OBJECTIVE: This study aimed to identify by in silico methods tropomyosin consensus B and T epitopes of shrimp species, house dust mites, insects, and nematodes associated with allergic diseases in tropical countries.
METHODS: In silico analysis included tropomyosin from mites (Der p 10, Der f 10, Blo t 10), insects (Aed a 10, Per a 7, Bla g 7), shrimp (Lit v 1, Pen m 1, Pen a 1), and nematode (Asc l 3) all sequences were taken from the UniProt database. Linear IgE epitopes were predicted with AlgPred 2.0 and validated with BepiPred 3.0. MHC-II binding T cell epitopes were predicted using the IEDB server, which implements nine predictive methods (consensus method, combinatorial library, NN-align-2.3, NN- align-2.2, SMM-align, Sturniolo, NetMHCIIpan 3.1, and NetMHCIIpan 3.2) these predictions focused on 10 HLA-DR and 2 HLA-DQ alleles associated with allergic diseases. Subsequently, consensus B and T epitopes present in all species were identified.
RESULTS: We identified 12 sequences that behaved as IgE-epitopes and B-cell epitopes, three of them: 160RKYDEVARKLAMVEA174, 192ELEEELRVVGNNLKSLEVSEEKAN215, 251KEVDRLEDELV261 were consensus in all species. Eleven peptides (T-epitopes) showed strong binding (percentile rank ≤ 2.0) to HLA-DRB1*0301, *0402, *0411, *0701, *1101, *1401, HLA-DQA1*03:01/DQB1*03:02, and HLA- DQA1*05:01/DQB1*02:01. Only two T-epitopes were consensus in all species: 167RKLAMVEADLERAEERAEt GEsKIVELEEELRV199, and 218EEeY KQQIKT LTaKLKEAEARAEFAERSV246. Subsequently, we identified 2 B and T epitope sequences and reached a consensus between species 167RKLAMVEA174 and 192ELEEELRV199.
CONCLUSIONS: These data describe three sequences that may explain the IgE cross-reactivity between the analyzed species. In addition, the consensus B and T epitopes can be used for further in vitro investigations and may help to design multiple-epitope protein-based immunotherapy for tropomyosin-related allergic diseases.
OBJECTIVE: Este estudio tuvo como objetivo identificar mediante métodos in silico epítopes B y T consenso de tropomiosina de especies de camarón, ácaros del polvo doméstico, insectos y nematodos asociados a enfermedades alérgicas en países tropicales.
UNASSIGNED: El análisis in silico incluyó tropomiosina de ácaros (Der p 10, Der f 10, Blo t 10), insectos (Aed a 10, Per a 7, Bla g 7), camarones (Lit v 1, Pen m 1, Pen a 1), y nematodo (Asc l 3). Todas las secuencias se tomaron de la base de datos UniProt. Los epítopes IgE lineales se predijeron con AlgPred 2.0 y se validaron con BepiPred 3.0. Los epítopes de células T de unión a MHC-II se predijeron utilizando el servidor IEDB, que implementa nueve métodos predictivos (método de consenso, biblioteca combinatoria, NN-align-2.3, NN-align-2.2, SMM-align, Sturniolo, NetMHCIIpan 3.1 y NetMHCIIpan 3.2). Estas predicciones se centraron en diez alelos HLA-DR y 2 HLA-DQ asociados con enfermedades alérgicas. Posteriormente, se identificaron epítopes consenso B y T presentes en todas las especies.
RESULTS: Se identificaron 12 secuencias que se comportaron como epítopes de IgE y, también, como epítopes de células B. Tres de ellas: 160RKYDEVARKLAMVEA174, 192ELEEELRVVGNNLKSLEVSEEKAN213 y 251KEVDRLEDELV261, fueron consenso en todas las especies. Once péptidos mostraron una fuerte unión (rango percentil ≤ 2,0) a HLA-DRB1*0301, *0402, *0411, *0701, *1101, *1401 y a HLA HLA-DQA1*03:01/DQB1*03:02, o HLA-DQA1*05:01/DQB1*02:01. Solo se encontraron dos secuencias: 167RKLAMVEADLERAEERAEtGEsKIVELEEELRV199 con fuerte afinidad por HLA-DQA1*03:01/DQB1*03:02, y HLA-DQA1*05:01/DQB1*02:01. Se identificaron dos secuencias que son epítopos B y T, y son consenso entre especies: 167RKLAMVEA174 y 192ELEEELRV199.
CONCLUSIONS: Estos datos describen tres secuencias que pueden explicar la reactividad cruzada de IgE entre las especies analizadas. Además, los epítopos B y T consenso se pueden usar para investigaciones in vitro adicionales, y pueden ayudar a diseñar inmunoterapia basada en proteínas de múltiepítopes para enfermedades alérgicas relacionadas con la tropomiosina.

