Protein identification and analysis tools in the ExPASy server

Genome-wide identification and salt stress expression analysis of the PLATZ transcription factor genes in Betula platyphylla

The PLATZ (Plant AT rich protein and zinc binding protein) transcription factor, which is a type of plant specific zinc dependent DNA binding protein, participates in regulating the process of plant growth and environmental stress responses. In order to clarify the characteristics of the PLATZ family genes in birch (Betula platyphylla), the members of the PLATZ family were screened and analyzed in this study. Totals of ten BpPLATZ genes were identified in birch genome and classified into five groups base on phylogenetic relationship, BpPLATZ genes in the same group usually possess a similar motif composition, exon or intron number. These ten genes distributed on eight chromosomes of fourteen chromosomes of birch. In addition, various cis-elements were distributed in the promoter regions of BpPLATZs, especially with abundant MYC, ABRE and MYB, which were reported to be involved in salt stress responses. The RT-qPCR analysis results show that most genes have the higher expression levels in the roots compared to leaves and stems in birch. BpPLATZ3, BpPLATZ5, BpPLATZ6, BpPLATZ7 and BpPLATZ8 are significantly induced expressed response to salt stress. These studies provide a basis for the further functional study of the BpPLATZ genes.

Construction of a Hybrid Vaccine Based on Der f 35-Derived Peptides with Reduced Allergenicity

INTRODUCTION

House dust mite is the primary trigger of allergic respiratory diseases worldwide, and allergen-specific immunotherapy (AIT) is the only disease-modifying treatment in the clinic. The use of allergen molecules instead of extracts is a promising strategy in AIT. In this study, we constructed a peptide hybrid vaccine against the major mite allergen Der f 35 and verified its hypoallergenicity, making it to be a promising candidate for AIT of mite allergy.

METHODS

The gene encoding Der f 35 was retrieved and synthesized. The hypoallergenic peptide fragments derived from the B-cell epitopes were synthesized based on the predicted profiles of B-cell or T helper-cell epitopes in Der f 35, they were verified by immunoglobulin E (IgE)-reaction test and fused to non-allergenic protein carrier to form the hybrid vaccine. Both the wild-type Der f 35 and the designed vaccine were expressed in Escherichia coli and purified by chromatography; their IgE-binding activity was compared by indirect enzyme-linked immunosorbent assay (ELISA), Western blot, inhibition ELISA, and basophil activation test (BAT). The blocking immunoglobulin G (IgG) against the designed vaccine was raised in rabbits and its ability to inhibit IgE binding of Der f 35 was evaluated by ELISA. The vaccine's effects on peripheral blood mononuclear cells (PBMCs) were investigated.

RESULTS

A total of 29 out of 60 (48.33%) IgE-positive sera against Der f 35 were screened. Five peptide fragments (residue 39-42, 60-67, 73-107, 111-118, 126-143) from Der f 35 were selected as candidates, in which four peptides exhibited almost no IgE reactivity and the fragment 73-107 had weak reactions. Only 5.98-24.02% inhibition rates could be achieved by the peptides when compared with Der f 35 (97.32%). The designed vaccine migrated at approximately 30 kDa by SDS-PAGE. The IgE-ELISA revealed a significant reduction in IgE-binding activity to the vaccine when compared to wild-type Der f 35 (p < 0.0001); the decreased allergenicity was further confirmed by IgE-Western blot, inhibition ELISA, and BAT, respectively. The IgE-reactivity of Der f 35 could be blocked by the vaccine-induced IgG (p < 0.01). The levels of IL-5 and IL-13 from PBMCs were significantly decreased after stimulation by the vaccine than that by Der f 35 (p < 0.05).

CONCLUSION

The designed B-cell epitope vaccine of Der f 35 showed greatly diminished allergenicity and Th2 activity. It could be an effective and safe candidate to prevent allergic adverse reactions during the immunotherapy of mite allergy and merits the further study.

Bioinformatics analysis to design a multi-epitope mRNA vaccine against S. agalactiae exploiting pathogenic proteins

Antibiotic resistance in bacterial pathogen infections is a growing global issue that occurs due to their adaptation to changing environmental conditions. Therefore, producing an efficient vaccine as an alternative approach can improve the immune system, eradicate related pathogens, and overcome this growing problem. Streptococcus agalactiae belongs to group B Streptococcus (GBS). Colonization of GBS during pregnancy is a significant risk factor for infants and young children. S. agalactiae infected population exhibits resistance to beta-lactams, including penicillin and the second-line antibiotics erythromycin and clindamycin. On the other hand, there are currently no commercial vaccines against this pathogen. Vaccination of pregnant women is a highly effective method to protect newborns and infants from S. agalactiae infection, and it has been identified as an urgent demand by the World Health Organization. This study employed various immunoinformatic tools to develop an effective vaccine that could trigger both humoral and cell-mediated immunity and prevent disease. For this purpose, three conserved antigenic proteins of the main pathogenic strains of S. agalactiae were utilized to predict CTL, HTL, and B-cell epitopes for producing an mRNA vaccine against different strains of S. agalactiae. The selected epitopes were fused using proper linkers. The Resuscitation promoting factor E (RpfE) sequence was incorporated in the designed vaccine construct as an adjuvant to boost its immune response. Different physicochemical characteristics of the final designed vaccine, modeling of the three-dimensional structure, molecular docking, molecular dynamics simulation, and immunological response simulation were screened following vaccine administration in an in vivo model. Computational immune simulation data identified that IgG1, IgM, INF γ, IL-2, T helper, and B-cell populations increased significantly after vaccination. These findings suggested that the vaccine candidate may provide good protection against S. agalactiae infection. However, experimental and animal model studies are required for additional validation and implementation in human vaccination programs.

Immunoinformatics investigation on pathogenic Escherichia coli proteome to develop an epitope-based peptide vaccine candidate

Escherichia coli (E. coli), a gram-negative bacterium, quickly colonizes in the human gastrointestinal tract after birth and typically sustains a long-term, symbiotic relationship with the host. However, certain virulent strains of E. coli can cause diseases such as urinary tract infections, meningitis, and enteric disorders. The rising antibiotic resistance among these strains has heightened the urgency for an effective vaccine. This study employs immunoinformatics and a reverse vaccinology technique to identify prospective antigens and create an efficient vaccine construct. In this study, we reported the "Attaching and Effacing Protein" a novel outer-membrane protein conserved in all pathogenic E. coli strains, based on proteome screening. We developed an in silico multi-epitope vaccine that includes helper T lymphocyte (HTL), cytotoxic T lymphocyte (CTL), B cell lymphocyte (BCL), and pan HLA DR-binding reactive epitope (PADRE) sequences, along with appropriate linkers and adjuvants. Machine Learning algorithms were used to evaluate antigenicity, solubility, stability, and non-allergenicity of the vaccine construct. Additionally, molecular docking analysis revealed that vaccine construct has a strong predicted binding affinity for human toll-like receptors on the cell surface. In this context, laboratory validations are necessary to demonstrate the effectiveness of the possible vaccine design that showed encouraging findings through computational validation.

Genome-Wide Analysis of the Common Fig (Ficus carica L.) R2R3-MYB Genes Reveals Their Structure, Evolution, and Roles in Fruit Color Variation

The R2R3-MYB transcription factor (TF) family is crucial for regulating plant growth, stress response, and fruit ripening. Although this TF family has been examined in a multitude of plants, the R2R3-MYB TFs in Ficus carica, a Mediterranean fruit species, have yet to be characterized. This study identified and classified 63 R2R3-MYB genes (FcMYB1 to FcMYB63) in the F. carica genome. We analyzed these genes for physicochemical properties, conserved motifs, phylogenetic relationships, gene architecture, selection pressure, and gene expression profiles and networks. The genes were classified into 29 clades, with members of the same clade showing similar exon-intron structures and motif compositions. Of the 54 orthologous gene pairs shared with mulberry (Morus notabilis), 52 evolved under negative selection, while two pairs (FcMYB55/MnMYB20 and FcMYB59/MnMYB31) experienced diversifying selection. RNA-Seq analysis showed that FcMYB26, FcMYB33, and FcMYB34 were significantly overexpressed in fig fruit peel during maturation phase III. Weighted gene co-expression network analysis (WGCNA) indicated that these genes are part of an expression module associated with the anthocyanin pathway. RT-qPCR validation confirmed these findings and revealed that the Tunisian cultivars 'Zidi' and 'Soltani' have cultivar-specific R2R3-FcMYB genes highly overexpressed during the final stage of fruit maturation and color acquisition. These genes likely influence cultivar-specific pigment synthesis. This study provides a comprehensive overview of the R2R3-MYB TF family in fig, offering a framework for selecting genes related to fruit peel color in breeding programs.

Molecular identification and expression patterns of sweet cherry HIPPs and functional analysis of PavHIPP16 in cold stress

MAIN CONCLUSION

The HIPP proteins are involved in low-temperature stress, the growth of sweet cherry, and may be potential targets for genetic improvement. PavHIPP16 improved cold resistance in Arabidopsis. In response to abiotic stressors, the heavy metal-associated isoprenylated plant protein (HIPP) proteins play a crucial regulatory role. Although the function of HIPP has been identified in some plants, there have been fewer systematic studies conducted on sweet cherry (Prunus avium L.). Therefore, we performed a comprehensive analysis and expression profiling of PavHIPPs using bioinformatics, RT-PCR, and qRT-PCR techniques. Our findings revealed that 28 PavHIPP genes were unevenly distributed across eight chromosomes. We predicted nine motifs in PavHIPP proteins and observed similar gene structures among highly homologous proteins. The promoter sequences of PavHIPPs contained numerous regulatory elements associated with an adversity of stress. The expression levels of some members showed varying degrees of change under low-temperature treatment. These genes were differentially expressed during flower and fruit development. Arabidopsis overexpressing the PavHIPP16 (OE) gene showed significantly lower relative conductivity and malondialdehyde (MDA) content compared with the wild-type (WT) plants under cold environment. Conversely, peroxidase (POD) activity, superoxide dismutase (SOD) activity, and proline content were significantly higher in OE Arabidopsis than in WT plants. Overall, our results suggest that PavHIPP16 OE Arabidopsis thaliana exhibited enhanced adaptability compared to WT plants under cold conditions. This study provides a foundation for future investigations of the pathways regulating sweet cherry growth and development mediated by the HIPP genes.

