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ABSTRACT The Alaskan red king crab (Paralithodes camtschaticus) fishery was once one of the most economically important single-species fisheries in the world, but is currently depressed. This fishery would benefit [...]

In 2003, the Alaska walleye pollock industry reported product quality issues attributed to an unspecified parasite in fish muscle. Using molecular and histological methods, we identified the parasite in Bering Sea pollock as Ichthyophonus. Infected pollock were identified throughout the study area, and prevalence was greater in adults than in juveniles. This study not only provides the first documented report of Ichthyophonus in any fish species captured in the Bering Sea, but also reveals that the parasite has been present in this region for nearly 20 years and is not a recent introduction. Sequence analysis of 18 S r DNA from Ichthyophonus in pollock revealed that consensus sequences were identical to published parasite sequences from Pacific herring and Yukon River Chinook salmon. Results from this study suggest potential for Ichthyophonus exposures from infected pollock via two trophic pathways; feeding on whole fish as prey and scavenging on industry-discharged offal. Considering the notable Ichthyophonus levels in pollock, the low host specificity of the parasite and the role of this host as a central prey item in the Bering Sea, pollock likely serve as a key Ichthyophonus reservoir for other susceptible hosts in the North Pacific. [ABSTRACT FROM AUTHOR]

The article discusses a study on the detection of Hematodinium in snow crabs Chionoecetes opilio and Tanner crabs C. bairdi using an optimized polymerase chain reaction (PCR)-based assay. The study involved C. bairdi from the Bering Sea, Gulf of Alaska and southern Alaska while C. opilio from the Bering Sea and Newfoundland in 2003 and 2004. The hemolymph from the crabs was centrifuged for DNA isolation. The recombinant DNA (rDNA) sequences of Hematodinium were found to be similar. Also explained is the variation between clades.

Muscle samples from 178 Merluccius productus were examined for two myxosporean parasites, Kudoa thyrsitis and K. paniformis. Kudoa paniformis was found in 51% of the samples, while K. thyrsitis and mixed infections were observed in 7% and \1% of the samples respectively. An inflammatory response that resulted in an encapsulation around a completely replaced muscle fibre was observed in infections with either parasite. Presporogenic and sporogenic stages were common while stages that may represent early forms of the parasites were only rarely observed. [ABSTRACT FROM AUTHOR]

The recent trend in using network and graph structures to represent a variety of different data types has renewed interest in the graph partitioning (GP) problem. This interest stems from the need for general methods that can both efficiently identify network communities and reduce the dimensionality of large graphs while satisfying various application-specific criteria. Traditional clustering algorithms often struggle to capture the complex relationships within graphs and generalize to arbitrary clustering criteria. The emergence of graph neural networks (GNNs) as a powerful framework for learning representations of graph data provides new approaches to solving the problem. Previous work has shown GNNs to be capable of proposing partitionings using a variety of criteria. However, these approaches have not yet been extended to Markov chains or kinetic networks. These arise frequently in the study of molecular systems and are of particular interest to the biomolecular modeling community. In this work, we propose several GNN-based architectures to tackle the GP problem for Markov Chains described as kinetic networks. This approach aims to maximize the Kemeny constant, which is a variational quantity and it represents the sum of time scales of the system. We propose using an encoder-decoder architecture and show how simple GraphSAGE-based GNNs with linear layers can outperform much larger and more expressive attention-based models in this context. As a proof of concept, we first demonstrate the method's ability to cluster randomly connected graphs. We also use a linear chain architecture corresponding to a 1D free energy profile as our kinetic network. Subsequently, we demonstrate the effectiveness of our method through experiments on a data set derived from molecular dynamics. We compare the performance of our method to other partitioning techniques, such as PCCA+. We explore the importance of feature and hyperparameter selection and propose a general strategy for large-scale parallel training of GNNs for discovering optimal graph partitionings.

