A Stimuli-Responsive Dual-Emitting Covalent Organic Framework Shows Selective Sensing of Highly Corrosive Acidic Media via Fluorescence Turn-On Signal with White Light Emission.

Luminescent covalent organic frameworks (LCOFs) have been employed as platforms for sensing analytes. Judicial incorporation of appropriate functional units inside the framework leads to the different electronic states in the presence of external stimuli, e.g., temperature, pH, etc. We report herein a new COF (TPEPy) as a solid-state acid sensor specific for the highly acidic environments that range from pH ∼0.5 to ∼3.0. This COF shows a protonation-induced reversible color change from bright yellow to deep red upon decreasing the pH from 3 to 0.5 and vice versa. No visual color change was, however, observed above pH 3.0. Photoluminescence (PL) studies show that the intrinsic emission peak of the TPEPy COF at 530 nm is shifted to 420 nm owing to the N-protonation of the imine nitrogen of COF within this pH range. Extensive studies demonstrate that the protonation behavior of the COF is counterion dependent. This was revealed when different acids, e.g., HCl, HNO3, HBr, and HI, were employed. The intensity of the proton-induced emission peak at 420 nm depends significantly upon the counterions with the order of HCl > HNO3 > HBr > HI. These anions interact with the protonated TPEPy COF by cation-anion and H-bonding interactions. Further, the pristine COF showed near white light emission at a particular pH of 2.5 (CIE coordinates 0.27, 0.32). From the PL spectrophotometric titrations, the deprotonation pKa was experimentally found to be 1.8 ± 0.02 for the TPEPy COF. The sensor reported herein is reversible, reusable, and regenerable and is useful for assessing pH fluctuations within a strongly acidic range via digital signaling.

Multi Epitopic Peptide Based Vaccine Development Targeting Immobilization Antigen of Ichthyophthirius multifiliis: A Computational Approach.

The white spot disease causes significant damage to global aquaculture production. A prominent vaccine, eliciting the immunogenicity of freshwater fishes against Ichthyophthirius multifiliis yet to be developed. Thus, an Immunoinformatic drive was implemented to find out the potential epitopes from the surface immobilization antigens. B-cell derived T-cell epitopes are promiscuous elements for new generation peptide-based vaccine designing. A total of eight common B and T-cell epitopes had filtered out with no overlapping manner. Subsequently, the common epitopes are linked up with EAAAKEAAAKEAAAK linker peptides, we also added L7/L12 ribosomal protein adjuvant at the N- terminal side of peptide sequence for eliciting the immune response in a better way. The secondary and tertiary structural properties of the modeled 3D protein revealed that the protein had all the properties required for a protective immunogen. Afterward, three globally used validation server: PROCKECK, ProSA and ERRAT were used to justify the proper coordinate. NMR, Crystallographic range and error plot calculation for vaccine model also been done respectively. This was followed by molecular docking, MD simulation, NMA analysis, in silico cloning and vaccine dose-based immune response simulation to evaluate the immunogenic potency of the vaccine construct. The in silico immune simulation in response to multi-epitopes show antibody generation and elevated levels of cell-mediated immunity during repeated exposure of the vaccine. The favourable results of the in silico analysis significantly specify that the vaccine construct is really a powerful vaccine candidate and ready to proceed to the next steps of experimental validation and efficacy studies. Supplementary Information: The online version contains supplementary material available at 10.1007/s10989-022-10475-1.

Regulatory role of miRNAs in Wnt signaling pathway linked with cardiovascular diseases.

MicroRNAs (miRNAs) are discovered in science about 23 years ago. These are short, a series of non-coding, single-stranded and evolutionary conserved RNA molecules found in eukaryotic cells. It involved post-transcriptional fine-tune protein expression and repressing the target of mRNA in different biological processes. These miRNAs binds with the 3'-UTR region of specific mRNAs to phosphorylate the mRNA degradation and inhibit the translation process in various tissues. Therefore, aberrant expression in miRNAs induces numerous cardiovascular diseases and developmental defects. Subsequently, the miRNAs and Wnt singling pathway are regulating a cellular process in cardiac development and regeneration, maintain the homeostasis and associated heart diseases. In Wnt signaling pathway majority of the signaling components are expressed and regulated by miRNAs, whereas the inhibition or dysfunction of the Wnt signaling pathway induces cardiovascular diseases. Moreover, inadequate studies about the important role of miRNAs in heart development and diseases through Wnt signaling pathway has been exist still now. For this reason in present review we summarize and update the involvement of miRNAs and the role of Wnt signaling in cardiovascular diseases. We have discussed the mechanism of miRNA functions which regulates the Wnt components in cellular signaling pathway. The fundamental understanding of Wnt signaling regulation and mechanisms of miRNAs is quite essential for study of heart development and related diseases. This approach definitely enlighten the future research to provide a new strategy for formulation of novel therapeutic approaches against cardiovascular diseases.

