Biology subjects

Hasan, M.

Publications and source records attributed to Hasan, M..

54 records · Page 3Linked to original sources

bioRxiv2020

In silico Identification and Functional Characterization of Conserved miRNAs in Fibre Biogenesis Crop Corchorus capsularis

Corchorus capsularis, commonly known as jute occupies the leading position in the production of natural fibre and fibre based products alongside lower environmental threat. Nowadays, the study of lignin biosynthesis pathways with other molecular basis of fibres formation are being more focused for its economic perspective. Small noncoding [~]21 to 24 nt nucleotides long microRNAs play significant roles in regulating the gene expression as well as different functions in cellular growth and development. Here, the study adopted a comprehensive in silico approach to identify and characterize the conserved miRNAs in the genome of C. capsularis including specific gene targets involved in the crucial cellular process. Expressed Sequence Tags (ESTs) based homology search of 3350 known miRNAs of dicotyledons were allowed against 763 non-redundant ESTs of jute genome resulted in the prediction of 5 potential miRNA candidates belonging five different miRNA families (miR1536, miR9567-3p, miR4391, miR11300, and miR8689). The putative miRNAs were 18 nucleotide length, within a range of -0.49 to -1.56 MFEI values and 55% to 61% of (A+U) content of their correspondence pre-miRNAs. A total of 1052 gene targets of putative miRNAs were identified and their functions were extensively analyzed. Most of the gene targets were involved in plant growth, cell cycle regulation, organelle synthesis, developmental process and environmental responses. The five gene targets, namely, NAC Domain Containing Protein, WRKY DNA binding protein, 3-dehydroquinate synthase, S-adenosyl-L-Met-dependent methyl transferase and Vascular-related NAC-Domain were found to be involved in the lignin biosynthesis, phenylpropanoid pathways and secondary wall formation which could play significant roles in the overall fibre biogenesis. The characterization of conserved miRNAs and their functional annotation of specific gene targets might enhance the more miRNA discovery, strengthening the complete understanding of miRNAs association in the cellular basis of lignin biosynthesis towards the production of high standard jute products.

genomics↗

bioRxiv2020

Identifying Novel Drug and Vaccine Molecules of Vibrio parahaemolyticus by Subtractive Proteomics and Vaccinomics Approach

Multidrug-resistant Vibrio parahaemolyticus has become a significant threat to human health as well as aquaculture, prioritizing the development of effective drug and vaccine candidates. Hence, the study was designed to identify novel therapeutics using a comprehensive genome-based analysis of V. parahaemolyticus. From V. parahaemolyticus proteome, a total of 4822 proteins were investigated in order to find out effective drug and vaccine targets. A range of diverse subtractive proteomics approaches - namely, identification of human non-homologous and pathogen-specific essential proteins, druggability and anti-target analysis, prediction of subcellular localization, human microbiome non-homology screening, analysis of virulence factors, protein-protein interactions studies. Among 16 novel cytoplasmic proteins, VIBPA Type II secretion system protein L and VIBPA Putative fimbrial protein Z were allowed to molecular docking with 350 human metabolites, which revealed that Eliglustat, Simvastatin and Hydroxocobalamin were the top drug molecules considering free binding energy. On the contrary, Sensor histidine protein kinase UhpB and Flagellar hook-associated protein of 25 novel membrane proteins were subjected to T and B cell epitope prediction, antigenicity testing, transmembrane topology screening, allergenicity and toxicity assessment, population coverage analysis and molecular docking were adopted to generate the most immunogenic epitopes. Three subunit vaccines were constructed by the combination of highly antigenic epitopes along with suitable adjuvant, PADRE sequence and linkers. The designed vaccine constructs (V1, V2, V3) were analyzed by their physiochemical properties and molecular docking with MHC molecules that suggested the superiority of construct V1. Besides, the binding affinity of human TLR1/2 heterodimer and construct V1 was also biologically significant. The vaccine-receptor complex exhibited deformability at a minimum level that also strengthened our prediction. The optimized codons of the designed construct was cloned into pET28a(+) vector of E. coli strain K12. However, the predicted drug molecules and vaccine constructs could be further studied to combat V. parahaemolyticus associated infections.

microbiology↗

bioRxiv2020

Genome based Evolutionary study of SARS-CoV-2 towards the Prediction of Epitope Based Chimeric Vaccine

