This study used computational tools to predict whether Bnm1, a pollen-specific protein from oilseed rape (Brassica napus), has potential to act as an allergen. Physicochemical properties of Bnm1, such as molecular weight and isoelectric point, were consistent with known allergens. Potential B cell and T cell epitopes were identified. B cell epitopes were mapped to the predicted 3D structure of Bnm1. The results suggest Bnm1 has potential to induce both humoral and cellular allergic immune responses. However, in vitro validation is still needed to confirm Bnm1's potency as an allergen.
Antibiogram and Genotypic Analysis using 16S rDNA after Biofield Treatment on...albertdivis
The aim of this study was to evaluate the effect of Mr. Trivedi’s biofield energy treatment on M. morganii in the lyophilized as well as revived state for antimicrobial susceptibility pattern, biochemical characteristics, biotype number and genotype.
American Journal of Bioterrorism, Biosecurity and Biodefense is an international scholarly peer reviewed Open Access journal, aims to promote the research in all the related fields of Bioterrorism, Biosecurity and Biodefence.
American Journal of Bioterrorism, Biosecurity and Biodefense is a comprehensive Open Access peer reviewed scientific Journal that covers multidisciplinary fields. We provide limitless access towards accessing our literature hub with colossal range of articles. The journal aims to publish high quality varied article types such as Research, Review, Short Communications, Case Reports, Perspectives (Editorials), Clinical Images.
American Journal of Bioterrorism, Biosecurity and Biodefense support the scientific modernization and enrichment in Bioterrorism, Biosecurity and Biodefense research community by magnifying access to peer reviewed scientific literary works. Austin also brings universally peer reviewed member journals under one roof thereby promoting knowledge sharing, collaborative and promotion of multidisciplinary science.
An Effect of Biofield Treatment on Multidrug-resistant Burkholderia cepacia: ...Mahendra Kumar Trivedi
Aim of the present study was to analyze the impact of biofield treatment on multidrug resistant B. cepacia. Clinicalsample of B. cepacia was divided into two groups i.e. control and biofield treated.
Anti-microbial resistance has become a world health issue today. Therefore it is imperative to know about the methods of acquiring resistance and ways to deal with the situation and prevent resistance.
Antibacterial resistance is a major global problem as many bacterial infections are becoming increasingly difficult to treat due to antibiotic resistance. There are two main issues - increased antibiotic resistance among bacteria and a declining antibiotic pipeline. Bacteria are developing resistance to existing antibiotics, especially gram-negative rods, leaving some infections with no effective treatment options. Meanwhile, the development of new antibiotics has slowed dramatically in recent years. Novel approaches are being explored to address the antibiotic resistance crisis, such as developing antibiotics from non-culturable bacteria and using bacteriophages and their gene products. However, the problem of antibiotic resistance worldwide remains serious without action.
Antimicrobial resistance (AMR) occurs when microorganisms become resistant to antimicrobial drugs that were previously able to treat infections. AMR arises through natural mutation and genetic transfer between microbes and is accelerated by misuse and overuse of antimicrobials. If not addressed, AMR could lead to increased mortality and healthcare costs as resistant organisms cause treatment failure. To combat AMR, proper antimicrobial use, hygiene, and surveillance are needed at the patient, clinical, agricultural, and policy levels. Education is also key to promoting appropriate antimicrobial usage.
Antibiogram and Genotypic Analysis using 16S rDNA after Biofield Treatment on...albertdivis
The aim of this study was to evaluate the effect of Mr. Trivedi’s biofield energy treatment on M. morganii in the lyophilized as well as revived state for antimicrobial susceptibility pattern, biochemical characteristics, biotype number and genotype.
American Journal of Bioterrorism, Biosecurity and Biodefense is an international scholarly peer reviewed Open Access journal, aims to promote the research in all the related fields of Bioterrorism, Biosecurity and Biodefence.
American Journal of Bioterrorism, Biosecurity and Biodefense is a comprehensive Open Access peer reviewed scientific Journal that covers multidisciplinary fields. We provide limitless access towards accessing our literature hub with colossal range of articles. The journal aims to publish high quality varied article types such as Research, Review, Short Communications, Case Reports, Perspectives (Editorials), Clinical Images.
