequences with moderate affinities like BAF250a ARID. However, distinct thermodynamic signatures were observed for binding of BAF250a ARID and BAF250b ARID to AT‐rich DNA sequence, suggesting that subtle sequence and structural differences in these two proteins influence their DNA‐binding. [ABSTRACT FROM AUTHOR]

Grid systems separate fish species primarily through physical means: fish size and body shape. On Georges Bank off the northeast USA, many species of flounders are overfished, and their catch needs to be reduced. Flat-bodied skates are also often discarded. We tested a European style horizontal-bar grid system to reduce these flat-bodied low quota species in a trawl targeting the haddock (Melanogrammus aeglefinus), whose population is robust. The grid system consisted of 4 grid sections, two on each side, with horizontal bars 70 mm apart. The alternating tow method was used to compare the catch characteristics between a trawl with a grid section and the same trawl without a grid section. A video camera was used to observe fish escape in the grid section. The results indicate that the grid system reduced the flounder catch rate (mainly winter flounder, Pseudopleuronectes americanus) by 51.3%, and skates (mainly winter skate, Leucoraja ocellata and little skate, Leucoraja erinacea) by 29.4%, while there were no differences in the catch of Atlantic cod (Gadus morhua). While haddock was reduced by 37% by weight, the reduction was primarily small undersized individuals. There was no reduction in large haddock greater than 50 cm. Video observations indicates that flounders and cod mainly escaped from the bottom half of the grid while haddock were from the top half. These finding suggest that this system reduced low quota flounders, as well as discarded skates and small haddock, while retaining Atlantic cod and large size haddock. Underwater observations indicate that differential spacing (narrower on the top and wider on the bottom) may improve the system performance by releasing more flat-bodied fish, that were observed to escape from the bottom part of the grid, while retaining more haddock, which typically escape from the top part of the grid.

State-space modeling is an emerging approach to age structured fisheries stock assessment that can accommodate multiple sources of variability in processes like recruitment, abundance, and selectivity. By maximizing the marginal likelihood by treating yearly deviations as random effects and then integrating them from the likelihood, these models can estimate multiple process variances. Several fisheries software packages have been developed that use a state-space framework with marginal likelihood, which has increased their popularity and usage across the U.S. Atlantic coast, Canada, and Europe. However, robust testing is still needed to gauge the applicability of these models and understand how they perform under a range of realistic variability in the process or observation error. Using an assessment model fit to Gulf of Maine Haddock as a baseline, we used a simulation-estimation procedure to test if state-space stock assessment models could produce approximately unbiased and precise estimates over a range of process variances that extended from zero to well above the levels estimated in the Gulf of Maine Haddock assessment, or when observations were noisier (i.e., more variable around their true value) than had been assumed in the assessment. We fit alternative estimation models that differed in which processes errors were included (of recruitment, expected survival, and fishery selectivity). State-space models which specify random effects in all three processes produced approximately unbiased and precise estimates of biomass and exploitation for most operating models and therefore are recommended except when variability in expected survival is absent (or very low), in which case the model is unlikely to converge. A conventional statistical-catch-at-age model with recruitment estimated as a fixed effect for each year, deterministic expected survival, and constant selectivity produced estimates that were comparable to the best state-space model, but do not provide internal estimates of process variances and did not perform well when recruitment was highly variable. This work will facilitate the use of state-space stock assessment models and choosing the parameterization that will produce the most accurate output to inform future predictions and management. [ABSTRACT FROM AUTHOR]

This study seeks to investigate the interaction profile of the L5 protein of oncolytic adenovirus with the overexpressed surface receptors of pancreatic cancer. This is an important area of research because pancreatic cancer is one of the most fatal malignancies with a very low patient survival rate. Multiple therapies to date to improve the survival rate are reported; however, they show a comparatively low success rate. Among them, oncolytic virus therapy is a type of immunotherapy that is currently under deliberation by researchers for multiple cancer types in various clinical trials. Talimogene laherparepvec (T-VEC) is the first oncolytic virus approved by the US Food and Drug Administration (FDA) for melanoma. The oncolytic virus not only kills cancer cells but also activates the anticancer immune response. Therefore, it is preferred over others to deal with aggressive pancreatic cancer. The efficacy of therapy primarily depends on how effectively the oncolytic virus enters and infects the cancer cell. Cell surface receptors and their interactions with virus coat proteins are a crucial step for oncolytic virus entry and a pivotal determinant. The L5 proteins of the virus coat are the first to interact with host cell surface receptors. Therefore, the objective of this study is to analyze the interaction profile of the L5 protein of oncolytic adenovirus with overexpressed surface receptors of pancreatic cancer. The L5 proteins of three adenovirus serotypes HAdV2, HAdV5, and HAdV3 were utilized in this study. Overexpressed pancreatic cancer receptors include SLC2A1, MET, IL1RAP, NPR3, GABRP, SLC6A6, and TMPRSS4. The protein structures of viral and cancer cell protein were docked using the High Ambiguity Driven protein–protein DOCKing (HADDOCK) server. The binding affinity and interaction profile of viral proteins against all the receptors were analyzed. Results suggest that the HAdV3 L5 protein shows better interaction as compared to HAdV2 and HAdV5 by elucidating high binding affinity with 4 receptors (NPR3, GABRP, SLC6A6, and TMPRSS4). The current study proposed that HAdV5 or HAdV2 virus pseudotyped with the L5 protein of HAdV3 can be able to effectively infect pancreatic cancer cells. Moreover, the current study surmises that the affinity maturation of HAdV3 L5 can enhance virus attachment with all the receptors of cancer cells. [ABSTRACT FROM AUTHOR]

