Publications by authors named "Mrutyunjay Suar"

115 Publications

Molecular Characterization and Designing of a Novel Multiepitope Vaccine Construct Against .

Int J Pept Res Ther 2022 17;28(2):49. Epub 2022 Jan 17.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, 751024 India.

Abstract: , an ESKAPE pathogen causes many fatal clinical diseases in humans across the globe. Despite an increase in clinical instances of Pseudomonas infection, there is currently no effective vaccine or treatment available. The major membrane protein candidate of the bacterial cell is known to be a critical component for cellular bacterial susceptibility to antimicrobial peptides and survival inside the host organisms. Therefore, the current computational study aims to examine major membrane protein, OprF, and OprI, in order to design linear B-cell, cytotoxic T-cell, and helper T-cell peptide-based vaccine constructs. Utilizing various immune-informatics tools and databases, a total of two B-cells and twelve T-cells peptides were predicted. The final vaccine design was simulated to generate a high-quality three-dimensional structure, which included epitopes, adjuvant, and linkers. The vaccine was shown to be nonallergenic, antigenic, soluble, and had the best biophysical properties. The vaccine and Toll-like receptor 4 have a strong and stable interaction, according to protein-protein docking and molecular dynamics simulations. Additionally, in silico cloning was employed to see how the developed vaccine expressed in the pET28a (+) vector. Ultimately, an immune simulation was performed to see the vaccine efficacy. In conclusion, the newly developed vaccine appears to be a promising option for a vaccine against infection.

Graphical Abstract:

Supplementary Information: The online version contains supplementary material available at 10.1007/s10989-021-10356-z.
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http://dx.doi.org/10.1007/s10989-021-10356-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8762192PMC
January 2022

Aurora Borealis in dentistry: The applications of cold plasma in biomedicine.

Mater Today Bio 2022 Jan 30;13:100200. Epub 2021 Dec 30.

School of Biotechnology, KIIT University, Bhubaneswar, 751024, India.

Plasma is regularly alluded to as the fourth form of matter. Its bounty presence in nature along with its potential antibacterial properties has made it a widely utilized disinfectant in clinical sciences. Thermal plasma and non-thermal (or cold atmospheric) plasma (NTP) are two types of plasma. Atoms and heavy particles are both available at the same temperature in thermal plasma. Cold atmospheric plasma (CAP) is intended to be non-thermal since its electrons are hotter than the heavier particles at ambient temperature. Direct barrier discharge (DBD), atmospheric plasma pressure jet (APPJ), etc. methods can be used to produce plasma, however, all follow a basic concept in their generation. This review focuses on the anticipated uses of cold atmospheric plasma in dentistry, such as its effectiveness in sterilizing dental instruments by eradicating bacteria, its advantage in dental cavity decontamination over conventional methods, root canal disinfection, its effects on tooth whitening, the benefits of plasma treatment on the success of dental implant placement, and so forth. Moreover, the limitations and probable solutions has also been anticipated. These conceivable outcomes thus have proclaimed the improvement of more up-to-date gadgets, for example, the plasma needle and plasma pen, which are efficient in treating the small areas like root canal bleaching, biofilm disruption, requiring treatment in dentistry.
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http://dx.doi.org/10.1016/j.mtbio.2021.100200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8743205PMC
January 2022

Structural investigation on SPI-6-associated Salmonella typhimurium VirG-like stress protein that promotes pathogen survival in macrophages.

Protein Sci 2022 04 15;31(4):835-849. Epub 2022 Feb 15.

Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India.

Enteric microbial pathogenesis, remarkably a complex process, is achieved by virulence factors encoded by genes located within regions of the bacterial genome termed pathogenicity islands. Salmonella pathogenicity islands (SPI) encodes proteins, that are essential virulence determinants for pathogen colonization and virulence. In addition to the well-characterized SPI-1 and SPI-2 proteins, which are required for bacterial invasion and intracellular replication, respectively, SPI-6 (formerly known as Salmonella enterica centisome 7 island [SCI]) encoding proteins are also known to play pivotal role in Salmonella pathogenesis. However, the underlying molecular mechanism of these proteins remained elusive. To gain molecular insights into SPI-6-associated proteins, in this study, a SPI-6 Salmonella typhimurium VirG-like protein (STV) is characterized using interdisciplinary experimental approaches including X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy and infection assays. The high-resolution crystal structure, determined by the single-wavelength anomalous dispersion (SAD) method, reveals that STV belongs to the LTxxQ motif family. Solution-state NMR spectroscopy studies reveal that STV form a dimer involving interconnected helices. Interestingly, functional studies show that STV influence pathogen persistence inside macrophages in vitro at later stages of infection. Altogether, our findings suggest that STV, a member of the LTxxQ stress protein family, modulates bacterial survival mechanism in macrophages through SPI-1 and SPI-2 genes, respectively.
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http://dx.doi.org/10.1002/pro.4272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8927873PMC
April 2022

Exploring capsule polysaccharide proteins to design multiepitope subunit vaccine to fight against pneumonia.

Expert Rev Vaccines 2022 Apr 4;21(4):569-587. Epub 2022 Jan 4.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, India.

Background: is an emerging human pathogen causing neonatal lung disease, catheter-associated infections, and nosocomial outbreaks with high fatality rates. Capsular polysaccharide (CPS) protein plays a major determinant in virulence and is considered as a promising target for vaccine development.

Research Design And Methods: In this study, we used immunoinformatic approaches to design a multi-peptide vaccine against K. pneumonia. The epitopes were selected through several immune filters, such as antigenicity, conservancy, nontoxicity, non-allergenicity, binding affinity to HLA alleles, overlapping epitopes, and peptides having common epitopes.

Results: Finally, a construct comprising 2 B-Cell, 8 CTL, 2 HTL epitopes, along with adjuvant, linkers was designed. Peptide-HLA interaction analysis showed strong binding of these epitopes with several common HLA molecules. The in silico immune simulation and population coverage analysis of the vaccine showed its potential to evoke strong immune responses.. Further, the interaction between vaccine and immune was evaluated by docking and simulation, revealing high affinity and complex stability. Codon adaptation and in silico cloning revealed higher expression of vaccine in E. coli K12 expression system.