Recombinant receptor-binding motif of spike COVID-19 vaccine candidate induces SARS-CoV-2 neutralizing antibody response

Introduction

The SARS-CoV-2 pandemic necessitates effective therapeutic solutions. The receptor-binding motif (RBM) is a subdomain of the spike protein's receptor-binding domain (RBD) and is critical for facilitating the binding of SARS-CoV-2 to the human ACE2 receptor. This study investigates the use of the receptor-binding motif (RBM) domain as an immunogen to produce potent neutralizing antibodies against SARS-CoV-2.

Methods

The RBM gene was codon-optimized and cloned into the pET17b vector for expression in E. coli BL21 (DE3) cells, induced with 1 mM IPTG. The recombinant RBM protein was purified using Ni-NTA affinity chromatography. After validating the recombinant RBM by Western blotting with anti-His tag antibodies, BALB/c mice were immunized with 20 µg of the purified RBM protein. Anti-RBM IgG was subsequently purified using protein G resin, and its neutralizing capacity was assessed using the Pishtaz Teb Zaman Neutralization Assay Kit.

Results

The recombinant RBM protein, with a molecular weight of 10 kDa, was expressed as inclusion bodies. the typical yield of purification was 27 mg/L of bacterial culture. The neutralization test demonstrated a concentration of 36 µg/mL of neutralizing antibodies in the immunized serum, preventing the spike protein from binding to ACE2.

Conclusion

Our study demonstrated that anti-RBM antibodies exhibited neutralization effects on SARS-CoV-2. These findings provide evidence for the development of a vaccine candidate through the induction of antibodies against the RBM, necessitating further studies with adjuvants suitable for human use to evaluate its potential for human vaccination.

Structural investigation, computational analysis, and theoretical cryoprotectant approach of antifreeze protein type IV mutants

Antifreeze proteins (AFPs) have unique features to sustain life in sub-zero environments due to ice recrystallization inhibition (IRI) and thermal hysteresis (TH). AFPs are in demand as agents in cryopreservation, but some antifreeze proteins have low levels of activity. This research aims to improve the cryopreservation activity of an AFPIV. In this in silico study, the helical peptide afp1m from an Antarctic yeast AFP was modeled into a sculpin AFPIV, to replace each of its four α-helices in turn, using various computational tools. Additionally, a new linker between the first two helices of AFPIV was designed, based on a flounder AFPI, to boost the ice interaction activity of the mutants. Bioinformatics tools such as ExPASy Prot-Param, Pep-Wheel, SOPMA, GOR IV, Swiss-Model, Phyre2, MODFOLD, MolPropity, and ProQ were used to validate and analyze the structural and functional properties of the model proteins. Furthermore, to evaluate the AFP/ice interaction, molecular dynamics (MD) simulations were executed for 20, 100, and 500 ns at various temperatures using GROMACS software. The primary, secondary, and 3D modeling analysis showed the best model for a redesigned antifreeze protein (AFP1mb, with afp1m in place of the fourth AFPIV helix) with a QMEAN (Swiss-Model) Z score value of 0.36, a confidence of 99.5%, a coverage score of 22%, and a p value of 0.01. The results of the MD simulations illustrated that AFP1mb had more rigidity and better ice interactions as a potential cryoprotectant than the other models; it also displayed enhanced activity in limiting ice growth at different temperatures.

In-silico evaluation of the T-cell based immune response against SARS-CoV-2 omicron variants

During of COVID-19 pandemic, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has continuously evolved, resulting in the emergence of several new variants of concerns (VOCs) with numerous mutations. These VOCs dominate in various regions due to increased transmissibility and antibody evasion, potentially reducing vaccine effectiveness. Nonetheless, it remains uncertain whether the recent SARS-CoV-2 VOCs have the ability to circumvent the T cell immunity elicited by either COVID-19 vaccination or natural infection. To address this, we conducted in-silico analysis to examine the impact of VOC-specific mutations at the epitope level and T cell cross-reactivity with the ancestral SARS-CoV-2. According to the in-silico investigation, T cell responses triggered by immunization or prior infections still recognize the variants in spite of mutations. These variants are expected to either maintain their dominant epitope HLA patterns or bind with new HLAs, unlike the epitopes of the ancestral strain. Our findings indicate that a significant proportion of immuno-dominant CD8 + and CD4 + epitopes are conserved across all the variants, implying that existing vaccines might maintain efficacy against new variations. However, further in-vitro and in-vivo studies are needed to validate the in-silico results and fully elucidate immune sensitivities to VOCs.

Designing a multi-epitope influenza vaccine: an immunoinformatics approach

Influenza continues to be one of the top public health problems since it creates annual epidemics and can start a worldwide pandemic. The virus's rapid evolution allows the virus to evade the host defense, and then seasonal vaccines need to be reformulated nearly annually. However, it takes almost half a year for the influenza vaccine to become accessible. This delay is especially concerning in the event of a pandemic breakout. By producing the vaccine through reverse vaccinology and phage display vaccines, this time can be reduced. In this study, epitopes of B lymphocytes, cytotoxic T lymphocytes, and helper T lymphocytes of HA, NA, NP, and M2 proteins from two strains of Influenza A were anticipated. We found two proper epitopes (ASFIYNGRL and LHLILWITDRLFFKC) in Influenza virus proteins for CTL and HTL cells, respectively. Optimal epitopes and linkers in silico were cloned into the N-terminal end of M13 protein III (pIII) to create a multi-epitope-pIII construct, i.e., phage display vaccine. Also, prediction of tertiary structure, molecular docking, molecular dynamics simulation, and immune simulation were performed and showed that the designed multi-epitope vaccine can bind to the receptors and stimulate the immune system response.

Development of novel multi-protein chimeric immunogens that protect against infection with the Lyme disease agent, Borreliella burgdorferi

Lyme disease is the most common tick-borne disease in North America. A vaccine for use in humans is not available. Here, we detail the development of two chimeric vaccine antigens, BAF and Chv2M. BAF elicits Abs that target proteins and protein variants produced by Borreliella species in ticks (OspB and OspA) and mammals (FtlA/B). OspB serves as the backbone structure for the BAF chimeric. Two OspA221-240 epitope-containing domain (ECD) variants (#A1 and #A15) were inserted into a loop in OspB. The N-terminal region of the FtlA protein was joined to the C-terminus of the chimeric. The second chimeric, Chv2M, consists of L5 (loop 5) and H5 (helix 5) ECDs derived from diverse OspC proteins. Borreliella species produce OspC upon exposure to the bloodmeal and during early infection in mammals. Here, we demonstrate that BAF and Chv2M are potent immunogens that elicit Abs that bind to each component protein (FtlA, FtlB, OspB, and multiple OspA and OspC variants). Anti-BAF and anti-Chv2M Abs kill Borreliella burgdorferi strains through Ab-mediated complement-dependent and complement-independent mechanisms. Eighty percent (32/40) of mice that received a three-dose vaccine regimen were protected from infection with B. burgdorferi B31. Efficacy increased to 90% (18/20) when the amount of Chv2M was increased in the third vaccine dose. Readouts for infection were flaB PCR and seroconversion to VlsE. This study establishes proof of principle for a chimeric immunogen vaccine formulation that elicits Abs to multiple targets on the B. burgdorferi cell surface produced during tick and mammalian stages of the enzootic cycle.IMPORTANCELyme disease is a growing public health threat across parts of the Northern Hemisphere. Regions that can support sustained tick populations are expanding, and the incidence of tick-borne diseases is increasing. In light of the increasing risk of Lyme disease, effective preventive strategies are needed. Most vaccine development efforts have focused on outer surface protein A, a Borreliella burgdorferi protein produced only in ticks. Herein, we describe the development of a novel vaccine formulation consisting of two multivalent chimeric proteins that are immunogenic and elicit antibodies with bactericidal activity that target several cell surface proteins produced by the Lyme disease spirochetes in feeding ticks and mammals. In a broader sense, this study advances efforts to develop custom-designed vaccinogens comprised of epitope-containing domains from multiple proteins.

Genome-wide analysis of Triticum aestivum bromodomain gene family and expression analysis under salt stress

MAIN CONCLUSION

This study identified 82 wheat BRD genes, revealing both conserved evolutionary and functional characteristics across plant species and novel features specific to wheat. GTE8-12 cluster TaBRDs were found as positive response to salt stress. Bromodomain-containing proteins (BRDs) are crucial in histone acetylation "reading" and chromatin remodeling in eukaryotes. Despite some of their members showing importance in various biological processes in plants, our understanding of the BRD family in wheat (Triticum aestivum) remains limited. This study comprehensively analyzes the T. aestivum BRD (TaBRD) family. We identified 82 TaBRD genes in wheat genome encoding hydrophobic proteins with a conserved pocket structure. Phylogenetic analysis classified these genes into 16 distinct clusters, with conserved protein motifs and gene structures within clusters but diverse patterns across clusters. Gene duplication analysis revealed that whole-genome or segmental duplication events were the primary expansion mechanism for the TaBRD family, with purifying selection acting on these genes. Subcellular localization and Gene Ontology (GO) analyses indicated that TaBRD proteins are predominantly nuclear-localized and involved in transcription regulation and RNA metabolism. Promoter analysis and interaction network prediction suggested diverse regulatory mechanisms for TaBRDs. Notably, TaBRDs from the GTE8-12 cluster were enriched with cis-elements responsive to abscisic acid (ABA), methyl jasmonate (MeJA), and light, implying their involvement in physiological functions and abiotic stress responses. Expression analysis confirmed tissue-specific patterns and responsiveness to salinity stress. This comprehensive study enhances our understanding of the BRD family in higher plants and provides a foundation for developing salt-tolerant wheat varieties.

