A comprehensive review on integrative approach for sustainable management of plastic waste and its associated externalities

The management of post-consumer discarded plastic wastes (PCPW) creates new challenges in developing countries due to the lack of amenities, technological interventions, and associated negative environmental externalities. The fate of untreated recyclable and non-recyclable plastic wastes lies in open dumping along with other solid waste, and improper management leads to environmental externalities such as pollution, global climate change, and health issues. Additionally, open dumping upsurges the emerging microplastics and nano plastics (MNPs) contaminants. The externalities depend on the waste generating sources (household, industries, commercial), waste composition, and its characteristics. However, urban mining can minimize environmental externalities where waste plastics can convert into potential anthropogenic resources and also helps in achieving the target of sustainable development goals (SDGs 11 & 12). Moreover, various treatment technologies that help in the sustainable utilization of plastic wastes are extensively reviewed in this study and evaluate the costs benefits arising during various stages of treating plastic waste through recycling (R), incineration (I), and landfilling (L). The recycling of plastic waste has demonstrated the lowest impact on global warming potential (GWP) and total energy use (TEU), followed by landfilling and incineration (R < L < I). Nevertheless, when energy is recovered from inert (non-recyclable) plastic waste in the form of fuel or by its utilization in construction purposes, the environmental impacts are more negligible (Incineration < Landfilling). Therefore, this study determines the significance of circular economy with legislative approach and standards on plastic waste management, which help in reducing environmental externalities besides yielding a secondary resource as energy and materials through urban mining. A sustainable plastic waste management (SPWM) model is proposed for developing countries to convert plastic waste into resources and use it as a sustainable tool in urban mining.

Decoding the Genetic Alteration in Genes of PARP Family and the Possible Association with HNSCC

Introduction: Genetic alterations have long been associated with the transformation of normal cells into malignant cells. Several genes are related to exhibiting the phenotype. The PARP gene family is mainly involved in maintaining genome stability. They play an important role in DNA repair and the programmed cell death process. Aim: To analyse the genetic alteration in PARP family and to determine its association with HNSCC. Materials and Methods: Cbioportal was used as the primary database for identifying the mutations and variations. The data generated in the form of oncoprint was further assessed for frequency of occurrence, type and novelty. Results and Discussion: It can be observed that greater amplification was found in the TIPARP gene which is 14% among all the 17 genes of the family. Also to add on, PARP 14 and PARP 15 show amplification patterns in similar groups of patients. Several types of mutations such as truncated, splicing deep deletion were found in most of the genes. The TIPARP gene was up-regulated in HNSCC patients. The Caucasians experiencing low/medium expression of TIPARP showed greater rates of survival than highly expressed African Americans. Similarly, males presenting with low or medium expression of TIPARP showed a greater rate of survival than the highly expressed females. Conclusion: TIPARP could be a promising prognostic marker for screening populations vulnerable to acquiring HNSCC.

Virtual Screening to Identify the Protein Network Interaction of Theophylline in Red Complex Pathogens

Background: Plants, herbs and plant derived compounds have been used since decades in folk and traditional medicine. These compounds were found to be non-toxic and compatible with the human cells. Screening of this exhaustive collection of compounds seems to be a herculean task. Hence, virtual screening methods have been developed to predict the potential targets of these compounds enabling researchers to acquire preliminary data on the compound intended to be tested in vitro. Aim: The present study aims to identify protein targets of theophylline in red complex pathogens which are mainly associated with periodontitis. Methods: The STITCH v5.0 pipeline was mainly used to classify drug-protein interactions, while VirulentPred and VICMPred were used to determine the proteins' virulence properties and functional classes. PSORTb v3.0 was used to determine the subcellular localization of viral proteins, and BepiPred v1.0 Linear Epitope Prediction was used to classify epitopes. Results: Proteins of red complex pathogens implicated in cellular process, metabolism, and virulence were identified to interact with theophylline. The virulent proteins attacked by the drugs were present in the cytoplasm, which would improve the drugs' antimicrobial efficacy even more. Finally, epitope prediction showed a number of epitopes in virulent proteins that can be targeted. Conclusions: Proteins involved in the cellular process, metabolism, and virulence of red complex pathogens targeted by theophylline were identified. To substantiate the true interactions between the drugs and the protein arsenal of pathogens, further in vitro experiments on a broad range of pathogens are required.

Genetic Alterations in CDH (Cadherin) Family of Genes and their Putative Association with Head and Neck Squamous Cell Carcinoma

Background: Head and neck squamous cell carcinoma is considered to be a common type of human cancer. It is highly invasive with limited therapeutic options outside surgery, chemotherapy and radiation.  Cadherin family genes comprises a family with more than 110 members which are calcium dependent transmembrane proteins which helps in cellular adhesion, signaling etc. There exist different functions of Cadherin genes in malignant cells. Uncontrolled mesenchymal- epithelial transition is seen in malignant situations where the cadherins serve as tumour suppressor genes but gets down regulated drastically to create tumour initiation and invasions. This study aims to study the association between genetic alterations in the cadherin family of genes and HNSCC patients. Materials and Methods: The datas were collected from a promising database, cBioportal and the demographic details of the selected individuals(HNSCC patients) were tabulated and noted. The genetic variations in the genes were analysed using GnomAD analysis, oncoprint analysis and their various genetic alterations,frequency were tabulated and represented figuratively. Results and Discussion: On analysing the various genetic alterations discovered in cadherin family genes of HNSCC patients, CDH2 gene showed maximum genetic alteration(%). The different genetic alterations documented were splicing, deep deletion, amplification, etc. the oncoprint data analysis shows the frequency of the types of different genetic alteration in the five genes considered, their combination with any other genetic alteration seen in the other genes along with their frequency. The graphical representation of Kaplan meier analysis, showing over expression of CDH2 genes helps understand the survival rate of HNSCC patients. These analysis and tabulated documents, figures prove the association between genetic alterations in the cadherin family of genes and HNSCC. Conclusion: There exists a significant association between HNSCC and genetic alterations seen in the cadherin family of genes.