Conclusions: Conclusively, the findings of the present study suggest that the designed novel multi-epitopic vaccine holds potential for further experimental validation against the pathogen.
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http://dx.doi.org/10.1080/14760584.2022.2021882DOI Listing
April 2022

Genome-based identification and comparative analysis of enzymes for carotenoid biosynthesis in microalgae.

World J Microbiol Biotechnol 2021 Nov 27;38(1). Epub 2021 Nov 27.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, 751024, India.

Microalgae are potential feedstocks for the commercial production of carotenoids, however, the metabolic pathways for carotenoid biosynthesis across algal lineage are largely unexplored. This work is the first to provide a comprehensive survey of genes and enzymes associated with the less studied methylerythritol 4-phosphate/1-deoxy-D-xylulose 5-phosphate pathway as well as the carotenoid biosynthetic pathway in microalgae through bioinformatics and comparative genomics approach. Candidate genes/enzymes were subsequently analyzed across 22 microalgae species of lineages Chlorophyta, Rhodophyta, Heterokonta, Haptophyta, Cryptophyta, and known Arabidopsis homologs in order to study the evolutional divergence in terms of sequence-structure properties. A total of 403 enzymes playing a vital role in carotene, lutein, zeaxanthin, violaxanthin, canthaxanthin, and astaxanthin were unraveled. Of these, 85 were hypothetical proteins whose biological roles are not yet experimentally characterized. Putative functions to these hypothetical proteins were successfully assigned through a comprehensive investigation of the protein family, motifs, intrinsic physicochemical features, subcellular localization, pathway analysis, etc. Furthermore, these enzymes were categorized into major classes as per the conserved domain and gene ontology. Functional signature sequences were also identified which were observed conserved across microalgal genomes. Additionally, the structural modeling and active site architecture of three vital enzymes, DXR, PSY, and ZDS catalyzing the vital rate-limiting steps in Dunaliella salina were achieved. The enzymes were confirmed to be stereochemically reliable and stable as revealed during molecular dynamics simulation of 100 ns. The detailed functional information about individual vital enzymes will certainly help to design genetically modified algal strains with enhanced carotenoid contents.
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http://dx.doi.org/10.1007/s11274-021-03188-yDOI Listing
November 2021

Glucose Starvation, Magnesium Ion Starvation, and Bile Stress Assays.

Bio Protoc 2021 Sep 20;11(18):e4157. Epub 2021 Sep 20.

School of Biotechnology, Kalinga Institute of Industrial Technology-(KIIT) University, Bhubaneswar, India.

serovar Enteritidis ( Enteritidis) is a leading causative pathogen for food-borne gastroenteritis. During its course of infection, it confronts myriads of physiological barriers inside the host, such as nutrient deprivation, low micronutrient availability, and toxicity from bile salts, to promote bacterial survival and infection inside the host. The ability of the pathogen to overcome these stressful conditions determines the degree of virulence in the host. Therefore, assessment of the survival of a pathogen during different stress conditions, like glucose starvation, magnesium starvation, and bile stress, are important parameters to assess the virulence of the pathogen. Here, we describe protocols for estimating the survival of the pathogen during the above-mentioned stress conditions. We culture Enteritidis in an appropriate growth medium to a required O.D. and treat it with glucose starvation (M9 minimal culture medium containing 0.03% glucose), magnesium starvation (M9 minimal culture medium containing 20 µM MgSO), and bile stress (bacterial cells treated with 15% bile salts in Luria Bertani (LB) culture medium) conditions. The number of surviving bacteria is obtained after the treatment by calculating the colony-forming units (CFU) of the surviving pathogen obtained on LB agar plates at relevant time intervals. The experiments are performed in biological replicates, and statistical analysis is performed to validate the experimental findings. The methodology of these stress response assays is simple and can be adapted to study the pathogenesis and stress response in other relevant and culturable enteric pathogens.
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http://dx.doi.org/10.21769/BioProtoc.4157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8481020PMC
September 2021

Prevalence and multidrug resistance in Salmonella enterica Typhimurium: an overview in South East Asia.

World J Microbiol Biotechnol 2021 Sep 28;37(11):185. Epub 2021 Sep 28.

School of Biotechnology, KIIT University, Bhubaneswar, India.

Acute/chronic gastroenteritis is caused by a few serovars of Salmonella enterica. Among different serovars, S. enterica Typhimurium is a potent pathogen that contributes significantly to self-limiting diarrhea related mortality worldwide. With no successful vaccine in hand against this pathogen, antibiotics are used as for gold standard for treatment against Salmonella induced gastroenteritis. Indispensably, rise in multi drug resistance against Salmonella Typhimurium poses challenge to treatment options. South East Asia, with 11 different countries, stands 3rd as super region for global burden of Salmonella induced gastroenteritis. In this review, we made an attempt to discuss on prevalence and multidrug resistance in Salmonella Typhimurium in 11 countries of South East Asia-the issue that has not been seriously addressed so far. By thorough analysis of reported data, we found varying frequencies for prevalence of Salmonella Typhimurium as well as subtle evidences on resistance of this pathogen to multiple antibiotics in different countries. Vietnam ranked top in terms of reports for prevalence and antimicrobial resistance. However, in countries such as Brunei and Timor Leste, no study has been performed so far to track the frequency of incidence and drug resistance of this pathogen. Our review, the first of its kind, emphasizes that, although the pathogen was not found as dominant serovar in South East Asia in last 20 years unlike sub-Saharan Africa, it may be still considered as a major threat in this region due to available evidences for infection in humans as well as contamination in several animal and food sources. More importantly, the importance as a public threat in this subregion of Asia is also due to resistance of this pathogen to multiple antibiotics. South East Asian countries showing incidence and multi drug resistance of Salmonella enterica Typhimurium in human and non-human sources (1969-2020). -Drug resistant S. enterica Typhimurium.
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http://dx.doi.org/10.1007/s11274-021-03146-8DOI Listing
September 2021

Development of a Conserved Chimeric Vaccine for Induction of Strong Immune Response against Using Immunoinformatics Approaches.

