Temperature modifies gene expression in subcuticular epithelial cells of white spot syndrome virus-infected Litopenaeus vannamei

Smart nano generation of transgenic algae expressing white spot syndrome virus in shrimps for inner ear-oral infection treatments using the spotted hyena optimizer (SHO)-Long short-term memory algorithm

Nanotechnology offers a promising avenue to amplify the effectiveness and precision of using transgenic algae in managing WSSV in shrimp by possibly crafting nano-carriers for targeted therapeutic agent delivery or modifying algae cells at a molecular level. Leveraging the capabilities of nano-scale interventions, this study could explore innovative means to manipulate cellular processes, control biological interactions, and enhance treatment efficacy while minimizing undesirable impacts in aquatic environments. The White Spot Syndrome Virus (WSSV) is a double-stranded DNA virus with a tail and rod form that belongs to theNimaviridaefamily. There is no workable way to manage this illness at the moment. This research proposes a new model based on the Long Short-Term Memory (LSTM) and Spotted Hyena Optimizer (SHO) method to control the inner ear-oral infection, utilizing transgenic algae (Chlamydomonas reinhardtii). It is pretty tricky to modify the weight matrix in LSTM. The output will be more accurate if the weight of the neurons is exact. Histological examinations and nested polymerase chain reaction (PCR) testing were performed on the challenged shrimp every 4 h to assess the degree of white spot disease. The SHO-LSTM has shown the highest accuracy and Roc value (98.12% and 0.93, respectively) and the lowest error values (MSE = 0.182 and MAE = 0.48). The hybrid optimized model improves the overall inner ear-oral linked neurological diseases detection ratio. Additionally, with the slightest technical complexity, it effectively controls the forecast factors required to anticipate the ENT. Algal cells were found to be particularly well-suited for inner ear-oral infections, and shrimps fed a transgenic line had the best survival ratio in WSSV infection studies, with 87% of the shrimp surviving. This shows that using this line would effectively stop the spread of WSSV in shrimp populations.

Validation of Real-time PCR Reference Genes of Muscle Metabolism in Harvested Spiny-Cheek Crayfish (Faxonius limosus) Exposed to Seasonal Variation

Real-time quantitative reverse transcription PCR (RT-qPCR) is a sensitive and broadly used technique of assessing gene activity. To obtain a reliable result, stably expressed reference genes are essential for normalization of transcripts in various samples. To our knowledge, this is the first systematic analysis of reference genes for normalization of RT-qPCR data in spiny-cheek crayfish (Faxonius limosus). In this study, expression of five candidate reference genes (actb, β-actin; gapdh, glyceraldehyde-3-phosphate dehydrogenase; eif, eukaryotic translation initiation factor 5a; ef-1α, elongation factor-1α; and tub, α-tubulin) in muscle samples from male and female F. limosus in spring and autumn was analyzed. Additionally, the most stable reference genes were used for accurate normalization of five target genes, i.e., tnnc, troponin c; ak, arginine kinase; fr, ferritin; ccbp-23, crustacean calcium-binding protein 23; and actinsk8, skeletal muscle actin 8. Results obtained using the geNorm and NormFinder algorithms showed high consistency, and differences in the activity of the selected actb with eif genes were successfully identified. The spring and autumn activities of the target genes (except ak) in the muscle tissue of males and females differed significantly, showing that both sexes are immensely involved in an array of breeding behaviors in spring, and females intensively recover in the autumn season. Characterization of first reference genes in spiny-cheek crayfish will facilitate more accurate and reliable expression studies in this key species.