Detection of 11 Multidrug Resistance Genes among the Strains of A. Baumannii by Computational Approach

Background: Acinetobacter baumannii is typically short, rod shaped gram negative bacterium. The World Health Organisation has declared it as an opportunistic pathogen in humans. Multi drug resistance involves different genetic determinants making the pathogen difficult to treat. So this study is undertaken to characterize the 11 different drug resistant genes from 19  virulent strains of A. baumannii using in-silico PCR. Aim: Detect the 11 multidrug resistance genes among strains of A. baumannii by computational approach. Materials & Methods: 11 multidrug resistance genes of A. baumannii were selected. Forward and reverse primers of the 11 genes as reported from earlier studies were used for in-silico PCR amplification. 19 strains of A .baumannii set as default strains on the server were chosen and the amplicon bands were observed.  Result: Among the 11 multidrug resistance genes only blaOXA-51like and blaADC were detected among the 19 virulent strains of A. bauamannii. Conclusion: The findings of the study documents the frequency of blaADC and blaOXA-51 like from the selected strains of A. baumannii. However further experimental validation must be done towards the periodical surveillance on the drug resistant strains of A. baumannii in hospital settings.

Prediction of Epitope Peptides for PTK Gene of Acinetobacter baumannii

Background: Acinetobacter baumannii is a gramnegative bacilli acquiring both intrinsic and adaptive patterns of multi drug resistance and virulence. Immune-informatics approach holds promise to detect putative epitope peptides from vital virulence factors which can be further synthesized and evaluated for their immunological response. Aim: The aim of the study was to predict the immuno-dominant peptides from the ptk gene of A. baumannii. Materials and Methods: Protein retrieval of the Ptk gene using CELLO V.2.5 was done with the evaluation of antigenicity and allergenicity of the predicted epitopes, using Vaxijen V2.0 server and AlgPred servers. Epitope structure prediction and validation by using RAMPAGE revealed the homology peptides. Molecular Docking of epitopes with HLA-alleles using ClusterPro server, and further identification of B cell epitope was performed by using Kolaskar and Tonganokar antigenicity method. Results: A total of 20 epitopes were predicted and 18 peptides were chosen based on antigenicity and stability analysis prediction. The structure predictions were carried out using pepfold server and based on Ramachandran plot analysis 10 epitopes were taken for further analysis. Conclusion: The present finding has detected and evaluated the desirable epitope as LFFSLIAQW using an immune-informatic approach. However, it needs further experimental validation for its immunological response using standard in-vitro studies.

Epitope Based Vaccine Peptide Predictions for fimH gene of Acinetobacter baumannii

Background: Acinetobacter baumannii is an opportunistic bacterial pathogen that is primarily associated with hospital-acquired infections. Recently, there is a dramatic increase in the incidence of multidrug-resistant (MDR) strains, which has significantly raised the profile of this emerging opportunistic pathogen. MDR is often associated with the formation of biofilms and various other virulence factors. Amidst all the genes, fimH gene is our area of interest in this research, because it is an important virulence factor in A. baumannii which encodes the Type 1 fimbriae, that helps bacteria bind to the surface of host cells initiating further infection. Aim: The aim of this study was to assess the epitope based vaccine epitope peptide predictions for the fimH protein of A. baumannii. Materials and Methods: The fimH gene for epitope prediction was selected. Druggability and physico-chemical properties were analysed. Antigenicity was predicted. Epitope mapping of T-cell MHC class 1, Class 1 immunogenicity, conservancy and toxicity analysis was done. T-cell class II epitopes were further mapped together with the immuno-dominant B-cell epitopes.  Results: From the selected 20 epitopes, 2 best epitopes (AALVASVCL and YSSGANAFT) were selected after analysing their antigenicity and allergenicity. The epitope YSSGANAFT showed better values in association with HLA alleles - HLA-DP, HLA-DQ, HLA-DR and TLR-2. Conclusion: The finding of the study documents a single immunodominant peptide (sequence) as a promising vaccine candidate to treat infections caused by A. baumannii. However further experimental analysis must be performed to assess the immunological memory and response of the peptide in both in-vitro and in-vivo studies.

Screening and in Silico Validation of Anti-Microbial Peptides Derived from Lysostaphin, Entero and Endolysin

Introduction: Antimicrobial peptides (AMPs) are small molecules which are known to exert destructive effects upon pathogenic microorganisms. AMPs are designed from proteins obtained from various sources and tested under in vitro conditions to deduce their antimicrobial activity. Materials and Methods: A few of the peptidoglycan hydrolases such as lysostaphin (AAB53783.1), enterolysin (AGG79281.1), and endolysin (YP_009901016.1) were selected for the study based on an extensive text mining process. The protein sequences of the proteins were retrieved from the NCBI (National Centre for Biotechnology Information) database in the FASTA format (https://www.ncbi.nlm.nih.gov/protein/). Results and Discussion :In the antimicrobial protein lysostaphin, three antimicrobial peptide are been found, in which two is active and other is inactive, and one has antifungal property with a score of -0.15, and one having cell penetrating property, in which all are non toxic. Conclusion: The present study predicts AMPs from lysostaphin, entero and endolysins. These peptides were found to possess antifungal, anti-biofilm properties. Most of the peptides predicted were found to be non-cell penetrating and non-toxic.