TN strain proteome mediated therapeutic target mapping and multi-epitopic peptide-based vaccine development for Mycobacterium leprae.

Leprosy is a significant universal health problem that is remarkably still a concern in developing countries due to infection frequency. New therapeutic molecules and next-generation vaccines are urgently needed to accelerate the leprosy-free world. In this direction, the present study was performed using two routes: proteome-mediated therapeutic target identification and mapping as well as multi-epitopic peptide-based novel vaccine development using state of the art of computational biology for the TN strain of M. leprae. The TN strain was selected from 65 Mycobacterium strains, and TN strain proteome mediated 83 therapeutic protein targets were mapped and characterized according to subcellular localization. Also, drug molecules were mapped with respect to protein targets localization. The Druggability potential of proteins was also evaluated. For multi-epitope peptide-based vaccine development, the four common types of B and T cell epitopes were identified (SLFQSHNRK, VVGIGQHAA, MMHRSPRTR, LGVDQTQPV) and combined with the suitable peptide linker. The vaccine component had an acceptable protective antigenic score (0.9751). The molecular docking of vaccine components with TLR4/MD2 complex exhibited a low ACE value (-244.12) which signifies the proper binding between the two molecules. The estimated free Gibbs binding energy ensured accurate protein-protein interactions (-112.46 kcal/mol). The vaccine was evaluated through adaptive immunity stimulation as well as immune interactions. The molecular dynamic simulation was carried out by using CHARMM topology-based parameters to minimize the docked complex. Subsequently, the Normal Mode Analysis in the internal coordinates showed a low eigen-value (1.3982892e-05), which also signifies the stability of molecular docking. Finally, the vaccine components were adopted for reverse transcription and codon optimization in E. coli strain K12 for the pGEX-4T1 vector, which supports in silico cloning of the vaccine components against the pathogen. The study directs the experimental study for therapeutics molecules discovery and vaccine candidate development with higher reliability.

Bioengineering of Novel Non-Replicating mRNA (NRM) and Self-Amplifying mRNA (SAM) Vaccine Candidates Against SARS-CoV-2 Using Immunoinformatics Approach.

Presently, the world needs safe and effective vaccines to overcome the COVID-19 pandemic. Our work has focused on formulating two types of mRNA vaccines that differ in capacity to copy themselves inside the cell. These are non-amplifying mRNA (NRM) and self-amplifying mRNA (SAM) vaccines. Both the vaccine candidates encode an engineered viral replicon which can provoke an immune response. Hence we predicted and screened twelve epitopes from the spike glycoprotein of SARS-CoV-2. We used five CTL, four HTL, and three B-cell-activating epitopes to formulate each mRNA vaccine. Molecular docking revealed that these epitopes could combine with HLA molecules that are important for boosting immunogenicity. The B-cell epitopes were adjoined with GPGPG linkers, while CTL and HTL epitopes were linked with KK linkers. The entire protein chain was reverse translated to develop a specific NRM-based vaccine. We incorporate gene encoding replicase in the upstream region of CDS encoding antigen to design the SAM vaccine. Subsequently, signal sequences were added to human mRNA to formulate vaccines. Both vaccine formulations translated to produce the epitopes in host cells, initiate a protective immune cascade, and generate immunogenic memory, which can counter future SARS-CoV-2 viral exposures before the onset of infection.

Evaluation and Designing of Epitopic-Peptide Vaccine Against Bunyamwera orthobunyavirus Using M-Polyprotein Target Sequences.