Vaccines (Basel) 2021 Sep 18;9(9). Epub 2021 Sep 18.

Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 63243, Korea.

is one of the most notorious Gram-positive bacteria with a very high mortality rate. The WHO has listed as one of the ESKAPE pathogens requiring urgent research and development efforts to fight against it. Yet there is a major layback in the advancement of effective vaccines against this multidrug-resistant pathogen. SdrD and SdrE proteins are attractive immunogen candidates as they are conserved among all the strains and contribute specifically to bacterial adherence to the host cells. Furthermore, these proteins are predicted to be highly antigenic and essential for pathogen survival. Therefore, in this study, using the immunoinformatics approach, a novel vaccine candidate was constructed using highly immunogenic conserved T-cell and B-cell epitopes along with specific linkers, adjuvants, and consequently modeled for docking with human Toll-like receptor 2. Additionally, physicochemical properties, secondary structure, disulphide engineering, and population coverage analysis were also analyzed for the vaccine. The constructed vaccine showed good results of worldwide population coverage and a promising immune response. For evaluation of the stability of the vaccine-TLR-2 docked complex, a molecular dynamics simulation was performed. The constructed vaccine was subjected to in silico immune simulations by C-ImmSim and Immune simulation significantly provided high levels of immunoglobulins, T-helper cells, T-cytotoxic cells, and INF-γ. Lastly, upon cloning, the vaccine protein was reverse transcribed into a DNA sequence and cloned into a pET28a (+) vector to ensure translational potency and microbial expression. The overall results of the study showed that the designed novel chimeric vaccine can simultaneously elicit humoral and cell-mediated immune responses and is a reliable construct for subsequent in vivo and in vitro studies against the pathogen.
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http://dx.doi.org/10.3390/vaccines9091038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8470666PMC
September 2021

Immunoinformatics and molecular docking studies reveal a novel Multi-Epitope peptide vaccine against pneumonia infection.

Vaccine 2021 10 21;39(42):6221-6237. Epub 2021 Sep 21.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar 751024, India; KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar 751024, India. Electronic address:

Pneumonia is a major endemic disease around the world, and an effective vaccine is the need of the hour to fight against the disease. When there are no appropriate antiviral and associated therapies available, vaccine development becomes even more essential. Therefore, in the present study, a variety of immunoinformatics techniques was utilized to develop a novel multi-epitope vaccine that targets the highly immunodominant type 3 fimbrial protein of Klebsiella pneumoniae, the causal organism for pneumonia. The putative B and T cell epitopes were predicted from the protein and screened for antigenicity, toxicity, allergenicity, and cross-reactivity with human proteomes. Subsequently, the selected epitopes were joined with the help of linkers to form a robust vaccine construct. In addition, an adjuvant was applied to the N-terminal of the construct to improve the immunogenicity of the vaccine. The physicochemical properties, solubility, the secondary and tertiary structure of the final vaccine were also established. MD simulations for 100 ns were employed to assess the stability of the vaccine-TLR-2 docked complex. The final vaccine was optimized and cloned in pET28a (+) vector with His-tag to achieve maximum vaccine protein expression for ease of purification. Immune simulation results indicated the potency of this vaccine candidate as a probable therapeutic agent. In conclusion, the overall results of various immunoinformatics tools and methods employed revealed that the constructed multi-epitope vaccine exhibits a high potential for stimulating both B and T-cells immune responses against pneumonia infection. However, experimental immunological studies are required to corroborate the viability of the novel multi-epitope construct as a commercial vaccine.
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http://dx.doi.org/10.1016/j.vaccine.2021.09.025DOI Listing
October 2021

Nanoparticle-biological interactions: the renaissance of bionomics in the myriad nanomedical technologies.

Nanomedicine (Lond) 2021 10 21;16(25):2249-2254. Epub 2021 Sep 21.

School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, 751024, India.

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http://dx.doi.org/10.2217/nnm-2021-0174DOI Listing
October 2021

B and T cell epitope-based peptides predicted from clumping factor protein of Staphylococcus aureus as vaccine targets.

Microb Pathog 2021 Nov 2;160:105171. Epub 2021 Sep 2.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, 751024, India; KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, 751024, India. Electronic address:

Staphylococcus aureus infection is emerging as a global threat because of the highly debilitating nature of the associated disease's unprecedented magnitude of its spread and growing global resistance to antimicrobial medicines. Recently WHO has categorized these bacteria under the high global priority pathogen list and is one of the six nosocomial pathogens termed as ESKAPE pathogens which have emerged as a serious threat to public health worldwide. The development of a specific vaccine can stimulate an optimal antibody response, thus providing immunity against it. Therefore, in the present study efforts have been made to identify potential vaccine candidates from the Clumping factor surface proteins (ClfA and ClfB) of S. aureus. Employing the immunoinformatics approach, fourteen antigenic peptides including T-cell, B-cell epitopes were identified which were non-toxic, non-allergenic, high antigenicity, strong binding efficiency with commonly occurring MHC alleles. Consequently, a multi-epitope vaccine chimera was designed by connecting these epitopes with suitable linkers an adjuvant to enhance immunogenicity. Further, homology modeling and molecular docking were performed to construct the three-dimensional structure of the vaccine and study the interaction between the modeled structure and immune receptor (TLR-2) present on lymphocyte cells. Consequently, molecular dynamics simulation for 100 ns period confirmed the stability of the interaction and reliability of the structure for further analysis. Finally, codon optimization and in silico cloning were employed to ensure the successful expression of the vaccine candidate. As the targeted protein is highly antigenic and conserved, hence the designed novel vaccine construct holds potential against emerging multi-drug-resistant organisms.
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http://dx.doi.org/10.1016/j.micpath.2021.105171DOI Listing
November 2021

Immunoinformatic approach employing modeling and simulation to design a novel vaccine construct targeting MDR efflux pumps to confer wide protection against typhoidal serovars.

J Biomol Struct Dyn 2021 Aug 31:1-13. Epub 2021 Aug 31.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India.