SARS-CoV-2 is known to infect the neurological, respiratory, enteric, and hepatic systems of human and has already become an unprecedented threat to global healthcare system. COVID-19, the most serious public condition caused by SARS-CoV-2 leads the world to an uncertainty alongside thousands of regular death scenes. Unavailability of specific therapeutics or approved vaccine has made the recovery of COVI-19 more troublesome and challenging. The present in silico study aimed to predict a novel chimeric vaccines by simultaneously targeting four major structural proteins via the establishment of ancestral relationship among different strains of coronaviruses. Conserved regions from the homologous protein sets of spike glycoprotein (S), membrane protein (M), envelope protein and nucleocapsid protein (N) were identified through multiple sequence alignment. The phylogeny analyses of whole genome stated that four proteins (S, E, M and N) reflected the close ancestral relation of SARS-CoV-2 to SARS-COV-1 and bat coronavirus. Numerous immunogenic epitopes (both T cell and B cell) were generated from the common fragments which were further ranked on the basis of antigenicity, transmembrane topology, conservancy level, toxicity and allergenicity pattern and population coverage analysis. Top putative epitopes were combined with appropriate adjuvants and linkers to construct a novel multiepitope subunit vaccine against COVID-19. The designed constructs were characterized based on physicochemical properties, allergenicity, antigenicity and solubility which revealed the superiority of construct V3 in terms safety and efficacy. Essential molecular dynamics and Normal Mode analysis confirmed minimal deformability of the refined model at molecular level. In addition, disulfide engineering was investigated to accelerate the stability of the protein. Molecular docking study ensured high binding affinity between construct V3 and HLA cells, as well as with different host receptors. Microbial expression and translational efficacy of the constructs were checked using pET28a(+) vector of E. coli strain K12. The development of preventive measures to combat COVID-19 infections might be aided the present study. However, the in vivo and in vitro validation might be ensured with wet lab trials using model animals for the implementation of the presented data.

immunology↗

bioRxiv2020

Antimicrobial Resistance Profile and mcr-1 gene Detection in Salmonella Isolates from Poultry in Bangladesh: Molecular and Bioinformatics Characterization

Antimicrobial resistance gene mcr-1 has been disseminated globally since its first discovery in Southern China in late 2015. However, the mcr-1 gene had not been identified previously in Salmonella isolates from poultry in Bangladesh. Here, we aimed to explore antimicrobial resistance gene mcr-1 in Salmonella isolates. Eighty two Salmonella isolates were isolated and characterized from suspected poultry specimens received from different zones of the country. A phenotypic disc diffusion assay with 15 antimicrobial agents was performed following CLSI standard. The disk diffusion assay showed that, all of the isolates presented high resistance to colistin (92.68%), oxytetracycline (86.59%), co-trimoxazole (76.83%), ciprofloxacin (73.17%) and enrofloxacin (65.85%). Further, randomly selected 10 Salmonella isolates were analyzed by polymerase chain reaction (PCR) targeting genus-specific invA and antimicrobial (colistin) resistance mcr-1 genes. Five were confirmed for the presence of the mcr-1 gene belonging to Salmonella spp. Further, sequencing followed by phylogenetic analysis revealed divergent evolutionary relation between the LptA and MCR proteins rendering them resistant to colistin. Three-dimensional homology structures of MCR-1 proteins were constructed and verified using different bioinformatics tools. Moreover, molecular docking interactions suggested that, MCR-1 and LptA share a similar substrate binding cavity which could be validated for the functional analysis. The results represent here is the first molecular and in silico analysis of colistin resistance mcr-1 gene of Salmonella in poultry in Bangladesh, which may emphasize the importance of the study on antibiotic resistance genes requiring for national monitoring and strategic surveillance in the country.

microbiology↗

bioRxiv2020

Scrutinizing surface glycoproteins and poxin-schlafen protein to design a heterologous recombinant vaccine against monkeypox virus

