Selection and Characterization of ssDNA Aptamers Targeting Largemouth Bass Virus Infected Cells With Antiviral Activities

Progress in Aptamer Research and Future Applications

Aptamers are short, single-stranded DNA, RNA or synthetic XNA molecules that bind to target molecules with high specificity and affinity. These intrinsically structured RNA or DNA oligonucleotides are not only substitutes for antibodies, but also show great potential for applications in diagnostics, specific drug delivery, and treatment of certain diseases. While the process of aptamer identification and its core functional mechanism known as systematic evolution of exponentially enriched ligands (SELEX), SELEX involves a number of single processes, each contributing to the success or failure of aptamer generation. Today, aptamers are widely used to facilitate basic research discoveries and clinical diagnostics. In addition, aptamers play a promising role as clinical diagnostic and therapeutic agents. This review provides recent advances in this rapidly growing field of research, with special emphasis on aptamer generation and screening, small molecule aptamers, the development of aptamer applications, and applications in clinical medicine. And it also discusses the problems that still exist today with aptamers.

Isolation and characterization of ssDNA aptamers against BipD antigen of Burkholderia pseudomallei

BACKGROUND

Melioidosis is difficult to diagnose due to its wide range of clinical symptoms. The culture method is time-consuming and less sensitive, emphasizing the importance of rapid and accurate diagnostic tests for melioidosis. Burkholderia invasion protein D (BipD) of Burkholderia pseudomallei is a potential diagnostic biomarker. This study aimed to isolate and characterize single-stranded DNA aptamers that specifically target BipD.

METHODS

The recombinant BipD protein was produced, followed by isolation of BipD-specific aptamers using Systematic Evolution of Ligands by EXponential enrichment. The binding affinity and specificity of the selected aptamers were evaluated using Enzyme-Linked Oligonucleotide Assay.

RESULTS

The fifth SELEX cycle showed a notable enrichment of recombinant BipD protein-specific aptamers. Sequencing analysis identified two clusters with a total of seventeen distinct aptamers. AptBipD1, AptBipD13, and AptBipD50 were chosen based on their frequency. Among them, AptBipD1 exhibited the highest binding affinity with a Kd value of 1.0 μM for the recombinant BipD protein. Furthermore, AptBipD1 showed significant specificity for B. pseudomallei compared to other tested bacteria.

CONCLUSION

AptBipD1 is a promising candidate for further development of reliable, affordable, and efficient point-of-care diagnostic tests for melioidosis.

Variation in the intestinal bacterial community composition under different water temperature culture conditions in largemouth bass (Micropterus salmoides)

AIMS

This study aimed to investigate the impact of temperature on the intestinal microbiota of largemouth bass using 16S rRNA gene amplicon sequencing, focusing on the under-explored role of abiotic factors in shaping the gut microbial community.

METHODS AND RESULTS

Five water temperature groups (20.0 ± 0.2°C, 25.0 ± 0.2°C, 28.0 ± 0.2°C, 31.0 ± 0.2°C, and 35.0 ± 0.2°C) were established, each with three replicates. Significant variations in intestinal bacterial community composition were observed across these conditions. Elevated temperatures (31.0 ± 0.2°C and 35.0 ± 0.2°C) led to an increase in opportunistic pathogens such as OTU180 Vibrio and OTU2015 Vogesella (P < 0.05). Species correlation network analysis showed a shift toward more positive relationships among intestinal microbes at higher temperatures (P < 0.05). Ecological process analysis highlighted a greater role of ecological drift in microbial community structure at 31.0 ± 0.2°C and 35.0 ± 0.2°C (P < 0.05).

CONCLUSIONS

The study suggests that higher temperatures may predispose largemouth bass to opportunistic pathogens by altering their intestinal microbiota. Effective water temperature management is crucial for largemouth bass aquaculture to mitigate pathogen risks and maintain a balanced intestinal microbiota. This research provides critical insights into the temperature-microbiota relationship and offers practical recommendations for aquaculture practices.

Updates on infectious diseases of largemouth bass: A major review

The largemouth bass (Micropterus salmoides) is native to North America and has now become a crucial economic species in aquaculture. With the rapid development of high-density intensive farming models, the continuous emergence and spread of diseases pose significant challenges to the sustainable development of largemouth bass aquaculture, including Micropterus salmoides rhabdovirus (MSRV), largemouth bass virus (LMBV), Nocardia spp. and Aeromonas spp. Here, we provide a comprehensive overview of the latest research progress on common diseases of largemouth bass, including pathogen isolation and identification, pathological characteristics, morphological features, epidemiological characteristics, pathogen-host interactions, detection and diagnosis, vaccines, and other control technologies. This information will enhance a more comprehensive understanding of the occurrence of diseases in largemouth bass, and provide insights into future research directions, facilitating more effective disease prevention and control. The collaborative progress among rapid detection technology, the interaction mechanism between pathogen and host, and prevention and control techniques will be the curial to achieving green prevention and control of largemouth bass disease and healthy aquaculture in future.