Overcoming multi drug resistance is one of the crucial challenges to control enteric typhoid fever caused by and Overexpression of efflux pumps predominantly causes drug resistance in microorganisms. Therefore, immunotherapy targeting the various efflux pumps antigens could be a promising strategy to increase the success of vaccines. An immunoinformatic approach was employed to design a Salmonellosis multi-epitope subunit vaccine peptide consisting of linear B-cell and T-cell epitopes of multidrug resistance protein families including ATP Binding Cassette (ABC), major facilitator superfamily (MFS), resistance nodulation cell division (RND), small multidrug resistance (SMR), and multidrug and toxin extrusion (MATE). The selected epitopes exhibited conservation in both and and thus could be helpful for cross-protection. Further, the final vaccine construct encompassing the peptides, adjuvants and specific linker sequences showed high immunogenicity, solubility, non-allergenic, nontoxic, and wide population coverage due to strong binding affinity to maximum HLA alleles. The three-dimensional structure was predicted, and validated using various structure validation tools. Additionally, protein-protein docking of the chimeric vaccine construct with the TLR-2 protein and molecular dynamics demonstrated stable and efficient binding. Conclusively, the immunoinformatic study showed that the novel multi epitopic vaccine construct can simulate the both T-cell and B-cell immune responses in typhoidal Salmonella serovars and could potentially be used for prophylactic or therapeutic applications.Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2021.1964600DOI Listing
August 2021

Next-Generation Bioinformatics Approaches and Resources for Coronavirus Vaccine Discovery and Development-A Perspective Review.

Vaccines (Basel) 2021 Jul 22;9(8). Epub 2021 Jul 22.

Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 63243, Korea.

COVID-19 is a contagious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To fight this pandemic, which has caused a massive death toll around the globe, researchers are putting efforts into developing an effective vaccine against the pathogen. As genome sequencing projects for several coronavirus strains have been completed, a detailed investigation of the functions of the proteins and their 3D structures has gained increasing attention. These high throughput data are a valuable resource for accelerating the emerging field of immuno-informatics, which is primarily aimed toward the identification of potential antigenic epitopes in viral proteins that can be targeted for the development of a vaccine construct eliciting a high immune response. Bioinformatics platforms and various computational tools and databases are also essential for the identification of promising vaccine targets making the best use of genomic resources, for further experimental validation. The present review focuses on the various stages of the vaccine development process and the vaccines available for COVID-19. Additionally, recent advances in genomic platforms and publicly available bioinformatics resources in coronavirus vaccine discovery together with related immunoinformatics databases and advances in technology are discussed.
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http://dx.doi.org/10.3390/vaccines9080812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8402397PMC
July 2021

Comprehensive sequence and structure analysis of algal lipid catabolic enzyme Triacylglycerol lipase: an study to vitalize the development of optimum engineered strains with high lipid productivity.

J Biomol Struct Dyn 2021 Aug 20:1-19. Epub 2021 Aug 20.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India.

Microalgae as an alternative renewable resource for biofuel production have captured much significance. Nonetheless, its economic viability is a field of major concern for researchers. Unraveling the lipid catabolic pathway and gaining insights into the sequence-structural features of its primary functioning enzyme, Triacylglycerol lipase, will impart valuable information to target microalgae for augmented lipid content. In the present study, a genome-wide comparative study on putative Triacylglycerol lipase (TAGL) enzyme from algal species belonging to varied phylogenetic lineages was performed. The comprehensive sequence analysis revealed that TAGL comprises of three distinct conserved domains, such as, Patatin, Class III Lipase, and Abhydro_lipase, and also confirmed the ubiquitous presence of GXSXG motif in the sequences analyzed. In the absence of a crystal structure of algal TAGL till date, we developed the first 3D model of patatin domain of TAGL from an oleaginous microalga, , employing homology modeling, docking and molecular dynamic simulations methods. The domain-substrate complex having the low-ranking docking score revealed the binding of palmitic acid to the TAGL patatin domain surface with strong hydrogen bond interactions. The simulation results implied that the substrate-complexed patatin domain and the free enzyme adopted a more stable conformation after 40 ns. This is the first ever attempt to provide insights into the structural and dynamical insights on catalytic mechanism of the TAGL patatin domain. Subsequently, these findings aided our understanding on their structural stability, folding mechanism and protein-substrate interactions, which could be further utilized to design site-specific mutagenic experiments for engineering microalgal strains.Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2021.1967194DOI Listing
August 2021

Switch to Autophagy the Key Mechanism for Trabecular Meshwork Death in Severe Glaucoma.

Clin Ophthalmol 2021 14;15:3027-3039. Epub 2021 Jul 14.

KIIT School of Biotechnology, Bhubaneswar, Odisha, India.

Purpose: The key differences in cell death mechanisms in the trabecular meshwork (TM) in adult moderate and severe primary glaucoma remain still unanswered. This study explored key differences in cell death mechanisms in the trabecular meshwork (TM) in adult moderate and severe primary glaucoma.

Design: In-vitro laboratory study on surgical specimens and primary cell lines.

Methods: Select cell death-related proteins differentially expressed on mass spectrometric analysis in ex-vivo dissected TM specimens patients with severe adult primary open-angle (POAG) or angle-closure glaucoma (PACG) compared to controls (cadaver donor cornea) were validated for temporal changes in cell death-related gene expression on in-vitro primary human TM cell culture after 48 hours (moderate) or 72 hours (severe) oxidative stress with HO (400-1000 uM concentration). These were compared with histone modifications after oxidative stress in human TM (HTM) culture and peripheral blood of patients with moderate and severe glaucoma.

Results: Autophagy-related proteins seemed to be the predominant cell-death mechanism over apoptosis in ex-vivo dissected TM specimens in severe glaucoma. Analyzing HTM cell gene expression at 48 hours and 72 hours of oxidative stress, autophagy genes were up-regulated at 48-72 hours of exposure in contrast to apoptosis-related genes, showing down-regulation at 72 hours. There was associated increased expression of H3K14ac in HTM after 72 hours of oxidative stress and in peripheral blood of severe POAG and PACG.

