N4-methylcytosine (4mC) is a modified form of cytosine found in DNA, contributing to epigenetic regulation. It exists in various genomes, including the Rosaceae family encompassing significant fruit crops like apples, cherries, and roses. Previous investigations have examined the distribution and functional implications of 4mC sites within the Rosaceae genome, focusing on their potential roles in gene expression regulation, environmental adaptation, and evolution. This research aims to improve the accuracy of predicting 4mC sites within the genome of Fragaria vesca, a Rosaceae plant species. Building upon the original 4mc-w2vec method, which combines word embedding processing and a convolutional neural network (CNN), we have incorporated additional feature encoding techniques and leveraged pre-trained natural language processing (NLP) models with different deep learning architectures including different forms of CNN, recurrent neural networks (RNN) and long short-term memory (LSTM). Our assessments have shown that the best model is derived from a CNN model using fastText encoding. This model demonstrates enhanced performance, achieving a sensitivity of 0.909, specificity of 0.77, and accuracy of 0.879 on an independent dataset. Furthermore, our model surpasses previously published works on the same dataset, thus showcasing its superior predictive capabilities.

Streptococcus suis is a bacterial pathogen that can cause significant economic losses in the swine industry due to high morbidity and mortality rates in infected animals. Vaccination with bacterins, which consist of inactivated bacteria and adjuvants to enhance the pig's immune response, is an effective approach to control S. suis infections in piglets. Here we provide a description of S. suis bacterins and the methods for vaccine preparation. Moreover, this chapter also describes the addition of recombinant Sao (rSao-L) protein to the S. suis bacterin, aiming to enhance the efficacy of the bacterins against S. suis in piglets. Furthermore, the methods for evaluating the immune response elicited by the bacterins are also covered in this chapter.

Bovine herpesvirus 1 (BoHV-1), a significant pathogen in the alpha-herpesvirus subfamily, primarily infects cattle and causes the upper respiratory disease known as infectious bovine rhinotracheitis (IBR). In silico studies evaluated the BoHV-1 D protein to be non-allergenic, non-toxic, and highly antigenic, highlighting its potential as an antigen for vaccine development. Therefore, this study aimed to evaluate the efficacy of a subunit vaccine using the ectodomain of glycoprotein D (gD34-380) as an antigen. The truncated gD was successfully cloned and expressed in both Escherichia coli (E. coli, termed EgD) and baculovirus (termed BgD) systems, with expected molecular weights of 65kDa and 50kDa, respectively. For the vaccine formulation, the gD proteins were used either alone or in combination with in-house inactivated BoHV-1. Vaccination of mice and bovines showed that baculovirus-expressed gD34-380 accelerated the antibody response. Moreover, the BgD-vaccinated group also showed significantly higher neutralizing antibody levels against BoHV-1 than the control group (p<0.0001). In conclusion, our study found that BgD from BoHV-1 can increase the immune response and enhance vaccine efficacy.

Here, we report for the first time, green-synthesized selenium nanoparticles (SeNPs) using pharmacologically potent herb of Polygonum bistorta Linn. for multiple biomedical applications. In the study, a facile and an eco-friendly approach is utilized for synthesis of SeNPs using an aqueous roots extract of P. bistorta Linn. followed by extensive characterization via Fourier transform infrared spectroscopy, X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and Energy Dispersive X-Ray (EDX) analysis. The XRD and FTIR data determine the phase composition and successful capping of plant extract onto the surface of NPs while SEM and TEM micrographic examination reveals the elliptical and spherical morphology of the particles with a mean size of 69 ± 23 nm. After comprehensive characterization, the NPs are investigated for antifungal, antibacterial, antileishmanial, antioxidant, and biocompatibility properties. The study reveals that Polygonum bistorta Linn. synthesized SeNPs exhibit significant antibacterial and antifungal activities with Staphylococcus aureus and Fusarium oxysporum inducing the highest zone of inhibition of 14 ± 1.0 mm and 20 ± 1.2 mm, respectively at the concentration of 40 mg/mL. The NPs are also found to have antiparasitic potential against promastigote and amastigote forms of Leishmania tropica. Furthermore, the NPs are discovered to have excellent potential in neutralizing harmful free radicals thus exhibiting considerable antioxidant potential. Most importantly, Polygonum bistorta Linn. synthesized SeNPs showed substantial compatibility against blood cells in vitro studies, which signifies the nontoxic nature of the NPs. The study thus concludes that medicinally important Polygonum bistorta Linn. roots can be utilized as an eco-friendly, sustainable, and green source for the synthesis of pharmacologically potent selenium nanoparticles.