Bunyamwera orthobunyavirus and its serogroup can cause several diseases in humans, cattle, ruminants, and birds. The viral M-polyprotein helps the virus to enter the host body. Therefore, this protein might serve as a potential vaccine target against Bunyamwera orthobunyavirus. The present study applied the immunoinformatics technique to design an epitopic vaccine component that could protect against Bunyamwera infection. Phylogenetic analysis revealed the presence of conserved patterns of M-polyprotein within the viral serogroup. Three epitopes common for both B-cell and T-cell were identified, i.e., YQPTELTRS, YKAHDKEET, and ILGTGTPKF merged with a specific linker peptide to construct an active vaccine component. The low atomic contact energy value of docking complex between human TLR4 (TLR4/MD2 complex) and vaccine construct confirms the elevated protein-protein binding interaction. Molecular dynamic simulation and normal mode analysis illustrate the docking complex's stability, especially by the higher Eigenvalue. In silico cloning of the vaccine construct was applied to amplify the desired vaccine component. Structural allocation of both the vaccine and epitopes also show the efficacy of the developed vaccine. Hence, the computational research design outcomes support that the peptide-based vaccine construction is a crucial drive target to limit the infection of Bunyamwera orthobunyavirus to an extent. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10989-021-10322-9.

A SARS-CoV-2 vaccine candidate: In-silico cloning and validation.

SARS-CoV-2 is spreading globally at a rapid pace. To contain its spread and prevent further fatalities, the development of a vaccine against SARS-CoV-2 is an urgent prerequisite. Thus, in this article, by utilizing the in-silico approach, a vaccine candidate for SARS-CoV-2 has been proposed. Moreover, the effectiveness and safety measures of our proposed epitopic vaccine candidate have been evaluated by in-silico tools and servers (AllerTOP and AllergenFP servers). We observed that the vaccine candidate has no allergenicity and successfully combined with Toll-like receptor (TLR) protein to elicit an inflammatory immune response. Stable, functional mobility of the vaccine-TLR protein binding interface was confirmed by the Normal Mode Analysis. The in-silico cloning model demonstrated the efficacy of the construct vaccine along with the identified epitopes against SARS-CoV-2. Taken together, our proposed in-silico vaccine candidate has potent efficacy against COVID-19 infection, and successive research work might validate its effectiveness in in vitro and in vivo models.

Epitope-Based Vaccine Designing of Nocardia asteroides Targeting the Virulence Factor Mce-Family Protein by Immunoinformatics Approach.

Nocardia asteroides is the main causative agent responsible for nocardiosis disease in immunocompromised patient viz. Acquired Immunodeficiency Syndrome (AIDS), malignancy, diabetic, organ recipient and genetic disorders. The virulence factor and outer membrane protein pertains immense contribution towards the designing of epitopic vaccine and limiting the robust outbreak of diseases. While epitopic based vaccine element carrying B and T cell epitope along with adjuvant is highly immunoprophylactic in nature. Present research equips immunoinformatics to figure out the suitable epitopes for effective vaccine designing. The selected epitopes VLGSSVQTA, VNIELKPEF and VVPSNLFAV amino acids sequence are identified by HLA-DRB alleles of both MHC class (MHC-I and II) molecules. Simultaneously, these also accessible to B-cell, confirmed through the ABCPred server. Antigenic property expression is validated by the Vaxijen antigenic prediction web portal. Molecular docking between the epitopes and T cell receptor delta chain authenticate the accurate interaction between epitope and receptor with significantly low binding energy. Easy access of epitopes to immune system also be concluded as transmembrane nature of the protein verified by using of TMHMM server. Appropriate structural identity of the virulence factor Mce-family protein generated through Phyre2 server and subsequently validated by ProSA and PROCHECK program suite. The structural configuration of theses epitopes also shaped using DISTILL web server. Both the structure of epitopes and protein will contribute a significant step in designing of epitopic vaccine against N. asteroides. Therefore, such immunoinformatics based computational drive definitely provides a conspicuous impel towards the development of epitopic vaccine as a promising remedy of nocardiosis.

Identification and Design of a Next-Generation Multi Epitopes Bases Peptide Vaccine Candidate Against Prostate Cancer: An In Silico Approach.