Monkeypox is a zoonotic disease caused by monkeypox virus with noteworthy mortality and morbidity. Several recent outbreaks and the need of dependable reconnaissance have raised the level of concern for this developing zoonosis. In the present study, a reverse vaccinology strategy was developed to construct a peptide vaccine against monkeypox virus by exploring cell surface binding protein, Poxin-Schlafen andenvelope protein. Both humoral and cell mediated immunity induction were the main concerned properties for the designed peptide vaccine. Therefore, both T cell and B cell immunity against monkeypox virus were analyzed from the conserver region of the selected protein. Antigenicity testing, transmembrane topology screening, allergenicity and toxicity assessment, population coverage analysis and molecular docking approach were used to create the superior epitopes of moneypox virus. The subunit vaccine was constructed using highly immunogenic epitopes with appropriate adjuvant and linkers. Molecular docking examination of the refined vaccine with various MHCs and human immune receptor illustrated higher binding interaction. The designed construct was reverse transcribed and adjusted for E. coli strain K12 earlier to inclusion inside pET28a(+) vector for its heterologous cloning and expression. The study could start in vitro and in vivo studies concerning effective vaccine development against monkeypox virus.

bioinformatics↗

bioRxiv2020

Proteome Exploration of Legionella pneumophila for Identifying Novel Therapuetics: A Hierarchical Subtractive Genomics and Reverse Vaccinology Approach

Legionella pneumophila, the causative agent of a serious type of pneumonia (lung infection) called Legionnaires disease. It is emerging as an antibacterial resistant strain day by day. Hence, the identification of novel drug targets and vaccine candidates is essential to fight against this pathogen. Herein attempts were taken through subtractive genomics approach on complete proteome of L. pneumophila to address the challenges of multidrug resistance. A total 2930 proteins from L. pneumophila proteome were investigated through diverse subtractive proteomics approaches, e.g., identification of human non-homologous and pathogen-specific essential proteins, druggability and anti-target analysis, prediction of subcellular localization, human microbiome non-homology screening, protein-protein interactions studies in order to find out effective drug and vaccine targets. Only 3 were identified that fulfilled all these criteria and proposed as novel drug targets against L. pneumophila. Furthermore, outer membrane protein TolB was identified as potential vaccine target with better antigenicity score and allowed for further in silico analysis to design a unique multiepitope subunit vaccine against it. Antigenicity and transmembrane topology screening, allergenicity and toxicity assessment, population coverage analysis, and molecular docking approach were adopted to generate the most potent epitopes. The final vaccine was constructed by the combination of highly immunogenic epitopes along with suitable adjuvant and linkers. The designed vaccine construct showed higher binding interaction with different MHC molecules and human immune TLR2 receptors with minimum deformability at molecular level. The translational potency and microbial expression of the vaccine protein was also analyzed using pET28a(+) vector. The present study aids in the development of novel therapeutics and vaccine candidates for efficient treatment of the infections caused by Legionella pneumophila. However, further wet lab-based investigations and in vivo trials are highly recommended to experimentally validate our prediction.

bioinformatics↗

bioRxiv2019

Conglomeration of highly antigenic nucleoproteins to inaugurate a heterosubtypic next generation vaccine candidate against Arenaviridae family

AbstractArenaviral infections often resulting in lethal Hemorrhagic Fevers (HF) affect primarily African and South American regions. To date, there is no FDA-approved licensed vaccine against arenaviruses and treatments have been limited to supportive therapies. Hence, the study was employed to design a highly immunogenic heterosubtypic vaccine candidate against Arenaviridae family. The whole proteomes of Lassa virus (LASV), Lymphocytic Chorio Meningitis Virus (LCMV), Lujo virus and Guanarito virus were retrieved from NCBI database and assessed to determine the most antigenic viral proteins. Only the conserved sequences were used for T cell and B cell epitope prediction to ensure protective response against a wide range of viral strains. For each virus, nucleoproteins were identified as most antigenic which generated a plethora of antigenic epitopes. The proposed epitopes were highly conserved (up to 100%) and showed high cumulative population coverage. Moreover, results revealed that among the top epitopes, T cell epitope GWPYIGSRS were conserved in Argentine mammarenavirus (Junin virus) and Brazilian mammarenavirus (Sabia virus), while B cell epitope NLLYKICLSG were conserved in Bolivian mammarenavirus (Machupo virus) and Brazilian mammarenavirus (Sabia virus), indicating the possibility of final vaccine constructs to confer broad range immunity in the host. A total 3 constructs were designed by the combination of top epitopes from each protein along with suitable adjuvant and linkers. Different physicochemical properties revealed the superiority of construct V1 in terms of safety and efficacy. Docking analysis of the refined vaccine structure with different MHC molecules and human immune receptors were also biologically significant. The vaccine receptor complex (V1-TLR3) showed minimal deformability at molecular level. Moreover, construct V1 was compatible for insertion into pET28a(+) vector and heterologous cloning in E. coli srain K12. However, the results were based on different sequence analysis and various immune databases. Further wet lab based studies using model animals are highly recommended for the experimental validation of the designed vaccine candidates.