Eukaryotic translation initiates upon recruitment of the EIF2‐GTP·Met‐tRNAi ternary complex (TC) to the ribosomes. EIF2 (α, β, γ subunits) is a GTPase. The GDP to GTP exchange within EIF2 is facilitated by the guanine nucleotide exchange factor EIF2B (α‐ε subunits). During stress‐induced conditions, phosphorylation of the α‐subunit of EIF2 turns EIF2 into an inhibitor of EIF2B. In turn, inhibition of EIF2B decreases TC formation and triggers the internal stress response (ISR), which determines the cell fate. Deregulated ISR has been linked to neurodegenerative disorders and cancer, positioning EIF2B as a promising therapeutic target. Hence, a better understanding of the mechanisms/factors that regulate EIF2B activity is required. Here, combining transcript and protein level analyses, we describe an intronically polyadenylated (IPA) transcript of EIF2B's γ‐subunit. We show that the IPA mRNA isoform is translated into a C‐terminus truncated protein. Using structural modeling, we predict that the truncated EIF2Bγ protein has unfavorable interactions with EIF2γ, leading to a potential decrease in the stability of the nonproductive EIF2:EIF2B complex. While we discovered and confirmed the IPA mRNA isoform in breast cancer cells, the expression of this isoform is not cancer‐specific and is widely present in normal tissues. Overall, our data show that a truncated EIF2Bγ protein co‐exists with the canonical protein and is an additional player to regulate the equilibrium between productive and nonproductive states of the EIF2:EIF2B complex. These results may have implications in stress‐induced translation control in normal and disease states. Our combinatorial approach demonstrates the need to study noncanonical mRNA and protein isoforms to understand protein interactions and intricate molecular mechanisms. [ABSTRACT FROM AUTHOR]

Research background. It is desirable to increase the consumption of pelagic fish rich in long-chain omega-3 fatty acids. Partial replacement of traditionally used white fish species by pelagic fish will increase the content of omega-3 fatty acids, and thus improve the nutritional value but it may also affect the consumer acceptance. The aim of this study is to assess the physicochemical and sensory quality of novel fish cake prototypes prepared from haddock and mackerel mince. Experimental approach. Fillets of haddock and Atlantic mackerel were used as raw material for preparation of fish cakes. The fish fillets were minced, mixed together (in haddock/mackerel mass ratio of 100:0, 75:25 and 50:50%) with salt, potato starch, pepper and full fat milk. Physicochemical and sensory analyses were further performed. Results and conclusions. The fatty acid composition analysis showed that the recommended daily intake of 250 mg of eicosapentaenoic acid and docosahexaenoic acid can easily be reached by consumption of fish cakes enriched with mackerel. The oxidation levels of all fish cakes were low in terms of peroxide value and thiobarbituric acid reactive substance assay (TBARS). Fish cakes prepared with higher mass fraction of mackerel mince (>50%) had significantly (p50%) fish cakes due to higher myoglobin content in the fish muscle. Moreover, fish cakes with higher amount of mackerel mince had increased yellowness due to the accumulation of water-soluble (r=0.990, p