Prostate cancer (PCa) is the second most diagnosed cancer in men and ranked fifth in overall cancer diagnosis. During the past decades, it has arisen as a significant life-threatening disease in men at an older age. At the early onset of illness when it is in localized form, radiation and surgical treatments are applied against this disease. In case of adverse situations androgen deprivation therapy, chemotherapy, hormonal therapy, etc. are widely used as a therapeutic element. However, studies found the occurrences of several side effects after applying these therapies. In current work, several immunoinformatic techniques were applied to formulate a multi-epitopic vaccine from the overexpressed antigenic proteins of PCa. A total of 13 epitopes were identified from the five prostatic antigenic proteins (PSA, PSMA, PSCA, STEAP, and PAP), after validation with several in silico tools. These epitopes were fused to form a vaccine element by (GGGGS)3 peptide linker. Afterward, 5, 6-dimethylxanthenone-4-acetic acid (DMXAA) was used as an adjuvant to initiate and induce STING-mediated cytotoxic cascade. In addition, molecular docking was performed between the vaccine element and HLA class I antigen with the low ACE value of -251 kcal/mol which showed a significant binding. Molecular simulation using normal mode analysis (NMA) illustrated the docking complex as a stable one. Therefore, this observation strongly indicated that our multi epitopes bases peptide vaccine molecule will be an effective candidate for the treatment of the PCa.

Computer aided novel antigenic epitopes selection from the outer membrane protein sequences of Aeromonas hydrophila and its analyses.

OBJECTIVES: Gram-negative bacteria are among the causative microorganisms for zoonotic diseases in humans and teleosts. Outer membrane proteins (Omps) of Aeromonas hydrophila, a gram-negative bacterium, are critical for the subcellular integration to eukaryotic cell that can modulate the functions of macrophages. Hence Omps are recognized as immune markers for the vaccine development. METHODS: In the present study, a 3-D model of Omps was identified using in silico technique and recognized through the Swiss model web-server and confirmed with Procheck and ProSA server.. The B-cell binding sites of the protein were selected from sequence alignment.. Further, the identification of B-cell epitope was carried out using modules of BCpred server (i.e., BCPred and Amino Acid Pairs). The identified antigenic amino acid sequences for B-cells were used to determine the T-cell epitope (both MHC I & II allelic binding sequences) using ProPred 1 and ProPred servers. RESULTS: The epitopic regions (9 mer: LAGKTTNES and GFDGSQYGK) in the Omps that are bound together with the MHC molecules (MHC-I & II), and have maximum possible numbers of MHC alleles are recognized. It was observed that Omps of A. hydrophila are conserved across the serotypes and are immunogenic. These epitopes can stimulate significant immune responses and can be advantageous while preparing peptide-based vaccines against A. hydrophila infections. Thus, suggesting the use of Omps in the development of vaccines and immunotherapeutics against the bacterial diseases in humans and teleosts.

Interaction between miRNAs and signaling cascades of Wnt pathway in chronic lymphocytic leukemia.

Chronic lymphocytic leukemia (CLL), a severe problem all over the world and represents around 25% of all total leukemia cases, is generating the need for novel targets against CLL. Wnt signaling cascade regulates cell proliferation, differentiation, and cell death processes. Thus, any alteration of the Wnt signaling pathway protein cascade might develop into various types of cancers, either by upregulation or downregulation of the Wnt signaling pathway protein components. In addition, it is reported that activation of the Wnt signaling pathway is associated with the transcriptional activation of microRNAs (miRNAs) by binding to its promoter region, suggesting feedback regulation. Considering the protein regulatory functions of various miRNAs, they can be approached therapeutically as modulatory targets for protein components of the Wnt signaling pathway. In this article, we have discussed the potential role of miRNAs in the regulation of Wnt signaling pathway proteins related to the pathogenesis of CLL via crosstalk between miRNAs and Wnt signaling pathway proteins. This might provide a clear insight into the Wnt protein regulatory function of various miRNAs and provide a better understanding of developing advanced and promising therapeutic approaches against CLL.

Computational characterization of epitopic region within the outer membrane protein candidate in Flavobacterium columnare for vaccine development.