bioinformatics↗

bioRxiv2019

Subtractive Genomic Analysis for Identification of Novel Drug Targets and Vaccine Candidates against Bartonella bacilliformis subsp. Ver097

Bartonella bacilliformis is the causative agent of Carrions disease, one of the truly neglected tropical diseases found in Peru, Colombia and Ecuador. Recent evidence predicts that Bartonella bacilliformis subsp. ver097 can emerge as an antibacterial resistant strain and hence identification of novel drug targets is a crying need. Subtractive genome analysis of B. bacilliformis subsp. ver097 was successfully done in order to address the challenges. Various computational tools and online based servers were used to screen out human homologous proteins of pathogen and proteins involved in common metabolic pathways of host and pathogen. Only 7 proteins involved in pathogen specific pathways were further analyzed to identify membrane proteins. Flagellar biosynthesis protein FlhA and ABC transporter permease were found to be novel as targets according to DrugBank database. To avoid side effects in human while administering drugs, human anti-targets analysis was performed to confirm non-homology of selected novel drug targets. Both predicted proteins also showed probability of antigenicity prediction through VaxiJen, however, Flagellar biosynthesis protein FlhA showed broad spectrum conservancy with Bartonella strains. Therefore, Flagellar biosynthesis protein FlhAcould facilitate the development of novel drugs and therapeutic compounds along with vaccines for efficient treatment of infections caused by Bartonella bacilliformis subsp. ver097.

bioinformatics↗

bioRxiv2019

Contriving a chimeric polyvalent vaccine to prevent infections caused by Herpes Simplex Virus (Type-1 and Type-2): an exploratory immunoinformatic approach

Herpes simplex virus type 1 (HSV-1) and 2 (HSV-2) cause a variety of infections including oral-facial infections, genital herpes, herpes keratitis, cutaneous infection and so on. To date, FDA-approved licensed HSV vaccine is not available yet. Hence, the study was conducted to identify and characterize an effective epitope based polyvalent vaccine against both types of Herpes Simplex Virus through targeting six viral proteins. The selected proteins were retrieved from viralzone and assessed to design highly antigenic epitopes by binding analyses of the peptides with MHC class-I and class-II molecules, antigenicity screening, transmembrane topology screening, allergenicity and toxicity assessment, population coverage analysis and molecular docking approach. The final vaccine was constructed by the combination of top CTL, HTL and BCL epitopes from each protein along with suitable adjuvant and linkers. Physicochemical and secondary structure analysis, disulfide engineering, molecular dynamic simulation and codon adaptation were further employed to develop a unique multi-epitope peptide vaccine. Docking analysis of the refined vaccine structure with different MHC molecules and human immune TLR-2 receptor demonstrated higher interaction. Complexed structure of the modeled vaccine and TLR-2 showed minimal deformability at molecular level. Moreover, translational potency and microbial expression of the modeled vaccine was analyzed with pET28a(+) vector for E. coli strain strain K12. The study enabled design of a novel chimeric polyvalent vaccine to confer broad range immunity against both HSV serotypes. However, further wet lab based research using model animals are highly recommended to experimentally validate our findings.

bioinformatics↗

bioRxiv2019

Phytochemical Constituency Profiling and Antimicrobial Activity Screening of Seaweeds Extracts Collected from the Bay of Bengal Sea Coasts