In recent years, the advancement and greater magnitude of products, which led to the intensification in shrimp aquaculture is the result of utilization of modern tools and synchronization with other fields of science like microbiology and biotechnology. This intensification led to the elevation of disorders such as the development of several diseases and complications associated with biofouling. The use of antibiotics in aquaculture is discouraged due to their certain hazardous paraphernalia. Consequently, there has been a growing interest in exploring alternative strategies, with probiotics and prebiotics emerging as environmentally friendly substitutes for antibiotic treatments in shrimp aquaculture. This review highlighted the results of probiotics and prebiotics administration in the improvement of water quality, enhancement of growth and survival rates, stress resistance, health status and disease resistance, modulation of enteric microbiota and immunomodulation of different shrimp species. Additionally, the study sheds light on the comprehensive role of prebiotics and probiotics in elucidating the mechanistic framework, contributing to a deeper understanding of shrimp physiology and immunology. Besides their role in growth and development of shrimp aquaculture, the eco-friendly behavior of prebiotics and probiotics have made them ideal to control pollution in aquaculture systems. This comprehensive exploration of prebiotics and probiotics aims to address gaps in our understanding, including the economic aspects of shrimp aquaculture in terms of benefit-cost ratio, and areas worthy of further investigation by drawing insights from previous studies on different shrimp species. Ultimately, this commentary seeks to contribute to the evolving body of knowledge surrounding prebiotics and probiotics, offering valuable perspectives that extend beyond the ecological dimensions of shrimp aquaculture.

Samples from multiple animals may be pooled and tested to reduce costs of surveillance for infectious agents in aquatic animal populations. The primary advantage of pooling is increased population-level coverage when prevalence is low (<10%) and the number of tests is fixed, because of increased likelihood of including target analyte from at least one infected animal in a tested pool. Important questions and a priori design considerations need to be addressed. Unfortunately, pooling recommendations in disease-specific chapters of the 2018 OIE Aquatic Manual are incomplete and, except for amphibian chytrid fungus, are not supported by peer-reviewed research. A systematic review identified only 12 peer-reviewed aquatic diagnostic accuracy and surveillance studies using pooled samples. No clear patterns for pooling methods and characteristics were evident across reviewed studies, although most authors agreed there is a negative effect on detection. Therefore, our purpose was to review pooling procedures used in published aquatic infectious disease research, present evidence-based guidelines, and provide simulated data examples for white spot syndrome virus in shrimp. A decision tree of pooling guidelines was developed for use by peer-reviewed journals and research institutions for the design, statistical analysis and reporting of comparative accuracy studies of individual and pooled tests for surveillance purposes.

The unique physical and chemical properties of graphene-based nanomaterials (GNMs) have inspired a diverse range of scientific and industrial applications. The market value of GNMs is predicted to reach $US 1.3 billion by 2023. Common to many nanomaterials, an important and unresolved question is the environmental consequences of the increases in GNMs use. The current deficiencies in studies reporting ecotoxicology data for GNMs include differences in analytical methodologies for quantification, no standardized test guidelines, differences in morphology of GNMs, the lack of Chemical Abstract Service numbers, and the quality of the reported data. The assessment of potential adverse effects on aquatic organisms typically relies on guideline values based on species sensitivity distributions (SSDs) of toxicity data. We present preliminary water quality guideline values for graphene oxide NMs in freshwaters. Data include 10 species from 7 phyla (bacteria and fungi were not included). The most sensitive organism was found to be the freshwater shrimp Palaemon pandaliformis. The derived guideline values for 99, 95, 90, and 80% species protection were 350, 600, 830, and 1300 μg/L, respectively. These results will contribute to the regulatory derivations of future water quality guideline values for graphene-based NMs. Environ Toxicol Chem 2018;37:1340-1348. © 2018 SETAC.