How do abiotic environmental conditions influence shrimp susceptibility to disease? A critical analysis focussed on White Spot Disease

White Spot Syndrome Virus (WSSV) causes White Spot Disease (WSD) and is historically the most devastating disease in the shrimp industry. Global losses from this disease have previously exceeded $3 bn annually, having a major impact on a global industry worth US$19 bn per annum. Shrimp are cultured predominantly in enclosed ponds that are subject to considerable fluctuations in abiotic conditions and WSD outbreaks are increasingly linked to periods of extreme weather, which may cause major fluctuations in pond culture conditions. Combined with the intensity of production in these systems, the resulting suboptimal physicochemical conditions have a major bearing on the susceptibility of shrimp to infection and disease. Current knowledge indicates that pond temperature and salinity are major factors determining outbreak severity. WSSV appears to be most virulent in water temperatures between 25 and 28 °C and salinities far removed from the isoosmotic point of shrimp. Elevated temperatures (>30 °C) may protect against WSD, depending on the stage of infection, however the mechanisms mediating this effect have not been well established. Other factors relating to water quality that may play key roles in determining outbreak severity include dissolved oxygen concentration, nitrogenous compound concentration, partial pressure of carbon dioxide and pH, but data on their impacts on WSSV susceptibility in cultured shrimps is scarce. This illustrates a major research gap in our understanding of the influence of environmental conditions on disease. For example, it is not clear whether temperature manipulations can be used effectively to prevent or mitigate WSD in cultured shrimp. Therefore, developing our understanding of the impact of environmental conditions on shrimp susceptibility to WSSV may provide insight for WSD mitigation when, even after decades of research, there is no effective practical prophylaxis or treatment.

Proliferation dynamics of WSSV in crayfish, Procambarus clarkii, and the host responses at different temperatures

The replication profile of white spot syndrome virus (WSSV) in crayfish, Procambarus clarkii, at different water temperature was investigated in this study. The WSSV detections were negative at 15 ± 1°C, and the natural infection ratio increased at 19 ± 1°C (24.2% ± 2.25%), reached 100% at 25 ± 1°C and decreased at 30 ± 1°C (93.2% ± 3.37%). The WSSV genome copies number was much higher at 25 ± 1°C (≥5 × 10^{6.45 ± 0.35} /mg) than at 15 ± 1°C (≤5 × 10^{1.13 ± 0.12} /mg), 19 ± 1°C (≤5 × 10^{2.74 ± 0.48} /mg) and 32 ± 1°C (≤5 × 10^{3.18 ± 0.27} /mg). Meanwhile, the significant transcription signals of immediate early gene ie1 and late gene vp28 and a large number of virus particles were detected in epitheliums of stomach, gut and gill, hepatopancreas, heart and muscle cells at 25 ± 1°C by using in situ hybridization (ISH) and transmission electron microscopy. The experimental infection of P. clarkii with WSSV infection showed reduced mortality and lower virus copies number at 19 ± 1°C (23.51% ± 0.84%, ≤5 × 10^{3.41 ± 0.11} /mg) and 32 ± 1°C (38.42% ^±  1.21%, ≤5 × 10^{3.72 ± 0.13} /mg) compared to 25 ± 1°C (100%, ≥5 × 10^{4.99 ± 0.24} /mg). The water temperature regulated the transcription of immune-related genes (crustin2, prophenoloxidase (proPO) and heat shock protein70 (Hsp70)), with some differences between WSSV treatments and control treatments. These results demonstrate that water temperature has effect on WSSV proliferation, which may due to transcriptional response of immune-related genes to temperature.

A crayfish Ras gene is involved in the defense against bacterial infection under high temperature

Temperature is an important environmental factor influencing crustacean resistance to pathogen infection. However, the mechanism underlying immune regulation by temperature remains unclear in crustacean. Here, we report a Ras gene of crayfish (designated as PcRAS1) which is involved in immune regulation of crayfish under high temperature. PcRAS1 is induced by both high temperature and bacterial infection and the induction by bacterial infection is associated with temperature. Significant changes of PcRAS1 expression was observed at 32 °C and 24 °C after infection with Aeromonas hydrophila, but relative moderate alternation was found at 16 °C after challenged with A. hydrophila. PcRAS1 silencing significantly reduced crayfish survival from high temperature (32 °C and 24 °C) or bacterial infection at 32 °C, but there was no significant effect on survival from bacterial infection at 24 °C or 16 °C. Further analysis reveals that PO activity is reduced by high temperature or enhanced by bacterial infection. Moreover, both the decreased PO activity and the enhanced PO activity are affected by PcRAS1 expression. PcRAS1 silencing further reduces PO activity under high temperature and compromises the enhanced PO activity by bacterial infection. Lipid peroxidation (LPO) and total antioxidant capacity (TAC) are also involved in the responses to high temperature. LPO is enhanced by lower temperature. TAC is reduced by high temperature and TAC change resulting from high temperature is amplified by PcRAS1 silencing. These results collectively indicate that PcRAS1 is involved in immune regulation against bacterial infection mediated by temperature.