Seaweeds are able to produce a great variety of secondary metabolites that are characterized by a broad spectrum of biological activities. Two seaweeds species, namely Hypnea musciformis and Enteromorpha intestinalis were studied to evaluate the phytochemical constituency and antimicrobial activities. First of all, crude extracts of both sea weeds were prepared by two different extraction methods (soaking and water bath) using different solvents. Phytochemicals profiling results revealed the presence of bioactive compounds (flavonoids, alkaloids, tannin, saponin and phenols) in both seaweed extracts. Quantification results for ethanolic extracts of H. musciformis and E. intestinalis estimated 51 mg and 43 mg tannins in per gram of dried samples and flavonoids contents were found 67 mg and 57 mg/g mg QE/g respectively. Total phenolic contents were determined in terms of gallic acid equivalent (GAE). H. musciformis exhibited higher amount of phenolics (59 {+/-} 0.0002 mg GAE/g) than E. intestinalis extracts (41 {+/-} 0.0002 mg GAE/g). In antimicrobial activity test, ethanol extracts of H. musciformis and E. intestinalis were found 10 mm of inhibition diameter against all of the bacterial strains. Besides, methanol extracts of E. intestinalis were more susceptible to Staphylococcus aureus and Pseudomonas which was close to the inhibition diameter (>15 mm) of the mainstream antibiotic; Gentamicin. Moreover, Klebsiella sp. was found more susceptible to ethanol and methanol extracts of Hypnea musciformis as it showed inhibition zone greater than 15 mm. Both Seaweed extracts possessed higher amount of phytochemicals and showed promising antimicrobial activities when compared with the standards.

pharmacology and toxicology↗

bioRxiv2019

Metabolic pathway rerouting in Paraburkholderia rhizoxinica evolved long-overlooked derivatives of coenzyme F420

Coenzyme F420 is a specialized redox cofactor with a highly negative redox potential. It supports biochemical processes like methanogenesis, degradation of xenobiotics or the biosynthesis of antibiotics. Although well-studied in methanogenic archaea and actinobacteria, not much is known about F420 in Gram-negative bacteria. Genome sequencing revealed F420 biosynthetic genes in the Gram-negative, endofungal bacterium Paraburkholderia rhizoxinica, a symbiont of phytopathogenic fungi. Fluorescence microscopy, high-resolution LC-MS, and structure elucidation by NMR demonstrated that the encoded pathway is active and yields unexpected derivatives of F420 (3PG-F420). Further analyses of a biogas-producing microbial community showed that these derivatives are more widespread in nature. Genetic and biochemical studies of their biosynthesis established that a specificity switch in the guanylyltransferase CofC re-programmed the pathway to start from 3-phospho-D-glycerate, suggesting a rerouting event during the evolution of F420 biosynthesis. Furthermore, the cofactor activity of 3PG-F420 was validated, thus opening up perspectives for its use in biocatalysis. The 3PG-F420 biosynthetic gene cluster is fully functional in Escherichia coli, enabling convenient production of the cofactor by fermentation.

biochemistry↗

bioRxiv2019

The degree of polymerization and sulfation patterns in heparan sulfate are critical determinants of cytomegalovirus infectivity

Several enveloped viruses, including herpesviruses attach to host cells by initially interacting with cell surface heparan sulfate (HS) proteoglycans followed by specific coreceptor engagement which culminates in virus-host membrane fusion and virus entry. Interfering with HS-herpesvirus interactions has long been known to result in significant reduction in virus infectivity indicating that HS play important roles in initiating virus entry. In this study, we provide a series of evidence to prove that specific sulfations as well as the degree of polymerization (dp) of HS govern human cytomegalovirus (CMV) binding and infection. First, purified CMV extracellular virions preferentially bind to sulfated longer chain HS on a glycoarray compared to a variety of unsulfated glycosaminoglycans including unsulfated shorter chain HS. Second, the fraction of glycosaminoglycans (GAG) displaying higher dp and sulfation has a larger impact on CMV titers compared to other fractions. Third, cell lines deficient in specific glucosaminyl sulfotransferases produce significantly reduced CMV titers compared to wild-type cells and virus entry is compromised in these mutant cells. Finally, cells pretreated with a peptide that specifically binds sulfated-HS produce significantly reduced virus titers compared to the control peptide treated cells. Taken together, these results highlight the significance of HS chain length and sulfation patterns in CMV attachment and infectivity. IMPORTANCEHeparan sulfate (HS) is a linear polysaccharide found in all animal tissues. It binds to a variety of protein ligands, including cytokines, chemokines, growth factors and morphogens and regulates a wide range of biological activities, including developmental processes, angiogenesis, blood coagulation, and tumor metastasis. The molecular diversity in HS chains generates unique binding sites for specific ligands and can offer preferential binding for a specific virus over other viruses or cellular ligands. In the current study human cytomegalovirus (CMV) was found to bind preferentially to uniquely sulfated and polymerized HS. The HS mimics designed with these properties inhibited CMV infection. The results were corroborated by parallel studies in mutant mouse cells as well as using peptide inhibition. Combined together, the data suggests that CMV preferentially attaches to uniquely modified HS and thus this virus-host interaction is amenable to targeting by specifically designed HS mimics or peptides.