Gram-negative bacteria is the main causative agents for columnaris disease outbreak to finfishes. The outer membrane proteins (OMPs) candidate of Flavobacterium columnare bacterial cell served a critical component for cellular invasion targeted to the eukaryotic cell and survival inside the macrophages. Therefore, OMPs considered as the supreme element for the development of promising vaccine against F. columnare. Implies advanced in silico approaches, the predicted 3-D model of targeted OMPs were characterized by the Swiss model server and validated through Procheck programs and Protein Structure Analysis (ProSA) web server. The protein sequences having B-cell binding sites were preferred from sequence alignment; afterwards the B cell epitopes prediction was prepared using the BCPred and amino acid pairs (AAP) prediction algorithms modules of BCPreds. Consequently, the selected antigenic amino acids sequences (B-cell epitopic regions) were analyzed for T-cell epitopes determination (MHC I and MHC II alleles binding sequence) performing the ProPred 1 and ProPred server respectively. The epitopes (9 mer: IKKYEPAPV, YGPNYKWKF and YRGLNVGTS) within the OMPs binds to both of the MHC classes (MHC I and MHC II) and covered highest number of MHC alleles are characterized. OMPs of F. columnare being conserved across serotypes and highly immunogenic for their exposed epitopes on the cell surface as a potent candidate focus to vaccine development for combating the disease problems in commercial aquaculture. The portrayed epitopes might be beneficial for practical designing of abundant peptide-based vaccine development against the columnaris through boosting up the advantageous immune responses.Communicated by Ramaswamy H. Sarma.

Promising approaches of small interfering RNAs (siRNAs) mediated cancer gene therapy.

RNA interference (RNAi) has extensive potential to revolutionize every aspect of clinical application in biomedical research. One of the promising tools is the Small interfering RNA (siRNA) molecules within a cellular component. Principally, siRNA mediated innovative advances are increasing rapidly in support of cancer diagnosis and therapeutic purposes. Conversely, it has some delivery challenges to the site of action within the cells of a target organ, due to the progress of nucleic acids engineering and advance material science research contributing to the exceptional organ-specific targeted therapy. This siRNA based therapeutic technique definitely favors a unique and effective prospect to cancer patients. Herein, the significant drive also takes to review and summarize the major organ specific targets of diverse siRNAs based gene silencing mechanism. This machinery promisingly served as the inhibitor components for cancer development in the human model. Furthermore, the focus is also given to current applications on siRNA based quantifiable therapy leading to the silencing of cancer related gene expression in a sequence dependent and selective manner for cancer treatment. That might be a potent tool against the traditional chemotherapy techniques. Therefore, the siRNA mediated cancer gene therapy definitely require sharp attention like future weapons in opposition to cancer by the method of non-invasive siRNA delivery and effective gene silencing approaches.

Efficacious Electrochemical Oxygen Evolution from a Novel Co(II) Porphyrin/Pyrene-Based Conjugated Microporous Polymer.

Oxygen evolution reaction (OER) is energetically challenging from the platform of making many photovoltaic devices such as metal-air batteries and water splitting systems because of its poor kinetics even when precious metals are used. Herein, a Co(II)-porphyrin/pyrene-comprised conjugated microporous polymer Co-MPPy-1 has been developed which shows efficient OER in alkaline medium. The material was characterized by Fourier transform infrared, solid-state 13C cross-polarization magic angle spinning nuclear magnetic resonance, N2 volumetric adsorption/desorption analysis, scanning electron microscopy, ultra high resolution-transmission electron microscopy, X-ray photoelectron spectroscopy, and other physical studies. Co-MPPy-1 showed Brunauer-Emmett-Teller surface area of ∼501 m2 g-1. Co-MPPy-1 achieved a current density of 1 and 10 mA/cm-2 at 340 and 420 mV, respectively. The turnover frequency calculated for the OER is 0.43 s-1. The heterogeneity of this electrocatalyst was tested by chronoamperometric measurement and 1000 cycle recyclability test with retainment of the excellent electrochemical catalytic activity. This can be attributed to the presence of high density of Co(II) porphyrin unit and efficient charge transport in the π-conductive conjugated polymeric backbone.

Therapeutic applications of zebrafish (Danio rerio) miRNAs linked with human diseases: A prospective review.