Functional elucidation of LvToll 3 receptor from P. vannamei through RNA interference and its potential role in the shrimp antiviral response

There is a continuing debate on whether an antiviral immunity similar to vertebrate interferon response exists in invertebrates. Recent advances in penaeid immunology identified several new members of the Toll receptor family and one of these is LvToll3 (Litopenaeus vannamei Toll3). It is hypothesized in this study that LvToll3 responds to pathogen associated molecular patterns (PAMPs) such as dsRNA, which then activates certain antiviral pathways in penaeids. RNA interference (RNAi) was used to determine differences in the expression levels of specific genes putatively involved in the antiviral response through qPCR. Results showed that LvToll3 upregulation could be elicited through the introduction of double stranded RNA (dsRNA) regardless of sequence relative to initial levels in the 3rd hour. Furthermore, statistically intriguing trend in the overall expression of Vago 4/5 and Interferon regulatory factor (IRF) suggests that both these genes are affected by the expression of LvToll3. Dicer showed no statistical difference between the experimentally treated (LvToll3-dsRNA), positive control (GFP-dsRNA), and control (PBS) samples corroborating the assertion that dicer is part of another antiviral mechanism that acts in concert with Toll system. These findings suggests that LvToll3 plays a critical role in penaeid antiviral immunity when molecular patterns associated with viruses are detected.

Surveying shrimp aquaculture pond activity using multitemporal VHSR satellite images - case study from the Perancak estuary, Bali, Indonesia

From the 1980's, Indonesian shrimp production has continuously increased through a large expansion of cultured areas and an intensification of the production. As consequences of diseases and environmental degradations linked to this development, there are currently 250,000ha of abandoned ponds in Indonesia. To implement effective procedure to undertake appropriate aquaculture ecosystem assessment and monitoring, an integrated indicator based on four criteria using very high spatial optical satellite images, has been developed to discriminate active from abandoned ponds. These criteria were: presence of water, aerator, feeding bridge and vegetation. This indicator has then been applied to the Perancak estuary, a production area in decline, to highlight the abandonment dynamic between 2001 and 2015. Two risk factors that could contribute to explain dynamics of abandonment were identified: climate conditions and pond locations within the estuary, suggesting that a spatial approach should be integrated in planning processes to operationalize pond rehabilitation.

White spot disease risk factors associated with shrimp farming practices and geographical location in Chanthaburi province, Thailand

Over the past 2 decades, shrimp aquaculture in Thailand has been impacted by white spot disease (WSD) caused by white spot syndrome virus (WSSV). Described here are results of a survey of 157 intensive shrimp farms in Chanthaburi province, Thailand, to identify potential farm management and location risk factors associated with the occurrence of WSD outbreaks. Logistic regression analysis of the survey responses identified WSD risks to be associated with farms sharing inlet water and culturing shrimp year round and with a single owner operating more than 1 farm. The analysis also showed WSD risks to be reduced at farms that used probiotics and applied lime to pond bottoms when fallow to neutralize acidity and kill microorganisms. Regression modeling identified no association of geographical location with WSD. The data should assist shrimp farms in mitigating the effects of WSD in Thailand.