Designing of neoepitopes based vaccine against breast cancer using integrated immuno and bioinformatics approach

Cancer is characterized by genetic instability due to accumulation of somatic mutations in the genes which generate neoepitopes (mutated epitopes) for targeting by Cytotoxic T lymphocytes (CTL). Breast cancer has a high transformation rate with unique composition of mutational burden and neoepitopes load that open a platform to designing a neoepitopes-based vaccine. Neoepitopes-based therapeutic cancer vaccines designed by neoantigens have shown to be feasible, nontoxic, and immunogenic in cancer patients. Stimulation of CTL by neoepitope-based vaccine of self-antigenic proteins plays a key role in distinguishing cancer cells from normal cells and selectively targets only malignant cells. A neoepitopes-based vaccine to combat breast cancer was designed by combining immunology and bioinformatics approaches. The vaccine construct was assembled by the fusion of CTL neoepitopes, helper sequences (used for better separation of the epitopes), and adjuvant together with linkers. The neoepitopes were identified from somatic mutations in the MUC16, TP53, RYR2, F5, DNAH17, ASPM, and ABCA13 self-antigenic proteins. The vaccine construct was undertaken to study the immune simulations (IS), physiochemical characteristics (PP), molecular docking (MD) and simulations, and cloning in appropriate vector. Together, these parameters establish safety, stability, and a strong binding affinity against class I MHC molecules capable of inducing a complete immune response against breast cancer cells.Communicated by Ramaswamy H. Sarma.

Association of Unc-51-like Kinase 4 (ULK4) with the reactivity of the extended reward system in response to conditioned stimuli

OBJECTIVES

ULK4 is an established candidate gene for mental disorders and antipsychotic treatment response. We investigated the association of functional genetic variation at the ULK4 locus with the human extended dopaminergic reward system using fMRI during the performance of a well-established reward paradigm.

METHODS

Two hundred and thirty-four patients were included in this study. Association of genetic variation in the ULK4 gene with reward system functioning were determined using the Desire-Reason-Dilemma (DRD) paradigm which allows to assess brain activation in response to conditioned reward stimuli.

RESULTS

Variant prioritisation revealed the strongest functional signatures for the ULK4 variant rs17215589, coding for amino acid exchange Ala715Thr. For rs17215589 minor allele carriers, we detected increased activation responses to conditioned reward stimuli in the ventral tegmental area, nucleus accumbens and several cortical brain regions of the extended reward system.

CONCLUSIONS

Our findings provide further evidence in humans that genetic variation in ULK4 may increase the vulnerability to mental disorders, by modulating the extended reward system function. Future studies are needed to confirm the modulation of the extended reward system by ULK4 and to specify the role of this mechanism in the pathogenesis of psychiatric disorders.

Pan-genome analysis of GT64 gene family and expression response to Verticillium wilt in cotton

BACKGROUND

The GT64 subfamily, belonging to the glycosyltransferase family, plays a critical function in plant adaptation to stress conditions and the modulation of plant growth, development, and organogenesis processes. However, a comprehensive identification and systematic analysis of GT64 in cotton are still lacking.

RESULTS

This study used bioinformatics techniques to conduct a detailed investigation on the GT64 gene family members of eight cotton species for the first time. A total of 39 GT64 genes were detected, which could be classified into five subfamilies according to the phylogenetic tree. Among them, six genes were found in upland cotton. Furthermore, investigated the precise chromosomal positions of these genes and visually represented their gene structure details. Moreover, forecasted cis-regulatory elements in GhGT64s and ascertained the duplication type of the GT64 in the eight cotton species. Evaluation of the Ka/Ks ratio for similar gene pairs among the eight cotton species provided insights into the selective pressures acting on these homologous genes. Additionally, analyzed the expression profiles of the GT64 gene family. Overexpressing GhGT64_4 in tobacco improved its disease resistance. Subsequently, VIGS experiments conducted in cotton demonstrated reduced disease resistance upon silencing of the GhGT64_4, may indicate its involvement in affecting lignin and jasmonic acid biosynthesis pathways, thus impacting cotton resistance. Weighted Gene Co-expression Network Analysis (WGCNA) revealed an early immune response against Verticillium dahliae in G. barbadense compared to G. hirsutum. Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR) analysis indicated that some GT64 genes might play a role under various biotic and abiotic stress conditions.

CONCLUSIONS

These discoveries enhance our knowledge of GT64 family members and lay the groundwork for future investigations into the disease resistance mechanisms of this gene in cotton.

Anti-Magnaporthe oryzae Activity of Streptomyces bikiniensis HD-087 In Vitro and Bioinformatics Analysis of Polyketide Synthase Gene pksL

Streptomyces bikiniensis HD-087 is capable of synthesizing various antimicrobial substances to counter the detrimental effects of hazardous microorganisms. To elucidate whether it produces polyketide antibiotics and the synthesis mechanism of antibiotic substances, the metabolites and related genes of S. bikiniensis HD-087 were analyzed through LC-MS, anti-Magnaporthe oryzae activity detection, and bioinformatics approaches. The result indicated that the strain HD-087 could produce erythromycin, a polyketide antibiotic. The inhibitory zones of the fermentation supernatant of strain HD-087 and methanol solution of erythromycin extract against M. oryzae were 40.84 ± 0.68 mm and 33.18 ± 0.81 mm, respectively. The IC50 value of erythromycin extract for inhibiting spore germination of erythromycin extract was 220.43 μg/mL. There are two polyketide synthesis gene clusters in the genome of strain HD-087, namely t1pks-nrps and t3pks-lantipeptide-t1pks-nrps. The key gene pksL in the t3pks-lantipeptide-t1pks-nrps gene cluster was predicted. The results suggested that it encodes a stable, hydrophilic, and acidic protein, mainly composed of α-helix and random coil. The PksL protein contains dehydrogenase (DH), ketone reductase (KR), acyl carrier protein (ACP), and ketone synthase (KS) domains. Moreover, it can form interaction networks with 11 proteins containing domains, such as polyketide synthase and ACP synthase. The molecular docking between PksL and acetyl-CoA is stable and strong, suggesting that PksL protein could catalyze the synthesis of polyketides with CoA as a substrate. This study provides a theoretical basis for further exploring the polyketides synthesis mechanism and developing antifungal metabolites in S. bikiniensis HD-087.

Inhibition of the EphA2-Sam/Ship2-Sam Association through Peptide Ligands: Studying the Combined Effect of Charge and Aromatic Character

The Sam (sterile alpha motif) domain from the lipid phosphatase Ship2 binds the Sam domain from the EphA2 receptor to negatively regulate receptor endocytosis and degradation. This interaction is primarily linked to pro-oncogenic effects. We report on the design and evaluation of EphA2-Sam/Ship2-Sam peptide inhibitors provided with positive charges and different aromatic characters. Starting from the sequence of previously identified Ship2-Sam targeting peptides, an in silico approach was set up to predict higher affinity peptide ligands. A few peptides were experimentally tested through an interdisciplinary approach. Interaction studies were performed by nuclear magnetic resonance spectroscopy and biolayer interferometry. 3D models of Ship2-Sam/peptide complexes were predicted by AlphaFold2. Cell-based assays were carried out to investigate whether such peptide sequences might have an influence on EphA2 signaling. The approach led to the identification of novel Ship2-Sam ligands and shed further light on original approaches to design inhibitors of the Ship2-Sam/EphA2-Sam interaction.

Overexpression of the Liriodendron tulipifera TPS32 gene in tobacco enhances terpenoid compounds synthesis

Liriodendron, a relic genus from the Magnoliaceae family, comprises two species, L. tulipifera and L. chinense. L. tulipifera is distinguished by its extensive natural distribution in Eastern North America. Conversely, L. chinense is nearing endangerment due to its low regeneration rate. A pivotal aspect in the difference of these species involves terpenoids, which play crucial roles in plant growth and attracting pollinators. However, the complex molecular mechanisms underlying terpenoid roles in Liriodendron are not well understood. Terpene Synthases (TPS) genes are widely reported to play a role in terpenoid biosynthesis, hence, this study centers on TPS genes in Liriodendron spp. Employing multiple bioinformatics methods, a differential expression gene in L. tulipifera, LtuTPS32, was discerned for further functional analysis. Subcellular localization results reveal the involvement of LtuTPS32 in chloroplast-associated processes, hence participate in terpenoid biosynthesis within chloroplasts. Heterologous transformation of the LtuTPS32 gene into tobacco significantly elevates the levels of common terpenoid compounds, including chlorophyll, gibberellin, and carotenoids. Collectively, these findings not only underscore the role of the LtuTPS32 gene in the biosynthesis of terpenoids but also lay a foundation for future research on interspecific differences in Liriodendron.

An immunoinformatics approach for a potential NY-ESO-1 and WT1 based multi-epitope vaccine designing against triple-negative breast cancer

Breast cancer emerges as one of the most prevalent malignancies in women, its incidence showing a concerning upward trend. Among the diverse array of breast cancer subtypes, triple-negative breast cancer (TNBC) assumes notable significance, due to lack of estrogen, progesterone, and HER-2 receptors. More focus has to be placed on creating effective therapy due to the high prevalence and rising incidence of TNBC. Currently, conventional passive treatments have several drawbacks that have not yet been resolved. On the other hand, as innovative immunotherapy approaches, cancer vaccines have offered promising prospects in combatting advanced stages of TNBC. Therefore, the main objective of this study was to utilize WT1 and NY-ESO-1 antigenic proteins in designing a multiepitope vaccine against TNBC. Initially, to generate robust immune responses, we identified antigenic epitopes of both proteins and assessed their immunogenicity. In order to reduce junctional immunogenicity, promiscuous epitopes were joined using the suitable adjuvant (50S ribosomal L7/L12 protein) and incorporated appropriate linkers (GPGPG, AAY, and EAAAK). The best predicted 3D model was refined and validated to achieve an excellent 3D model. Molecular docking analysis and dynamic simulation were conducted to demonstrate the structural stability and integrity of the vaccine/TLR-4 complex. Finally, the vaccine was cloned into the vector pET28 (+). Thus, analysis of the constructed vaccine through immunoinformatics indicates its capability to elicit robust humoral and cellular immune responses in the targeted organism. As such, it holds promise as a therapeutic weapon against TNBC and may open doors for further research in the field.