Fowl cholera, caused by Pasteurella multocida infection, poses challenges for prevention because of its many serotypes. Bacterins are currently widely used for vaccination against fowl cholera, but protection is limited to homologous strains. Live attenuated vaccines of P. multocida provide some heterologous protection, but side effects are considerable. More recently, protein-based antigens are promising subunit vaccines when their low immunogenicity has been addressed with effective adjuvants. Bacterial flagellin has been widely considered a promising adjuvant for vaccines. In this study, we tested the adjutancy of flagellin in a subunit vaccine against P. multocida in a mice and chicken models. For vaccine formulation, the antigen fPlpE (P. multocida liporotein E) was combined with fFliC (Salmonella Typhimurium flagellin). The recombinant proteins of fPlpE and fFliC were successfully expressed using the Escherichia coli system as the expected sizes of 55 kDa and 70 kDa, respectively. The fFliC elicited strong expression levels of proinflammatory cytokine (IL-1β, IL-8, and IL-6) when stimulated in native chicken peripheral blood mononuclear cells. Immunization of mice and chickens with the subunit vaccines containing fFliC accelerated the antibody response. In the challenge tests, fFliC increased vaccine protective efficacy against the heterologous strain P. multocida A1 and highly virulent strain Chu01 in mice and chickens, respectively. These data indicated potential possibilities of using fFliC as an immunostimulant adjuvant in developing a subunit vaccine against fowl cholera.

Recombinant Pasterurella multocida lipoprotein E (PlpE) has been shown to protect against fowl cholera. This study aimed to determine if the signal sequence may contribute to the antigenicity and protec-tive efficacy of recombinant PlpE. A small antigenic domain of PlpE (termed truncated PlpE, tPlpE) was constructed with (SP-tPlpE) or without (tPlpE) the signal sequence and evaluated in vitro and in vivo. In vitro, the HEK-Bule hTLR2 Cells were used to evaluate the activation of NF-kB in the test associated with the stimulation of the SP-tPlpE and tPlpE proteins. When chickens were immunized, compared to the tPlpE vac-cine group, the SP-tPlpE group showed higher antibody levels and enhanced CD4+ T cell response. In a challenge test, the SP-tPlpE group showed a survival rate of 87.5% (n = 8), compared to 25% for the tPlpE group. It is confirmed that the inclusion of the native signal sequence enhanced protective efficacy against fowl chol-era and may act as a vaccine adjuvant. The short SP-tPlpE construct is amenable to further vaccine engineer-ing and has potential to be developed as a fowl cholera vaccine.

Flagellin activates the immune system through Toll-like receptor 5 (TLR5) and can work as an adjuvant for subunit vaccines. In this study, we tested the adjuvancy of two different N-terminal fragments of flagellin, (1) FliC99, residues 1–99, and (2) FliC176, residues 1–176, to incorporate larger areas of the hotspot region for potentially higher levels of TLR5 activation and immune response. A truncated version of the VP2 protein (name tVP2, residues 199–356) of the Infectious bursal disease virus (IBDV) was genetically linked to the flagellin constructs, and the immune response was evaluated in chickens. Results showed that both chimeric antigen–adjuvant constructs increased humoral (total IgG titers), cellular and cytokine immune response (IL-4, IFN-γ). The resulting antibody also successfully neutralized IBDV. We conclude that the N-terminus of flagellin can act as an immune activator to enhance vaccine efficacy.

Suilysin (Sly) from Streptococcus suis has been shown to elicit strong immune responses and may act as a vaccine adjuvant. In the present study, we tested the adjuvant effect of Sly using an engineered Pasteurella multocida toxin, rPMT-NC, as the antigen. The antigen was also formulated with other conventional adjuvants (aluminum hydroxide, water-in-oil-in-water) for comparison. The efficacy of these vaccine formulations were evaluated in mice. The optimal dosage of purified rSly for enhancing immune responses in mice was first determined to be 40 μg/ml based on significantly (p < 0.05) increased serum antibody titers, expression of cytokines, including interleukin (IL)-4, IL-12, and interferon (IFN)-γ and the survival rate after challenge with P. multocida. Mice immunized with rPMT-NC + rSly had augmented antibody production and cellular immunity compare to those immunized with rPMT-NC plus other adjuvants. In addition, the survival rate of mice immunized with rPMT-NC + rSly was the highest (70% v.s. 30% of mice immunized with rPMT-NC alone) among all groups. In conclusion, rSly has the potential to be used as a biological adjuvant to enhance immune responses and protective efficacy of protein-based vaccines.

Flagellin from bacteria elicits a proinflammatory immune response and may act as a vaccine adjuvant. In this study, we evaluated the adjuvant effect of the N-terminus of flagellin (residues 1–99) when linked to an antigen (a truncated, conserved domain of lipoprotein E of Pasteurella multocida). Immunization of chickens with the antigen-adjuvant chimeric protein showed that the N-terminus of flagellin accelerated the antibody response and enhanced the cellular immunity (CD8+ T cell expansion). Stimulation of peripheral blood mononuclear cells from vaccinated chickens showed both TH1 (IFN-γ and IL-12) and TH2 (IL-4)-type cytokine gene expressions. In a challenge test, the N-terminus of flagellin increased the survival rate to 75%, compared to 25% in the antigen-only group. In conclusion, our study found that the N-terminus of flagellin can increase the immune response and enhance vaccine protection.