Can three-dimensional nitrate structure be reconstructed from surface information with artificial intelligence? - A proof-of-concept study.

Nitrate is one of the essential variables in the ocean that is a primary control of the upper ocean pelagic ecosystem. Its three-dimensional (3D) structure is vital for understanding the dynamic and ecosystem. Although several gridded nitrate products exist, the possibility of reconstructing the 3D structure of nitrate from surface data has never been exploited. In this study, we employed two advanced artificial intelligence (AI) networks, U-net and Earthformer, to reconstruct nitrate concentration in the Indian Ocean from surface data. Simulation from an ecosystem model was utilized as the labeling data to train and test the AI networks, with wind vectors, wind stress, sea surface temperature, sea surface chlorophyll-a, solar radiation, and precipitation as the input. We compared the performance of two networks and different pre-processing methods. With the input features decomposed into climatology and anomaly components, the Earthformer achieved optimal reconstruction results with a lower normalized mean square error (NRMSE = 0.1591), spatially and temporally, outperforming U-net (NRMSE = 0.2007) and the climatology prediction (NRMSE = 0.2089). Furthermore, Earthformer was more capable of identifying interannual nitrate anomalies. With a network interpretation technique, we quantified the spatio-temporal importance of every input feature in the best case (Earthformer with decomposed inputs). The influence of different input features on nitrate concentration in the adjacent Java Sea exhibited seasonal variation, stronger than the interannual one. The feature importance highlighted the role of dynamic factors, particularly the wind, matching our understanding of the dynamic controls of the ecosystem. Our reconstruction and network interpretation technique can be extended to other ecosystem variables, providing new possibilities in studies of marine environment and ecology from an AI perspective.

Cross-immunity in Nile tilapia vaccinated with Streptococcus agalactiae and Streptococcus iniae vaccines.

Streptococcus agalactiae and Streptococcus iniae are major bacterial pathogens of tilapia that can cause high mortality concomitant with large economic losses to aquaculture. Although development of vaccines using formalin-killed bacteria to control these diseases has been attempted, the mechanism of immunity against streptococcal infections and the cross-protective ability of these two bacteria remains unclear. To explore the immunological role of these vaccines, we compared the immune responses of tilapia after immunization with both vaccines and compared the relative percent survival (RPS) and cross-immunization protection of tilapia after separate infection with S. agalactiae and S. iniae. All results revealed that vaccinated fish had significantly higher (P < 0.05) levels of specific antibodies than control fish 14 days post secondary vaccination (PSV) and 7 days post challenge. In vaccinated fish, the mRNA expression of interleukin-8 (IL-8), interleukin-12 (IL-12), caspase-3 (C-3), tumour necrosis factor (TNF), and interferon (IFN) was significantly up regulated (P < 0.05) in the head kidney after immunized; similar results were found for IL-8, TNF and IFN in the posterior kidney, meanwhile the expression levels of C-3 and IFN were significantly increased (P < 0.05) in the spleen of vaccinated fish. Additionally, the levels of acid phosphatase (ACP), alkaline phosphatase (AKP), superoxide dismutase (SOD), and lysozyme (LZM) in vaccinated fish were improved at different degree when compared to the control fish. These results showed that vaccination with formalin-killed cells (FKCs) of either S. agalactiae or S. iniae conferred protection against infection by the corresponding pathogen in Nile tilapia, resulting in RPS values of 92.3% and 91.7%, respectively. Furthermore, cross-protection was observed, as the S. agalactiae FKC vaccine protected fish from S. iniae infection, and vice versa. These results suggested that the S. agalactiae and S. iniae FKC vaccines can induce immune responses and generate excellent protective effects in Nile tilapia.

Generation of a novel Streptococcus agalactiae ghost vaccine and examination of its immunogenicity against virulent challenge in tilapia.

Streptococcus agalactiae (S. agalactiae) is a gram-positive pathogen that causes a wide range of infections in fish and other animals including humans. Bacterial ghosts (BGs) are nonliving, empty cell envelopes and are well represented as novel vaccine candidates. In this study, we examined the immunogenicity and protective efficacy of S. agalactiae ghosts (SAG) against a virulent challenge in tilapia. Nonliving SAG was generated by a culture with Penicillin and Streptolysin, and then treated with the MIC of sodium hydroxide. The formation of a transmembrane lysis tunnel structure in SAG was visualized by electron microscopy. To investigate the SAG as a vaccine candidate, fish were divided into three groups, A (SAG immunized), B [Formalin-inactivated S. agalactiae (FSA) immunized] and C (phosphate-buffered saline, PBS-immunized control). The IgM antibody responses were significantly stronger in the SAG-immunized group than in FSA-immunized group, which was higher than in the non-immunized control group (P < 0.05). Moreover, phagocytic activity (percent phagocytes, PP) was significantly higher (p < 0.05) in the SAG-immunized group than in FSA-immunized group, which was higher than in the non-immunized control group (P < 0.05). In addition, non-specific immune immunity, such as lysozyme and superoxide dismutase activities, in the SAG-immunized fish showed significantly higher activities than FSA-immunized fish and the control group fish (P < 0.05). Also, fish immunized with SAG and FSA showed significantly higher (p < 0.05) gene expression of IL-1ß, TNF-α, IFN-γ and TGF-ß in the head kidney and spleen than fish treated with PBS during the whole observed period. In addition, fish immunized with SAG showed significantly higher gene expression of L-1ß, TNF-α, and TGF-ß in the spleen than in the FSA-immunized fish. Although there was no significant (P > 0.05) difference of survival rate (SR) or relative percent survival (RPS) between SAG and FSA immunized groups, they were all significantly more protected against the S. agalactiae challenge (SR: 86.67%, RPS: 76.395) and (SR: 80.00%, RPS: 67.50%) respectively, compared to the PBS-treated group (SR: 33.33%). These results suggest that immunization with SAG induces immune responses and provides protection against a virulent S. agalactiae challenge.

Genome size and identification of abundant repetitive sequences in Vallisneria spinulosa.

Vallisneria spinulosa is a freshwater aquatic plant of ecological and economic importance. However, there is limited cytogenetic and genomics information on Vallisneria. In this study, we measured the nuclear DNA content of Vallisneria spinulosa by flow cytometry, performed a de novo assembly, and annotated repetitive sequences by using a combination of next-generation sequencing (NGS) and bioinformatics tools. The genome size of Vallisneria spinulosa is approximately 3,595 Mbp, in which nearly 60% of the genome consists of repetitive sequences. The majority of the repetitive sequences are LTR-retrotransposons comprising 43% of the genome. Although the amount of sequencing data used in this study was not sufficient for a whole-genome assembly, it could generate an overview of representative elements in the genome. These results will lay a new foundation for further studies on various species that belong to the Vallisneria genus.