This study seeks to investigate the interaction profile of the L5 protein of oncolytic adenovirus with the overexpressed surface receptors of pancreatic cancer. This is an important area of research because pancreatic cancer is one of the most fatal malignancies with a very low patient survival rate. Multiple therapies to date to improve the survival rate are reported; however, they show a comparatively low success rate. Among them, oncolytic virus therapy is a type of immunotherapy that is currently under deliberation by researchers for multiple cancer types in various clinical trials. Talimogene laherparepvec (T-VEC) is the first oncolytic virus approved by the US Food and Drug Administration (FDA) for melanoma. The oncolytic virus not only kills cancer cells but also activates the anticancer immune response. Therefore, it is preferred over others to deal with aggressive pancreatic cancer. The efficacy of therapy primarily depends on how effectively the oncolytic virus enters and infects the cancer cell. Cell surface receptors and their interactions with virus coat proteins are a crucial step for oncolytic virus entry and a pivotal determinant. The L5 proteins of the virus coat are the first to interact with host cell surface receptors. Therefore, the objective of this study is to analyze the interaction profile of the L5 protein of oncolytic adenovirus with overexpressed surface receptors of pancreatic cancer. The L5 proteins of three adenovirus serotypes HAdV2, HAdV5, and HAdV3 were utilized in this study. Overexpressed pancreatic cancer receptors include SLC2A1, MET, IL1RAP, NPR3, GABRP, SLC6A6, and TMPRSS4. The protein structures of viral and cancer cell protein were docked using the High Ambiguity Driven protein–protein DOCKing (HADDOCK) server. The binding affinity and interaction profile of viral proteins against all the receptors were analyzed. Results suggest that the HAdV3 L5 protein shows better interaction as compared to HAdV2 and HAdV5 by elucidating high binding affinity with 4 receptors (NPR3, GABRP, SLC6A6, and TMPRSS4). The current study proposed that HAdV5 or HAdV2 virus pseudotyped with the L5 protein of HAdV3 can be able to effectively infect pancreatic cancer cells. Moreover, the current study surmises that the affinity maturation of HAdV3 L5 can enhance virus attachment with all the receptors of cancer cells.

With its fast-paced mutagenesis, the SARS-CoV-2 Omicron variant has threatened many societies worldwide. Strategies for predicting mutagenesis such as the computational prediction of SARS-CoV-2 structural diversity and its interaction with the human receptor will greatly benefit our understanding of the virus and help develop therapeutics against it. We aim to use protein structure prediction algorithms along with molecular docking to study the effects of various mutations in the Receptor Binding Domain (RBD) of the SARS-CoV-2 and its key interactions with the angiotensin-converting enzyme 2 (ACE-2) receptor. The RBD structures of the naturally occurring variants of SARS-CoV-2 were generated from the WUHAN-Hu-1 using the trRosetta algorithm. Docking (HADDOCK) and binding analysis (PRODIGY) between the predicted RBD sequences and ACE-2 highlighted key interactions at the Receptor-Binding Motif (RBM). Further mutagenesis at conserved residues in the Original, Delta, and Omicron variants (P499S and T500R) demonstrated stronger binding and interactions with the ACE-2 receptor. The predicted T500R mutation underwent some preliminary tests in vitro for its binding and transmissibility in cells; the results correlate with the in-silico analysis. In summary, we suggest conserved residues P499 and T500 as potential mutation sites that could increase the binding affinity and yet do not exist in nature. This work demonstrates the use of the trRosetta algorithm to predict protein structure and future mutations at the RBM of SARS-CoV-2, followed by experimental testing for further efficacy verification. It is important to understand the protein structure and folding to help develop potential therapeutics.

The less virulent human (h) coronaviruses (CoVs) 229E, NL63, OC43, and HKU1 cause mild, self-limiting respiratory tract infections, while the more virulent SARS-CoV-1, MERS-CoV, and SARS-CoV-2 have caused severe outbreaks. The CoV envelope (E) protein, an important contributor to the pathogenesis of severe hCoV infections, may provide insight into this disparate severity of the disease. We, therefore, generated full-length E protein models for SARS-CoV-1 and -2, MERS-CoV, HCoV-229E, and HCoV-NL63 and docked C-terminal peptides of each model to the PDZ domain of the human PALS1 protein. The PDZ-binding motif (PBM) of the SARS-CoV-1 and -2 and MERS-CoV models adopted a more flexible, extended coil, while the HCoV-229E and HCoV-NL63 models adopted a less flexible alpha helix. All the E peptides docked to PALS1 occupied the same binding site and the more virulent hCoV E peptides generally interacted more stably with PALS1 than the less virulent ones. We hypothesize that the increased flexibility of the PBM in the more virulent hCoVs facilitates more stable binding to various host proteins, thereby contributing to more severe disease. This is the first paper to model full-length 3D structures for both the more virulent and less virulent hCoV E proteins, providing novel insights for possible drug and/or vaccine development.

T cell receptor (TCR) recognition of peptides presented by major histocompatibility complex (MHC) molecules is a fundamental process in the adaptive immune system. An understanding of this recognition process at the molecular level is crucial for TCR based therapeutics and vaccine design. The broad nature of TCR diversity and cross-reactivity presents a challenge for traditional structural resolution. Computational modelling of TCR-pMHC complexes offers an efficient alternative. This study compares the ability of four general-purpose docking platforms (ClusPro, LightDock, ZDOCK and HADDOCK) to make use of varying levels of binding interface information for accurate TCR-pMHC modelling. Each platform was tested on an expanded benchmark set of 44 TCR-pMHC docking cases. In general, HADDOCK is shown to be the best performer. Docking strategy guidance is provided to obtain the best models for each platform for future research. The TCR-pMHC docking cases used in this study can be downloaded from https://github.com/innate2adaptive/ExpandedBenchmark.