Effect of Ocimum Sanctum Bio Compounds against csuE Gene Protein of Acinetobacter baumanii

Background: Acinetobacter baumannii is a Gram-negative bacillus that is aerobic, pleomorphic and non-motile. Multi-drug resistance and biofilm formation contributes to the virulence and pathogenicity of the bacterium. Among many virulence factors, csuE is critical for initiation and assembly, showing much homology to type 1 and P pili. With much propensity of drug resistance, in recent years alternative medications have spurred renewed interest in targeting potent pathogens. Ocimum sanctum, also known as holy basil or tulsi possess various bio-active properties and can be used as alternative medicine to treat systemic ailments. Aim: This study was aimed to analyze the drug-ligand interactions between csuE protein of A. baumannii and the bio-compounds from O.sanctum using in-silico docking analysis. Material and Methods: csuE protein was retrieved and optimisation of protein was done. Ligands were selected and were assessed for drug likeness using molinspiration parameters. Further the compounds were subjected for docking analysis and the interacted molecules were visualized for binding energy and hydrogen bonds. Results: Out of the 9 compounds of Ocimum sanctum, benzofuran showed good interaction with csuE protein of Acinetobacter baumannii with a least docking energy of -5.31Kcal/Mol. Conclusion: The present study recommends benzofuran as the potent candidate for novel drug design to treat the infections caused by A.baumannii upon further evaluations for its safety and immunological response.

Distribution of Four Biofilm Associated Gene among A. baumannii by in Silico-PCR

Background: A.baumannii is an opportunistic pathogen known for its efficient biofilm formation that is attributed for its virulence. Acinetobacter baumannii is an inhabitant of oral biofilms as well. Many gene operons are involved in the biofilm formation that need to be monitored frequently. Aim: The aim of the present study was to detect the distribution of four biofilm associated genes among A.baumannii. Materials and Methods: Four biofilm forming genes viz., bfms, ptk, pgaB, and fimH of A.baumannii were selected. Forward and reverse primers of those four genes were used for in-silico PCR amplification. 19 strains of A.baumannii set as default on the server were chosen and the amplicon bands were observed Results: The present investigation documents the distribution of four vital biofilm associated gene among 19 different strains of A.baumannii among which bfms was distributed at a higher frequency followed by pgaB and ptk Conclusion: The finding of the study suggests the presence of pgaB, bfms, ptk among the 19 different strains of A.baumannii. However further experimental validation must be done to frequently monitor the presence of the genes among the clinical strains of A.baumannii.

A Computational Approach on the Anti-biofilm Effect of Ocimum sanctum Bio-compounds Against ptk of Acinetobacter baumannii

Introduction: Acinetobacter baumannii is a gram negative coccobacilli often considered as a nosocomial pathogen and as an opportunistic pathogen in immunocompromised patients. It is considered to be multi-drug resistant and a potent bacteria forming vital biofilms. Ptk which is protein tyrosine kinase is a protein coding gene involved with the synthesis of capsular polysaccharide. Ocimum sanctum is a perennial plant belonging to the Lamiaceae family. Tulsi and holy basil are the common names of this plant. In-silico docking approach method is much more convenient and cost effective to assess the bioactive properties of the natural drugs against any target ligands. Aim: The aim of the study to assess the inhibitory effect of Ocimum sanctum bio-compounds against ptk of Acinetobacter baumannii using a computational approach. Materials and Methods: Retrieval of the structure of ptk was followed by Ligand preparation and optimisation. Further drug likeliness was assessed using Molinspiration parameters, docking simulations and visualisation for the binding energy and hydrogen bonds. Results: Among the bio compounds of O.sanctum, benzofuran is selected as an active inhibitory compound with -11.12 as its binding energy showing a high affinity. Conclusion: The findings of the present study documents benzofuran as the promising candidate to design novel drugs from O.sanctum and to target the ptk of A.baumannii. However further experimental validation must be done to observe its efficacy and safety in the treatment of nosocomial infections caused by A.baumannii.

Distribution of Biofilm-associated Genes among Acinetobacter baumannii by in-silico PCR

Background: Acinetobacter baumannii is a coccobacillus that is Gram negative, non motile, non fermentative and oxidase negative. It is the most common and successful nosocomial pathogen recognised by WHO. This dreadful pathogen causes urinary tract infections, ventilator associated pneumonia (VAP), bacteremia, etc., These infections are most common in hospital wards especially Intensive Care Unit (ICU). The infections are due to biofilm formation by the virulent genes of A. baumannii, and the common biofilm-associated genes of A. baumannii were bap, csuE, fimH, epsA, bfmS, ptk, pgaB, ompA, blaPER-1. Among these, bap, epsA and ompA genes are highly prevalent among the clinical strains of A. baumannii. Aim:  To detect the three vital biofilm-associated genes of A. baumannii by in-silico PCR analysis. Materials and Methods: 19 isolates of A. baumannii were selected and 3 target genes, namely epsA, ompA and bap gene were used for the amplification process through in-silico PCR simulation tools. Evolutionary analysis was done for the ompA gene. Results: The epsA gene was expressed in 10.52% of the total strains selected with the highest occurrence of ompA gene as 57.89%. bap gene was not observed from the study strains included. From evolutionary analysis based on ompA distributed strains, the Acinetobacter baumannii SDF and Acinetobacter baumannii BJAB0715 might be the parental strains where the evolution of strains would have started. Through successive generations, the Acinetobacter baumannii MDR-ZJ06 and Acinetobacter baumannii TYTH-1 had become the multidrug resistant strains present in the environment. Conclusion: The findings of the study confirms the distribution of epsA and ompA genes among the 19 different strains of A. baumannii. The study suggests periodical monitoring of biofilm based virulence genes among the clinical strains and to curtail the A. baumannii infections.

