Aquatic ecosystems that form major biodiversity hotspots are critically threatened due to environmental and anthropogenic stressors. We believe that, in this genomic era, computational methods can be applied to promote aquatic biodiversity conservation by addressing questions related to the evolutionary history of aquatic organisms at the molecular level. However, huge amounts of genomics data generated can only be discerned through the use of bioinformatics. Here, we examine the applications of next-generation sequencing technologies and bioinformatics tools to study the molecular evolution of aquatic animals and discuss the current challenges and future perspectives of using bioinformatics toward aquatic animal conservation efforts.

The spread of infectious illnesses has been a significant factor restricting aquaculture production. To maximise aquatic animal health, vaccination tactics are very successful and cost-efficient for protecting fish and aquaculture animals against many disease pathogens. However, due to the increasing number of immunological cases and their complexity, it is impossible to manage, analyse, visualise, and interpret such data without the assistance of advanced computational techniques. Hence, the use of immunoinformatics tools is crucial, as they not only facilitate the management of massive amounts of data but also greatly contribute to the creation of fresh hypotheses regarding immune responses. In recent years, advances in biotechnology and immunoinformatics have opened up new research avenues for generating novel vaccines and enhancing existing vaccinations against outbreaks of infectious illnesses, thereby reducing aquaculture losses. This review focuses on understanding in silico epitope-based vaccine design, the creation of multi-epitope vaccines, the molecular interaction of immunogenic vaccines, and the application of immunoinformatics in fish disease based on the frequency of their application and reliable results. It is believed that it can bridge the gap between experimental and computational approaches and reduce the need for experimental research, so that only wet laboratory testing integrated with in silico techniques may yield highly promising results and be useful for the development of vaccines for fish.

(1) Background: Quorum sensing (QS) is the chemical communication between bacteria that sense chemical signals in the bacterial population to control phenotypic changes through the regulation of gene expression. The inhibition of QS has various potential applications, particularly in the prevention of bacterial infection. QS can be inhibited by targeting the LuxP, a periplasmic receptor protein that is involved in the sensing of the QS signaling molecule known as the autoinducer 2 (AI-2). The sensing of AI-2 by LuxP transduces the chemical information through the inner membrane sensor kinase LuxQ protein and activates the QS cascade. (2) Methods: An in silico approach was applied to design DNA aptamers against LuxP in this study. A method combining molecular docking and molecular dynamics simulations was used to select the oligonucleotides that bind to LuxP, which were then further characterized using isothermal titration calorimetry. Subsequently, the bioactivity of the selected aptamer was examined through comparative transcriptome analysis. (3) Results: Two aptamer candidates were identified from the ITC, which have the lowest dissociation constants (K_d) of 0.2 and 0.5 micromolar. The aptamer with the lowest K_d demonstrated QS suppression and down-regulated the flagellar-assembly-related gene expression. (4) Conclusions: This study developed an in silico approach to design an aptamer that possesses anti-QS properties.

Tagatose is a high value low calorie sweetener that is used as a sugar substitute in the food and pharmaceutical industry. The production of tagatose requires the conversion of galactitol-1-phosphate to tagatose-6-phosphate by galactitol-1-phosphate 5-dehydrogenase (PdGPDH). The objective of this work is to study the protein-ligand interaction between PdGPDH and its ligands; galactitol-1-phosphate, Zn2+ and NAD+. Understanding of this mechanism will provide an insight into the possible catalytic events in these domains, thus providing information for potential protein engineering to improve the tagatose production. A 3D model of PdGPDH was constructed to identify the catalytic and coenzyme binding domains. In order to understand the interaction of PdGPDH with its ligands, a docking analysis of PdGPDH-substrate, PdGPDH-Zn2+ and PdGPDH-NAD+ complex was performed using CDOCKER in Discovery Studio 4.0 (DS 4.0). A series of docking events were performed to find the most stable binding interaction for the enzyme and its ligands. This study found that Cys 37, His 58, Glu 59, Glu 142 residues from PdGPDH form an active site pocket similar to known GPDH. A catalytic Zn2+ binding domain and a cofactor NAD+ binding domain with strong hydrogen bonding contacts with the substrate and the cofactor were identified. The binding pockets of the enzyme for galactitol-1-phosphate, NAD+ and Zn2+ has been defined. The stability of PdGPDH with its ligand was verified by utilizing the molecular dynamic simulation of docked complex. The results from this study will assist future mutagenesis study and enzyme modification work to improve the tagatose production.