Owing to its clinical significance, modulation of functionally relevant amino acids in protein-protein complexes has attracted a great deal of attention. To this end, many approaches have been proposed to predict the partner-selecting amino acid positions in evolutionarily close complexes. These approaches can be grouped into sequence-based machine learning and structure-based energy-driven methods. In this work, we assessed these methods’ ability to map the specificity-determining positions of Axl, a receptor tyrosine kinase involved in cancer progression and immune system diseases. For sequence-based predictions, we used SDPpred, Multi-RELIEF, and Sequence Harmony. For structure-based predictions, we utilized HADDOCK refinement and molecular dynamics simulations. As a result, we observed that (i) sequence-based methods overpredict partner-selecting residues of Axl and that (ii) combining Multi-RELIEF with HADDOCK-based predictions provides the key Axl residues, covered by the extensive molecular dynamics simulations. Expanding on these results, we propose that a sequence-structure-based approach is necessary to determine specificity-determining positions of Axl, which can guide the development of therapeutic molecules to combat Axl misregulation.

Protein-protein interactions are indispensable physiological processes regulating several biological functions. Despite the availability of structural information on protein-protein complexes, deciphering their complex topology remains an outstanding challenge. Raf kinase inhibitory protein (RKIP) has gained substantial attention as a favorable molecular target for numerous pathologies including cancer and Alzheimer’s disease. RKIP interferes with the RAF/MEK/ERK signaling cascade by endogenously binding with C-Raf (Raf-1 kinase) and preventing its activation. In the current investigation, the binding of RKIP with C-Raf was explored by knowledge-based protein-protein docking web-servers including HADDOCK and ZDOCK and a consensus binding mode of C-Raf/RKIP structural complex was obtained. Molecular dynamics (MD) simulations were further performed in an explicit solvent to sample the conformations for when RKIP binds to C-Raf. Some of the conserved interface residues were mutated to alanine, phenylalanine and leucine and the impact of mutations was estimated by additional MD simulations and MM/PBSA analysis for the wild-type (WT) and constructed mutant complexes. Substantial decrease in binding free energy was observed for the mutant complexes as compared to the binding free energy of WT C-Raf/RKIP structural complex. Furthermore, a considerable increase in average backbone root mean square deviation and fluctuation was perceived for the mutant complexes. Moreover, per-residue energy contribution analysis of the equilibrated simulation trajectory by HawkDock and ANCHOR web-servers was conducted to characterize the key residues for the complex formation. One residue each from C-Raf (Arg398) and RKIP (Lys80) were identified as the druggable “hot spots” constituting the core of the binding interface and corroborated by additional long-time scale (300 ns) MD simulation of Arg398Ala mutant complex. A notable conformational change in Arg398Ala mutant occurred near the mutation site as compared to the equilibrated C-Raf/RKIP native state conformation and an essential hydrogen bonding interaction was lost. The thirteen binding sites assimilated from the overall analysis were mapped onto the complex as surface and divided into active and allosteric binding sites, depending on their location at the interface. The acquired information on the predicted 3D structural complex and the detected sites aid as promising targets in designing novel inhibitors to block the C-Raf/RKIP interaction.

T cell receptor (TCR) recognition of peptides presented by major histocompatibility complex (MHC) molecules is a fundamental process in the adaptive immune system. An understanding of this recognition process at the molecular level is crucial for TCR based therapeutics and vaccine design. The broad nature of TCR diversity and cross-reactivity presents a challenge for traditional structural resolution. Computational modelling of TCR-pMHC complexes offers an efficient alternative. This study compares the ability of four general-purpose docking platforms (ClusPro, LightDock, ZDOCK and HADDOCK) to make use of varying levels of binding interface information for accurate TCR-pMHC modelling. Each platform was tested on an expanded benchmark set of 44 TCR-pMHC docking cases. In general, HADDOCK is shown to be the best performer. Docking strategy guidance is provided to obtain the best models for each platform for future research. The TCR-pMHC docking cases used in this study can be downloaded from https://github.com/innate2adaptive/ExpandedBenchmark. [ABSTRACT FROM AUTHOR]