MALDI-TOF MS combined with AUC method for tigecycline susceptibility testing in Escherichia coli

Objectives

The wide spread of tet(X4) gene orthologues in the environment, food, poultry and humans is causing serious tigecycline resistance. Consequently, developing a fast and universal method to detect tigecycline resistance has become increasingly important.

Methods

During 2019-2022, 116 Escherichia coli isolates were obtained from nine provinces in China. All isolates were tested for their susceptibility to antimicrobial agents by the microdilution broth method and for the tet(X4) gene by PCR. Ten tet(X4)-positive E. coli isolates were used to confirm certain conditions, including the optimal incubation time, the optimal concentration of tigecycline, and the cut-off of the relative growth (RG) value.

Results

The optimal time and concentration of tigecycline for separation of susceptible and resistant isolates was 2 h and 4 mg/L, and the RG cut-off value was 0.4. We validated whether the experiment was feasible using 116 isolates of E. coli. The method yielded a susceptibility of 94.9% (95% CI: 81.4%-99.1%) and a specificity of 96.1% (95% CI: 88.3%-99.0%).

Conclusions

This research has shown that this optical antimicrobial susceptibility testing method can rapidly differentiate between susceptible and resistant phenotypes in isolates of E. coli. In the same range as the current gold-standard methods, the clinical turnaround time is reduced from 48 h to 2.5 h. The above results suggest that the method has splendid specificity and operationality.

Isolation, Characterization, and Transcriptome Analysis of an ISKNV-Like Virus from Largemouth Bass

Largemouth bass (Micropterus salmoides) is an important commercial fish farmed in China. Challenges related to diseases caused by pathogens, such as iridovirus, have become increasingly serious. In 2017, we detected iridovirus-infected diseased largemouth bass in Zunyi, Guizhou Province. The isolated virus was identified as an infectious spleen and kidney necrosis virus (ISKNV)-like virus (ISKNV-ZY). ISKNV-ZY induces a cytopathic effect after infecting mandarin fish brain (MFB) cells. Abundant hexagonal virus particles were observed in the cytoplasm of ISKNV-ZY-infected MFB cells, using electron microscopy. The whole genome of ISKNV-ZY contained 112,248 bp and 122 open reading frames. Phylogenetic tree analysis showed that ISKNV-ZY was most closely related to BCIV, indicating that it is an ISKNV-like megalocytivirus. ISKNV-ZY-infected largemouth bass started to die on day six and reached a death peak on days 7-8. Cumulative mortality reached 100% on day 10. Using RNA sequencing-based transcriptome analysis after ISKNV-ZY infection, 6254 differentially expressed unigenes (DEGs) were identified, of which 3518 were upregulated and 2673 downregulated. The DEGs were associated with endocytosis, thermogenesis, oxidative phosphorylation, the JAK-STAT signaling pathway, the MAPK signaling pathway, etc. These results contribute to understanding the molecular regulation mechanism of ISKNV infection and provide a basis for ISKNV prevention.

Effect of EGCG Extracted from Green Tea against Largemouth Bass Virus Infection

(1) Background: Largemouth bass virus (LMBV) is a major viral pathogen in largemouth bass (Micropterus salmoides) aquaculture that often causes high mortality and heavy economic losses, thus developing treatments to combat this pathogen is of great commercial importance. Green tea is a well-known medicinal plant that contains active ingredients with antiviral, antibacterial, and other biological activities. The goals of this study were to explore the effect and mechanism of green tea source compounds on LMBV and provide data to serve as the basis for the screening of targeted drugs in the future. In this study, we evaluated the effects of the main component of green tea, epigallocatechin-3-gallate (EGCG), against LMBV infection. (2) Methods: The safe working concentration of EGCG was identified by cell viability detection and light microscopy. The antiviral activity and mechanism of action of EGCG against LMBV infection were evaluated with light microscopy, an aptamer 6-carboxy-fluorescein-based fluorescent molecular probe, and reverse transcription quantitative PCR. (3) Results: The safe working concentration of EGCG was ≤10 μg/mL. EGCG showed significant anti-LMBV infection activity in a concentration-dependent manner, and it also destroyed the structure of virus particles. EGCG impacted the binding of virus particles to cell receptors and virus invasion into the host cells. Inhibitory effects of EGCG on LMBV particles, LMBV binding to the host-cell membrane, and LMBV invasion were 84.89%, 98.99%, and 95.23%, respectively. Meanwhile, the effects of EGCG subsequently were verified in vivo. The fatality rate of the LMBV + EGCG group was significantly lower than that of the LMBV group. (4) Conclusions: Our results suggest that EGCG has effective antiviral properties against LMBV and may be a candidate for the effective treatment and control of LMBV infections in largemouth bass aquaculture.

