Development of multi epitope subunit vaccines against emerging carp viruses Cyprinid herpesvirus 1 and 3 using immunoinformatics approach.

Cyprinid herpesvirus is a causative agent of a destructive disease in common and koi carp (Cyprinus carpio), which leads to substantial global financial losses in aquaculture industries. Among the strains of C. herpesvirus, C. herpesvirus 1 (CyHV-1) and C. herpesvirus 3 (CyHV-3) are known as highly pathogenic to carp fishes in Europe, Asia, and Africa. To date, no effective vaccine has been developed to combat these viruses. This study aimed to develop unique multi-epitope subunit vaccines targeting the CyHV-1 and CyHV-3 using a reverse vaccinology approach. The study began with a comprehensive literature review to identify the most critical proteins, which were then subjected to in silico analyses to predict highly antigenic epitopes. These analyses involved assessing antigenicity, transmembrane topology screening, allergenecity, toxicity, and molecular docking approaches. We constructed two multi-epitope-based vaccines incorporating a suitable adjuvant and appropriate linkers. It revealed that both the vaccines are non-toxic and immunogenic. The tertiary structures of the vaccine proteins were generated, refined, and validated to ensure their suitability. The binding affinity between the vaccine constructs and TLR3 and TLR5 receptors were assessed by molecular docking studies. Molecular dynamics simulations indicated that vaccine construct V1 exhibited greater stability with both TLR3 and TLR5 based on RMSD analysis. Hydrogen bond analysis revealed a stronger binding affinity between the vaccine constructs and TLR5 compared to TLR3. Furthermore, MM-PBSA analysis suggested that both vaccine constructs exhibited a better affinity for TLR5. Considering all aspects, the results suggest that in silico development of CyHV vaccines incorporating multiple epitopes holds promise for management of diseases caused by CyHV-1 and CyHV-3. However, further in vivo trials are highly recommended to validate the efficacies of these vaccines.

Surface water, sediment, and biota: The first multi-compartment analysis of microplastics in the Karnafully river, Bangladesh.

The Karnafullly River, which flows through Chattogram and falls into the Bay of Bengal, Bangladesh, is vulnerable to microplastic contamination. In this study, we looked at microplastics in the Karnafully River's surface water (5 sites), sediment (9 sites), and biota (4 species). Microplastic concentrations ranged from 0.57 ± 0.07 to 6.63 ± 0.52 items/L in surface water, 143.33 ± 3.33 to 1240 ± 5.77 items/kg dry weight in sediment, and 5.93 ± 0.62 to 13.17 ± 0.76 items/species in biota. A significant difference (P < 0.05) was found in the concentration of MPs in the Karnafully River's sediment, biota, and surface water. High percentage of fiber-shaped and small-sized MPs (<1 mm) were detected throughout the samples. Water and sediment MPs were often transparent/white and blue, whereas biota MPs were mostly black and red, indicating a color preference during biological uptake. The Bay of Bengal received 61.3 × 109 microplastic items per day. The feeding zone of biota influenced the level of microplastics, with a trend of pelagic > demersal > benthic > benthopelagic. Polyethylene and polyethylene terephthalate were the most abundant polymer. Using the average fish intake rate in Bangladesh, we computed a possible consumption of 4015-7665 items of MPs/person/year.

Insights into ß-diversity of periphytic protozoan fauna along the water column of marine ecosystems.

It has been increasingly recognized that there is high relevance in determining the ß-diversity of communities along an environmental gradient for bioassessment of environmental quality status. To evaluate the vertical variations in ß-diversity of periphytic protozoan fauna, in response to environmental heterogeneity in marine ecosystems, a baseline survey was conducted at the four water depths in the coastal waters of the Yellow Sea, northern China. Results demonstrated that (1) the species distribution presented different patterns at four water depths; (2) both compositional and community structure showed a significant vertical variation in multivariate dispersions from surface layer to the deeper layers; and (3) ß-diversity measures generally increased from depths of 1 m to 5 m. These findings suggest that the homogeneity in the periphytic communities are of a high variability along the water column of marine ecosystems.