We present a comparative study that evaluates the performance of a machine learning potential (ANI-2x), a conventional force field (GAFF), and an optimally tuned GAFF-like force field in the modeling of a set of 10 γ-fluorohydrins that exhibit a complex interplay between intra- and intermolecular interactions in determining conformer stability. To benchmark the performance of each molecular model, we evaluated their energetic, geometric, and sampling accuracies relative to quantum-mechanical data. This benchmark involved conformational analysis both in the gas phase and chloroform solution. We also assessed the performance of the aforementioned molecular models in estimating nuclear spin-spin coupling constants by comparing their predictions to experimental data available in chloroform. The results and discussion presented in this study demonstrate that ANI-2x tends to predict stronger-than-expected hydrogen bonding and overstabilize global minima and shows problems related to inadequate description of dispersion interactions. Furthermore, while ANI-2x is a viable model for modeling in the gas phase, conventional force fields still play an important role, especially for condensed-phase simulations. Overall, this study highlights the strengths and weaknesses of each model, providing guidelines for the use and future development of force fields and machine learning potentials.

Conformational analysis is of paramount importance in drug design: it is crucial to determine pharmacological properties, understand molecular recognition processes, and characterize the conformations of ligands when unbound. Molecular Mechanics (MM) simulation methods, such as Monte Carlo (MC) and molecular dynamics (MD), are usually employed to generate ensembles of structures due to their ability to extensively sample the conformational space of molecules. The accuracy of these MM-based schemes strongly depends on the functional form of the force field (FF) and its parametrization, components that often hinder their performance. High-level methods, such as ab initio MD, provide reliable structural information but are still too computationally expensive to allow for extensive sampling. Therefore, to overcome these limitations, we present a multilevel MC method that is capable of generating quantum configurational ensembles while keeping the computational cost at a minimum. We show that FF reparametrization is an efficient route to generate FFs that reproduce QM results more closely, which, in turn, can be used as low-cost models to achieve the gold standard QM accuracy. We demonstrate that the MC acceptance rate is strongly correlated with various phase space overlap measurements and that it constitutes a robust metric to evaluate the similarity between the MM and QM levels of theory. As a more advanced application, we present a self-parametrizing version of the algorithm, which combines sampling and FF parametrization in one scheme, and apply the methodology to generate the QM/MM distribution of a ligand in aqueous solution.

The ensemble of structures generated by molecular mechanics (MM) simulations is determined by the functional form of the force field employed and its parameterization. For a given functional form, the quality of the parameterization is crucial and will determine how accurately we can compute observable properties from simulations. While accurate force field parameterizations are available for biomolecules, such as proteins or DNA, the parameterization of new molecules, such as drug candidates, is particularly challenging as these may involve functional groups and interactions for which accurate parameters may not be available. Here, in an effort to address this problem, we present ParaMol, a Python package that has a special focus on the parameterization of bonded and nonbonded terms of druglike molecules by fitting to ab initio data. We demonstrate the software by deriving bonded terms' parameters of three widely known drug molecules, viz. aspirin, caffeine, and a norfloxacin analogue, for which we show that, within the constraints of the functional form, the methodologies implemented in ParaMol are able to derive near-ideal parameters. Additionally, we illustrate the best practices to follow when employing specific parameterization routes. We also determine the sensitivity of different fitting data sets, such as relaxed dihedral scans and configurational ensembles, to the parameterization procedure, and discuss the features of the various weighting methods available to weight configurations. Owing to ParaMol's capabilities, we propose that this software can be introduced as a routine step in the protocol normally employed to parameterize druglike molecules for MM simulations.