American Journal of Bioterrorism, Biosecurity and Biodefense support the scientific modernization and enrichment in Bioterrorism, Biosecurity and Biodefense research community by magnifying access to peer reviewed scientific literary works. Austin also brings universally peer reviewed member journals under one roof thereby promoting knowledge sharing, collaborative and promotion of multidisciplinary science.
An Effect of Biofield Treatment on Multidrug-resistant Burkholderia cepacia: ...Mahendra Kumar Trivedi
Aim of the present study was to analyze the impact of biofield treatment on multidrug resistant B. cepacia. Clinicalsample of B. cepacia was divided into two groups i.e. control and biofield treated.
Anti-microbial resistance has become a world health issue today. Therefore it is imperative to know about the methods of acquiring resistance and ways to deal with the situation and prevent resistance.
Antibacterial resistance is a major global problem as many bacterial infections are becoming increasingly difficult to treat due to antibiotic resistance. There are two main issues - increased antibiotic resistance among bacteria and a declining antibiotic pipeline. Bacteria are developing resistance to existing antibiotics, especially gram-negative rods, leaving some infections with no effective treatment options. Meanwhile, the development of new antibiotics has slowed dramatically in recent years. Novel approaches are being explored to address the antibiotic resistance crisis, such as developing antibiotics from non-culturable bacteria and using bacteriophages and their gene products. However, the problem of antibiotic resistance worldwide remains serious without action.
Antimicrobial resistance (AMR) occurs when microorganisms become resistant to antimicrobial drugs that were previously able to treat infections. AMR arises through natural mutation and genetic transfer between microbes and is accelerated by misuse and overuse of antimicrobials. If not addressed, AMR could lead to increased mortality and healthcare costs as resistant organisms cause treatment failure. To combat AMR, proper antimicrobial use, hygiene, and surveillance are needed at the patient, clinical, agricultural, and policy levels. Education is also key to promoting appropriate antimicrobial usage.
The document discusses hypersensitivity reactions, immune stimulation, and immune suppression. It defines hypersensitivity as increased reactivity to an antigen that an animal has been previously exposed to. Immune stimulation refers to stimulating the immune system through external sources like vaccines to confer a protective effect against microbes. Immune suppression involves deliberately or unintentionally suppressing the immune system through diseases, drugs before transplants, or chemotherapy which increases risk of infection.
Antimicrobial Susceptibility, Biochemical Characterization and Molecular Typi...wilhelm mendel
Pathogenic isolates of Klebsiella pneumoniae (K. pneumoniae), particularly the extended-spectrum β-lactamase (ESBL) producing strains, are mostly associated with the failure of antibiotic therapy in nosocomial infections. The present work was designed to evaluate the impact of Mr. Trivedi’s biofield energy treatment on phenotypic and genotypic characteristics of K. pneumoniae. The strain of K. pneumoniae bearing ATCC 15380 (American Type Culture Collection) was procured from the Bangalore Genei, in sealed pack and divided into control and treated groups. Treated group was subjected to Mr. Trivedi’s biofield energy treatment and analyzed for the antimicrobial susceptibility, minimum inhibitory concentration (MIC), biochemical reactions, and biotyping using automated MicroScan Walk-Away® system. Further, the effect of biofield treatment was also evaluated using Random Amplified Polymorphic DNA (RAPD) in order to determine their epidemiological relatedness and genetic characteristics of biofield treated K. pneumoniae samples. The antimicrobial susceptibility results showed an improve sensitivity (i.e. from intermediate to susceptible) of ampicillin/sulbactam and chloramphenicol, while altered sensitivity of cephalothin (i.e. from susceptible to intermediate) was also reported as compared to the control sample. The MIC value showed two-fold decrease in MIC value of ampicillin/sulbactam (i.e. 16/8 to ≤8/4 μg/mL) and chloramphenicol (i.e. 16 to ≤ 8 μg/mL) as compared to the control. The cephalothin showed two-folds change (i.e. ≤ 8 to 16 μg/mL) in the MIC value as compared with the control. Biofield treatment showed 9.09% alterations in biochemical reactions followed by a change in biotype number (7774 4272) in the treated group with respect to the control (7774 4274). Genetic fingerprinting was performed on control and treated samples using RAPD-PCR biomarkers, which showed an average range of 11 to 15% of polymorphism among the treated samples with respect to the control. These results suggested that Mr. Trivedi’s biofield energy treatment has a significant impact on K. pneumoniae.