Genome-wide identification of the GATA gene family in melon (Cucumis melo) and analysis of their expression characteristics under biotic and abiotic stresses

GATA transcription factors are an important class of transcription factors in plants, known for their roles in tissue development, signal transduction, and responses to biotic and abiotic stresses. To date, there have been no reports on the GATA gene family in melon (Cucumis melo). In this study, 24 CmGATA genes were identified from the melon genome. These family members exhibit significant differences in protein length, molecular weight, and theoretical isoelectric point and are primarily located in the nucleus. Based on the classification of Arabidopsis thaliana GATA members, the phylogenetic tree divided them into four groups: group I, group II, group III, and group IV, containing 10, 8, 4, and 2 genes, respectively. Notably, CmGATA genes within the same group have highly conserved protein motifs and similar exon-intron structures. The CmGATA family members are unevenly distributed across 10 chromosomes, with six pairs of segmentally duplicated genes and one pair of tandemly duplicated genes, suggesting that gene duplication may be the primary factor in the expansion of the CmGATA family. Melon shares 21, 4, 38, and 34 pairs of homologous genes with A. thaliana, Oryza sativa, Cucumis sativus, and Citrullus lanatus, respectively. The promoter regions are enriched with various cis-acting elements related to growth and development (eight types), hormone regulation (nine types), and stress responses (six types). Expression patterns indicate that different CmGATA family members are significantly expressed in seeds, roots, stems, leaves, tendrils, mesocarp, and epicarp, exhibiting distinct tissue-specific expression characteristics. Quantitative fluorescence analysis revealed that five genes, CmGATA3, CmGATA7, CmGATA16, CmGATA22, and CmGATA24, may be highly active under 48-h drought stress, while CmGATA1 and CmGATA22 may enhance melon resistance to heavy metal lead stress. Additionally, CmGATA22 and CmGATA24 are suggested to regulate melon resistance to Fusarium wilt infection. CmGATA22 appears to comprehensively regulate melon responses to both biotic and abiotic stresses. Lastly, potential protein interaction networks were predicted for the CmGATA family members, identifying CmGATA8 as a potential hub gene and predicting 2,230 target genes with enriched GO functions. This study preliminarily explores the expression characteristics of CmGATA genes under drought stress, heavy metal lead stress, and Fusarium wilt infection, providing a theoretical foundation for molecular mechanisms in melon improvement and stress resistance.

Genome-wide identification of oxidosqualene cyclase genes regulating natural rubber in Taraxacum kok-saghyz

MAIN CONCLUSION

Nine TkOSC genes have been identified by genome-wide screening. Among them, TkOSC4-6 might be more crucial for natural rubber biosynthesis in Taraxacum kok-saghyz roots. Taraxacum kok-saghyz Rodin (TKS) roots contain large amounts of natural rubber, inulin, and valuable metabolites. Oxidosqualene cyclase (OSC) is a key member for regulating natural rubber biosynthesis (NRB) via the triterpenoid biosynthesis pathway. To explore the functions of OSC on natural rubber producing in TKS, its gene family members were identified in TKS genome via genome-wide screening. Nine TkOSCs were identified, which were mainly distributed in the cytoplasm. Their family genes experienced a neutral selection during the evolution process. Overall sequence homology analysis OSC proteins revealed 80.23% similarity, indicating a highly degree of conservation. Pairwise comparisons showed a multiple sequence similarity ranging from 57% to 100%. Protein interaction prediction revealed that TkOSCs may interact with baruol synthase, sterol 1,4-demethylase, lupeol synthase and squalene epoxidase. Phylogenetic analysis showed that OSC family proteins belong to two branches. TkOSC promoter regions contain cis-acting elements related to plant growth, stress response, hormones response and light response. Protein accumulation analysis demonstrated that TkOSC4, TkOSC5 and TkOSC6 proteins had strong expression levels in the root, latex and plumular axis. Comparison of gene expression patterns showed TkOSC1, TkOSC4, TkOSC5, TkOSC6, TkOSC7, TkOSC8 and TkOSC9 might be important in regulating NRB. Combination of gene and protein results revealed TkOSC4-6 might be more crucial, and the data might contribute to a more profound understanding of the roles of OSCs for NRB in TKS roots.

Molecular characterization, expression and in-silico analysis of fibrinogen-related protein 1 (frep1) in malaria vector Anopheles stephensi

BACKGROUND

Fibrinogen-related protein 1 (frep1) is a member of the pattern-recognizing receptor family (PRR) which generates an innate immune response after recognizing the pattern associated molecular pattern (PAMP) that occurs on the surface of microorganisms. The main objective of this study is to characterize frep1 and its in-silico analysis in Anopheles stephensi.

METHODS AND RESULT

The DNA was extracted from female Anopheles stephensi. PCR was performed for complete analysis of frep1 using specific primers. The gene sequence of frep1 was identified by Sanger sequencing. The bioinformatics structure analysis approach revealed the presence of 3 exons and 4 introns in the frep1. The sequence of frep1 was submitted to NCBI GeneBank with accession number ON817187.1. Quantitative real-time PCR was performed to analyze frep1 expression. At the developmental stage, frep1 is highly expressed in the L1 stage, egg, and adult female mosquito. In addition, frep1 is highly expressed in the tissue fat body, midgut, and salivary gland. After blood-fed, an upregulation of frep1 at 48 h in the midgut, and downregulation in fat body were observed at different time intervals.

CONCLUSION

The genomic data of frep1 is encoded by 12,443 bp. The frep1 has a significant role in the early metamorphosis. Its expression in fat body and midgut suggests it could be important for fat metabolism and post-blood digestion. The conserved domain could be targeted for vector control. Further study is required to elucidate its function against malaria parasites to confirm its agonist role in malaria transmission.

Genome-wide identification of the E-class gene family in wheat: evolution, expression, and interaction

Introduction

Wheat (Triticum aestivum L.) is among themost important crop worldwide. Given a growing population and changing climate, enhancing wheat yield is of great importance. Yield is closely associated with flower and spike development, and E-class genes play important roles in the flower and kernel development of plants. Currently, the absence of systematic analysis on the E gene family hinders our comprehension of their roles in plant growth and development.

Methods

Identify E-class genes based on homologous sequence searches. Analyze the identified E-class genes through a series of gene family analyses. Determine the expression levels of wheat E-class genes by searching public databases. Validate the functions of these genes by transforming them into Arabidopsis. Finally, determine the interactions between the genes through yeast two-hybrid experiments.

Results

Fifteen E-class genes (TaEs) were identified in common wheat. Nine E-class genes were detected in five ancestral/closely related species, including one in Aegilops tauschii (AtE), one in T. Urartu (TuEs), two in T. turgidum (TtEs), two in T. dicoccoides (TdEs), and three in T. spelta (TsEs). The 24 E-class genes were classified into three subgroups using a phylogenetic approach. All genes were highly expressed in spikes, and most were only highly expressed at the floret meristem stage. The effects of TaSEP5-A on flowering and growth cycles were confirmed in homologous mutants and transgenic Arabidopsis thaliana. The E-class genes were able to regulate the growth cycle of Arabidopsis. Finally, we confirmed the interactions between TaSEP5-A and other wheat E-class genes based on yeast two-hybrid assays.

Discussion

Our findings provide information regarding the E-class genes in wheat and will potentially promote the application of these genes in wheat improvement.

Exploring liquid-liquid phase separation in the organisation of Golgi matrix proteins

The Golgi apparatus is a critical organelle in protein sorting and lipid metabolism. Characterized by its stacked, flattened cisternal structure, the Golgi exhibits distinct polarity with its cis- and trans-faces orchestrating various protein maturation and transport processes. At the heart of its structural integrity and organisation are the Golgi Matrix Proteins (GMPs), predominantly comprising Golgins and GRASPs. These proteins contribute to this organelle's unique stacked and polarized structure and ensure the precise localization of Golgi-resident enzymes, which is crucial for accurate protein processing. Despite over a century of research since its discovery, the Golgi architecture's intricate mechanisms still need to be fully understood. Here, we discuss that GMPs across different Eukaryotic lineages present a significant tendency to form biomolecular condensates. Moreover, we validated experimentally that members of the GRASP family also exhibit a strong tendency. Our findings offer a new perspective on the possible roles of protein disorder and condensation of GMPs in the Golgi organisation.