Water quality guidelines for suspended solids generally rely on the percentage departure from reference condition, an approach that has been criticized. Attempts to develop a biological effects-base guideline have, however, been confounded by low data availability. Furthermore, the high biological response variability to suspended solids exposure suggests that organisms are responding not only to exposure concentration and duration but also to other mechanisms of effect associated with suspended particles (e.g., size, shape, and geochemical composition). An alternative option is to develop more situation and site specific guidelines by generating biological effects data to suspended particles of a particular geochemistry and restricted size range. With this in mind, aquatic organism responses to kaolin clay particle exposure were collated from the literature and incorporated into 2 exposure-response relationship approaches. The species sensitivity distribution approach produced a hazardous concentration affecting 5% of species estimate of 58 mg/L for mortality responses, and 36 mg/L for sublethal data. The severity-of-ill-effect approach produced similar estimates for lethal and sublethal data. These results suggest that aquatic organisms are slightly more tolerant of kaolin clay particles than particles from barite or bentonite clays, based on results from previous studies on these clay types. This type of information can enable better estimates of the risk faced by aquatic organisms exposed to suspended solids. For example, when the sediments of a particular water body are dominated by a particular type of clay particle, then the most appropriate exposure-response relationship can be applied.

The purpose of this study was to investigate how well single-species laboratory data predict real-world pesticide toxicity effects on Crustacea. Data from field pesticide exposures from experimental mesocosm and small pond studies were converted into toxicity units (TUs) by dividing measured pesticide concentrations by the L(E)C50 for Daphnia or acute 5% hazard concentration for Crustacea (HC5-C). The proportion of crustacean taxa significantly affected by the pesticide treatment, called the count ratio of effect, was used in logistic regression models. Of 200 possible logistic model combinations of the TUs, fate, physicochemical variables, and structural variables versus the count ratio of effect for the mesocosm data, the best model was found to incorporate log(TU HC5-C). This model was used to convert pesticide water quality guidelines from around the world into estimates of the proportion of crustacean taxa predicted to be impacted by exposure to a pesticide at the water quality guideline concentration. This analysis suggests 64% of long-term water quality guidelines and 88% of short-term pesticide water quality guidelines are not protective of the aquatic life they are designed to protect. We conclude that empirically derived data from mesocosm studies should be incorporated into water quality guideline derivation for pesticides where available. Also, interspecific differences in susceptibility should be accounted for more accurately to ensure water quality guidelines are adequately protective against the adverse effects of pesticide exposure.

This paper presents an overview of current hypotheses of higher-level crustacean phylogeny in order to assist and help focus further research. It concentrates on hypotheses proposed or debated in the recent literature based on morphological, molecular and combined evidence phylogenetic analyses. It can be concluded that crustacean phylogeny remains essentially unresolved. Conflict is rife, irrespective of whether one compares different morphological studies, molecular studies, or both. Using the number of recently proposed alternative sister group hypotheses for each of the major tetraconatan taxa as a rough estimate of phylogenetic uncertainty, it can be concluded that the phylogenetic position of Malacostraca remains the most problematic, closely followed by Branchiopoda, Cephalocarida, Remipedia, Ostracoda, Branchiura, Copepoda and Hexapoda. Future progress will depend upon a broader taxon sampling in molecular analyses, and the further exploration of new molecular phylogenetic markers. However, the need for continued revision and expansion of morphological datasets remains undiminished given the conspicuous lack of agreement between molecules and morphology for positioning several taxa. In view of the unparalleled morphological diversity of Crustacea, and the likely nesting of Hexapoda somewhere within Crustacea, working out a detailed phylogeny of Tetraconata is a crucial step towards understanding arthropod body plan evolution.

The goal of this study was to assess coastal marine pollution in the Mar Piccolo and Taranto Gulf (Ionian Sea, Southern Italy) by combining chemical and toxicological data in order to compare and integrate both approaches. Pollutants levels, traditionally, have limited ability to predict adverse effects on living resources. Moreover, in order to provide information on the ecological impact of sediment contamination on aquatic biota Numerical Sediment Quality Guidelines (SQGs) and sediment toxicity bioassays were carefully recommended. In this study ERL (effect range low)/ERM (effect range medium value) and TEL (threshold effect level)/PEL (probable effect level) guidelines have been used. Bioassays were performed with two species of amphipods Gammarus aequicauda and Corophium insidiosum, one species of isopod Idotea baltica and bivalve Mytilus galloprovincialis larvae. The TEL/PEL analysis suggested that, especially for stations 1 and 2, sediments in Mar Piccolo should contain acutely toxic concentrations of metals. In particular Hg content, in station 1, was about 17 times PEL value. 96 h LC(50) and 48 h EC(50) values were estimated for cadmium, copper and mercury in these species using the static acute toxicity test. M. galloprovincialis larvae was more sensitive than other species to all the reference toxicants tested (EC(50) determined for cadmium copper and mercury were of 0.59, 0.11 and 0.01 mg/l respectively). Significant differences in sensitivity of species tested to all reference toxicants (ANOVA p < 0.001) were recorded. Bioassays with these species allowed to estimated sediment toxicity from the different studied sites. On the basis of results obtained a good agreement was reported between chemical data and response of the biological endpoints tested.