Immunoglobulins, also known as antibodies, are Y-shaped proteins produced by B lymphocytes that bind to pathogens like bacteria and viruses. They have a variable region that changes to bind different antigens and a constant region. The five major classes of immunoglobulins are IgG, IgM, IgA, IgE, and IgD. Immunoglobulins recognize and bind to specific antigens, which can trigger immune responses like phagocytosis. While antibodies are a type of immunoglobulin, not all immunoglobulins function as antibodies.
Research topic was come from successful inactivation of some plant viruses by gamma irradiation like Citrus tristeza virus, Necrotic ring spot virus and Prune dwarf virus. Gamma irradiation has been also used to sterilize agricultural products in order to increase their conservation time or to reduce pathogen when being traded from a country to another. Gamma radiation is high-energy radiation emitted from certain radioactive isotopes as cobalt 60, these isotopes are potential sources of gamma radiation. Therefore, this research was conducted to find out the inactivation possibility of Hibiscus witches' broom (HibWB)-phytoplasma using gamma irradiation through tissue culture technique with clarify their effect on in vitro growth and survival rate.
The document discusses recombinant DNA technology. It begins by defining recombinant DNA as DNA molecules formed by joining DNA from two different species. It then discusses the key steps in recombinant DNA technology, including isolating DNA, cutting DNA with restriction enzymes, joining DNA together with DNA ligase, and amplifying the recombinant DNA by inserting it into a host cell. The document also covers applications of recombinant DNA technology such as producing insulin, vaccines, and monoclonal antibodies.
Gentic engineering for disease resistance in cropsChainika Gupta
Genetic engineering can be used to develop transgenic disease resistance in crops. First generation strategies introduced single antimicrobial genes, but second generation strategies manipulate entire signaling pathways for more durable resistance. Targets for second generation strategies include modifying defense signaling pathways using hormones, defense modulators like NPR1, transcription factors like WRKY, and R-genes. Other strategies express virulence factor detoxifiers, antimicrobial peptides/metabolites, phytoalexins, viral coat proteins or replicases, and antisense RNA to inhibit various plant pathogens. While promising, developing transgenic resistance also faces challenges like durability and effects on other pathogens.
Phytopathogen induced changes to plant methylomesroshni mohan
This document summarizes a seminar presentation on phytopathogen-induced changes to plant methylomes. It discusses various methods for profiling genome-wide DNA methylation in plants and provides examples of plant methylome changes induced by different pathogens, including bacteria, fungi, viruses, cyst nematodes, and rhizobium. It also describes a case study that analyzed differential DNA methylation and gene expression changes in Arabidopsis roots infected with the cyst nematode Heterodera schachtii using methylation profiling and RNA-sequencing. The study found H. schachtii preferentially induces hypomethylation and targets specific transposable elements and genes for differential methylation.
Transgenics, Environmental Concerns & Biosafety Issues Related To BT GeneVikas Verma
1. The document discusses Bacillus thuringiensis (Bt), a soil bacterium that produces Cry proteins toxic to insect pests. Genes coding for these Cry proteins have been inserted into crops like cotton, making them insect resistant.
2. The development of transgenic crops involves identifying genes for desired traits, copying the genes, transferring them to plant tissues, regenerating plants, and extensive safety testing before commercialization.
3. Major concerns regarding Bt crops include their potential effects on human health, development of insect resistance, gene transfer to wild plants, and impacts on biodiversity. Proper regulation and labeling are important to address these environmental and safety issues.
A mutation is a change in a DNA sequence that can be caused by errors during DNA replication, exposure to mutagens like radiation or chemicals, or infection by viruses. Mutations can be passed on to offspring or occur somatically in body cells. Some mutations can cause genetic disorders like sickle cell anemia, Down syndrome, or Edwards syndrome, while others may have no effect or even provide an advantage to survival. Mutants arise from mutations in existing genomes due to errors in DNA replication or repair.