Study on aptamer based high throughput approach identifies natural ingredients against RGNNV

Nervous necrosis virus (NNV) is one of the most destructive pathogens in marine fish aquaculture and is capable of infecting more than 50 fish species worldwide, which resulted in great economic losses. Effective drugs for managing NNV infection are urgently required. Medicinal plants have been known for thousands of years and benefit of medicinal plants against pathogens in aquaculture have emerged. Nowadays, the most commonly used method for detecting virus infection and assessing antiviral drugs efficacy is reverse transcription-quantitative real-time PCR. However, the application is limited on account of high reagent costs, complex time-consuming operations and long detection time. Aptamers have been widely applied in application of pathogens or diseases diagnosis and treatments because of high specificity, strong affinity, good stability, easy synthesized and low costs. This study aimed to establish an aptamer (GBN34)-based high-throughput screening (GBN34-AHTS) model for efficient selection and evaluation of natural ingredients against NNV infection. GBN34-AHTS is an expeditious rapid method for selecting natural ingredients against NNV, which is characterized with high-speed, dram, sensitive and accurate. AHTS strategy could reduce work intensity and experimental costs and shorten the whole screening cycle of effective ingredients. AHTS should be suitable for rapid selection of effective ingredients against other viruses, which is important for improving the prevention and controlling of aquatic diseases.

High-Sensitive FAM Labeled Aptasensor Based on Fe3O4/Au/g-C3N4 for the Detection of Sulfamethazine in Food Matrix

In this study, we developed a fluorescent aptasensor based on Fe₃O₄/Au/g-C₃N₄ and a FAM-labeled aptamer (FAM-SMZ1S) against sulfamethazine (SMZ) for the specific and sensitive detection of SMZ in food matrix. The FAM-SMZ1S was adsorbed by the Fe₃O₄/Au/g-C₃N₄ via π–π stacking and electrostatic adsorption, serving as a basis for the ultrasensitive detection of SMZ. Molecular dynamics was used to explain the reasons why SMZ1S and SMZ were combined. This aptasensor presented sensitive recognition performance, with a limit of detection of 0.16 ng/mL and a linear range of 1–100 ng/mL. The recovery rate ranged from 91.6% to 106.8%, and the coefficient of variation (CV) ranged from 2.8% to 13.4%. In addition, we tested the aptasensor for the monitoring of SMZ in various matrix samples, and the results were well-correlated (R² ≥ 0.9153) with those obtained for HPLC detection. According to these results, the aptasensor was sensitive and accurate, representing a potentially useful tool for the detection of SMZ in food matrix.

Simultaneous Isolation and Identification of Largemouth Bass Virus and Rhabdovirus from Moribund Largemouth Bass (Micropterus salmoides)

Largemouth bass is an important commercially farmed fish in China, but the rapid expansion of its breeding has resulted in increased incidence of diseases caused by bacteria, viruses and parasites. In this study, moribund largemouth bass containing ulcer foci on body surfaces indicated the most likely pathogens were iridovirus and rhabdovirus members and this was confirmed using a combination of immunohistochemistry, cell culture, electron microscopy and conserved gene sequence analysis. We identified that these fish had been co-infected with these viruses. We observed bullet-shaped virions (100−140 nm long and 50−100 nm in diameter) along with hexagonal virions with 140 nm diameters in cell culture inoculated with tissue homogenates. The viruses were plaque purified and a comparison of the highly conserved regions of the genome of these viruses indicated that they are most similar to largemouth bass virus (LMBV) and hybrid snakehead rhabdovirus (HSHRV), respectively. Regression infection experiments indicated fish mortalities for LMBV-FS2021 and HSHRV-MS2021 were 86.7 and 11.1%, respectively. While co-infection resulted in 93.3% mortality that was significantly (p < 0.05) higher than the single infections even though the viral loads differed by >100-fold. Overall, we simultaneously isolated and identified LMBV and a HSHRV-like virus from diseased largemouth bass, and our results can provide novel ideas for the prevention and treatment of combined virus infection especially in largemouth bass.