Single-cell sequencing of miRNAs: A modified technology

The recent development of next-generation sequencing technologies has offered valuable insights into individual cells. This technology is centered on the characterization of single cells for epigenomics, genomics, and transcriptomics. Ever since the first report appeared in 2009, the single-cell RNA-sequencing saga started to explore deeper into the mechanics intrigued within a single cell. microRNA (miRNA) has been increasingly recognized as an essential molecule triggering an additional layer for gene regulation. Therefore, single-cell sequencing of miRNAs is crucial to explore the logical riddles surrounding the epigenomics, genomics, and transcriptomics of an individual cell. Scientists from the Vienna Biocenter Campus have lately performed single-cell sequencing of miRNAs in the fly, Drosophila, and nematode, Caenorhabditis elegans. In this review, we present the latest scientific explorations supported by all-inclusive data on this novel subject matter of next-generation sequencing.

Probable Molecular Mechanism of Remdesivir for the Treatment of COVID-19: Need to Know More

COVID-19 is now pandemic throughout the world. Scientist, doctors are searching for effective therapy of this diseases. The remdesivir, an antiviral drug, is appeared as ‘molecule of hope’ for the treatment of this disease. USFDA gave emergency approval to this drug for the treatment of COVID-19. The molecular mechanism is unknown. In this paper, we tried to describe the probable molecular mechanism of remdesivir to inhibit the RNA synthesis of SARS-CoV-2. However, more detail mechanism is needed to understand mechanism of action of remdesivir.

SARS-CoV-2 causing pneumonia-associated respiratory disorder (COVID-19): diagnostic and proposed therapeutic options

SARS-CoV-2 is responsible for the outbreak of severe respiratory illness (COVID-19) in Wuhan City, China and is now spreading rapidly throughout the world. The prompt outbreak of COVID-19 and its quick spread without any controllable measure defines the severity of the situation. In this crisis, a collective pool of knowledge about the advancement of clinical diagnostic and management for COVID-19 is a prerequisite. Here, we summarize all the available updates on the multidisciplinary approaches for the advancement of diagnosis and proposed therapeutic strategies for COVID-19. Moreover, the review discusses different aspects of the COVID-19, including its epidemiology; incubation period; the general clinical features of patients; the clinical features of intensive care unit (ICU) patients; SARS-CoV-2 infection in the presence of co-morbid diseases and the clinical features of pediatric patients infected with the SARS-CoV-2. Advances in various diagnostic approaches, such as the use of real-time polymerase chain reaction (RT-PCR), chest radiography, and computed tomography (CT) imaging; and other modern diagnostic methods, for this infection have been highlighted. However, due to the unavailability of adequate evidence, presently there are no officially approved drugs or vaccines available against SARS-CoV-2. Additionally, we have discussed various therapeutic strategies for COVID-19 under different categories, like the possible treatment plans with drug (antiviral drugs and anti-cytokines) therapy for disease prevention. Lastly, potentials candidates for the vaccines against SARS-CoV-2 infection have been described. Collectively, the review provides an overview of the SARS-CoV-2 infection outbreak along with the recent advancements and strategies for diagnosis and therapy of COVID-19.

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.

Development of epitope-based peptide vaccine against novel coronavirus 2019 (SARS-COV-2): Immunoinformatics approach

Recently, a novel coronavirus (SARS‐COV‐2) emerged which is responsible for the recent outbreak in Wuhan, China. Genetically, it is closely related to SARS‐CoV and MERS‐CoV. The situation is getting worse and worse, therefore, there is an urgent need for designing a suitable peptide vaccine component against the SARS‐COV‐2. Here, we characterized spike glycoprotein to obtain immunogenic epitopes. Next, we chose 13 Major Histocompatibility Complex‐(MHC) I and 3 MHC‐II epitopes, having antigenic properties. These epitopes are usually linked to specific linkers to build vaccine components and molecularly dock on toll‐like receptor‐5 to get binding affinity. Therefore, to provide a fast immunogenic profile of these epitopes, we performed immunoinformatics analysis so that the rapid development of the vaccine might bring this disastrous situation to the end earlier.

The potential epitopes of coronavirus (SARS‐CoV‐2) are identified.

The docking complex of the construct vaccine and TLR5 is described.