Transcriptome-wide identification of the Hsp70 gene family in Pugionium cornutum and functional analysis of PcHsp70-5 under drought stress

MAIN CONCLUSION

The PcHsp70-5 enhances drought stress tolerance in transgenic Arabidopsis thaliana by upregulating stress tolerance genes and antioxidant enzyme activities. Heat shock proteins (HSPs) constitute a class of evolutionarily conserved proteins synthesized by organisms in response to various adverse environmental stimuli such as elevated temperatures, drought, hormonal fluctuations, high salt concentrations, and mechanical stress. However, research on HSPs has predominantly focused on model plants and crops, whereas their functions in desert plants have not been well investigated. This study analyzed the transcriptome of Pugionium cornutum and identified the complete ORFs of 25 genes of the PcHsp70 family genes. Their expression levels under drought stress were investigated using existing RNA-seq data. PcHsp70-5 genes exhibited high expression levels in both roots and leaves under drought stress. Consequently, the PcHsp70-5 genes were cloned and transformed into Arabidopsis thaliana for further analysis of their roles in drought stress response. Real-time fluorescence quantitative PCR (qRT-PCR) analysis demonstrated that both, drought stress and ABA, induced PcHsp70-5 expression. Under drought conditions, transgenic Arabidopsis plants exhibited markedly enhanced growth compared to wild-type plants, as evidenced by improved survival rates, root length, fresh weight, chlorophyll content, and reduced levels of malondialdehyde (MDA) and hydrogen peroxide (H2O2) in leaves, indicating that PcHsp70-5 overexpression mitigated growth inhibition and oxidative damage induced by drought stress. Subsequent research revealed that PcHsp70-5 overexpression significantly augmented the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and increased the proline content in transgenic Arabidopsis under drought conditions, alongside a significant increase in the expression levels of genes related to stress tolerance. This suggests that PcHsp70-5 enhances drought stress tolerance in transgenic Arabidopsis by upregulating stress tolerance genes and antioxidant enzyme activities.

Genome-level therapeutic targets identification and chimeric Vaccine designing against the Blastomyces dermatitidis

Blastomyces dermatitidis is a thermally dimorphic fungus that can cause serious and sometimes fatal infections, including blastomycosis. After spore inhalation, a pulmonary infection develops, which can be asymptomatic and have lethal effects, such as acute respiratory distress syndrome. Its most common extra-pulmonary sites are the central nervous system, bones, skin, and genito-urinary systems. Currently, no vaccine has been approved by the FDA to prevent this infection. In the study, a peptide-based vaccine was developed against blastomycosis by using subtractive proteomics and reverse vaccinology approaches. It focuses on mining the whole genome of B. dermatitidis, identifying potential therapeutic targets, and pinpointing potential epitopes for both B- and T-cells that are immunogenic, non-allergenic, non-toxic, and highly antigenic. Multi-epitope constructs were generated by incorporating appropriate linker sequences. A linker (EAAAK) was also added to incorporate an adjuvant sequence to increase immunological potential. The addition of adjuvants and linkers ultimately resulted in the formation of a vaccine construct in which the number of amino acids was 243 and the molecular weight was 26.18 kDa. The designed antigenic and non-allergenic vaccine constructs showed suitable physicochemical properties. The vaccine's structures were predicted, and further analysis verified their interactions with the human TLR-4 receptor through protein-protein docking. Additionally, MD simulation showed a potent interaction between prioritized vaccine-receptor complexes. Immune simulation predicted that the final vaccine injections resulted in significant immune responses for the T- and B-cell immune responses. Moreover, in silico cloning ensured a high expression possibility of the lead vaccine in the E. coli (K12) vector. This study offers an initiative for the development of effective vaccines against B. dermatitidis; however, it is necessary to validate the designed vaccine's immunogenicity experimentally.

Systematic Analysis of the BrHAT Gene Family and Physiological Characteristics of Brassica rapa L. Treated with Histone Acetylase and Deacetylase Inhibitors under Low Temperature

Brassica rapa L. is an important overwintering oilseed crop in Northwest China. Histone acetyltransferases (HATs) play an important role in epigenetic regulation, as well as the regulation of plant growth, development, and responses to abiotic stresses. To clarify the role of histone acetylation in the low-temperature response of B. rapa L., we identified 29 HAT genes in B. rapa L. using bioinformatics tools. We also conducted a comprehensive analysis of the physicochemical properties, gene structure, chromosomal localization, conserved structural domains and motifs, cis-acting regulatory elements, and evolutionary relationships of these genes. Using transcriptome data, we analyzed the expression patterns of BrHAT family members and predicted interactions between proteins; the results indicated that BrHATs play an important role in the low-temperature response of B. rapa L. HAT inhibitor (curcumin; CUR) and histone deacetylase inhibitor (Trichostatin A; TSA) were applied to four B. rapa L. varieties varying in cold resistance under the same low-temperature conditions, and changes in the physiological indexes of these four varieties were analyzed. The inhibitor treatment attenuated the effect of low temperature on seed germination, and curcumin treatment was most effective, indicating that the germination period was primarily regulated by histone acetylase. Both inhibitor treatments increased the activity of protective enzymes and the content of osmoregulatory substances in plants, suggesting that histone acetylation and deacetylation play a significant role in the response of B. rapa L. to low-temperature stress. The qRT-PCR analyses showed that the expression patterns of BrHATs were altered under different inhibitor treatments and low-temperature stress; meanwhile, we found three significantly differentially expressed genes. In sum, the process of histone acetylation is involved in the cold response and the BrHATs gene plays a role in the cold stress response.

Design of a Helicobacter pylori multi-epitope vaccine based on immunoinformatics

Helicobacter pylori (H. pylori) is an infectious bacterium that colonizes the stomach of approximately half of the global population. It has been classified as a Group I carcinogen by the World Health Organization due to its strong association with an increased incidence of gastric cancer and exacerbation of stomach diseases. The primary treatment for H. pylori infection currently involves triple or quadruple therapy, primarily consisting of antibiotics and proton pump inhibitors. However, the increasing prevalence of antibiotic resistance poses significant challenges to this approach, underscoring the urgent need for an effective vaccine. In this study, a novel multi-epitope H. pylori vaccine was designed using immunoinformatics. The vaccine contains epitopes derived from nine essential proteins. Software tools and online servers were utilized to predict, evaluate, and analyze the physiochemical properties, secondary and tertiary structures, and immunogenicity of the candidate vaccine. These comprehensive assessments ultimately led to the formulation of an optimal design scheme for the vaccine. Through constructing a novel multi-epitope vaccine based on immunoinformatics, this study offers promising prospects and great potential for the prevention of H. pylori infection. This study also provides a reference strategy to develop multi-epitope vaccines for other pathogens.

DNA Vaccines Encoding HTNV GP-Derived Th Epitopes Benefited from a LAMP-Targeting Strategy and Established Cellular Immunoprotection

Vaccines has long been the focus of antiviral immunotherapy research. Viral epitopes are thought to be useful biomarkers for immunotherapy (both antibody-based and cellular). In this study, we designed a novel vaccine molecule, the Hantaan virus (HTNV) glycoprotein (GP) tandem Th epitope molecule (named the Gnc molecule), in silico. Subsequently, computer analysis was used to conduct a comprehensive and in-depth study of the various properties of the molecule and its effects as a vaccine molecule in the body. The Gnc molecule was designed for DNA vaccines and optimized with a lysosomal-targeting membrane protein (LAMP) strategy. The effects of GP-derived Th epitopes and multiepitope vaccines were initially verified in animals. Our research has resulted in the design of two vaccines based on effective antiviral immune targets. The effectiveness of molecular therapies has also been preliminarily demonstrated in silico and in laboratory animals, which lays a foundation for the application of a vaccines strategy in the field of antivirals.

Metabolic Engineering of Candida tropicalis for the De Novo Synthesis of β-Ionone

β-ionone, a norisoprenoid, is a natural aromatic compound derived from plants, which displays various biological activities including anticancer, antioxidant and deworming properties. Due to its large biomass and strong environmental tolerance, the nonconventional oleaginous yeast Candida tropicalis was selected to efficiently synthesize β-ionone. We initially investigated the capacity of the cytoplasm and subcellular compartments to synthesize β-ionone independently. Subsequently, through adaptive screening of enzymes, functional identification of subcellular localization signal peptides and subcellular compartment combination strategies, a titer of 152.4 mg/L of β-ionone was achieved. Finally, directed evolution of rate-limiting enzyme and overexpression of key enzymes were performed to enhance β-ionone production. The resulting titer was 400.5 mg/L in shake flasks and 730 mg/L in a bioreactor. This study demonstrates the first de novo synthesis of β-ionone in C. tropicalis, providing a novel cellular chassis for terpenoid fragrances with considerable industrial potential.

Miniaturized Fab' imaging probe derived from a clinical antibody: Characterization and imaging in CRISPRi-attenuated mammary tumor models

Clinical imaging-assisted oncosurgical navigation requires cancer-specific miniaturized optical imaging probes. We report a near-infrared (NIR) Fab'-based epidermal growth factor receptor (EGFR)-specific probe carrying 3 NIR fluorophores (Fab'-800CW), which retained high-affinity binding to EGFR ectodomain (equilibrium KD E = 1 nM). Fab'-800CW showed a robust 4-times gain of fluorescence intensity (FI) and a 20% lifetime (FLT) increase under the conditions mimicking intracellular degradation. The probe was tested by using triple-negative breast cancer (TNBC) cell lines obtained by applying CRISPR interference (CRISPRi) effect of EGFR-targeting sgRNA and dCas9-KRAB chimera coexpression in MDA-MB-231 cells (WT cells). FI imaging in cell culture proved a 50% EGFR expression attenuation by CRISPRi. FI imaging in animals harboring attenuated or WT TNBC tumors with ex vivo corroboration identified differences between WT and CRISPRi tumors FI at 30 min post injection. Our results suggest the feasibility of EGFR expression imaging using a Fab'-based probe relevant for imaging-guided cancer surgery.

Bioinformatic elucidation of conserved epitopes to design a potential vaccine candidate against existing and emerging SARS-CoV-2 variants of concern

The COVID-19 pandemic caused by SARS-CoV-2 poses a significant adverse effects on health and economy globally. Due to mutations in genome, COVID-19 vaccine efficacy decreases. We used immuno-informatics to design a Multi epitope vaccine (MEV) candidate for SARS-CoV-2 variants of concern (VOCs). Hence, we predicted binders/epitopes MHC-I, CD8+, MHC-II, CD4+, and CTLs from spike, membrane and envelope proteins of VOCs. In addition, we assessed the conservation of these binders and epitopes across different VOCs. Subsequently, we designed MEV by combining the predicted CTL and CD4+ epitopes from spike protein, peptide linkers, and an adjuvant. Further, we evaluated the binding of MEV candidate against immune receptors namely HLA class I histocompatibility antigen, HLA class II histocompatibility antigen, and TLR4, achieving binding scores of -1265.3, -1330.7, and -1337.9. Molecular dynamics and normal mode analysis revealed stable docking complexes. Moreover, immune simulation suggested MEV candidate elicits both innate and adaptive immune response. We anticipate that this conserved MEV candidate will provide protection from VOCs and emerging strains.