The first detection of white spot syndrome virus in naturally infected cultured Chinese mitten crabs, Eriocheir sinensis in China

An epidemic with a high mortality rate (80-100%) recently occurred in the cultured Chinese mitten crab, Eriocheir sinensis, which is a very important economic crustacean species in China. Using negative stain, histopathology and nested PCR supplemented by sequencing we identified white spot syndrome virus (WSSV) in these crabs. Challenge experiments revealed that the disease was caused by WSSV and confirmed the crab's susceptibility to this virus, which was consistent with previous laboratory-based studies. A cumulative mortality of 100% was observed within 10 days post WSSV injection. This is the first report of WSSV-associated disease outbreaks in the Chinese mitten crab, which is normally reported as an important penaeid-shrimp viral pathogen. Furthermore, this is only the second report to describe a significant pathogen in pond-cultured E. sinensis. These results will enhance the early diagnosis of WSSV in the crab farms and help in monitoring efforts directed at determining the prevalence of the virus in E. sinensis.

Transcriptome analysis of the initial stage of acute WSSV infection caused by temperature change

White spot syndrome virus (WSSV) is the most devastating virosis threatening the shrimp culture industry worldwide. Variations of environmental factors in shrimp culture ponds usually lead to the outbreak of white spot syndrome (WSS). In order to know the molecular mechanisms of WSS outbreak induced by temperature variation and the biological changes of the host at the initial stage of WSSV acute infection, RNA-Seq technology was used to analyze the differentially expressed genes (DEGs) in shrimp with a certain amount of WSSV cultured at 18°C and shrimp whose culture temperature were raised to 25°C. To analyze whether the expression changes of the DEGs were due to temperature rising or WSSV proliferation, the expression of selected DEGs was analyzed by real-time PCR with another shrimp group, namely Group T, as control. Group T didn't suffer WSSV infection but was subjected to temperature rising in parallel. At the initial stage of WSSV acute infection, DEGs related to energy production were up-regulated, whereas most DEGs related to cell cycle and positive regulation of cell death and were down-regulated. Triose phosphate isomerase, enolase and alcohol dehydrogenase involved in glycosis were up-regulated, while pyruvate dehydrogenase, citrate synthase and isocitrate dehydrogenase with NAD as the coenzyme involved in TCA pathway were down-regulated. Also genes involved in host DNA replication, including DNA primase, DNA topoisomerase and DNA polymerase showed down-regulated expression. Several interesting genes including crustin genes, acting binding or inhibiting protein genes, a disintegrin and metalloproteinase domain-containing protein 9 (ADAM9) gene and a GRP 78 gene were also analyzed. Understanding the interactions between hosts and WSSV at the initial stage of acute infection will not only help to get a deep insight into the pathogenesis of WSSV but also provide clues for therapies.

Identification of differentially expressed genes of Trichinella spiralis larvae after exposure to host intestine milieu

Although it has been known for many years that T. spiralis muscle larvae (ML) can not invade intestinal epithelial cells unless they are exposed to the intestinal milieu and activated into intestinal infective larvae (IIL), which genes in IIL are involved in the process of invasion is still unknown. In this study, suppression subtractive hybridization (SSH) was performed to identify differentially expressed genes between IIL and ML. SSH library was constructed using cDNA generated from IIL as the ‘tester’. About 110 positive clones were randomly selected from the library and sequenced, of which 33 T. spiralis genes were identified. Thirty encoded proteins were annotated according to Gene Ontology Annotation in terms of molecular function, biological process, and cellular localization. Out of 30 annotated proteins, 16 proteins (53.3%) had binding activity and 12 proteins (40.0%) had catalytic activity. The results of real-time PCR showed that the expression of nine genes (Ts7, Ndr family protein; Ts8, serine/threonine-protein kinase polo; Ts11, proteasome subunit beta type-7; Ts17, nudix hydrolase; Ts19, ovochymase-1; Ts22, fibronectin type III domain protein; Ts23, muscle cell intermediate filament protein OV71; Ts26, neutral and basic amino acid transport protein rBAT and Ts33, FACT complex subunit SPT16) from 33 T. spiralis genes in IIL were up-regulated compared with that of ML. The present study provide a group of the potential invasion-related candidate genes and will be helpful for further studies of mechanisms by which T. spiralis infective larvae recognize and invade the intestinal epithelial cells.