Peptide‐based vaccine developed and in silico validation is provided.

Common epitopes of coronavirus (SARS‐CoV‐2) against B‐cells and T‐cells are listed.

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.

Insight into Evolution and Conservation Patterns of B1-Subfamily Members of GPCR

The diverse, evolutionary architectures of proteins can be regarded as molecular fossils, tracing a historical path that marks important milestones across life. The B1-subfamily of GPCRs (G-protein-coupled receptors) are medically significant proteins that comprise 15 transmembrane receptor proteins in Homo sapiens. These proteins control the intracellular concentration of cyclic AMP as well as various vital processes in the body. However, little is known about the evolutionary correlation and conservational blueprint of this GPCR subfamily. We performed a comprehensive analysis to understand the evolutionary architecture among 13 members of the B1-subfamily. Multiple sequence alignment analysis exhibited six multiple sequence aligned blocks and five highly aligned blocks. Molecular phylogenetics indicated that CRHR1 and CRHR2 share a typical ancestral relationship and are siblings in 100% bootstrap replications with a total of 24 nodes observed in the cladogram. CRHR2 has the maximum number of extremely conserved amino acids followed by ADCYAP1R1. The longest continuous number sequence logos (74) were found between sequence location 349 and 423, and consequently, the maximum and minimum logo height recorded was 3.6 bits and 0.18 bits, respectively. Finally, to understand the model and pattern of evolutionary relatedness, the conservation blueprint, and the diversification among the members of a protein family, GPCR distribution from several species throughout the animal kingdom was analysed. Together, the study provides an evolutionary insight and offers a rapid method to explore the potential of depicting the evolutionary relationship, conservation blueprint, and diversification among the B1-subfamily of GPCRs using bioinformatics, algorithm analysis, and mathematical models.

Higher order correlations in a levitated nanoparticle phonon laser

We present theoretical and experimental investigations of higher order correlations of mechanical motion in the recently demonstrated optical tweezer phonon laser, consisting of a silica nanosphere trapped in vacuum by a tightly focused optical beam [R. M. Pettit et al., Nature Photonics 13, 402 (2019)]. The nanoparticle phonon number probability distribution is modeled with the master equation formalism in order to study its evolution across the lasing threshold. Up to fourth-order equal-time correlation functions are then derived from the probability distribution. Subsequently, the master equation is transformed into a nonlinear quantum Langevin equation for the trapped particle's position. This equation yields the non-equal-time correlations, also up to fourth order. Finally, we present experimental measurements of the phononic correlation functions, which are in good agreement with our theoretical predictions. We also compare the experimental data to existing analytical Ginzburg-Landau theory where we find only a partial match.

Effect of temperature on Pi54-mediated leaf blast resistance in rice

Assessment of temperature effect on plant resistance against diseases has become essential under climate change scenario as temperature rise is anticipated to modify host resistance. To determine temperature influence on resistance gene, a pair of near-isogenic rice lines differing for the Pi54 resistance gene was assessed against leaf blast. Blast resistance was determined as the extent of infection efficiency (IE) and sporulation (SP) at suboptimal (22 °C and 32 °C) and optimal temperature (27 °C) of pathogen aggressiveness. Relative resistance for IE and SP was higher at suboptimal temperature as compared to that of optimal temperature. Maximum level of resistance was at 22 °C where higher levels of expression of Pi54 and defence-regulatory transcription factor WRKY45 were also noted. At 32 °C, although some level of resistance noted, but level of Pi54 and WRKY45 expression was too low, suggesting that resistance recorded at higher temperature was due to reduced pathogen aggressiveness. At the optimal temperature for pathogen aggressiveness, comparatively lower levels of Pi54 and WRKY45 expression suggest possible temperature-induced interruption of the defence processes. The variation in resistance patterns modulated by temperature is appeared to be due to pathogen's sensitivity to temperature that leads to varying levels of Pi54 gene activation. Quick and violent activity of the pathogen at optimal temperature came into sight for the interruption of defence process activated by Pi54 gene. Evaluation of blast resistance genes under variable temperature conditions together with weather data could be applied in screening rice genotypes for selection of resistance having resilience to temperature rise.

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.

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.