Reverse vaccinology uses genomics and bioinformatics to identify antigens that could be used in vaccines, rather than relying on culturing pathogens. It sequences the genome of a pathogen and predicts potential antigens, allowing development of vaccines for pathogens that cannot be grown in culture. This approach was used to develop a vaccine for Neisseria meningitidis serogroup B, the first reverse vaccinology vaccine approved for use. Traditional vaccinology is limited by only being able to use antigens that are abundant during infection and that the pathogen can be cultured, whereas reverse vaccinology makes all antigens available for vaccine development.
Management of host plant resistance through immunizationAnshul Arya
it is a small presentation prepared for seminar purpose .immunization is a new technique very few people know about it even i did not get any slide prepared by it earlier even whatever i got was not purchased .so i prepared it for those who are interested to know about it without having problems to find the matter for it.
Antimicrobial Sensitivity Pattern of Pseudomonas fluorescens after Biofield T...Mahendra Kumar Trivedi
Objective of this study was to investigate the effect of biofield treatment on antimicrobial sensitivity patternof P. fluorescens. P. fluorescens cells were procured from MicroBioLogics in sealed packs bearing the AmericanType Culture Collection (ATCC 49838) number.
Multi-drug resistant tuberculosis (MDR-TB) arises from inadequate or incomplete treatment that allows bacteria to develop resistance to multiple drugs. MDR-TB bacteria resist key first-line drugs like isoniazid and rifampin and require lengthy treatment with second-line drugs. The development of drug resistance threatens global TB control and highlights the need for improved diagnostics, treatment monitoring, and antibiotic stewardship to limit resistance.
The document discusses plant disease resistance genes (R-genes) and their importance in crop breeding for disease resistance. It contains the following key points:
1. R-genes encode receptors that recognize pathogen effector proteins and trigger plant immune responses. Most R-genes contain nucleotide binding and leucine-rich repeat domains.
2. Dozens of R-genes have been cloned from various plants using map-based cloning, transposon tagging, or a new method called MutRenSeq that enriches for R-gene sequences.
3. Introducing R-genes from wild crop relatives into domestic crops can provide natural and sustainable resistance to diseases while avoiding pesticide use and potential environmental damage.
Antimicrobial resistance, Dr Soumya Dey and Dr Tapas BaikarTapas Baikar
This document provides an overview of antimicrobial resistance (AMR). It defines AMR and discusses the types (natural vs acquired), mechanisms (mutation, gene transfer), and evolution of antibiotic resistance. Types of acquired resistance include mutation (single or multi-step) and gene transfer (conjugation, transformation, transduction). Common resistance mechanisms include drug tolerance, destruction, and impermeability. Examples are given of resistance mechanisms for antimalarial, antiretroviral, and antitubercular drugs. The global prevalence of multi-drug resistant tuberculosis and trends in AMR for various pathogens like E. coli, Salmonella, and Staphylococcus aureus in India are summarized. Interventions to address AMR include
This document summarizes research on the plant pathogenic bacterium Pseudomonas syringae and one of its virulence factors, HrpZ1. Key findings include:
1) HrpZ1 is a type III secreted protein that can form ion-conducting pores in lipid membranes and trigger plant immune responses. However, pore formation and immune activation are separate functions localized to different domains.
2) The C-terminal domain of HrpZ1 is necessary and sufficient for binding to plant membranes and stimulating immunity responses, but not for pore formation.
3) Insertional mutations in the C-terminal domain disrupt HrpZ1's ability to activate immunity, suggesting this domain contains motifs recognized by plant
Fungal biocontrol agents like Trichoderma spp. can induce systemic resistance in plants against pathogens through several mechanisms. They compete with pathogens for space and nutrients, produce antibiotics, or act as mycoparasites against other fungi. Trichoderma elicits plant defenses by inducing the expression of pathogenesis-related proteins and antioxidant enzymes. Case studies showed Trichoderma reduced disease severity in cotton, barley, and maize by triggering the plants' terpenoid defenses or increasing their tolerance to salt and drought stress. Fungal biocontrol is an environmentally sustainable alternative to chemicals for managing plant diseases.