Immunoinformatic-guided novel mRNA vaccine designing to elicit immunogenic responses against the endemic Monkeypox virus

Monkeypox virus (MPXV) is an orthopoxvirus, causing zoonotic infections in humans with smallpox-like symptoms. The WHO reported MPXV cases in May 2022 and the outbreak caused significant morbidity threats to immunocompromised individuals and children. Currently, no clinically validated therapies are available against MPXV infections. The present study is based on immunoinformatics approaches to design mRNA-based novel vaccine models against MPXV. Three proteins were prioritized based on high antigenicity, low allergenicity, and toxicity values to predict T- and B-cell epitopes. Lead T- and B-cell epitopes were used to design vaccine constructs, linked with epitope-specific linkers and adjuvant to enhance immune responses. Additional sequences, including Kozak sequence, MITD sequence, tPA sequence, Goblin 5', 3' UTRs, and a poly(A) tail were added to design stable and highly immunogenic mRNA vaccine construct. High-quality structures were predicted by molecular modeling and 3D-structural validation of the vaccine construct. Population coverage and epitope-conservancy speculated broader protection of designed vaccine model against multiple MPXV infectious strains. MPXV-V4 was eventually prioritized based on its physicochemical and immunological parameters and docking scores. Molecular dynamics and immune simulations analyses predicted significant structural stability and binding affinity of the top-ranked vaccine model with immune receptors to elicit cellular and humoral immunogenic responses against the MPXV. The pursuance of experimental and clinical follow-up of these prioritized constructs may lay the groundwork to develop safe and effective vaccine against MPXV.Communicated by Ramaswamy H. Sarma.

Designing multi-epitope vaccine against human cytomegalovirus integrating pan-genome and reverse vaccinology pipelines

Human cytomegalovirus (HCMV) is accountable for high morbidity in neonates and immunosuppressed individuals. Due to the high genetic variability of HCMV, current prophylactic measures are insufficient. In this study, we employed a pan-genome and reverse vaccinology approach to screen the target for efficient vaccine candidates. Four proteins, envelope glycoprotein M, UL41A, US23, and US28, were shortlisted based on cellular localization, high solubility, antigenicity, and immunogenicity. A total of 29 B-cell and 44 T-cell highly immunogenic and antigenic epitopes with high global population coverage were finalized using immunoinformatics tools and algorithms. Further, the epitopes that were overlapping among the finalized B-cell and T-cell epitopes were linked with suitable linkers to form various combinations of multi-epitopic vaccine constructs. Among 16 vaccine constructs, Vc12 was selected based on physicochemical and structural properties. The docking and molecular simulations of VC12 were performed, which showed its high binding affinity (-23.35 kcal/mol) towards TLR4 due to intermolecular hydrogen bonds, salt bridges, and hydrophobic interactions, and there were only minimal fluctuations. Furthermore, Vc12 eliciting a good response was checked for its expression in Escherichia coli through in silico cloning and codon optimization, suggesting it to be a potent vaccine candidate.

Multiple Protein Profiler 1.0 (MPP): A Webserver for Predicting and Visualizing Physiochemical Properties of Proteins at the Proteome Level

Determining the physicochemical properties of a protein can reveal important insights in their structure, biological functions, stability, and interactions with other molecules. Although tools for computing properties of proteins already existed, we could not find a comprehensive tool that enables the calculations of multiple properties for multiple input proteins on the proteome level at once. Facing this limitation, we developed Multiple Protein Profiler (MPP) 1.0 as an integrated tool that allows the profiling of 12 individual properties of multiple proteins in a significant manner. MPP provides a tabular and graphic visualization of properties of multiple proteins. The tool is freely accessible at https://mproteinprofiler.microbiologyandimmunology.dal.ca/ .

Contriving a novel of CHB therapeutic vaccine based on IgV_CTLA-4 and L protein via immunoinformatics approach

Chronic infection induced by immune tolerance to hepatitis B virus (HBV) is one of the most common causes of hepatic cirrhosis and hepatoma. Fortunately, the application of therapeutic vaccine can not only reverse HBV-tolerance, but also serve a potentially effective therapeutic strategy for treating chronic hepatitis B (CHB). However, the clinical effect of the currently developed CHB therapeutic vaccine is not optimistic due to the weak immunogenicity. Given that the human leukocyte antigen CTLA-4 owns strong binding ability to the surface B7 molecules (CD80 and CD86) of antigen presenting cell (APCs), the immunoglobulin variable region of CTLA-4 (IgV_CTLA-4) was fused with the L protein of HBV to contrive a novel therapeutic vaccine (V_C4HBL) for CHB in this study. We found that the addition of IgV_CTLA-4 did not interfere with the formation of L protein T cell and B cell epitopes after analysis by means of immunoinformatics approaches. Meanwhile, we also found that the IgV_CTLA-4 had strong binding force to B7 molecules through molecular docking and molecular dynamics (MD) simulation. Notably, our vaccine V_C4HBL showed good immunogenicity and antigenicity by in vitro and in vivo experiments. Therefore, the V_C4HBL is promising to again effectively activate the cellular and humoral immunity of CHB patients, and provides a potentially effective therapeutic strategy for the treatment of CHB in the future.Communicated by Ramaswamy H. Sarma.

PON-Tm: A Sequence-Based Method for Prediction of Missense Mutation Effects on Protein Thermal Stability Changes

Proteins, as crucial macromolecules performing diverse biological roles, are central to numerous biological processes. The ability to predict changes in protein thermal stability due to mutations is vital for both biomedical research and industrial applications. However, existing experimental methods are often costly and labor-intensive, while structure-based prediction methods demand significant computational resources. In this study, we introduce PON-Tm, a novel sequence-based method for predicting mutation-induced thermal stability variations in proteins. PON-Tm not only incorporates features predicted by a protein language model from protein sequences but also considers environmental factors such as pH and the thermostability of the wild-type protein. To evaluate the effectiveness of PON-Tm, we compared its performance to four well-established methods, and PON-Tm exhibited superior predictive capabilities. Furthermore, to facilitate easy access and utilization, we have developed a web server.

Genomic characterization of bZIP gene family and patterns of gene regulation on Cercospora beticola Sacc resistance in sugar beet (Beta vulgaris L.)

Sugar beet (Beta vulgaris L.) is one of the most important sugar crops, accounting for nearly 30% of the world's annual sugar production. And it is mainly distributed in the northwestern, northern, and northeastern regions of China. However, Cercospora leaf spot (CLS) is the most serious and destructive foliar disease during the cultivation of sugar beet. In plants, the bZIP gene family is one of important family of transcription factors that regulate many biological processes, including cell and tissue differentiation, pathogen defense, light response, and abiotic stress signaling. Although the bZIP gene family has been mentioned in previous studies as playing a crucial role in plant defense against diseases, there has been no comprehensive study or functional analysis of the bZIP gene family in sugar beet with respect to biotic stresses. In this study, we performed a genome-wide analysis of bZIP family genes (BvbZIPs) in sugar beet to investigate their phylogenetic relationships, gene structure and chromosomal localization. At the same time, we observed the stomatal and cell ultrastructure of sugar beet leaf surface during the period of infestation by Cercospora beticola Sacc (C. beticola). And identified the genes with significant differential expression in the bZIP gene family of sugar beet by qRT-PCR. Finally we determined the concentrations of SA and JA and verified the associated genes by qRT-PCR. The results showed that 48 genes were identified and gene expression analysis indicated that 6 BvbZIPs were significantly differential expressed in C. beticola infection. It is speculated that these BvbZIPs are candidate genes for regulating the response of sugar beet to CLS infection. Meanwhile, the observation stomata of sugar beet leaves infected with C. beticola revealed that there were also differences in the surface stomata of the leaves at different periods of infection. In addition, we further confirmed that the protein encoded by the SA signaling pathway-related gene BVRB_9g222570 in high-resistant varieties was PR1, which is closely related to systemic acquired resistance. One of the protein interaction modes of JA signal transduction pathway is the response of MYC2 transcription factor caused by JAZ protein degradation, and there is a molecular interaction between JA signal transduction pathway and auxin. Despite previous reports on abiotic stresses in sugar beet, this study provides very useful information for further research on the role of the sugar beet bZIP gene family in sugar beet through experiments. The above research findings can promote the development of sugar beet disease resistance breeding.

Genome-wide identification and expression analysis of the U-box E3 ubiquitin ligase gene family related to bacterial wilt resistance in tobacco (Nicotiana tabacum L.) and eggplant (Solanum melongena L.)

The E3 enzyme in the UPS pathway is a crucial factor for inhibiting substrate specificity. In Solanaceae, the U-box E3 ubiquitin ligase has a complex relationship with plant growth and development, and plays a pivotal role in responding to various biotic and abiotic stresses. The analysis of the U-box gene family in Solanaceae and its expression profile under different stresses holds significant implications. A total of 116 tobacco NtU-boxs and 56 eggplant SmU-boxs were identified based on their respective genome sequences. Phylogenetic analysis of U-box genes in tobacco, eggplant, tomato, Arabidopsis, pepper, and potato revealed five distinct subgroups (I-V). Gene structure and protein motifs analysis found a high degree of conservation in both exon/intron organization and protein motifs among tobacco and eggplant U-box genes especially the members within the same subfamily. A total of 15 pairs of segmental duplication and 1 gene pair of tandem duplication were identified in tobacco based on the analysis of gene duplication events, while 10 pairs of segmental duplication in eggplant. It is speculated that segmental duplication events are the primary driver for the expansion of the U-box gene family in both tobacco and eggplant. The promoters of NtU-box and SmU-box genes contained cis-regulatory elements associated with cellular development, phytohormones, environment stress, and photoresponsive elements. Transcriptomic data analysis shows that the expression levels of the tobacco and eggplant U-box genes in different tissues and various abiotic stress conditions. Using cultivar Hongda of tobacco and cultivar Yanzhi of eggplant as materials, qRT-PCR analysis has revealed that 15 selected NtU-box genes and 8 SmU-box may play important roles in response to pathogen Ras invasion both in tobacco and eggplant.