Conclusion: A preference of autophagy over apoptosis may underlie stage transition from moderate to severe glaucoma in the trabecular meshwork or peripheral blood, which may be tightly regulated by epigenetic modulators.
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http://dx.doi.org/10.2147/OPTH.S292218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8286731PMC
July 2021

The interrelation of COVID-19 and neurological modalities.

Neurol Sci 2021 06 12;42(6):2157-2160. Epub 2021 Mar 12.

Infection Bio-engineering Group, Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453552, India.

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http://dx.doi.org/10.1007/s10072-021-05177-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7953374PMC
June 2021

The Hha-TomB toxin-antitoxin module in Salmonella enterica serovar Typhimurium limits its intracellular survival profile and regulates host immune response.

Cell Biol Toxicol 2022 02 2;38(1):111-127. Epub 2021 Mar 2.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India.

The key to bacterial virulence relies on an exquisite balance of signals between microbe and hosts. Bacterial toxin-antitoxin (TA) system is known to play a vital role in response to stress adaptation, drug resistance, biofilm formation, intracellular survival, persistence as well as pathogenesis. In the present study, we investigated the role of Hha-TomB TA system in regulating virulence of Salmonella enterica serovar Typhimurium (S. Typhimurium) in a host model system, where we showed that deletion of hha and tomB genes displayed impaired cell adhesion, invasion, and uptake. The isogenic hha and tomB mutant strain was also found to be deficient in intracellular replication in vitro, with a highly repressed Salmonella Pathogenicity Island-2 (SPI-2) genes and downregulation of Salmonella Pathogenicity Island-1 (SPI-1) genes. In addition, the Δhha and ΔtomB did not show acute colitis in C57BL/6 mice and displayed less dissemination to systemic organs followed by their cecal pathology. The TA mutants also showed reduction in serum cytokine and nitric oxide levels both in vitro and in vivo. However, the inflammation phenotype was restored on complementing strain of TA gene to its mutant strain. In silico studies depicted firm interaction of Hha-TomB complex and the regulatory proteins, namely, SsrA, SsrB, PhoP, and PhoQ. Overall, we demonstrate that this study of Hha-TomB TA system is one of the prime regulating networks essential for S. Typhimurium pathogenesis. 1. Role of Hha-TomB toxin-antitoxin (TA) system in Salmonella pathogenesis was examined. 2. The TA mutants resulted in impaired invasion and intracellular replication in vitro. 3. The TA mutants displayed alteration in SPI-1 and SPI-2 regulatory genes inside host cells. 4. Mutation in TA genes also limited systemic colonization and inflammatory response in vivo.
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http://dx.doi.org/10.1007/s10565-021-09587-zDOI Listing
February 2022

Intrinsic atomic interaction at molecular proximal vicinity infer cellular biocompatibility of antibacterial nanopepper.

Nanomedicine (Lond) 2021 02 27;16(4):307-322. Epub 2021 Jan 27.

School of Biotechnology, KIIT University, Bhubaneswar 751024, India.

Fabrication of nanopepper (NP) for antibacterial application and elucidation of its molecular and cellular biocompatibility. Synthesis of NP was achieved using a high-energy ball milling method. Following characterization, its antibacterial activity and cellular and molecular biocompatibility were evaluated by experimental and computational approaches. A total of 15 h of milling pepper produced NP with a size of 44 ± 12 nm and zeta potential of -22 ± 12 mV. Bulk pepper and NP showed antibacterial activity and an LC of 1.9 μM and 2.1 μM in HCT116 colon cells. Components of pepper, piperine and β-caryophyllene were found to interact with superoxide dismutase [Cu-Zn] and apoptotic protease-activating factor-1-caspase-9 through different amino acids via H-bonds. NP exhibits significant antibacterial activity with cellular biocompatibility due to intrinsic atomic interaction. Fabrication of nanopepper (NP) for antibacterial application and elucidation of its molecular and cellular biocompatibility. Synthesis of NP was achieved using a high-energy ball milling method. Following characterization, its antibacterial activity and cellular and molecular biocompatibility were evaluated by experimental and computational approaches. A total of 15 h of milling pepper produced NP with a size of 44 ± 12 nm and zeta potential of -22 ± 12 mV. Bulk pepper and NP showed antibacterial activity and an LC of 1.9 μM and 2.1 μM in HCT116 colon cells. Components of pepper, piperine and β-caryophyllene were found to interact with superoxide dismutase [Cu-Zn] and apoptotic protease-activating factor-1-caspase-9 through different amino acids via H-bonds. NP exhibits significant antibacterial activity with cellular biocompatibility due to intrinsic atomic interaction.
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http://dx.doi.org/10.2217/nnm-2020-0395DOI Listing
February 2021

Next-generation computational tools and resources for coronavirus research: From detection to vaccine discovery.

Comput Biol Med 2021 01 1;128:104158. Epub 2020 Dec 1.

KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India; School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Bhubaneswar, 751024, India. Electronic address:

The COVID-19 pandemic has affected 215 countries and territories around the world with 60,187,347 coronavirus cases and 17,125,719 currently infected patients confirmed as of the November 25, 2020. Currently, many countries are working on developing new vaccines and therapeutic drugs for this novel virus strain, and a few of them are in different phases of clinical trials. The advancement in high-throughput sequence technologies, along with the application of bioinformatics, offers invaluable knowledge on genomic characterization and molecular pathogenesis of coronaviruses. Recent multi-disciplinary studies using bioinformatics methods like sequence-similarity, phylogenomic, and computational structural biology have provided an in-depth understanding of the molecular and biochemical basis of infection, atomic-level recognition of the viral-host receptor interaction, functional annotation of important viral proteins, and evolutionary divergence across different strains. Additionally, various modern immunoinformatic approaches are also being used to target the most promiscuous antigenic epitopes from the SARS-CoV-2 proteome for accelerating the vaccine development process. In this review, we summarize various important computational tools and databases available for systematic sequence-structural study on coronaviruses. The features of these public resources have been comprehensively discussed, which may help experimental biologists with predictive insights useful for ongoing research efforts to find therapeutics against the infectious COVID-19 disease.
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http://dx.doi.org/10.1016/j.compbiomed.2020.104158DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7705366PMC
January 2021

DBCOVP: A database of coronavirus virulent glycoproteins.