Trichocyst morphology and development were explored using transmission electron microscopy in Hematodinium spp. isolated directly from Atlantic snow crab (Chionoecetes opilio) hemolymph and from in vitro cultures. Appearance of trichocysts defines the initiation of a morphological transition in the parasites life cycle from vegetative stage to the transmission stage. Trichocysts within sporonts were found in distinct clusters near the nucleus in close apposition to the Golgi. As cells transitioned to more mature dinospores however, trichocysts were found randomly distributed throughout the cytoplasm. Clusters contained both primordial and maturing trichocysts at various stages indicating an asynchronous development. The random distribution of mature trichocysts suggests deployment to the cell membrane for future extrusion. Mature trichocysts of Hematodinium spp. appeared structurally similar to trichocysts from photosynthetic dinoflagellates. Hematodinium spp. trichocysts differed by the presence of peripheral tubules associated with novel cuboidal appendages in the apical region rather than a network of central electron dense fibres as found in photosynthetic dinoflagellates. Additionally, the trichocyst membrane of Hematodinium spp. was in close apposition to the square crystalline core. Trichocyst expulsion was not observed during our study which along with features of development and maturation within Hematodinium life stages should provide insight into proposed roles in host attachment or defense that could further our understanding of the mechanisms of pathogenesis and transmission of the parasite., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Members of the genus Ichthyophonus are trophically transmitted, cosmopolitan parasites that affect numerous fish species worldwide. A quantitative PCR (qPCR) assay specific for genus Ichthyophonus 18S ribosomal DNA was developed for parasite detection and surveillance. The new assay was tested for precision, repeatability, reproducibility, and both analytical sensitivity and specificity. Diagnostic sensitivity and specificity were estimated using tissue samples from a wild population of walleye pollock Theragra chalcogramma. Ichthyophonus sp. presence in tissue samples was determined by qPCR, conventional PCR (cPCR), and histology. Parasite prevalence estimates varied depending upon the detection method employed and tissue type tested. qPCR identified the greatest number of Ichthyophonus sp.-positive cases when applied to walleye pollock skeletal muscle. The qPCR assay proved sensitive and specific for Ichthyophonus spp. DNA, but like cPCR, is only a proxy for infection. When compared to cPCR, qPCR possesses added benefits of parasite DNA quantification and a 100-fold increase in analytical sensitivity. Because this novel assay is specific for known members of the genus, it is likely appropriate for detecting Ichthyophonus spp. DNA in various hosts from multiple regions. However, species-level identification and isotype variability would require DNA sequencing. In addition to distribution and prevalence applications, this assay could be modified and adapted for use with zooplankton or environmental samples. Such applications could aid in investigating alternate routes of transmission and life history strategies typical to members of the genus Ichthyophonus.

Inhibition of proteasome activity and the resulting protein accumulation are now known to be important events in the development of many neurological disorders, including Alzheimer's and Parkinson's diseases. Abnormal or over expressed proteins cause endoplasmic reticulum and oxidative stress leading to cell death, thus, normal proteasome function is critical for their removal. We have shown previously, with cultured SH-SY5Y neuroblastoma cells, that proteasome inhibition by the drug epoxomicin results in accumulation of ubiquitinated proteins. This causes obligatory loading of the mitochondria with calcium (Ca(2+)), resulting in mitochondrial damage and cytochrome c release, followed by programmed cell death (PCD). In the present study, we demonstrate that all-trans-retinoic acid (RA) pretreatment of SH-SY5Y cells protects them from PCD death after subsequent epoxomicin treatment which causes proteasome inhibition. Even though ubiquitinated protein aggregates are present, there is no evidence to suggest that autophagy is involved. We conclude that protection by RA is likely by mechanisms that interfere with cell stress-PCD pathway that otherwise would result from protein accumulation after proteasome inhibition. In addition, although RA activates both the AKT and ERK phosphorylation signaling pathways, only pretreatment with LY294002, an inhibitor of PI3-kinase in the AKT pathway, removed the protective effect of RA from the cells. This finding implies that RA activation of the AKT signaling cascade takes precedence over its activation of ERK1/2 phosphorylation, and that this selective effect of RA is key to its protection of epoxomicin-treated cells. Taken together, these findings suggest that RA treatment of cultured neuroblastoma cells sets up conditions under which proteasome inhibition, and the resultant accumulation of ubiquitinated proteins, loses its ability to kill the cells and may likely play a therapeutic role in neurodegenerative diseases., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

Protists are a diverse group of eukaryotes that possess a unicellular level of organization. As unicellular organisms, the differentiation of cells into tissues does not occur, although when cell differentiation does occur, it is limited to sexual reproduction, alternate vegetative morphologies or quiescent life history stages. Protistan parasites may possess simple or complex life histories that are important factors to consider when investigating protistan diseases of decapods. Unfortunately, the life histories of many protistan parasites of decapods are insufficiently described, resulting in the fact that modes of infection and transmission are often unidentified. This is surprising considering the economic importance of many marine decapods and the ability of protistan parasites to produce significant, but generally transient and area limited mortalities. However, the marine disease landscape is changing and will continue to change as climate change and ocean acidification will play important roles in disease occurrence and distribution. As a result, the following discussion attempts to summarize current knowledge on several crab diseases, their protistan etiological agents, the impact of disease on economically important crab populations and draw attention to areas of needed research. The discussion is not complete as only selected diseases are addressed, or perfect as the Microsporidia are included in the discussion (a traditional error continued in this summary) despite the recent, but controversial placement of the taxon with the fungi., (Published by Elsevier Inc.)