Detection of Drug Resistant Genes among A. baumannii by In silico PCR Method

Background: Acinetobacter baumannii is a gram-negative bacterium classified as an opportunistic pathogen in humans by the World Health Organization. Different genetic determinants contribute to multidrug resistance, and transform it as a nosocomial pathogen. Aim: Using in-silico PCR, this analysis aims to characterize the 13 distinct drug resistant genes found in 19 virulent A.baumannii strains. Materials & Methods: There were 11 A.baumannii multidrug resistance genes chosen. In-silico PCR amplification was performed using forward and reverse primers from the 11 genes described in previous research. The amplicon bands were detected in 19 strains of A.baumannii that were set as default on the server. Results: Among the 13 multidrug resistance genes studied, tet A, tet B, Sul 1, Sul 2, DfrA1,  ISAba-1 and ISAba-125 were detected among the 19 virulent strains of ​A.baumannii​. Conclusion: The findings of the study documents the frequency of tet A, tet B, Sul 1, Sul 2, DfrA1, ISAba-1 and ISAba-125 like from the selected strains of A. baumannii. However, more experimental validation is needed in order to conduct routine surveillance on drug-resistant A. baumannii strains in hospital settings.

In silico Analysis of Plant Based Quorum Sensing Inhibitor against Chromobacterium violaceum CviR

Background: Chromobacterium violaceum (C. violaceum), a Gram-negative, facultative anaerobic, non-sporing coccobacillus has a quorum-sensing system consisting of CviI/CviR, a homologous gene. Quorum sensing (QS) is a mechanism of intercellular communication in bacteria that received substantial attention as an alternate strategy for combating bacterial resistance and the development of new anti-infective agents. Methods: DATA SET Information of photochemical from the natural source deposited as a machine readable format in PubChem database was utilized to retrieve the compound for the study. To study ligand - receptor interactions, docking paves way to accomplish the protein ligand interaction was docked through rigid docking CviR protein (PDB ID: 3QP5) was prepared and energy minimized to evaluate the best affinity among the complex. Results: The results showed that the Alpha.,2.Alpha.- Epoxy-1.Beta.- Methyl Cholesta-4,6- Dien-3-One had high affinity for CviR receptor protein and Alpha.,2.Alpha.- Epoxy-1.Beta.- Methyl Cholesta-4,6- Dien-3-One binds to the active site of CviR with binding energy of -9.6 kcal/mol. Conclusion: Overall study concluded that 1. Alpha., 2. Alpha.- Epoxy-1.Beta.-Methyl Cholesta-4,6-Dien-3-One with highest binding affinity for the CviR protein possessing strong inhibitory binding interaction. Hence, we concluded that 1.Alpha.,2.Alpha.-Epoxy-1.Beta.- Methyl Cholesta-4, 6-Dien-3-One good serves as potential an anti-quorum sensing molecule for treating C. violaceum infection.

Virtual Screening to Identify the Protein Network Interaction of Hypericin with Red Complex Pathogens

Introduction: Hypericin is the anthraquinone derivative and has many properties like antiviral, antifungal and antibacterial. The red complex pathogens which include Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia in association with other microbes found in the periodontal pockets, cause severe inflammation resulting in periodontitis. Novel bioactive agents from several sources have been tested against the microbial pathogens to deduce antimicrobial activity.  Aim: The aim of the study is to virtually screen and identify the protein network interaction of hypericin in red complex pathogens. Methodology: The STITCH v5.0 pipeline was primarily used to identify the drug-protein interactions. The VirulentPred and VICMPred software were used for elucidating the functional class of the proteins and virulence property. The sub cellular localization of virulent proteins was analysed with pSORTb v3.0 software. Further, the epitopes in virulent proteins were identified using BepiPred v1.0 linear epitope prediction tool. Results: Heat shock protein 90 of Porphyromonas gingivalis were found to involve in the cellular process and DNA topoisomerase IV subunit B, heat shock protein 90, DNA gyrase subunit A and DNA gyrase subunit B of Treponema denticola were found to be the virulent factors. The virulent proteins were located in the cytoplasm, which would further increase the potential effect of the drug to serve as antimicrobial agents. Finally, epitopes were predicted on the virulent proteins which can be specifically docked to further ascertain their interactions with the phytocompound. Conclusion: Hypericin with all its potential and biological benefits can be addressed, can be used as an antimicrobial agent to eradicate dental pathogens which are recalcitrant to treatment. The mode of action of hypericin is, it is targeting crucial proteins in red complex pathogens. Further in vitro studies should be performed on a wide range of pathogens to substantiate the true interactions between the drugs and the protein repertoire of pathogens.

Targeting Omp-A Protein of Acinetobacter Baumannii with the Bio-Active Compounds from Azadirachta Indica - an in-silico Approach

Background: Acinetobacter baumannii is a gram negative bacterium which is typically short, round, coccobacillus and was named after the bacteriologist Paul Baumann. It is an emerging dental pathogen since it acquires  drug resistance and expression of several virulence genes. It is an opportunistic pathogen in humans, affecting people with compromised immune systems. Acinetobacter baumannii is an arising nosocomial microorganism causing serious complications because of the propensity of its multi-drug resistant property. Aim: The aim of the present study was to target omp-A protein of Acinetobacter baumannii with the bio active compounds from Azadirachta indica an in-silico approach. Materials and Methods: The crystal structure of ompA protein was obtained from the PDB protein data bank. The structures of the bio-active derivatives of A. indica were obtained from the chemsketch software. The generated 3D structures were then optimised. Auto Dock instrument was utilized for docking investigation to interpret the affinity between bio-compounds of A. indica against ompA protein of A. baumannii. Results: The 3D crystal structure of OmpA-like domain from A.baumannii was retrieved from PDB database and its PDB ID was 3TD3 – A chain. 3D Structure of OmpA visualization using Biovia-Discovery studio visualizer. The 2D structure of compounds from Azadirachta indica was drawn using ACD chemsketch and saved in MDL-mol format and converted to PDB format using open babel converter. The final docked structures for the drug ligand interactions were assessed for their binding energies and hydrogen bonds. Conclusion: The present study had achieved the anti-biofilm inhibitory effect of imidazole-2-carboxylic acid from A. indica exhibiting a great interaction between activity with ompA utilizing computational investigation.