Mean sediment quality guideline quotients (mean SQGQs) were developed to represent the presence of chemical mixtures in sediments and are derived by normalizing a suite of chemicals to their respective numerical sediment quality guidelines (SQGs). Mean SQGQs incorporate the number of SQGs exceeded and the degree to which they are exceeded and are used for comparison with observed biological effects in the laboratory or field. The current research makes it clear, however, that the number and type of SQGs used in the derivation of these mean quotients can influence the ability of mean SQGQ values to correctly predict acute toxicity to marine amphipods in laboratory toxicity tests. To determine the optimal predictive ability of mean SQGQs, a total of 18 different chemical combinations were developed and compared. The ability of each set of mean SQGQs to correctly predict the presence and absence of acute toxicity to amphipods was determined using three independent databases (n = 605, 2753, 226). Calculated mean SQGQ values for all chemical combinations ranged from 0.002 to 100. The mean SQGQ that was most predictive of acute toxicity to amphipods is calculated as SQGQ1 = ((sigma ([cadmium]/4.21 )([copper]/270)([lead]/ 12.18)([silver]/1.77)([zinc]/ 410)([total chlordane]/6)([dieldrin]/8)([total PAHoc]/1,800)([total PCB]/400))/9). Both the incidence and magnitude of acute toxicity to amphipods increased with increasing SQGQI values. To provide better comparability between regions and national surveys, SQGQ1 is recommended to serve as the standard method for combination of chemicals and respective SQGs when calculating mean SQGQs.

The objectives of this study were to compare approaches for evaluating the combined effects of chemical mixtures on the toxicity in field-collected sediments and to evaluate the ability of consensus-based probable effect concentrations (PECs) to predict toxicity in a freshwater database on both a national and regional geographic basis. A database was developed from 92 published reports, which included a total of 1,657 samples with high-quality matching sediment toxicity and chemistry data from across North America. The database was comprised primarily of 10- to 14-day or 28- to 42-day toxicity tests with the amphipod Hyalella azteca (designated as the HA10 or HA28 tests) and 10- to 14-day toxicity tests with the midges Chironomus tentans or C. riparius (designated as the CS10 test). Mean PEC quotients were calculated to provide an overall measure of chemical contamination and to support an evaluation of the combined effects of multiple contaminants in sediments. There was an overall increase in the incidence of toxicity with an increase in the mean quotients in all three tests. A consistent increase in the toxicity in all three tests occurred at a mean quotient > 0.5, however, the overall incidence of toxicity was greater in the HA28 test compared to the short-term tests. The longer-term tests, in which survival and growth are measured, tend to be more sensitive than the shorter-term tests, with acute to chronic ratios on the order of six indicated for H. azteca. Different patterns were observed among the various procedures used to calculate mean quotients. For example, in the HA28 test, a relatively abrupt increase in toxicity was associated with elevated polychlorinated biphenyls (PCBs) alone or with elevated polycyclic aromatic hydrocarbons (PAHs) alone, compared to the pattern of a gradual increase in toxicity observed with quotients calculated using a combination of metals, PAHs, and PCBs. These analyses indicate that the different patterns in toxicity may be the result of unique chemical signals associated with individual contaminants in samples. Though mean quotients can be used to classify samples as toxic or nontoxic, individual quotients might be useful in helping identify substances that may be causing or substantially contributing to the observed toxicity. An increase in the incidence of toxicity was observed with increasing mean quotients within most of the regions, basins, and areas in North America for all three toxicity tests. The results of these analyses indicate that the consensus-based PECs can be used to reliably predict toxicity of sediments on both a regional and national basis.