microbiology↗

bioRxiv2019

Reconstruction of 1,000 projection neurons reveals new cell types and organization of long-range connectivity in the mouse brain

Neuronal cell types are the nodes of neural circuits that determine the flow of information within the brain. Neuronal morphology, especially the shape of the axonal arbor, provides an essential descriptor of cell type and reveals how individual neurons route their output across the brain. Despite the importance of morphology, few projection neurons in the mouse brain have been reconstructed in their entirety. Here we present a robust and efficient platform for imaging and reconstructing complete neuronal morphologies, including axonal arbors that span substantial portions of the brain. We used this platform to reconstruct more than 1,000 projection neurons in the motor cortex, thalamus, subiculum, and hypothalamus. Together, the reconstructed neurons comprise more than 75 meters of axonal length and are available in a searchable online database. Axonal shapes revealed previously unknown subtypes of projection neurons and suggest organizational principles of long-range connectivity.

neuroscience↗

bioRxiv2019

Prevalence and risk factors of postpartum depression among women living in urban slums of Dhaka, Bangladesh

Postpartum depression (PPD) is a serious pubic health concern and known to have the adverse effects on mothers perinatal wellbeing; and childs physical and codnitive development. There were limited literatures on PPD in Bangladesh, especially in urban slum context. The aim of this study was to assess the burden and risk factors of PPD among the urban slum women. A cross-sectional study was conducted between November-December 2017 in three urban slums on 376 women within first 12 months of postpartum. A validated Bangla version of Edinburgh Postnatal Depression Scale was used to measure the depression status. Respondents socio-economic characteristics and other risk factors were collected with structured validated questionaire by trained interviewers. Unadjusted Prevalence Ratio (PR) and Adjusted Prevalence Ratio (APR) were estimated with Generalized Linear Model(GLM) and Generalized Estimating Equation (GEE) respectively to identify the risk factors of PPD. The prevalence of PPD was 39.4% within first 12 months following the child birth. Job involvement after child delivery (APR=1.9, 95% CI= 1.1, 3.3), job loss due to pregnancy (APR=1.5, 95% CI= 1.0, 2.1), perinatal and postnatal death (APR=1.4, 95% CI= 0.97, 2.0), unintended pregnancy (APR=1.8, 95% CI= 1.3, 2.5), management of delivery cost by borrowing, selling or mortgaging assets (APR=1.3, 95% CI= 0.94, 1.9), depressive symptom during pregnancy (APR=2.5, 95% CI= 1.7, 3.8) and intimate partner violence (APR=2.0, 95% CI= 1.2, 3.3), were identified as risk factors. PPD was not associated with poverty, mother in law and any child related factors. The burden of postpartum depression is high in the urban slum of Bangladesh. Maternal mental health services should be integrated with existing maternal health services. Research is required for the innovation of effective, low cost and culturally appropriate PPD case management and preventive intervention in urban slum of Bangladesh.

epidemiology↗

bioRxiv2018

Vaccinomics strategy for developing a unique multi-epitope monovalent vaccine against Marburg marburgvirus

Marburg virus causes severe hemorrhagic fever in both humans and non-human primates with high degree of infectivity and lethality. To date no approved treatment is available for Marburg virus infection. A study was employed to design a novel chimeric vaccine against Marburg virus by adopting reverse vaccinology approach. Envelope glycoprotein and matrix protein VP40 were identified as most antigenic viral proteins which generated a plethora of antigenic epitopes. Results showed that vaccine construct V1 was superior in terms of various physicochemical properties and structural stability. Molecular docking analysis of the refined vaccine with different MHCs and human immune TLR8 receptor demonstrated higher binding affinity. Moreover, complexed structure of the modeled vaccine and TLR8 indicated minimal deformability at molecular level. Translational potency and microbial expression of the modeled vaccine within E. coli strain K12 by pET28a(+) vector were also biologically significant. However, further in vitro and in vivo investigation could be implemented for the acceptance and validation of the designed vaccine against Marburg virus.

bioinformatics↗

bioRxiv2018

Reverse vaccinology approach to design a novel multi-epitope subunit vaccine against avian influenza A (H7N9) virus