An apostome ciliate, Collinia oregonensis n. sp., is reported inhabiting the cephalothorax and abdomen of 3 euphausiid species from the Oregon-Washington coast: Euphausia pacifica Hansen, 1911, Thysanoessa spinifera Holmes, 1900, and Thysanoessa gregaria G.O. Sars, 1883. This ciliate is the 7th species described for the genus Collinia and the 2nd species known to infect euphausiids. Disease progression and ciliate morphology are described using (1) modified protargol stain, (2) hematoxylin counterstained with Fast Green, and (3) Scanning Electron Microscopy (SEM). All endoparasitic developmental stages (trophont, tomont, tomitogenesis, protomite, and tomite) of C. oregonensis are astomatous and possess between 14 and 22 kineties. C. oregonensis is smaller than C. beringensis Capriulo & Small, 1986, which infects the euphausiid Thysanoessa inermis Krøyer, 1846 in the Bering Sea and which possesses between 24 and 80 kineties. The ciliate is a parasitoid because it must kill the host to complete its life cycle. Infections and mortalities in multiple host species likely reflect the virulent nature of the ciliate. Adult euphausiids infected with this parasitoid possess a swollen and bright orange cephalothorax. C. oregonensis feeds and proliferates inside euphausiids, producing fulminating infections that rupture the cephalothorax and release large numbers of tomites into the surrounding water. After several hours in the free swimming stage under shipboard conditions in the present study, the tomites adhered to each other, forming filaments. Infection rates ranged between 3 and 20% within individual euphausiid aggregations, but infected aggregations were randomly and sparingly distributed. Infected euphausiids were found at 6.7% of 316 stations sampled during 3 summer cruises. No infected euphausiids were collected in winter. Because E. pacifica and T. spinifera account for about 90% of the euphausiid standing stock in the northern California Current System, this parasitoid ciliate may have a significant impact on euphausiid population abundance, distribution and secondary productivity.

This study characterizes intracytoplasmic infections with prokaryote microorganisms in Dreissena sp. (near Dreissena polymorpha) from northeastern Greece and represents the first report of such infections in freshwater bivalves. Light microscope observations of stained tissues revealed basophilic, cytoplasmic inclusion bodies in 87.5% (28/32) of the mussels sectioned. Inclusions in epithelial cells and connective tissues were noted, respectively, in 34.4 and 71.9% of the sample, with 5 mussels (15.6%) having both tissue types infected. Epithelial cell infections were observed in histological sections only in digestive gland tubules and ducts; within tubules, inclusions were present more often in secretory than digestive cells. Connective tissue infections, however, were systemic; among the 32 mussels sectioned, inclusions were found in the gills (65.6%), foot (12.5%), mantle (9.4%), labial palps (6.3%), digestive gland (6.3%), stomach (6.3%), and gonads (3.1%). Cytoplasmic inclusions (maximum dimension, 138 microm) were prominent enough in the gills to be visible in 17.0% of the 247 mussels dissected. Ultrastructurally, prokaryote cells in gill connective tissues were clearly characteristic of Chlamydiales-like organisms, with each intracytoplasmic inclusion containing a loosely packed mixture of elementary, reticulate, intermediate bodies, and blebs. Prokaryote colonies in digestive gland epithelial cells exclusively contained 1 of 4 morphological cell types and were considered Rickettsiales-like. Hexagonal, virus-like particles were present in the cytoplasm of the largest of these Rickettsiales-like prokaryotes. Although host stress was evident from localized cell necrosis and dense hemocyte infiltration, overall infection was fairly benign, with no major, adverse impact on body condition evident among sectioned or dissected mussels. A possible negative effect was partial constriction of gill water tubes, but at the infection intensity observed (typical range 1 to 7 inclusion bodies per section), significant interference with respiration and other metabolic functions of the gills was highly unlikely.