A downscaled version of an electrical dry stunner used in aquaculture has been adapted for use on fishing vessels to immobilize the catch (cod, haddock and saithe) shortly after capture to facilitate immediate and easy catch handling, and to minimize downgrading due to poor bleed-out. Possible effects of electrical stimulation of white muscle (blood lactate, initial pH and twitch ability) were determined. Eye roll, respiration, equilibrium, swim ability and noxious stimuli were assessed after stunning and fillets were examined with respect to color shade, possible blood spots and discolorations. Suitable voltages, exposure times to electricity, and rows of electrodes were 40 and 70 V, 4 to 6 s, and 3 to 5 rows of electrodes, respectively. Cod and haddock can be immobilized without skeletal damages and occurrence of blood spots and discolorations. In contrast, 11% of the saithe had fractured spine usually accompanied by a single large blood spot. [ABSTRACT FROM AUTHOR]

From 2005 to 2019, three gadoid species, Atlantic cod (Gadus morhua), haddock (Melanogrammus aeglefinus) and saithe (Pollachius virens), were sampled approximately every third year in the northeastern part of the North Sea. Liver samples were analyzed to investigate levels and temporal trends of six groups of persistent organic pollutants (POPs): polychlorinated biphenyls (PCBs), dichlorodiphenyltrichloroethane (DDT) and its degradation products, hexachlorocyclohexanes (HCHs), hexachlorobenzene (HCB), trans -nonachlor (TNC), and polybrominated diphenyl ethers (PBDEs). Some of the highest average concentrations were found in cod, the levels otherwise being similar between the three species and mostly below established threshold values. The levels of all the contaminants except HCB and TNC were higher than previously reported for cod and haddock in the Barents Sea. Significantly decreasing levels were found for Σ7PCBs, ΣDDTs, ΣHCHs and Σ15PBDEs in all three species, and for TNC in haddock and saithe, while there was no significant trend for TNC in cod. HCB levels increased significantly in cod and haddock and showed only a minor decrease in saithe. The observed time trends of legacy POPs demonstrate the persistence of some of the studied pollutants despite efforts to eliminate them from the marine environment. [Display omitted] • Levels of four POPs show a significant decrease in Atlantic cod, haddock and saithe. • The most recently banned group of POPs, Σ15PBDEs, shows the strongest decrease. • HCB shows a significant increase in cod and haddock, and a weak decrease in saithe. • Differences in time trends between the species are due to their diet and behavior. • The levels are higher than in the Barents Sea for four out of six groups of POPs. [ABSTRACT FROM AUTHOR]

The effect of different type of fish, marination methods, temperature, and cooking time as well as foil type on Al leaching into baked fish, was determinated. Two fish types, Al foils, and marinating ingredients were procured from a hypermarket. Fish was cooked in the baking tray of oven, using two foil types, at 150°C for 40 min and at 200°C for 20 min. Al content was determined. It was found that increase in acidity caused significant increase in Al leaching. When the relationship between temperature-time and Al leaching based on meat type was analysed, it was found that when the temperature was increased the extent of Al leaching was higher in salmon. Even in the highest estimated weekly exposure to Al (1.228 ± 0.1631 mg/kg per week), Al PTWI suggested by JECFA was not exceeded. Although using different Al foil did not leach significant amounts of Al into the fish and exposure values of Al did not exceed the PTWI, exposure of Al from fish samples may be dangerous to vulnerable groups such as children, elderly and people with kidney disease.

Discarding fish has been a part of the fisheries for centuries but it has been very difficult to monitor how much is discarded, especially in areas where it is an illegal activity. In this study the ecological and economic effects of discarding were investigated using the Atlantis model for Icelandic waters. Five different scenarios were compared, using different discarding rates and selectivities. The results showed that a complete stop of discarding fish (cod and haddock) and landing everything instead had little ecological and economic impact. Improved selectivity, which would result in not catching the fish that would be discarded, had great beneficial economic effects. The increase in biomass led to higher landings, which consequently led to higher revenue. Also, the cost decreased with increasing biomass, which increased the profit of the fisheries. None of the five scenarios had great ecological effects but only discarding of cod and haddock, which have low discard rates, were considered in this study.