Attenuation of Quorum Sensing Controlled Virulence Factors and Biofilm Formation by Edible Fruit Extract of Coccinia indica against Pseudomonas aeruginosa

Background: Pseudomonas aeruginosa is a Gram-negative opportunistic human pathogen that mainly infects immunocompromised individuals and patients with urinary tract infection and chronic infections of the respiratory pathways, including cystic fibrosis. Many quorum sensing (QS) controlled components such as bio surfactants and swarming motilities play an important role in the establishment of biofilms. Targeting these factors through anti-QS strategies prevent biofilm formation and treating infections. Coccinia indica commonly called little gourd is used to treat diabetes, wound, burn infections and has antioxidant, antibacterial and antitussive properties. Methods: The methanolic fruit extract of C. indica was prepared and screened for anti-QS and anti-biofilm formation activity. Pyocyanin inhibition, rhamnolipid, crystal violet staining assay tests was performed and the extract was observed under fluorescent microscope. Results: The results obtained are as follows - the fruit extract inhibits the pyocyanin at 58.13% and 42.27% at 0.5 mg/ml and 1.0 mg/ml, biofilm at 69.86% and 49.06% at 0.5 mg/ml and 1.0 mg/ml, inhibits rhamnolipid assay and under fluorescent microscope it is seen scattered whereas control produce biofilm matrix like appearance. Conclusion: Since less study has been made on the quorum sensing and biofilm activity of C.indica our study aimed to fulfil it and it was found that it exhibits good biofilm formation and thus can be used for treating infections.

Virtual Screening to Identify the Protein Network Interactions of Triclosan with Streptococcus mutans and Enterococcus faecalis

Introduction: Triclosan is considered to be an important ingredient in toothpastes and mouth rinses. Several studies have reported contradictory results regarding the antimicrobial effect of triclosan. Hence, the present in silico study intends to identify the potential targets of triclosan in two common dental pathogens Streptococcus mutans and Enterococcus faecalis. Aim: To identify the protein network interactions of triclosan in Streptococcus mutans and Enterococcus faecalis by virtual screening method. Materials and Methods: The STITCH v5.0 database was initially used for identifying drug-protein interactions followed by VICMPred and VirulentPred which was employed to identify functional class of the proteins and its virulence property. Finally, BepiPred v1.0 Linear Epitope Prediction tool was used to identify the potential epitopes of the virulent proteins. Results: Triclosan was found to interact with crucial proteins in S. mutans and E. faecalis which could contribute to severe forms of periodontitis and endodontic diseases. Conclusion: Taken together, the present study provides the preliminary data on the potential targets of triclosan in common dental pathogens. Further experimental validation is warranted to provide concrete evidence on the molecular targets of dental pathogens. 

Detection of Immuno Dominant Peptides against pgaB of Acinetobacter baumannii

Background: Acinetobacter baumannii is a gram negative non-motile coccobacillus, which was considered as a low priority pathogen with low virulence. Recently, it was declared as the priority pathogen under the critical category of the most dangerous pathogen by WHO. Acinetobacter Baumannii is an inhabitant of oral biofilms, and it also increases the risk of refractory periodontitis. It causes nosocomial infections with pgaB, a part of pgaABCD operon which is involved in the biofilm formation. Aim: The aim of the present study was to detect the immunodominant peptides against pgaB of Acinetobacter baumannii using bioinformatic tools and databases. Materials and Methods: The present study was carried out using immune informatics. The protein sequence of the pgaB protein from A.baumannii was subjected to assess allergenicity, secondary structure, antigenicity and stability prediction of selected T cell epitopes, physico-chemical analysis, Identification of MHC class 2 binders, Final selection of B-cell epitopes was done with IEDB B-cell epitope tool Results: Final docking of the peptides were interpreted by hydrogen bonds and interac- tion scores with TLR-2. Promising scores on antigenicity, instability were obtained. Based on the combinatorial scores, one vaccine peptide (LNLTLGLAL) was suggested to be a promising vaccine candidate against pgaB of A.baumannii. Conclusion: The findings of the present study suggest epitope LNLTLGLAL as a promising vaccine candidate against pgaB of A.baumannii. The vaccine peptides targeting the pgaB Gene in A.baumannii using an immune-informatics approach suggests promising results in the present study. However, the predicted epitope peptides need further experimentation in animal models for its application against A.baumannii.

Virtual Screening to Identify the Protein Network Interaction of Berberine with Red Complex Pathogens

Introduction: Periodontal disease is an infection of the tissues that hold your teeth in place. It's typically caused by poor brushing and flossing habits that allow plaque, a sticky film of bacteria, to build up on the teeth and harden. Elimination of these pathogens from the site of infection remains a perplexing task, which demands the use of antibiotics. The emergence of drug resistant forms has spurred interest into identifying novel therapeutic targets against these pathogens. Aim: The present study employs virtual screening method to identify the protein network interaction of berberine with red complex pathogens. Materials and Methods: Computational tools were used to identify the targets, assess their functional role and virulence property. Further, the peptide epitopes present in the virulence factors were identified using the BepiPred tool. The subcellular location of the virulence proteins was also elucidated using PSORTb. Results: Berberine was found to target vital protein transporters such as TetR family transcriptional regulator and MerR family transcriptional regulator, which is known to play a crucial role in the survival of bacterial cells. Conclusion: Hence the present study provides preliminary data on the protein targets of berberine against red complex pathogens. However, in vitro studies using the compound is warranted to further confirm the efficacy of the compound.