Comput Biol Med 2021 02 21;129:104131. Epub 2020 Nov 21.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, Odisha, India; KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, Odisha, India. Electronic address:

Since the emergence of SARS-CoV-1 (2002), novel coronaviruses have emerged periodically like the MERS- CoV (2012) and now, the SARS-CoV-2 outbreak which has posed a global threat to public health. Although, this is the third zoonotic coronavirus breakout within the last two decades, there are only a few platforms that provide information about coronavirus genomes. None of them is specific for the virulence glycoproteins and complete sequence-structural features of these virulence factors across the betacoronavirus family including SARS-CoV-2 strains are lacking. Against this backdrop, we present DBCOVP (http://covp.immt.res.in/), the first manually-curated, web-based resource to provide extensive information on the complete repertoire of structural virulent glycoproteins from coronavirus genomes belonging to betacoronavirus genera. The database provides various sequence-structural properties in which users can browse and analyze information in different ways. Furthermore, many conserved T-cell and B-cell epitopes predicted for each protein are present that may perform a significant role in eliciting the humoral and cellular immune response. The tertiary structure of the epitopes together with the docked epitope-HLA binding-complex is made available to facilitate further analysis. DBCOVP presents an easy-to-use interface with in-built tools for similarity search, cross-genome comparison, phylogenetic, and multiple sequence alignment. DBCOVP will certainly be an important resource for experimental biologists engaged in coronavirus research studies and will aid in vaccine development.
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http://dx.doi.org/10.1016/j.compbiomed.2020.104131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7679231PMC
February 2021

Role of OB-Fold Protein YdeI in Stress Response and Virulence of Salmonella enterica Serovar Enteritidis.

J Bacteriol 2020 12 7;203(1). Epub 2020 Dec 7.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT) University, Bhubaneswar, India

An essential feature of the pathogenesis of the serovar Enteritidis wild type (WT) is its ability to survive under diverse microenvironmental stress conditions, such as encountering antimicrobial peptides (AMPs) or glucose and micronutrient starvation. These stress factors trigger virulence genes carried on pathogenicity islands (SPIs) and determine the efficiency of enteric infection. Although the oligosaccharide/oligonucleotide binding-fold (OB-fold) family of proteins has been identified as an important stress response and virulence determinant, functional information on members of this family is currently limited. In this study, we decipher the role of YdeI, which belongs to OB-fold family of proteins, in stress response and virulence of Enteritidis. When was deleted, the Δ mutant showed reduced survival during exposure to AMPs or glucose and Mg starvation stress compared to the WT. Green fluorescent protein (GFP) reporter and quantitative real-time PCR (qRT-PCR) assays showed was transcriptionally regulated by PhoP, which is a major regulator of stress and virulence. Furthermore, the Δ mutant displayed ∼89% reduced invasion into HCT116 cells, ∼15-fold-reduced intramacrophage survival, and downregulation of several SPI-1 and SPI-2 genes encoding the type 3 secretion system apparatus and effector proteins. The mutant showed attenuated virulence compared to the WT, confirmed by its reduced bacterial counts in feces, mesenteric lymph node (mLN), spleen, and liver of C57BL/6 mice. qRT-PCR analyses of the Δ mutant displayed differential expression of 45 PhoP-regulated genes, which were majorly involved in metabolism, transport, membrane remodeling, and drug resistance under different stress conditions. YdeI is, therefore, an important protein that modulates Enteritidis virulence and adaptation to stress during infection. Enteritidis during its life cycle encounters diverse stress factors inside the host. These intracellular conditions allow activation of specialized secretion systems to cause infection. We report a conserved membrane protein, YdeI, and elucidate its role in protection against various intracellular stress conditions. A key aspect of the study of a pathogen's stress response mechanism is its clinical relevance during host-pathogen interaction. Bacterial adaptation to stress plays a vital role in evolution of a pathogen's resistance to therapeutic agents. Therefore, investigation of the role of YdeI is vital for understanding the molecular basis of regulation of pathogenesis. In conclusion, our findings may contribute to finding potential targets to develop new intervention strategies for treatment and prevention of enteric diseases.
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http://dx.doi.org/10.1128/JB.00237-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7723950PMC
December 2020

Designing an efficient multi-epitope vaccine displaying interactions with diverse HLA molecules for an efficient humoral and cellular immune response to prevent COVID-19 infection.

Expert Rev Vaccines 2020 09 24;19(9):871-885. Epub 2020 Sep 24.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT-DU) , Bhubaneswar 751024, India.

Background: The novel SARS-CoV-2 coronavirus, the causative agent of the ongoing pandemic COVID-19 disease continues to infect people globally and has infected millions of humans worldwide. However, no effective vaccine against this virus exists.

Method: Using Immunoinformatics, epitopic sequences from multiple glycoproteins that play crucial role in pathogenesis were identified. Particularly, epitopes were mapped from conserved receptor-binding domain of spike protein which have been experimentally validated in SARS-CoV-1 as a promising target for vaccine development.

Results: A multi-epitopic vaccine construct comprising of B-cell, CTL, HTL epitopes was developed along with fusion of adjuvant and linkers. The epitopes identified herein are reported for the first time and were predicted to be highly antigenic, stable, nonallergen, nontoxic and displayed conservation across several SARS-CoV-2 isolates from different countries. Additionally, the epitopes associated with maximum HLA alleles and population coverage analysis shows the proposed epitopes would be a relevant representative of large proportion of the world population. A reliable three-dimensional structure of the vaccine construct was developed. Consequently, docking and molecular-dynamics simulation ensured the stable interaction between vaccine and innate-immune receptor.
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http://dx.doi.org/10.1080/14760584.2020.1811091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7544970PMC
September 2020

Effect of mutation on structure, function and dynamics of receptor binding domain of human SARS-CoV-2 with host cell receptor ACE2: a molecular dynamics simulations study.

J Biomol Struct Dyn 2021 11 7;39(18):7231-7245. Epub 2020 Aug 7.