• Haddock express multiple classical and non-classical MHC-I molecules. • Haddock MHC-I molecules lack endosomal sorting signals involved in cross-presentation. • De-glycosylation trials reveal Atlantic cod and haddock β2 M are N-linked glycosylated. • β2M glycosylation sites appear frequently within Gadiformes and Perciformes lineages. The Atlantic cod immune system deviates from antigen presentation processes seen in other vertebrates in that it lacks the necessary genes for exogenous antigen presentation (i.e., MHC-II and li) and a key MHC-II interacting molecule necessary for T-helper cell function (i.e., CD4), while possessing an expanded repertoire of MHC-I genes that facilitate endogenous antigen presentation. These observations, combined with the identification of putative endosomal sorting signals in MHC-I cytoplasmic tails, have led to speculation that cod rely on cross-presentation of exogenous antigens to elicit cytotoxic T-lymphocyte responses against extracellular threats. In light of this suggestion, we investigated MHC-I transcriptional profiles and endosomal sorting signals in a closely related gadoid species, the haddock. Analysis of transcripts from one individual identified 13 unique MHC-I molecules, including two non-classical molecules as determined by the level of conservation at their peptide anchoring sites. This suggests that like the cod, the haddock has an expanded MHC-I repertoire. Analysis of haddock MHC-I cytoplasmic tail sequences revealed that the dileucine- and tyrosine-based endosomal signaling motifs, that are suggested to facilitate cross-presentation in cod, were absent. Closer examination of the cod signaling motifs, including their relative position in the cytoplasmic tail region, indicates that these motifs might be non-functional, further supporting the need for functional studies to assess cross-presentation. Finally, in silico analysis and in vitro N-type de-glycosylation experiments demonstrate that haddock and cod beta-2-microglobulin (β2M) are glycosylated at the same NQT sequon. Interestingly, whole genome tBLASTn searches also revealed that putative β2 M glycosylation sites appear frequently within the Gadiformes lineage, as the predictive NQT and other N-X-S/T sequons were located in β2M orthologues from 19 of the 25 additional gadoid genomes analyzed. Though the exact significance of β2M glycosylation has yet to be elucidated, phylogenetic comparisons predict that the same NQT glycosylation sequence occurs in 13 additional species comprising four different orders of Actinopterygii (Gymnotiformes, Esociformes, Beryciformes and Perciformes). This suggests either that this feature has arisen independently in multiple lineages or that it comes from a common ancestor and has been lost or modified in many species. Together, the analysis of gadoid MHC-I genes and β2M molecules highlights the challenges in generalizing immune system paradigms across the most diverse vertebrate lineage (i.e., fish) and between fish and more well-studied mammals. [ABSTRACT FROM AUTHOR]

Research background. It is desirable to increase the consumption of pelagic fish rich in long-chain omega-3 fatty acids. Partial replacement of traditionally used white fish species by pelagic fish will increase the content of omega-3 fatty acids, and thus improve the nutritional value but it may also affect the consumer acceptance. The aim of this study is to assess the physicochemical and sensory quality of novel fish cake prototypes prepared from haddock and mackerel mince. Experimental approach. Fillets of haddock and Atlantic mackerel were used as raw material for preparation of fish cakes. The fish fillets were minced, mixed together (in haddock/mackerel mass ratio of 100:0, 75:25 and 50:50) with salt, potato starch, pepper and full fat milk. Physicochemical and sensory analyses were further performed. Results and conclusions. The fatty acid composition analysis showed that the recommended daily intake of 250 mg of eicosapentaenoic acid and docosahexaenoic acid can easily be reached by consumption of fish cakes enriched with mackerel. The oxidation levels of all fish cakes were low in terms of peroxide value and thiobarbituric acid reactive substance assay (TBARS). Fish cakes prepared with higher mass fraction of mackerel mince (>50 %) had significantly (p<0.05) softer texture than other fish cakes due to higher amount of fat in their formulations. At the same time, these fish cakes were significantly darker than haddock-based (>50 %) fish cakes due to higher myoglobin content in the fish muscle. Moreover, fish cakes with higher amount of mackerel mince had increased yellowness due to the accumulation of water-soluble (r=0.990, p<0.05) and fat-soluble (r=0.976, p<0.05) TBARS. Metabolites relevant for taste and quality were quantified by using 1H nuclear magnetic resonance (NMR) spectroscopy. The mass fractions of anserine, trimethylamine oxide and β-alanine decreased, while the mass fractions of histidine, glutamic acid and alanine increased with the addition of mackerel. Sensory tests have shown the addition of mackerel did not reduce consumer acceptability of the new fish cakes. Novelty and scientific contribution. The research demonstrates that Atlantic mackerel can be successfully used for partial replacement of white fish species in fish cake formulations to produce healthy and tasty ready-to-cook products and increase the consumption of small pelagic fish in Europe. [ABSTRACT FROM AUTHOR]