In vitro Evaluation of Antimicrobial Activity of Opuntia ficus-indica Seed Oil

Introduction: Opuntia ficus-indica is a well adapted cactus to extreme climatic environments. In the usual diet and food industry, it is an interesting source of food ingredients. In general, the protective role of prickly pears has been due to their antioxidant components, phenolic compounds, and some minor components present in the content of seed oil and seed protein and the oil from cactus pear seed has been found with high levels of unsaturated fatty acids ,with antioxidant  and antimicrobial activity as well as cardioprotective, antithrombotic, anti-inflammatory, antiarrhythmic, hypolipidemic, and antihyperglycemic effect. Aim: To evaluate the in vitro antimicrobial activity of Opuntia ficus-indica seed oil against Streptococcus mutans. Materials and Methods: Broth microdilution assay was performed by following modifications: Brain heart infusion (BHI) broth was prepared and sterilise at 121c for 15lbs, the 100 microlitre of streptococcus mutans inoculated at freshly prepared broth and incubated at 37c for 24 hours. Then BHI broth prepared with sucrose and serial two fold dilution were done with 160microlitre broth and 40 microlitre prickly pear seed oil. Then 20 microlitre of culture was added. Column 11 contains BHI using sterile micro pipettes and the plates were incubated at 30 c for 18 hours. The growth of bacteria was visualised and lowest concentration with no visible growth was recorded as MIC. Results: This study results shows that, by broth microdilution method at concentration ranging from 10%-0.039% v/v, Opuntia ficus-indica seed oil potentially inhibits the growth of streptococcus mutans at the concentration of 0.03% (v/v). Conclusion: From the study, the results demonstrated that Opuntia ficus-indica seed oil shows noticeable antimicrobial activity against streptococcus mutans. Use of essential oils against oral pathogens can be an alternative to other antimicrobial agents which could be cheap and effective modules used in control of bacteria which are responsible for oral infections.

Decoding the Genetic Alterations in Genes of Fibroblast Growth Factor Family and Their Possible Association with HNSCC

Introduction: HNSCC is a type of cancer in the oral and pharynx region. Several mutations/variations are observed in these cancer phenotypes. Fibroblast growth factor belongs to the family of heparin binding growth factors. FGFs are multifunctional proteins with a wide variety of effects; they are most commonly mitogens. Their expression pattern correlates with invasion of HNSCC. Aim: To assess the genetic alterations in genes of the fibroblast growth factor family and their association with HNSCC. Materials and Methods: The demographic data and samples of 528 HNSCC patients was collected from the cBioportal database. Oncoprint analysis was done to assess the amplification and genetic alterations of the members of the FGF gene family. String analysis was performed to evaluate the protein-protein interaction. The information about previous reported mutation and correlation with novel and reported mutation was obtained using GnomAD analysis. Results and Discussion: FGF3,4 and 19 genes showed maximum variation (25%). FGF4 and FGF19 genes showed maximum amplification in addition to deletion mutation. Excitingly FGF3, FGF4 and FGF19 genes showed similar amplification patterns in most of the HNSCC patients. Statistical significant difference in the gene expression of FGF3 9.578 x 10-3 observed between normal and primary tumour. S.  Findings showed many novel mutations and also 4 reported mutations ie:FGF1, FGF12, FGF20, FGF21 Conclusion: Our present study concludes that more evidence is required to confirm their association with HNSCC.

Virtual Screening to Identify the Protein Network Interaction of Triclosan in Red Complex Pathogens

Background: Antimicrobial drug resistance is the major problem encountered world-wide. Novel therapeutic leads have been identified and are regularly tested for their activity against microbial pathogens. Aim: To identify the protein network interactions of triclosan in red complex pathogens. Materials and Methods: The present study follows an observational study design which aims to screen for the interaction of triclosan in red complex pathogens. The interaction was analyzed using the STITCH v.5 pipeline. The functional class of proteins identified were assessed using VICMPred and VirulentPred softwares. The microbial pathogens Treponema denticola ATCC 35405, Tannerella forsythia ATCC 43037, Porphyromonas gingivalis ATCC 33277 are the strains of red complex pathogens that are included in the present study. Results and Discussion: Several proteins were found to interact with triclosan. Among the protein interactions, interactions of triclosan with virulent proteins seems to have a greater impact. The NAD-dependent nucleotide-diphosphate-sugar epimerase [PGN_1370], Putative NAD dependent epimerase [PGN_1886], GDP-fucose synthetase [PGN_1079], Probable oxidoreductase [PGN_1360] of Porphyromonas gingivalis, Conserved hypothetical protein [TDE_2401],  Epimerase/dehydratase family protein [TDE_1439] of Treponema denticola, NAD dependent epimerase/dehydratase family protein [BFO_2919], Hypothetical protein [BFO_1782],  Nitroreductase family protein [BFO_1604] and Nitroreductase family protein [BFO_1516] Tannerella forsythia were found to be exhibit virulence nature. Conclusion: This study identifies the molecular targets of triclosan on red complex pathogens. As triclosan interacts with the red complex pathogens, in future it can be used as a primary medicine for periodontitis and some oral conditions.