MicroRNAs (miRNAs) are the class of small, non-coding RNAs that are produced from precursor transcripts by subsequent processing steps mediated by members of the RNaseIII family, Dicer and Drosha protein within cell. The importance of zebrafish miRNAs in regulation of normal cellular development and support to various kinds of metabolism process. Although the zebrafish model provides a fundamental platform for the study of developmental biology but recent work with zebrafish model has expanded its appliance to a broad range of experimental studies relevant to different kind of human diseases. Presently, the zebrafish model is used for the study of cardiovascular disease, schizophrenia, bipolar I disorder in eyes, psoriasis, spinal cord injury, cancer and diabetes that showing in some selected miRNAs are regulate these diseases in molecular levels. Here, a superior drive performed to depict the fundamental utilization of the zebrafish miRNAs that targeted to several clinical diseases connected to human. This review aims to provide a summary of understanding of the cellular mechanism which is responsible for selected diseases and suggests some therapeutic application for inhibition of miRNA functions.

The crucial role and regulations of miRNAs in zebrafish development.

To comprehend the events during developmental biology, fundamental knowledge about the basic machinery of regulation is a prerequisite. MicroRNA (miRNAs) act as regulators in most of the biological processes and recently, it has been concluded that miRNAs can act as modulatory factors even during developmental process from lower to higher animal. Zebrafish, because of its favorable attributes like tiny size, transparent embryo, and rapid external embryonic development, has gained a preferable status among all other available experimental animal models. Currently, zebrafish is being utilized for experimental studies related to stem cells, regenerative molecular medicine as well drug discovery. Therefore, it is important to understand precisely about the various miRNAs that controls developmental biology of this vertebrate model. In here, we have discussed about the miRNA-controlled zebrafish developmental stages with a special emphasis on different miRNA families such as miR-430, miR-200, and miR-133. Moreover, we have also reviewed the role of various miRNAs during embryonic and vascular development stages of zebrafish. In addition, efforts have been made to summarize the involvement of miRNAs in the development of different body parts such as the brain, eye, heart, muscle, and fin, etc. In each section, we have tried to fulfill the gaps of zebrafish developmental biology with the help of available knowledge of miRNA research. We hope that precise knowledge about the miRNA-regulated developmental stages of zebrafish may further help the researchers to efficiently utilize this vertebrate model for experimental purpose.

MicroRNAs mediated regulation of MAPK signaling pathways in chronic myeloid leukemia.

Chronic myeloid leukemia (CML) is a severe problem throughout the world and requires identification of novel targets for its treatment. This multifactorial disease accounts for about 15% of the all diagnosed leukemia cases. Mitogen-activated protein kinase (MAPK) signaling pathway is crucial for the cell survival and its dysregulation is being implicated in various types of cancers. In here, we have discussed the potential role of various miRNAs that are found involved in regulating the proteins cascades of MAPK signaling pathway associated with CML. An emphasis has been paid to summarize the influence of various miRNAs in elevating or suppressing the expression level of significant proteins such as miR-203, miR-196a, miR-196b, miR-30a, miR-29b, miR-138 in BCR-ABL tyrosine kinase; miR-126, miR-221, miR-128, miR-15a, miR-188-5p, miR-17 in CRK family proteins; miR-155, miR-181a with SOS proteins; miR-155, miR-19a, with KRAS proteins; miR-19a with RAF1 protein; and miR-17, miR-19a, miR-17-92 cluster with MAPK/ERK proteins. In light of ever-increasing importance and ever-widening regulatory roles of miRNAs in cells, we have reviewed the recent progress in the field of miRNAs and have tried to suggest them as controlling targets for various protein cascades of MAPK signaling pathway. An understanding of the supervisory mechanism of MAPK by miRNAs might provide novel targets for treating CML.

DNA barcoding to fishes: current status and future directions.

DNA barcoding appears to be a promising approach for taxonomic identification, characterization, and discovery of newer species, facilitating biodiversity studies. It helps researchers to appreciate genetic and evolutionary associations by collection of molecular, morphological, and distributional data. Fish DNA barcoding, based on the sequencing of a uniform area of Cytochrome C Oxidase type I (COI) gene, has received significant interest as an accurate tool for species identification, authentication, and phylogenetic analysis. The aim of this review article was to investigate recent global status, approaches, and future direction of DNA barcoding in fisheries sectors. We have tried to highlight its possible impacts, complications, and validation issues at species levels for biodiversity analysis. Moreover, an effort has been put forward to understand issues related to various marker genes associated with barcode process as primer sequences and have concluded barcode promotion as an indispensable tool of molecular biology for the development of taxonomic support systems.