The Ca2+-mediated S100 family protein S100A6 has a crucial task in various intracellular and extracellular activities thereby demonstrating a possible involvement in the advancement and development of malignant tumors. S100A6 has been found to associate with receptor for advanced glycation end products, RAGE, through its extracellular extension. This extension is famously identified as a prominent receptor for many S100 family associates. Additionally, S100A6 binds to S100B protein and forms a heterodimer. Thus, we consider the S100B protein to be a prospective drug molecule to obstruct the interacting regions amongst S100A6 and RAGE V domain. We applied the NMR spectroscopy method to locate the binding area amid the S100A6m (mutant S100A6, cysteine at 3rd position of S100A6 is replaced with serine, C3S) and S100B proteins. The 1H–15N HSQC NMR titrations revealed the probable requisite dynamics of S100A6m and S100B interfaces. Utilizing data from the NMR titrations as input parameters, we ran the HADDOCK program and created a S100A6m-S100B heterodimer complex. The obtained complex was then superimposed with the reported complex of S100A6m-RAGE V domain. This superimposition displayed the possibility of S100B to be a potential antagonist that can block the interface area of the S100A6m and the RAGE V domain. Moreover, an in vitro cancer model using SW480 cells in water-soluble tetrazolium-1 assay (WST-1) showed a noticeable change in the cell proliferation as an effect of these proteins. Our study indicates the possibility to develop a S100B-like competitor that could play a key role in the treatment of S100- and RAGE-mediated human diseases. • S100A6m and S100B protein interacts with each other. • S100A6m and S100B forms a heterodimer complex successfully. • S100B blocks the interaction between S100A6m and RAGE-V. • S100B interfering with the interaction of S100A6m and RAGE-V domain is demonstrated by the WST-1 assay in vitro using SW480 Cells. [ABSTRACT FROM AUTHOR]

Abstract Background Increased availability of genome assemblies for non-model organisms has resulted in invaluable biological and genomic insight into numerous vertebrates, including teleosts. Sequencing of the Atlantic cod (Gadus morhua) genome and the genomes of many of its relatives (Gadiformes) demonstrated a shared loss of the major histocompatibility complex (MHC) II genes 100 million years ago. An improved version of the Atlantic cod genome assembly shows an extreme density of tandem repeats compared to other vertebrate genome assemblies. Highly contiguous assemblies are therefore needed to further investigate the unusual immune system of the Gadiformes, and whether the high density of tandem repeats found in Atlantic cod is a shared trait in this group. Results Here, we have sequenced and assembled the genome of haddock (Melanogrammus aeglefinus) – a relative of Atlantic cod – using a combination of PacBio and Illumina reads. Comparative analyses reveal that the haddock genome contains an even higher density of tandem repeats outside and within protein coding sequences than Atlantic cod. Further, both species show an elevated number of tandem repeats in genes mainly involved in signal transduction compared to other teleosts. A characterization of the immune gene repertoire demonstrates a substantial expansion of MCHI in Atlantic cod compared to haddock. In contrast, the Toll-like receptors show a similar pattern of gene losses and expansions. For the NOD-like receptors (NLRs), another gene family associated with the innate immune system, we find a large expansion common to all teleosts, with possible lineage-specific expansions in zebrafish, stickleback and the codfishes. Conclusions The generation of a highly contiguous genome assembly of haddock revealed that the high density of short tandem repeats as well as expanded immune gene families is not unique to Atlantic cod – but possibly a feature common to all, or most, codfishes. A shared expansion of NLR genes in teleosts suggests that the NLRs have a more substantial role in the innate immunity of teleosts than other vertebrates. Moreover, we find that high copy number genes combined with variable genome assembly qualities may impede complete characterization of these genes, i.e. the number of NLRs in different teleost species might be underestimates.

Abstract Background The WRKY transcription factors are a class of DNA-binding proteins involved in diverse plant processes play critical roles in response to abiotic and biotic stresses. Genome-wide divergence analysis of WRKY gene family in Hordeum vulgare provided a framework for molecular evolution and functional roles. So far, the crystal structure of WRKY from barley has not been resolved; moreover, knowledge of the three-dimensional structure of WRKY domain is pre-requisites for exploring the protein-DNA recognition mechanisms. Homology modelling based approach was used to generate structures for WRKY DNA binding domain (DBD) and its variants using AtWRKY1 as a template. Finally, the stability and conformational changes of the generated model in unbound and bound form was examined through atomistic molecular dynamics (MD) simulations for 100 ns time period. Results In this study, we investigated the comparative binding pattern of WRKY domain and its variants with W-box cis-regulatory element using molecular docking and dynamics (MD) simulations assays. The atomic insight into WRKY domain exhibited significant variation in the intermolecular hydrogen bonding pattern, leading to the structural anomalies in the variant type and differences in the DNA-binding specificities. Based on the MD analysis, residual contribution and interaction contour, wild-type WRKY (HvWRKY46) were found to interact with DNA through highly conserved heptapeptide in the pre- and post-MD simulated complexes, whereas heptapeptide interaction with DNA was missing in variants (I and II) in post-MD complexes. Consequently, through principal component analysis, wild-type WRKY was also found to be more stable by obscuring a reduced conformational space than the variant I (HvWRKY34). Lastly, high binding free energy for wild-type and variant II allowed us to conclude that wild-type WRKY-DNA complex was more stable relative to variants I. Conclusions The results of our study revealed complete dynamic and structural information about WRKY domain-DNA interactions. However, no structure base information reported to date for WRKY variants and their mechanism of interaction with DNA. Our findings highlighted the importance of selecting a sequence to generate newer transgenic plants that would be increasingly tolerance to stress conditions.