In silico Analysis of a Novel Peptide Vaccine against Hepatitis B Virus (HBV)

Background : Hepatitis B is a potentially life-threatening liver infection caused by the Hepatitis B virus (HBV). It is a major global health problem and the most serious type of viral hepatitis. It can cause chronic liver disease and puts people at high risk of death from cirrhosis of the liver and liver cancer. HBV is found in highest concentrations in blood and in lower concentrations in other body fluids. Methods: Target protein was retrieved from the swissprot database. Epitopes were predicted using the BCEPRED server. After running the BLAST algorithm for the target protein, the template with the best identity was selected. After modeling, target protein is verified by using the swiss model workspace and after this process the obtained target protein is allowed to interact with the MHC which is studied by using patchdock, finally these results were viewed by using the deepview tool. Results: The target protein for vaccine development was downloaded from the SwissProt database. Its SwissProt ID was p29178. The protein was isolated from hepatitis B virus genotype G. The virus was isolated from the United States of America. The length of the target protein was found to be 195 amino acids. To confirm that the target protein could be used for vaccine development, the Presence of epitopes in the protein was confirmed using the BCEPRED tool. Results from the SAVS server showed 95.80 of the residues of the protein had an average 3D-1D score greater than 0.2. The protein attained a pass with an ERRAT value of 90.299. Conclusion: The present investigation recognized the promising complex formed between the HBV peptide and MHC molecules. All the downloaded MHC molecules were found to interact with the target protein through the formation of hydrogen bonds. Since these interactions are necessary during an immune response to invading pathogens, the target protein would ultimately trigger an immune response if it is administered as a vaccine for Hepatitis B virus genotype G.

Genetic Alterations in HSPA Family of Genes and their Putative Association with HNSCC

Introduction: Head and neck squamous cell carcinoma (HNSCC) is an aggressive life-threatening disease associated with high mortality rates. Several genes related to stress response have been studied extensively to reveal their possible association with HNSCC. Members of the HSPA (heat shock protein family A) family are exclusively expressed under stress conditions suggesting that these are specialised to function in the stress response. Aim: The aim of the present study is to demonstrate the genetic alterations in the HSPA gene family and their putative association with HNSCC. Materials and Methods: The source of the patient's data was procured from the cBioportal database. The TCGA Firehose Legacy comprised 528 head and neck squamous cell carcinoma cases. Oncoprint data analysis can be used to derive a putative association between the disease phenotype and genotype, to identify the variations and to identify any novel variations which can be associated with the disease phenotype. The gnomAD data analysis was used to compare between the observed variants documented in the present study with that of reported variants deposited in the gnomAD repository. Results and Discussion: The HSPA1A&HSPA1B genes harboured high frequency of amplification and deep deletions. The expression of two genes HSPA8 and HSPA13 was found to be up-regulated in the primary tumor sample in comparison to normal tissues. In Kaplan Meier analysis, HSPA8 gene expression was compared with gender, here, high expression in females shows low survival rate. Similarly, HSPA13 gene expression was compared with race, here low expression in africanamerican population shows low survival rate. Conclusion: The present study provides preliminary data on the involvement of the HSPA family of genes with HNSCC, which has to be validated using experimental evidence in other populations.

Experimental exposure of Burkholderia pseudomallei crude culture filtrate upregulates PD-1 on T lymphocytes

Burkholderia pseudomallei is the causative agent for melioidosis. Because of its intracellular nature, the bacterium is capable of replicating within a plethora of eukaryotic cell lines. B. pseudomallei can remain dormant within host cells without symptoms for years, causing recrudescent infections. Here, we investigated the pathogenesis mechanism behind the suppression of T cell responses by B. pseudomallei . Peripheral blood mononuclear cells (1×10⁶ cells/well) isolated by Ficoll Paque (Sigma-Aldrich) density gradient centrifugation were incubated with optimized concentrations of bacterial crude culture filtrate antigens (CFAs) (10 ug ml^-1) and heat-killed bacteria [1 : 10 multiplicity of infection (m.o.i.)]. Following incubation, cells were investigated for surface expression of coinhibitory molecules by flow cytometry. We found that B. pseudomallei induced the upregulation of programmed death 1 (PD-1), a molecule responsible for T cell exhaustion, on T cells in vitro following exposure to crude CFAs of B. pseudomallei . This upregulation of PD-1 probably contributes to poor immune surveillance and disease pathogenesis.

Attenuation of quorum-sensing-dependent virulence factors and biofilm formation by medicinal plants against antibiotic resistant Pseudomonas aeruginosa

Pseudomonas aeruginosa use small signaling molecules such as acyl homoserine lactones (AHLs), which play an important role in release virulence factors and toxin for further establishment of host infection. Thus, involving with the QS system would provide alternative ways of preventing the pathogenicity. In the present study, totally six medicinal plants (Terminalia bellerica, Celastrus paniculatus, Kingiodendron pinnatum, Schleichera oleosa, Melastoma malabathricum, Garcinia gummi-gutta) were screened for anti-QS activity using biomonitor strain of Chromobacterium violaceum CV12472. The primary screening of antimicrobial activity of all the plant extracts have inhibited the growth of tested bacterial species. Of these at the sub-minimum inhibitory concentration the methanol extract of T. bellerica (0.0625–0.5 mg/ml) has significantly inhibited violacein production (20.07–66.22%) in C. violaceum (CV12472). Consequently, the extract of T. bellerica has reduced the production of pyocyanin, exopolysaccharide and biofilm formation in P. aeruginosa strains. Fluorescence and scanning electron microscopy analysis confirmed the reduction of biofilm formation in P. aeruginosa strains when treated with T. bellerica. GC–MS analysis showed the active compounds inhibited the production of virulence factors of P. aeruginosa. The results suggest the possible use of this T. bellerica as an anti-QS and anti-biofilm agent to control Pseudomonas infection. Interference of QS provides an important means for the inhibition of bacterial virulence and thus aids in treatment strategies.