Comparative analysis among the degradation potential of enzymes obtained from Escherichia coli against the toxicity of sulfur dyes through molecular docking

The common bacterium Escherichia coli has demonstrated potential in the field of biodegradation. E. coli is naturally capable of biodegradation because it carries a variety of enzymes that are essential for the breakdown of different substances. The degradation process is effectively catalyzed by these enzymes. The collaborative effects of E. coli's aryl sulfotransferase, alkanesulfonate moonoxygenase, and azoreductase enzymes on the breakdown of sulfur dyes from industrial effluents are investigated in this work. ExPASY ProtParam was used to confirm the stability of the enzyme, showing an instability index less than 40. We determined the maximum binding affinities of these enzymes with sulfur dye pollutants - 1-naphthalenesulfonic acid, sulfogene, sulfur green 3, sulfur red 6, sulfur red 1, sulfur yellow 2, thianthrene, thiazone, and thional - using comparative molecular docking. Significantly, the highest binding affinity was shown by monooxygenase (-12.1), whereas aryl sulfotransferase and azoreductase demonstrated significant energies of -11.8 and -11.4, respectively. The interactions between proteins and ligands in the docked complexes were examined. To evaluate their combined effects, co-expression analysis of genes and enzyme bioengineering were carried out. Using aryl sulfotransferase, alkanesulfonate monooxygenase, and azoreductase, this study investigates the enzymatic degradation of sulfur dye pollutants, thereby promoting environmentally friendly and effective sulfur dye pollutant management.

Metagenome-derived SusD-homologs affiliated with Bacteroidota bind to synthetic polymers

Starch utilization system (Sus)D-homologs are well known for their carbohydrate-binding capabilities and are part of the sus operon in microorganisms affiliated with the phylum Bacteroidota. Until now, SusD-like proteins have been characterized regarding their affinity toward natural polymers. In this study, three metagenomic SusD homologs (designated SusD1, SusD38489, and SusD70111) were identified and tested with respect to binding to natural and non-natural polymers. SusD1 and SusD38489 are cellulose-binding modules, while SusD70111 preferentially binds chitin. Employing translational fusion proteins with superfolder GFP (sfGFP), pull-down assays, and surface plasmon resonance (SPR) has provided evidence for binding to polyethylene terephthalate (PET) and other synthetic polymers. Structural analysis suggested that a Trp triad might be involved in protein adsorption. Mutation of these residues to Ala resulted in an impaired adsorption to microcrystalline cellulose (MC), but not so to PET and other synthetic polymers. We believe that the characterized SusDs, alongside the methods and considerations presented in this work, will aid further research regarding bioremediation of plastics.

IMPORTANCE

SusD1 and SusD38489 can be considered for further applications regarding their putative adsorption toward fossil-fuel based polymers. This is the first time that SusD homologs from the polysaccharide utilization loci (PUL), largely described for the phylum Bacteroidota, are characterized as synthetic polymer-binding proteins.

Development of a broad-spectrum therapeutic Fc-nanobody for human noroviruses

Human norovirus was discovered more than five decades ago and is a widespread cause of outbreaks of acute gastroenteritis. There are no approved vaccines or antivirals currently available. However, norovirus inhibitors, including capsid-specific monoclonal antibodies (Mabs) and nanobodies, have recently shown promising results. Several Mabs and nanobodies were found to inhibit norovirus replication using a human intestinal enteroid (HIE) culture system and/or could block norovirus attachment to histo-blood group antigen (HBGA) co-factors. In our pursuit to develop a single broad-spectrum norovirus therapeutic, we continued our analysis and development of a cross-reactive and HBGA interfering nanobody (NB26). To improve NB26 binding capacity and therapeutic potential, we conjugated NB26 onto a human IgG Fc domain (Fc-NB26). We confirmed that Fc-NB26 cross-reacts with genetically diverse GII genotype capsid protruding (P) domains (GII.8, GII.14, GII.17, GII.24, GII.26, and GII.NA1) using a direct enzyme-linked immunosorbent assay. Furthermore, X-ray crystallography structures of these P domains and structures of other GII genotypes reveal that the NB26 binding site is largely conserved, validating its broad reactivity. We showed that Fc-NB26 has ~100-fold higher affinity toward the norovirus P domain compared to native NB26. We also found that both NB26 and Fc-NB26 neutralize human norovirus replication in the HIE culture system. Furthermore, the mode of inhibition confirmed that like NB26, Fc-NB26 caused norovirus particle disassembly and aggregation. Overall, these new findings demonstrate that structural modifications to nanobodies can improve their therapeutic potential.IMPORTANCEDeveloping vaccines and antivirals against norovirus remains a challenge, mainly due to the constant genetic and antigenic evolution. Moreover, re-infection with genetically related and/or antigenic variants is not uncommon. We further developed our leading norovirus nanobody (NB26) that indirectly interfered with norovirus binding to HBGAs, by converting NB26 into a dimeric Fc-linked Nanobody (Fc-NB26). We found that Fc-NB26 had improved binding affinity and neutralization capacity compared with native NB26. Using X-ray crystallography, we showed this nanobody engaged highly conserved capsid residues among genetically diverse noroviruses. Development of such broadly reactive potent therapeutic nanobodies delivered as a slow-releasing prophylactic could be of exceptional value for norovirus outbreaks, especially for the prevention or treatment of severe acute gastroenteritis in high-risk groups such as the young, elderly, and immunocompromised.

Production, purification, and quality assessment of borrelial proteins CspZ from Borrelia burgdorferi and FhbA from Borrelia hermsii

Borrelia, spirochetes transmitted by ticks, are the etiological agents of numerous multisystemic diseases, such as Lyme borreliosis (LB) and tick-borne relapsing fever (TBRF). This study focuses on two surface proteins from two Borrelia subspecies involved in these diseases: CspZ, expressed by Borrelia burgdorferi sensu stricto (also named BbCRASP-2 for complement regulator-acquiring surface protein 2), and the factor H binding A (FhbA), expressed by Borrelia hermsii. Numerous subspecies of Borrelia, including these latter, are able to evade the immune defenses of a variety of potential vertebrate hosts in a number of ways. In this context, previous data suggested that both surface proteins play a role in the immune evasion of both Borrelia subspecies by interacting with key regulators of the alternative pathway of the human complement system, factor H (FH) and FH-like protein 1 (FHL-1). The recombinant proteins, CspZ and FhbA, were expressed in Escherichia coli and purified by one-step metal-affinity chromatography, with yields of 15 and 20 mg or pure protein for 1 L of cultured bacteria, respectively. The purity was evaluated by SDS-PAGE and HPLC and is close to about 95%. The mass of CspZ and FhbA was checked by mass spectrometry (MS). Proper folding of CspZ and FhbA was confirmed by circular dichroism (CD), and their biological activity, namely their interaction with purified FH from human serum (recombinant FH15-20 and recombinant FHL-1), was characterized by SPR. Such a study provides the basis for the biochemical characterization of the studied proteins and their biomolecular interactions which is a necessary prerequisite for the development of new approaches to improve the current diagnosis of LB and TBRF. KEY POINTS: • DLS, CD, SEC-MALS, NMR, HPLC, and MS are tools for protein quality assessment • Borrelia spp. possesses immune evasion mechanisms, including human host complement • CspZ and FhbA interact with high affinity (pM to nM) to human FH and rFHL-1.

Screening of Bovine Coronavirus Multiepitope Vaccine Candidates: An Immunoinformatics Approach

Bovine coronavirus (BCoV) is a causative agent of enteric and respiratory disease in cattle. BCoV has been reported to cause a variety of animal diseases and is closely related to human coronaviruses; moreover, it has attracted extensive attention from both cattle farmers and researchers. With the rise of BCoV, a vaccine that is prophylactic and immunotherapeutic has to be utilized for a preemptive and adroit therapeutic approach. The aim of this study was to develop a novel multiepitope-based BCoV vaccine that can induce an immune response using a silicon reverse vaccinology approach. In this study, an immunoinformatics approach was employed to identify potential vaccine targets against BCoV, and four candidate antigen proteins were selected to predict B-cell and T-cell epitopes. To identify dominant epitopes, we employed a variety of bioinformatics techniques, including antigenicity prediction, immunogenicity assessment, allergenicity analysis, conservative analysis, and toxicity assessment. Finally, six multiepitope vaccines were developed using dominant epitopes, suitable adjuvants, Pan HLADR-binding epitope (PADRE), and linkers. Then based on the antigenicity score, solubility analysis, allergenicity evaluation, physicochemical property assessment, and tertiary structure verification score, construct 6 was selected as the best candidate vaccine; it was named CY. Molecular modeling and structural validation ensured the high-quality 3D structure of construct CY. The immunogenicity and complex stability of the vaccine were evaluated by molecular docking and kinetic simulation. In silicon clones, the BCoV vaccine had high levels of gene expression in the insect expression system. These results may contribute to the development of experimental BCoV vaccines with higher potency and safety.