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India.

Recent studies have pointed the role of angiotensin-converting enzyme-II (ACE2) in mediating the entry of SARS-CoV-2 to the host cell by binding to the receptor-binding domain (RBD) of viral spike protein, and successive priming by cellular proteases initiates the infection. SARS-CoV replication rate and disease severity is controlled by the binding affinity of RBD with ACE2. To understand, how mutations in the conserved residues of RBD affect the molecular interaction with ACE2, we generated five alanine mutants i.e. Y449A, N487A, Y489A, N501A and Y505A in the receptor binding motif (RBM) of the ACE2-RBD SARS-CoV-2 complex (PDB: 6M0J). Computational site directed mutagenesis induced dynamics in wild-type and mutant complexes were extensively studied through all-atoms molecular dynamics (MD) simulations of 150 ns. In silico mutational analysis revealed loss of important intermolecular hydrogen bonds and other non-bonded contacts, critical for molecular recognition of SARS-CoV-2 RBD to ACE2, which is well supported by saturation mutagenesis study of binding interface residues. MD simulations results showed that RBM motif is flexible, where mutant residues are relatively more mobile than corresponding wild-type residues. Global motion analysis through principal component studies revealed that RBD exhibits protuberant in-ward motion towards the human ACE2 binding interface which may be crucial for molecular interaction. Conclusively, the present finding are in congruence with previous experimental reports and provides detailed information on the structural basis of receptor binding by human SARS-CoV-2, which will crucial for the development of novel inhibitors or drugs to combat against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2020.1802348DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7484587PMC
November 2021

Structure-based drug designing and immunoinformatics approach for SARS-CoV-2.

Sci Adv 2020 07 10;6(28):eabb8097. Epub 2020 Jul 10.

Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.

The prevalence of respiratory illness caused by the novel SARS-CoV-2 virus associated with multiple organ failures is spreading rapidly because of its contagious human-to-human transmission and inadequate globalhealth care systems. Pharmaceutical repurposing, an effective drug development technique using existing drugs, could shorten development time and reduce costs compared to those of de novo drug discovery. We carried out virtual screening of antiviral compounds targeting the spike glycoprotein (S), main protease (M), and the SARS-CoV-2 receptor binding domain (RBD)-angiotensin-converting enzyme 2 (ACE2) complex of SARS-CoV-2. PC786, an antiviral polymerase inhibitor, showed enhanced binding affinity to all the targets. Furthermore, the postfusion conformation of the trimeric S protein RBD with ACE2 revealed conformational changes associated with PC786 drug binding. Exploiting immunoinformatics to identify T cell and B cell epitopes could guide future experimental studies with a higher probability of discovering appropriate vaccine candidates with fewer experiments and higher reliability.
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http://dx.doi.org/10.1126/sciadv.abb8097DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319274PMC
July 2020

Crystal structure of the usher chaperone YadV reveals a monomer with the proline lock in closed conformation suggestive of an intermediate state.

FEBS Lett 2020 09 23;594(18):3057-3066. Epub 2020 Jul 23.

Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India.

Cell surface pili assembled by the chaperone-usher (CU) pathway play a crucial role in the adhesion of uropathogenic Escherichia coli. YadV is the chaperone component of the CU pathway of Yad pili. Here, we report the crystal structure of YadV from E. coli. In contrast to major usher chaperones, YadV is a monomer in solution as well as in the crystallographic symmetry, and the monomeric form is a preferred state for interacting with pilus subunits. Moreover, we observed a closed conformation for the proline lock, a crucial structural element for chaperone-pilus subunit interaction. MD simulation shows that the closed state of the proline lock is not energetically stable. Thus, the structure of monomeric YadV with its closed proline lock may serve as an intermediate state to provide suitable access to pilus subunits.
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http://dx.doi.org/10.1002/1873-3468.13883DOI Listing
September 2020

Cocaine-regulated microRNA miR-124 controls poly (ADP-ribose) polymerase-1 expression in neuronal cells.

Sci Rep 2020 07 8;10(1):11197. Epub 2020 Jul 8.

Center for AIDS Health Disparities Research, Meharry Medical College, Old Hospital Bldg-CAHDR, Room 5023, 1005 Dr. DB Todd Jr Blvd., Nashville, TN, 37208, USA.

MiR-124 is a highly expressed miRNA in the brain and regulates genes involved in neuronal function. We report that miR-124 post-transcriptionally regulates PARP-1. We have identified a highly conserved binding site of miR-124 in the 3'-untranslated region (3'UTR) of Parp-1 mRNA. We demonstrate that miR-124 directly binds to the Parp-1 3'UTR and mutations in the seed sequences abrogate binding between the two RNA molecules. Luciferase reporter assay revealed that miR-124 post-transcriptionally regulates Parp-1 3'UTR activity in a dopaminergic neuronal cell model. Interestingly, the binding region of miR-124 in Parp-1 3'UTR overlapped with the target sequence of miR-125b, another post-transcriptional regulator of Parp-1. Our results from titration and pull-down studies revealed that miR-124 binds to Parp-1 3'UTR with greater affinity and confers a dominant post-transcriptional inhibition compared to miR-125b. Interestingly, acute or chronic cocaine exposure downregulated miR-124 levels concomitant with upregulation of PARP-1 protein in dopaminergic-like neuronal cells in culture. Levels of miR-124 were also downregulated upon acute or chronic cocaine exposure in the mouse nucleus accumbens (NAc)-a key reward region of brain. Time-course studies revealed that cocaine treatment persistently downregulated miR-124 in NAc. Consistent with this finding, miR-124 expression was also significantly reduced in the NAc of animals conditioned for cocaine place preference. Collectively, these studies identify Parp-1 as a direct target of miR-124 in neuronal cells, establish miR-124 as a cocaine-regulated miRNA in the mouse NAc, and highlight a novel pathway underlying the molecular effects of cocaine.
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http://dx.doi.org/10.1038/s41598-020-68144-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7343862PMC
July 2020

RpoS-regulated gene promotes resistance to stress and influences serovar enteritidis virulence.