Structural information of Fc-Fc receptor interaction may contribute to the design of drugs or therapeutic antibodies associated with the interaction. Computational protein-protein docking can be employed in structural study of protein-protein interaction, but its efficiency and reliability are still unstable and need to be validated and optimized for respective target protein complexes. In this study, we investigated and assessed the computational modeling efficiency of Fc-FcγR complex through HADDOCK by defining five different sets of active residues, a major parameter to determine the prediction efficiency of HADDOCK. The binding residues identified experimentally or the residues in the binding pocket were confirmed to be efficient active residues to achieve a high prediction efficiency, and too narrower or wider specification of active residues led to poor prediction efficiency. Most binding residues and crucial molecular interactions such as conserved interactions and hydrogen bonds in the crystal structure were reproduced in the best model. The HADDOCK docking condition determined in this study is expected to be applied to the computational characterization of various Fc-Fc receptor complexes and mutants. [ABSTRACT FROM AUTHOR]

Protein–protein interactions (PPIs) are important biochemical processes that represent a major challenge in modern biology. Current approaches, which include high-throughput screening and computer aided ligand design, have limitations regarding the identification of hit matter. This current investigation focuses on computational study for protein–protein docking of hypoxia inducible factor-1α (HIF-1α), a tumor inducible factor, and Raf-1 kinase inhibitory protein (RKIP), a tumor metastasis suppressor. These are individually crystallized structures of interacting proteins, which interact to generate a conformational space. HIF activity in pancreatic tumors is determined by hypoxia and HIF-1α subunit availability. RKIP can be used as a prognostic indicator in a number of tumors. The interaction of RKIP with HIF-1α protects against pancreatic cancer (PC) metastasis by inhibiting its hypoxia function. We have explored the binding affinity between both the proteins with the HADDOCK (high ambiguity driven protein–protein docking) server, which determined that 158 structures in 11 clusters represent 79.0% of water-refined models. Of the best 10 clusters, the structures of cluster 2 were found to be better, as they had the lowest Z-score. Further supporting HIF-1α-RKIP interaction, pulldown assay has shown dissociation of RKIP from HIF-1α after CoCl2 treatment in both PC cell lines. [ABSTRACT FROM AUTHOR]

The elimination of unwanted catch in mixed species fisheries is technically challenging given the complexity of fish behaviour within nets. Most approaches to date have employed technologies that modify the nets themselves or use physical sorting grids within the gear. There is currently increasing interest in the use of artificial light to either deter fish from entering the net, or to enhance their escapement from within the net. Here, we evaluated the differences in catch retained in a standard otter trawl, relative to the same gear fitted with a square mesh panel, or a square mesh panel fitted with LEDs. We found that the selectivity of the gear differed depending on water depth. When using a square mesh panel in shallow depths of 29–40 m the unwanted bycatch of whiting and haddock was reduced by 86% and 58% respectively. In deep, darker water (45–95 m), no change in catch was observed in the square-mesh panel treatment, however when LEDs were added to the square-mesh panel, haddock and flatfish catches were reduced by 47% and 25% respectively. These findings demonstrate the potential to improve the performance of bycatch reduction devices through the addition of light devices to enhance selectivity. The results also highlight species-specific and site-specific differences in the performance of bycatch reduction devices, and hence a more adaptive approach to reduce bycatch is probably required to maximize performance. [ABSTRACT FROM AUTHOR]

We report the performance of our newly introduced Ensemble Docking with Enhanced sampling of pocket Shape (EDES) protocol coupled to a template-based algorithm to generate near-native ligand conformations in the 2019 iteration of the Grand Challenge (GC4) organized by the D3R consortium. Using either AutoDock4.2 or HADDOCK2.2 docking programs (each software in two variants of the protocol) our method generated native-like poses among the top 5 submitted for evaluation for most of the 20 targets with similar performances. The protein selected for GC4 was the human beta-site amyloid precursor protein cleaving enzyme 1 (BACE-1), a transmembrane aspartic-acid protease. We identified at least one pose whose heavy-atoms RMSD was less than 2.5 Å from the native conformation for 16 (80%) and 17 (85%) of the 20 targets using AutoDock and HADDOCK, respectively. Dissecting the possible sources of errors revealed that: (i) our EDES protocol (with minor modifications) was able to sample sub-ångstrom conformations for all 20 protein targets, reproducing the correct conformation of the binding site within ~ 1 Å RMSD; (ii) as already shown by some of us in GC3, even in the presence of near-native protein structures, a proper selection of ligand conformers is crucial for the success of ensemble-docking calculations. Importantly, our approach performed best among the protocols exploiting only structural information of the apo protein to generate conformations of the receptor for ensemble-docking calculations. [ABSTRACT FROM AUTHOR]