Seasonal variability in body-size spectrum of periphytic protozoa during colonization of artificial substrates for marine bioassessment.

To identify the seasonal variability of body-size spectrum for monitoring surveys based on periphytic protozoa, a one-year baseline survey was carried out in a coastal region of Yellow Sea, northern China. A total of 240 glass slides were collected after immersion times of 3, 7, 10, 14, 21 and 28 days in a four season cycle, i.e., winter, spring, summer, and autumn. Body-size ranks S2 and S5 dominated the periphytic protozoan communities from the initial stage (from day 3) to the next periods in spring and autumn, while body-size ranks S7, S8 and S4 showed high variety at the equilibrium stages (from day 10) in summer and winter. The expectation analysis revealed that the samples had different patterns of departure from the anticipated body-size spectrum in each season. This study shows that an ideal sampling approach needs to be established when protozoa is used as bioindicators of marine water quality.

Seasonal variations in colonization dynamics of periphytic protozoa in coastal waters of the Yellow Sea, northern China.

The colonization features of periphytic protozoa have proved to be a useful tool for indicating water quality status in aquatic ecosystems. In order to reveal the seasonal variations in colonization dynamics of the protozoa, a 1-year baseline survey was carried out in coastal waters of the Yellow Sea, northern China. Using glass slides as artificial substrates, a total of 240 slides were collected at a depth of 1 m in four seasons after colonization periods of 3, 7, 10, 14, 21, and 28 days. A total of 122 ciliate species were identified with 21 dominant species. The colonization dynamics of the protozoa were well fitted to the MacArthur-Wilson and logistic models in all four seasons (P < 0.05). However, the equilibrium species numbers (Seq), colonization rates (G), and the time to 90% Seq (T90%) represented a clear seasonal variability: (1) more or less similar levels in spring and autumn (Seq = 29/23; G = 0.301/0.296; T90%=7.650/7.779); (2) with a significant difference in summer and winter (Seq = 32/121; G = 0.708/0.005; T90% = 3.252/479.705). Multivariate approaches demonstrated that the exposure time for the species composition and community structure of the protozoa to an equilibrium period were 10-14 days in spring and autumn, but less and more time periods were needed in summer and winter, respectively. Based on the results, we suggest that the colonization dynamics of periphytic protozoa were different within four seasons, and an optimal sampling strategy for monitoring surveys should be modified during different seasons in marine ecosystems.

Seasonal variability in taxonomic breadth of biofilm-dwelling ciliates in colonization surveys for marine bioassessment.

To determine an optimal sampling strategy for collecting samples with an expected taxonomic breadth, a 1-year baseline colonization survey was conducted in Chinese coastal waters using glass slides as an artificial substratum for biofilm-dwelling ciliates. A total of 240 slide samples were collected at a depth of 1 m in a four-season cycle. The taxonomic composition and structure of the ciliate communities differed from spring to winter. The colonization dynamics in taxonomic distinctness showed a significant variability among the four seasons. Expectation tests on the pairs of average taxonomic distinctness indices demonstrated a seasonal variability in taxonomic breadth of the ciliates, with high expectation levels in spring and autumn and low levels in the other two seasons. These findings suggest that there was a significant seasonal variability in taxonomic breadth for colonization surveys of biofilm-dwelling ciliates, and that an optimal sampling strategy should be determined for bioassessment in marine ecosystems.

Seasonal variability in biological trait pattern of biofilm-dwelling protozoa in colonization surveys for marine bioassessment.