H7N9, a novel strain of avian origin influenza was the first recorded incidence where a human was transited by a N9 type influenza virus. Effective vaccination against influenza A (H7N9) is a major concern, since it has emerged as a life threatening viral pathogen. Here, an in silico reverse vaccinology strategy was adopted to design a unique chimeric subunit vaccine against avian influenza A (H7N9). Induction of humoral and cell-mediated immunity is the prime concerned characteristics for a peptide vaccine candidate, hence both T cell and B cell immunity of viral proteins were screened. Antigenicity testing, transmembrane topology screening, allergenicity and toxicity assessment, population coverage analysis and molecular docking approach were adopted to generate the most antigenic epitopes of avian influenza A (H7N9) proteome. Further, a novel subunit vaccine was designed by the combination of highly immunogenic epitopes along with suitable adjuvant and linkers. Physicochemical properties and secondary structure of the designed vaccine were assessed to ensure its thermostability, hydrophilicity, theoretical PI and structural behavior. Homology modeling, refinement and validation of the designed vaccine allowed to construct a three dimensional structure of the predicted vaccine, further employed to molecular docking analysis with different MHC molecules and human immune TLR8 receptor present on lymphocyte cells. Moreover, disulfide engineering was employed to lessen the high mobility region of the designed vaccine in order to extend its stability. Furthermore, we investigated the molecular dynamic simulation of the modeled subunit vaccine and TLR8 complexed molecule to strengthen our prediction. Finally, the suggested vaccine was reverse transcribed and adapted for E. coli strain K12 prior to insertion within pET28a(+) vector for checking translational potency and microbial expression.

bioinformatics↗

bioRxiv2018

Phylogeny and distinct properties of major intrinsic proteins in the genomes of six Phytophthora species suggest their novel functions in Phytophthora

ABSTRACTMajor intrinsic proteins (MIPs), commonly known as aquaporins, facilitate the membrane diffusion of water and some other non- polar solutes. MIPs might be involved in host-pathogen interactions. Herein, we identified 17, 24, 27, 19, 19, and 22 full-length MIPs, respectively, in the genomes of six Phytophthora species, P. infestans, P. parasitica, P. sojae, P. ramorum, P. capsici, and P. cinnamomi. These Phytophthora species are devastating plant pathogens and members of oomycetes, a distinct lineage of fungus-like eukaryotic microbes. Phylogenetic analysis showed that the Phytophthora MIPs (PMIPs) formed a completely distinct clade from their counterparts in other taxa and were clustered into nine subgroups. Sequence and structural properties indicated that the primary selectivity-related constrictions, including aromatic arginine (ar/R) selectivity filter and Froger’s positions in PMIPs were distinct from those in other taxa. The substitutions in the conserved Asn-Pro-Ala motifs in loops B and E of many PMIPs were also divergent from those in plants. We further deciphered group-specific consensus sequences/motifs in different loops and transmembrane helices of PMIPs, which were distinct from those in plants, animals, and microbes. The data collectively supported the notion that PMIPs might have novel functions.Competing Interest StatementThe authors have declared no competing interest.View Full Text

bioinformatics↗

bioRxiv2017

Unique ATP-cone-driven allosteric regulation of ribonucleotide reductase via the radical-generating subunit

Ribonucleotide reductases (RNRs) are key enzymes in DNA synthesis and repair, with sophisticated allosteric mechanisms controlling both substrate specificity and overall activity. In RNRs, the activity master-switch, the ATP-cone, has been found exclusively in the catalytic subunit. In two class I RNR subclasses whose catalytic subunit lacks the ATP-cone, we discovered ATP-cones in the radical-generating subunit. The ATP-cone in the Leewenhoekiella blandensis radical-generating subunit regulates activity via modifications of quaternary structure induced by binding of nucleotides. ATP induces enzymatically competent dimers, whereas dATP induces non-productive tetramers, resulting in different holoenzyme complexes. The tetramer forms solely by interactions between ATP-cones, as evidenced by a 2.45 [A] crystal structure. We also present evidence for an MnIIIMnIV metal center. In summary, lack of an ATP-cone domain in the catalytic subunit was compensated by evolutionary capture of the domain by the radical-generating subunit. Our findings present a novel opportunity for dATP-regulation of engineered proteins.

biochemistry↗