Identification of differentially transcribed genes in shrimp Litopenaeus vannamei exposed to osmotic stress and challenged with WSSV virus

The effects of hyposmotic stress and white spot syndrome virus (WSSV) challenge in expression was studied in the marine shrimp Litopenaeus vannamei. Messenger RNA from gills of shrimp submitted to osmotic stress was isolated to identify genes differentially expressed through the suppressive subtractive hybridization (SSH) method. Two subtractive libraries forward and two reverse were constructed to identify up and down-regulated genes under these conditions. About 192 clones were sequenced, of which 46 genes were identified. These genes encode proteins corresponding to a wide range of biological roles, including defense, cell signaling, electron transfer, cell proliferation and differentiation, apoptosis, intermediary metabolism, cytoskeleton and digestion. Among the identified genes, 19 were up-regulated and 27 were down-regulated in the animals kept at a lower ion concentration. We evaluated the expression of eight genes by RT-qPCR in shrimp submitted to hyposmotic conditions with and without WSSV challenge. The SSH enabled the identification of genes that are influenced by hyposmotic stress. A significant up-regulation was observed in lectin-C, QM, TGF beta inducible nuclear protein 1, ciclophilin, malate dehydrogenase, mitochondrial ATP synthase F chain and ATP synthase subunit 9 precursor transcripts. However, the expression of these genes in L. vannamei was not affected by WSSV infection both at isosmotic and hyposmotic conditions.

Viral disease emergence in shrimp aquaculture: origins, impact and the effectiveness of health management strategies

Shrimp aquaculture has grown rapidly over several decades to become a major global industry that serves the increasing consumer demand for seafood and has contributed significantly to socio-economic development in many poor coastal communities. However, the ecological disturbances and changes in patterns of trade associated with the development of shrimp farming have presented many of the pre-conditions for the emergence and spread of disease. Shrimp are displaced from their natural environments, provided artificial or alternative feeds, stocked in high density, exposed to stress through changes in water quality and are transported nationally and internationally, either live or as frozen product. These practices have provided opportunities for increased pathogenicity of existing infections, exposure to new pathogens, and the rapid transmission and transboundary spread of disease. Not surprisingly, a succession of new viral diseases has devastated the production and livelihoods of farmers and their sustaining communities. This review examines the major viral pathogens of farmed shrimp, the likely reasons for their emergence and spread, and the consequences for the structure and operation of the shrimp farming industry. In addition, this review discusses the health management strategies that have been introduced to combat the major pathogens and the reasons that disease continues to have an impact, particularly on poor, small-holder farmers in Asia.

Differential expression of genes encoding anti-oxidant enzymes in Sydney rock oysters, Saccostrea glomerata (Gould) selected for disease resistance