Virulence 2020 12;11(1):295-314

School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, India.

serovar Enteritidis (. Enteritidis; wild type (WT)) is a major cause of foodborne illness globally. The ability of this pathogen to survive stress inside and outside the host, such as encountering antimicrobial peptides and heat stress, determines the efficiency of enteric infection. These stressors concertedly trigger virulence factors encoded on pathogenicity islands (SPIs). Although RpoS is a well-known central transcriptional stress and virulence regulator, functional information regarding the genes of the regulon is currently limited. Here, we identified as a conserved RpoS-regulated gene belonging to the KGG protein superfamily. We further assessed its role in pathogenic stress responses and virulence. When was deleted (Δ1538), the pathogen showed reduced survival during antimicrobial peptide introduction and heat stress at 55°C compared to WT. The mutant displayed 70% reduced invasion in the HCT116 colon epithelial cell line, 5-fold attenuated phagocytic survival in RAW264.7 cells, and downregulation of several SPI-1 and SPI-2 genes encoding the three secretion system apparatus and effector proteins. Δ1538 also showed decreased virulence compared to WT, demonstrated by its reduced bacterial counts in the feces, mLN, spleen, and cecum of C57BL/6 mice. Comparative transcriptomic analysis of Δ1538 against WT revealed 111 differentially regulated genes, 103 of which were downregulated (fold change ≤ -1.5, P < 0.05). The majority of these genes were in clusters for metabolism, transporters, and pathogenesis, driving pathogenic stress responses and virulence. is, therefore, an important virulence determinant contributing to the resilience of . Enteritidis to stress factors during infection.
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http://dx.doi.org/10.1080/21505594.2020.1743540DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7161692PMC
December 2020

A ROD9 island encoded gene in Salmonella Enteritidis plays an important role in acid tolerance response and helps in systemic infection in mice.

Virulence 2020 12;11(1):247-259

School of Biotechnology, KIIT University, Bhubaneswar, India.

, like other pathogenic bacteria has undergone multiple genomic alterations to adapt itself into specific host environments executing varied degrees of virulence through evolution. Such variations in genome content have been assumed to lead the closely related non-typhoidal serovars, . Enteritidis, and . Typhimurium to exhibit Type Three Secretion System -2 (T3SS-2) based diverse colonization and inflammation kinetics. Mutually exclusive genes present in either of the serovars are recently being studied and in our currentwork, we focused on a particular island ROD9, present in . Enteritidis but not in . Typhimurium. Earlier reports have identified a few genes from this island to be responsible for virulence as well as . In this study, we have identified another gene, from the same island encoding a hypothetical protein to be a potential virulence determinant showing systemic attenuation upon mutation in C57BL/6 mice infection model. The isogenic mutant strain displayed reduced adhesion to epithelial cells as well as was highly immotile. It was also deficient in intracellular replication , with a highly suppressed SPI-2and failed to cause acute colitis at 72-h p.i.. Moreover, on acid exposure, showed 17 folds and 2 fold up-regulations during adaptation and challenge phases,respectively and Δ failed to survive during ATR assay, indicating its role under acid stress. Together, our findings suggested Δ to be significantly attenuated and we propose this gene to be a potent factor responsible for . Enteritidis pathogenesis.
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http://dx.doi.org/10.1080/21505594.2020.1733203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7051147PMC
December 2020

Selective in vivo molecular and cellular biocompatibility of black peppercorns by piperine-protein intrinsic atomic interaction with elicited oxidative stress and apoptosis in zebrafish eleuthero embryos.

Ecotoxicol Environ Saf 2020 Apr 13;192:110321. Epub 2020 Feb 13.

School of Biotechnology, KIIT University, Bhubaneswar, 751024, India; Advance Science and Technology Research Centre, Vinoba Bhave University, Hazaribag, 825301, India. Electronic address:

Day to day consumption of black pepper raise concern about the detailed information about their medicinal, pharmaceutical values and knowledge about the biocompatibility with respect to ecosystem. This study investigates the in vivo selective molecular biocompatibility of its seed cover (SC) and seed core (SP) powder extract using embryonic zebrafish model. Gas chromatography mass spectrometry (GCMS) analysis of the extract prepared by grinding showed presence of different components with "piperine" as principle component. Biocompatibility analysis showed dose and time dependent selective effect of SC and SP with LC50 of 30.4 μg/ml and 35.6 μg/ml, respectively on survivability, hatching and heartbeat rate in embryonic zebrafish. Mechanistic investigation elucidated it as effect of accumulation and internalization of black pepper leading to their influence on structure and function of cellular proteins hatching enzyme (he1a), superoxide dismutase (sod1) and tumor protein (tp53) responsible for delayed hatching, oxidative stress induction and apoptosis. The study provided insight to selective biocompatibility of black pepper expedient to produce higher quality spices with respect to pharmaceutical, clinical and environmental aspects.
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http://dx.doi.org/10.1016/j.ecoenv.2020.110321DOI Listing
April 2020

dEMBF v2.0: An Updated Database of Enzymes for Microalgal Biofuel Feedstock.

Plant Cell Physiol 2020 May;61(5):1019-1024

School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar 751024, India.

In light of increasing algal genomics data and knowledge of biosynthetic pathways responsible for biofuel production, an integrated resource for easy access to all information is essential to improve our understanding of algal lipid metabolism. Against this backdrop, dEMBF v2.0, a significantly updated and improved version of our database of microalgae lipid biosynthetic enzymes for biofuel production, has been developed. dEMBF v2.0 now contains a comprehensive annotation of 2018 sequences encoding 35 enzymes, an increase of over 7-fold as compared with the first version. Other improved features include an increase in species coverage to 32 algal genomes, analysis of additional metabolic pathways, expanded annotation thoroughly detailing sequence and structural features, including enzyme-ligand interactions, and integration of supporting experimental evidence to demonstrate the role of enzymes in increasing lipid content. Along with a complete redesign of the interface, the updated database provides several inbuilt tools and user-friendly functionalities for more interactive and dynamic visualization of data.
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http://dx.doi.org/10.1093/pcp/pcaa015DOI Listing
May 2020
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