Influence of single nucleotide polymorphisms (SNPs) in genetic susceptibility towards periprosthetic osteolysis

Wear debris-induced inflammatory osteolysis remains a significant limiting factor for implant replacement surgeries. Hence, a comprehensive understanding of the complex network of cellular and molecular signals leading to these inflammatory responses is required. Both macrophages and monocytes have a critical role in the instigation of the inflammatory reaction to wear debris but differ in the extent to which they induce cytokine expression in patients. Lately, single nucleotide polymorphisms (SNPs) have been associated with genetic susceptibility among individual patients with implant failure. Studies have shown that SNPs in key pro-inflammatory cytokines and their receptors are associated with osteolytic susceptibility. Likewise, SNPs within several genes involved in the regulation of bone turnover have also been found to be associated with wear debris induced osteolysis. It is presumed that SNP variance might play a decisive role in the activation and signaling of macrophages, osteoblasts, chondrocytes, fibroblasts and other cells involved in inflammatory bone loss. Understanding the extent to which SNPs exist among genes that are responsible for inflammatory bone loss may provide potential targets for developing future therapeutic interventions. Herein, we attempt to summarize the various susceptible genes with possible SNP variance that could contribute to the severity of periprosthetic osteolysis in patients with implants.

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.

In silico structural and functional modelling of Antifreeze protein (AFP) sequences of Ocean pout (Zoarces americanus, Bloch & Schneider 1801)

Antifreeze proteins (AFPs) are known to polypeptide components formed by certain plants, animals, fungi and bacteria which support to survive in sub-zero temperature. Current study highlighted the seven different antifreeze proteins of fish Ocean pout (Zoarces americanus), in which protein (amino acids sequence) were collected from National Centre for Biotechnology Information and finely characterized using several in silico tools. Such biocomputational techniques applied to figure out the physicochemical, functional and conformational characteristics of targeted AFPs. Multiple physicochemical properties such as Isoelectric Point, Extinction Coefficient and Instability Index, Aliphatic Index, Grand Average Hydropathy were calculated and analysed by ExPASy-ProtParam prediction web server. EMBOSS: pepwheel online tool was used to represent the protein sequences in a helical form. The primary structure analysis shows that most of the AFPs are hydrophobic in nature due to the high content of non-polar residues. The secondary structure of these proteins was calculated using SOPMA tool. SOSUI server and CYS_REC program also run for ideal prediction of transmembrane helices and disulfide bridges of experimental proteins respectively. The modelling of 3D structures of seven desired AFPs were executed by the homology modelling programmes; SWISS MODEL and ProSA web server. UCSF Chimera, Antheprot 3D, PyMOL and RAMPAGE were used to visualize and analysis of the structural variation of the predicted protein model. MEGA7.0.9 software used to know the phylogenetic relationship among these AFPs. These models offered excellent and reliable baseline information for functional characterization of the experimentally derived protein domain composition by using the advanced tools and techniques of Computational Biology.

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.

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.

Magnetometry via spin-mechanical coupling in levitated optomechanics

We analyze magnetometry using an optically levitated nanodiamond. We consider a configuration where a magnetic field gradient couples the mechanical oscillation of the diamond with its spin degree of freedom provided by a nitrogen vacancy center. First, we investigate the measurement of the position spectrum of the mechanical oscillator. We find that conditions of ultrahigh vacuum and feedback cooling allow a magnetic field gradient sensitivity of 1μTm^-1/Hz. At high pressure and room temperature, this sensitivity degrades and can attain a value of the order of 100mTm^-1/Hz. Subsequently, we characterize the magnetic field gradient sensitivity obtainable by maneuvering the spin degrees of freedom using Ramsey interferometry. We find that this technique can offer photon-shot noise and spin-projection noise limited magnetic field gradient sensitivity of 100μTm^-1/Hz. We conclude that this hybrid levitated nanomechanical magnetometer provides a favorable and versatile platform for sensing applications.

Exploiting Le Chatelier's principle for a one-pot synthesis of nontoxic HHogGNPs with the sharpest nanoscopic features suitable for tunable plasmon spectroscopy and high throughput SERS sensing

Le Chatelier's principle leads to the generation of nontoxic, stable and highly anisotropic HHogGNPs.

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.