Accumulation of Trace Metals by Mangrove Plants in Indian Sundarban Wetland: Prospects for Phytoremediation

The work investigates on the potential of ten mangrove species for absorption, accumulation and partitioning of trace metal(loid)s in individual plant tissues (leaves, bark and root/pneumatophore) at two study sites of Indian Sundarban Wetland. The metal(loid) concentration in host sediments and their geochemical characteristics were also considered. Mangrove sediments showed unique potential in many- fold increase for most metal(loid)s than plant tissues due to their inherent physicochemical properties. The ranges of concentration of trace metal(loid)s for As, Cd, Co, Cr, Cu, Fe, Hg, Mn, Ni, Pb and Zn in plant tissue were 0.006-0.31, 0.02-2.97, 0.10-4.80, 0.13-6.49, 4.46-48.30, 9.2-938.1, 0.02-0.13, 9.8-1726, 11-5.41, 0.04-7.64, 3.81-52.20 μg g (-1)respectively. The bio- concentration factor (BCF) showed its maximum value (15.5) in Excoecaria agallocha for Cd, suggesting that it can be considered as a high-efficient plant for heavy metal bioaccumulation. Among all metals, Cd and Zn were highly bioaccumulated in E. agallocha (2.97 and 52.2 μg g (-1) respectively. Our findings suggest that the species may be classified as efficient metal trap for Cd in aerial parts, as indicated by higher metal accumulation in the leaves combined with BCF and translocation factor (TF) values.

Vermicomposting of the leaf litter of acacia (Acacia auriculiformis): possible roles of reactor geometry, polyphenols, and lignin

Vermicomposting of the pre-composted leaf litter of acacia (Acacia auriculiformis) was studied in reactors of identical volume but with surface area: height ratios varying from 4 to 250. In separate sets of experiments with these reactors, epigeic earthworm species Eudrilus eugeniae and anecic earthworm species Lampito mauritii were employed at densities of 75 and 150 adult animals per litre of reactor volume. The results reveal that greater the surface area: volume ratio of the reactor, higher is the vermicast output in terms of vermicast output per animal; the more densely populated reactors were comparatively under-productive. Even as the vermicast production remained consistently high in all the reactors, there was significant earthworm mortality throughout the course of the experiments and the worms who survived, steadily lost weight with time. A detailed investigation of the possible causes revealed that, whereas the C:N ratio of acacia compost was comparable with that of other substrates; the polyphenols and lignin content were much higher. Studies by other authors on leaf litter consumption by earthworms in natural or man-made forests have indicated that leaf litter rich in polyphenols and lignin are not preferred by most species of earthworm. This may perhaps be the reason for the high rate of mortality and weight loss in earthworms forced to feed upon acacia in the experiments conducted by the authors.

Recovery of methane-rich gas from solid-feed anaerobic digestion of ipomoea (Ipomoea carnea)

Studies are presented on new types of anaerobic digesters in which chopped or dry crushed Ipomoea carnea was fed without any other pretreatment, in an attempt to develop commercially viable means of utilizing the otherwise very harmful plant. Two types of solid-feed anaerobic digesters (SFADs) were studied. The first type had a single vessel in which the bottom 35% portion was separated from the top portion by a perforated PVC disk. The weed was charged from the top and inoculated with anaerobically digested cowdung-water slurry. The fermentation of the weed in the reactor led to the formation of volatile fatty acids (VFAs) plus some biogas. The leachate, rich in the VFAs, was passed through the perforated PVC sheet and collected in the lower portion of the vessel. The other type of reactors had two vessels, the first one was fully charged with the weed and the second received the VFA leachate. With both types were attached upflow anaerobic filters (UAFs) which converted the leachate into combustible biogas consisting of approximately 70% methane. All SFADs developed very consistent performance in terms of biogas yield within 17 weeks of start. The two-compartment reactors yielded significantly more biogas than the single-compartment reactors of corresponding total volume, and the reactors with which anaerobic filters (AF) were attached yielded more biogas than the ones without AF. The best performing units generated 2.41m(3) of biogas per m(3) of digester volume, as compared to 0.1-0.2m(3) of biogas, m(-3)d(-1), obtainable with conventional digesters. This indicates the viability of this technology. The spent weed can be vermicomposted directly to obtain good soil-conditioner cum fertilizer; earthworm Eudrilus eugeniae produced 540mg vermicast per animal every day, achieving near total conversion of feed to vermicast in 20 days. The proposed systems, thus, makes it possible to accomplish total utilization of ipomoea.

Modeling of ion permeation in calcium and sodium channel selectivity filters

Structure-function studies have shown that it is possible to convert a sodium channel to a calcium-selective channel by a single amino acid substitution in the selectivity filter locus. Ion permeation through the "model selectivity filter" was modeled with a reduced set of functional groups representative of the constituent amino acid side chains. Force-field minimizations were conducted to obtain the energy profile of the cations as they get desolvated and bind to the "model selectivity filter." The calculations suggest that the ion selectivity in the calcium channel is due to preferential binding, whereas in the sodium channel it is due to exclusion. Energetics of displacement of a bound cation from the calcium "model selectivity filter" by another cation suggest that "multi-ion mechanism" reduces the activation barrier for ion permeation. Thus, the simple model captures qualitatively most of the conduction characteristics of sodium and calcium channels. However, the computed barriers for permeation are fairly large, suggesting that ion interaction with additional residues along the transport path may be essential to effect desolvation.