Biological trait analysis (BTA) has been proved to be a powerful tool to evaluate marine water quality. The species trait distributions of biofilm-dwelling protozoa were studied in a coastal region of the Yellow Sea, northern China, during a four-season cycle. The BTA demonstrated that: (1) the protozoa showed a significant seasonal variability in biological trait pattern during the colonization process across four seasons; (2) the colonization dynamics in species trait distribution followed different temporal models; (3) the functional dynamics in spring and summer were significantly different from those in autumn and winter (P < 0.05); and (4) functional diversity showed lower values in spring and summer than in autumn and winter. These findings suggest that BTA is subject to a high seasonal variability during colonization surveys when protozoa are used as bioindicators of marine water quality.

Seasonal variation in biological trait distribution of periphytic protozoa in coastal ecosystem: A baseline study for marine bioassessment.

To reveal the seasonal variability in biological trait distribution for monitoring surveys based on periphytic protozoa, a baseline survey was carried out in a coastal region of Yellow Sea, northern China. A total of 40 slide samples were collected in a four season cycle after an exposure time period of 14 days. The results demonstrated that: (1) the community-weighted means (CWM) of algivores with large and medium sizes were high in spring and summer, while bacterivores with small size were high in autumn and winter; (2) there was a significant seasonal variation in the protozoan community functions, especially from spring/summer to autumn and winter; and (3) functional diversity indices generally peaked in spring or summer. Thus, there was a significant seasonal variation in protozoan community functions and this approach may be used to determine an optimal sampling strategy for monitoring programs in marine ecosystems.

Spatial variations in trophic-functional patterns of periphytic ciliates and indications to water quality in coastal waters of the Yellow Sea.

To evaluate the water quality status using ecological features of the periphytic ciliate communities, a 1-year (Jan. to Dec., 2016) investigation was conducted in coastal waters of the Yellow Sea, northern China. Four trophic-functional groups (TFgrs) were recorded from a total of 141 species-abundance dataset: algivores (A); bacterivores (B); non-selectives (N); and predators (R), comprising of 65, 34, 26, and 16 species, respectively. In terms of species number, TFgr A was predominant in clean areas while TFgrs B and N were dominant in heavy polluted areas and TFgr R was dominant in slightly polluted area. The trophic-functional patterns of the periphytic ciliate communities showed a clear spatial variation within the pollution gradient. Trophic-functional trait diversity measures represented a clear increasing trend from polluted stations to the clean area regarding the pollution gradients. Multivariate correlation and best matching analysis revealed that the spatial pattern of the trophic-functional groupings were significantly shaped by environmental variable nutrients and chemical oxygen demand, alone or in combination with pH, dissolved oxygen, salinity, and transparency. Thus, we suggest that the ecological features based on the trophic-functional patterns of periphytic ciliate communities might be used for bioassessment of water quality in marine ecosystems.

Identifying indicator redundancy of biofilm-dwelling protozoa for bioassessment in marine ecosystems.

A multivariate peeling method of data analysis was applied to determine indicator redundancy and for identifying indicator units (IUs) among biofilm-dwelling ciliate communities used for bioassessment of marine water quality. Samples were taken monthly over a 1-year period at four stations in coastal waters of the Yellow Sea: one heavily polluted, one moderately polluted, one intermittently polluted, and one unpolluted. Four IUs (IU1-4) were identified consisting of 22, 13, 14, and 17 species, respectively, out of a total of 144 species. The IUs showed significant correlation with temporal and spatial variations in environmental variables. The redundancy levels of IUs were interchangeable in time and space. However, IU1 and IU2 generally dominated the communities in moderately and intermittently polluted areas during cool (e.g., early spring, late autumn, and winter) and warm (late spring and early autumn) seasons; IU3 dominated in warm seasons (e.g., late spring to autumn) in the heavily polluted area; and IU4 mainly dominated the samples in the unpolluted and moderately polluted areas during the late summer and early autumn. Furthermore, different trophic-functional groupings were represented within the four IUs and these were generally associated with water quality status. These findings suggest that there is high indicator redundancy in marine biofilm-dwelling ciliate communities subjected to different levels of water quality.