Bioactivity of synthetic peptides from Ecuadorian frog skin secretions against Leishmania mexicana, Plasmodium falciparum, and Trypanosoma cruzi

Chagas disease, leishmaniasis, and malaria are major parasitic diseases disproportionately affecting the underprivileged population in developing nations. Finding new, alternative anti-parasitic compounds to treat these diseases is crucial because of the limited number of options currently available, the side effects they cause, the need for long treatment courses, and the emergence of drug-resistant parasites. Anti-microbial peptides (AMPs) derived from amphibian skin secretions are small bioactive molecules capable of lysing the cell membrane of pathogens while having low toxicity against human cells. Here, we report the anti-parasitic activity of five AMPs derived from skin secretions of three Ecuadorian frogs: cruzioseptin-1, cruzioseptin-4 (CZS-4), and cruzioseptin-16 from Cruziohyla calcarifer; dermaseptin-SP2 from Agalychnis spurrelli; and pictuseptin-1 from Boana picturata. These five AMPs were chemically synthesized. Initially, the hemolytic activity of CZS-4 and its minimal inhibitory concentration against Escherichia coli, Staphylococcus aureus, and Candida albicans were determined. Subsequently, the cytotoxicity of the synthetic AMPs against mammalian cells and their anti-parasitic activity against Leishmania mexicana promastigotes, erythrocytic stages of Plasmodium falciparum and mammalian stages of Trypanosoma cruzi were evaluated in vitro. The five AMPs displayed activity against the pathogens studied, with different levels of cytotoxicity against mammalian cells. In silico molecular docking analysis suggests this bioactivity may occur via pore formation in the plasma membrane, resulting in microbial lysis. CZS-4 displayed anti-bacterial, anti-fungal, and anti-parasitic activities with low cytotoxicity against mammalian cells. Further studies about this promising AMP are required to gain a better understanding of its activity.IMPORTANCEChagas disease, malaria, and leishmaniasis are major tropical diseases that cause extensive morbidity and mortality, for which available treatment options are unsatisfactory because of limited efficacy and side effects. Frog skin secretions contain molecules with anti-microbial properties known as anti-microbial peptides. We synthesized five peptides derived from the skin secretions of different species of tropical frogs and tested them against cultures of the causative agents of these three diseases, parasites known as Trypanosoma cruzi, Plasmodium falciparum, and Leishmania mexicana. All the different synthetic peptides studied showed activity against one of more of the parasites. Peptide cruzioseptin-4 is of special interest since it displayed intense activity against parasites while being innocuous against cultured mammalian cells, which indicates it does not simply hold general toxic properties; rather, its activity is specific against the parasites.

Advancing vaccine development against Opisthorchis viverrini: A synergistic integration of omics technologies and advanced computational tools

The liver fluke O. viverrini (Opisthorchis viverrini), a neglected tropical disease (NTD), endemic to the Great Mekong Subregion (GMS), mainly afflicts the northeastern region of Thailand. It is a leading cause of cholangiocarcinoma (CCA) in humans. Presently, the treatment modalities for opisthorchiasis incorporate the use of the antihelminthic drug praziquantel, the rapid occurrence of reinfection, and the looming threat of drug resistance highlight the urgent need for vaccine development. Recent advances in "omics" technologies have proven to be a powerful tool for such studies. Utilizing candidate proteins identified through proteomics and refined via immunoproteomics, reverse vaccinology (RV) offers promising prospects for designing vaccines targeting essential antibody responses to eliminate parasite. Machine learning-based computational tools can predict epitopes of candidate protein/antigens exhibiting high binding affinities for B cells, MHC classes I and II, indicating strong potential for triggering both humoral and cell-mediated immune responses. Subsequently, these vaccine designs can undergo population-specific testing and docking/dynamics studies to assess efficacy and synergistic immunogenicity. Hence, refining proteomics data through immunoinformatics and employing computational tools to generate antigen-specific targets for trials offers a targeted and efficient approach to vaccine development that applies to all domains of parasite infections. In this review, we delve into the strategic antigen selection process using omics modalities for the O. viverrini parasite and propose an innovative framework for vaccine design. We harness omics technologies to revolutionize vaccine development, promising accelerated discoveries and streamlined preclinical and clinical evaluations.

Biophysical and structural studies of fibulin-2

Fibulin-2 is a multidomain, disulfide-rich, homodimeric protein which belongs to a broader extracellular matrix family. It plays an important role in the development of elastic fiber structures. Malfunction of fibulin due to mutation or poor expression can result in a variety of diseases including synpolydactyly, limb abnormalities, eye disorders leading to blindness, cardiovascular diseases and cancer. Traditionally, fibulins have either been produced in mammalian cell systems or were isolated from the extracellular matrix, a procedure that results in poor availability for structural and functional studies. Here, we produced seven fibulin-2 constructs covering 62% of the mature protein (749 out of 1195 residues) using a prokaryotic expression system. Biophysical studies confirm that the purified constructs are folded and that the presence of disulfide bonds within the constructs makes them extremely thermostable. In addition, we solved the first crystal structure for any fibulin isoform, a structure corresponding to the previously suggested three motifs related to anaphylatoxin. The structure reveals that the three anaphylatoxins moieties form a single-domain structure.

Identification of novel T-cell epitopes on monkeypox virus and development of multi-epitopes vaccine using immunoinformatics approaches

Monkeypox virus (MPV) is closely related to the smallpox virus, and previous data from Africa suggest that the smallpox vaccine (VARV) is at least 85% effective in preventing MPV. No multi-epitope vaccine has yet been developed to prevent MPV infection. In this work, we used in silico structural biology and advanced immunoinformatic strategies to design a multi-epitope subunit vaccine against MPV infection. The designed vaccine sequence is adjuvanted with CpG-ODN and includes HTL/CTL epitopes for similar proteins between vaccinia virus (VACV) that induced T-cell production in vaccinated volunteers and the first draft sequence of the MPV genome associated with the suspected outbreak in several countries, May 2022. In addition, the specific binding of the modified vaccine and the immune Toll-like receptor 9 (TLR9) was estimated by molecular interaction studies. Strong interaction in the binding groove as well as good docking scores confirmed the stringency of the modified vaccine. The stability of the interaction was confirmed by a classical molecular dynamics simulation and normal mode analysis. Then, the immune simulation also indicated the ability of this vaccine to induce an effective immune response against MPV. Codon optimization and in silico cloning of the vaccine into the pET-28a (+) vector also showed its expression potential in the E. coli K12 system. The promising data obtained from the various in silico studies indicate that this vaccine is effective against MPV. However, additional in vitro and in vivo studies are still needed to confirm its efficacy.Communicated by Ramaswamy H. Sarma.

Integrating pan-genome and reverse vaccinology to design multi-epitope vaccine against Herpes simplex virus type-1

Herpes simplex virus type-1 (HSV-1), the etiological agent of sporadic encephalitis and recurring oral (sometimes genital) infections in humans, affects millions each year. The evolving viral genome reduces susceptibility to existing antivirals and, thus, necessitates new therapeutic strategies. Immunoinformatics strategies have shown promise in designing novel vaccine candidates in the absence of a clinically licensed vaccine to prevent HSV-1. However, to encourage clinical translation, the HSV-1 pan-genome was integrated with the reverse-vaccinology pipeline for rigorous screening of universal vaccine candidates. Viral targets were screened from 104 available complete genomes. Among 364 proteins, envelope glycoprotein D being an outer membrane protein with a high antigenicity score (> 0.4) and solubility (> 0.6) was selected for epitope screening. A total of 17 T-cell and 4 B-cell epitopes with highly antigenic, immunogenic, non-toxic properties and high global population coverage were identified. Furthermore, 8 vaccine constructs were designed using different combinations of epitopes and suitable linkers. VC-8 was identified as the most potential vaccine candidate regarding chemical and structural stability. Molecular docking revealed high interactive affinity (low binding energy: - 56.25 kcal/mol) of VC-8 with the target elicited by firm intermolecular H-bonds, salt-bridges, and hydrophobic interactions, which was validated with simulations. Compatibility of the vaccine candidate to be expressed in pET-29(a) + plasmid was established by in silico cloning studies. Immune simulations confirmed the potential of VC-8 to trigger robust B-cell, T-cell, cytokine, and antibody-mediated responses, thereby suggesting a promising candidate for the future of HSV-1 prevention.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04022-6.

Identification of m6A RNA methylation genes in Oryza sativa and expression profiling in response to different developmental and environmental stimuli

Eukaryotic messenger RNAs (mRNAs) transcend their predominant function of protein encoding by incorporating auxiliary components that ultimately contribute to their processing, transportation, translation, and decay. In doing so, additional layers of modifications are incorporated in mRNAs at post-transcriptional stage. Among them, N6-methyladenosine (m6A) is the most frequently found mRNA modification that plays crucial roles in plant development and stress response. In the overall mechanism of m6A methylation, key proteins classified based on their functions such as writers, readers, and erasers dynamically add, read, and subtract methyl groups respectively to deliver relevant functions in response to external stimuli. In this study, we identified 30 m6A regulatory genes (9 writers, 5 erasers, and 16 readers) in rice that encode 53 proteins (13 writers, 7 erasers, and 33 readers) where segmental duplication was found in one writer and four reader gene pairs. Reproductive cells such as sperm, anther and panicle showed high levels of expression for most of the m6A regulatory genes. Notably, writers like OsMTA, OsMTD, and OsMTC showed varied responses in different stress and infection contexts, with initial upregulation in response to early exposure followed by downregulation later. OsALKBH9A, a noteworthy eraser, displayed varied expression in response to different stresses at different time intervals, but upregulation in certain infections. Reader genes like OsECT5, OsCPSF30-L3, and OsECT8 showed continuous upregulation in exertion of all kinds of stress relevant here. Conversely, other reader genes along with OsECT11 and OsCPSF30-L2 were observed to be consistently downregulated. The apparent correlation between the expression patterns of m6A regulatory genes and stress modulation pathways in this study underscores the need for additional research to unravel their intricate regulatory mechanisms that could ultimately contribute to the substantial development of enhanced stress tolerance in rice through mRNA modification.