Sydney rock oysters (Saccostrea glomerata) selectively bred for disease resistance (R) and wild-caught control oysters (W) were exposed to a field infection of disseminating neoplasia. Cumulative mortality of W oysters (31.7%) was significantly greater than R oysters (0.0%) over the 118 days of the experiment. In an attempt to understand the biochemical and molecular pathways involved in disease resistance, differentially expressed sequence tags (ESTs) between R and W S. glomerata hemocytes were identified using the PCR technique, suppression subtractive hybridisation (SSH). Sequencing of 300 clones from two SSH libraries revealed 183 distinct sequences of which 113 shared high similarity to sequences in the public databases. Putative function could be assigned to 64 of the sequences. Expression of nine ESTs homologous to genes previously shown to be involved in bivalve immunity was further studied using quantitative reverse-transcriptase PCR (qRT-PCR). The base-line expression of an extracellular superoxide dismutase (ecSOD) and a small heat shock protein (sHsP) were significantly increased, whilst peroxiredoxin 6 (Prx6) and interferon inhibiting cytokine factor (IK) were significantly decreased in R oysters. From these results it was hypothesised that R oysters would be able to generate the anti-parasitic compound, hydrogen peroxide (H(2)O(2)) faster and to higher concentrations during respiratory burst due to the differential expression of genes for the two anti-oxidant enzymes of ecSOD and Prx6. To investigate this hypothesis, protein extracts from hemolymph were analysed for oxidative burst enzyme activity. Analysis of the cell free hemolymph proteins separated by native-polyacrylamide gel electrophoresis (PAGE) failed to detect true superoxide dismutase (SOD) activity by assaying dismutation of superoxide anion in zymograms. However, the ecSOD enzyme appears to generate hydrogen peroxide, presumably via another process, which is yet to be elucidated. This corroborates our hypothesis, whilst phylogenetic analysis of the complete coding sequence (CDS) of the S. glomerata ecSOD gene is supportive of the atypical nature of the ecSOD enzyme. Results obtained from this work further the current understanding of the molecular mechanisms involved in resistance to disease in this economically important bivalve, and shed further light on the anomalous oxidative processes involved.

Contributions of functional genomics and proteomics to the study of immune responses in the Pacific white leg shrimp Litopenaeus vannamei

The need for better control of infectious diseases in shrimp aquaculture and the ecological importance of crustacea in marine ecosystems have prompted interest in the study of crustacean immune systems, particularly those of shrimp. As shrimp and other crustacea are poorly understood from the immunological point of view, functional genomic and proteomic approaches have been applied as a means of quickly obtaining molecular information regarding immune responses in these organisms. In this article, a series of results derived from transcriptomic and proteomic studies in shrimp (Litopenaeus vannamei) are discussed. Expressed Sequence Tag analysis, differential expression cloning through Suppression Subtractive Hybridization, expression profiling using microarrays, and proteomic studies using mass spectrometry, have provided a wealth of useful data and opportunities for new avenues of research. Examples of new research directions arising from these studies in shrimp include the molecular diversity of antimicrobial effectors, the role of double stranded RNA as an inducer of antiviral immunity, and the possible overlap between antibacterial and antiviral responses in the shrimp.

White spot syndrome virus proteins and differentially expressed host proteins identified in shrimp epithelium by shotgun proteomics and cleavable isotope-coded affinity tag

Shrimp subcuticular epithelial cells are the initial and major targets of white spot syndrome virus (WSSV) infection. Proteomic studies of WSSV-infected subcuticular epithelium of Penaeus monodon were performed through two approaches, namely, subcellular fractionation coupled with shotgun proteomics to identify viral and host proteins and a quantitative time course proteomic analysis using cleavable isotope-coded affinity tags (cICATs) to identify differentially expressed cellular proteins. Peptides were analyzed by offline coupling of two-dimensional liquid chromatography with matrix-assisted laser desorption ionization-tandem time of flight mass spectrometry. We identified 27, 20, and 4 WSSV proteins from cytosolic, nuclear, and membrane fractions, respectively. Twenty-eight unique WSSV proteins with high confidence (total ion confidence interval percentage [CI%], >95%) were observed, 11 of which are reported here for the first time, and 3 of these novel proteins were shown to be viral nonstructural proteins by Western blotting analysis. A first shrimp protein data set containing 1,999 peptides (ion score, > or =20) and 429 proteins (total ion score CI%, >95%) was constructed via shotgun proteomics. We also identified 10 down-regulated proteins and 2 up-regulated proteins from the shrimp epithelial lysate via cICAT analysis. This is the first comprehensive study of WSSV-infected epithelia by proteomics. The 11 novel viral proteins represent the latest addition to our knowledge of the WSSV proteome. Three proteomic data sets consisting of WSSV proteins, epithelial cellular proteins, and differentially expressed cellular proteins generated in the course of WSSV infection provide a new resource for further study of WSSV-shrimp interactions.