Lecture 8 digital printing of textiles (condensed)Adane Nega
Digital printing of textiles allows for mass customization by printing designs directly from digital files without screens or plates. It provides benefits like quick design changes and short runs but adoption has been slow due to limitations in printing speed. Improvements are being made and digital printing is gaining acceptance for applications like sampling and short runs while conventional printing remains dominant for bulk production. In the future, further increases in printing speeds may allow digital printing to compete for more bulk production applications and even be used in a woven format like looms.
Lecture 5 dyeing of cotton with reactive dyesAdane Nega
The document discusses the discovery and development of reactive dyes for dyeing cotton fabrics. Reactive dyes were discovered in 1956 and allow for covalent bonding between dye molecules and cellulose fibers. They are classified as mono-functional or bi-functional depending on whether they contain one or two reactive groups. Common reactive groups include dichlorotriazine, monochlorotriazine, and vinyl sulphone. The document also describes different dyeing methods for reactive dyes such as batch, pad-batch, pad-dry, and pad-dry-bake and provides statistics on global cotton dyeing with reactive dyes.
The document discusses hypersensitivity reactions, immune stimulation, and immune suppression. It defines hypersensitivity as increased reactivity to an antigen that an animal has been previously exposed to. Immune stimulation refers to stimulating the immune system through external sources like vaccines to confer a protective effect against microbes. Immune suppression involves deliberately or unintentionally suppressing the immune system through diseases, drugs before transplants, or chemotherapy which increases risk of infection.
Antimicrobial Susceptibility, Biochemical Characterization and Molecular Typi...wilhelm mendel
Pathogenic isolates of Klebsiella pneumoniae (K. pneumoniae), particularly the extended-spectrum β-lactamase (ESBL) producing strains, are mostly associated with the failure of antibiotic therapy in nosocomial infections. The present work was designed to evaluate the impact of Mr. Trivedi’s biofield energy treatment on phenotypic and genotypic characteristics of K. pneumoniae. The strain of K. pneumoniae bearing ATCC 15380 (American Type Culture Collection) was procured from the Bangalore Genei, in sealed pack and divided into control and treated groups. Treated group was subjected to Mr. Trivedi’s biofield energy treatment and analyzed for the antimicrobial susceptibility, minimum inhibitory concentration (MIC), biochemical reactions, and biotyping using automated MicroScan Walk-Away® system. Further, the effect of biofield treatment was also evaluated using Random Amplified Polymorphic DNA (RAPD) in order to determine their epidemiological relatedness and genetic characteristics of biofield treated K. pneumoniae samples. The antimicrobial susceptibility results showed an improve sensitivity (i.e. from intermediate to susceptible) of ampicillin/sulbactam and chloramphenicol, while altered sensitivity of cephalothin (i.e. from susceptible to intermediate) was also reported as compared to the control sample. The MIC value showed two-fold decrease in MIC value of ampicillin/sulbactam (i.e. 16/8 to ≤8/4 μg/mL) and chloramphenicol (i.e. 16 to ≤ 8 μg/mL) as compared to the control. The cephalothin showed two-folds change (i.e. ≤ 8 to 16 μg/mL) in the MIC value as compared with the control. Biofield treatment showed 9.09% alterations in biochemical reactions followed by a change in biotype number (7774 4272) in the treated group with respect to the control (7774 4274). Genetic fingerprinting was performed on control and treated samples using RAPD-PCR biomarkers, which showed an average range of 11 to 15% of polymorphism among the treated samples with respect to the control. These results suggested that Mr. Trivedi’s biofield energy treatment has a significant impact on K. pneumoniae.
Immunoglobulins, also known as antibodies, are Y-shaped proteins produced by B lymphocytes that bind to pathogens like bacteria and viruses. They have a variable region that changes to bind different antigens and a constant region. The five major classes of immunoglobulins are IgG, IgM, IgA, IgE, and IgD. Immunoglobulins recognize and bind to specific antigens, which can trigger immune responses like phagocytosis. While antibodies are a type of immunoglobulin, not all immunoglobulins function as antibodies.
Research topic was come from successful inactivation of some plant viruses by gamma irradiation like Citrus tristeza virus, Necrotic ring spot virus and Prune dwarf virus. Gamma irradiation has been also used to sterilize agricultural products in order to increase their conservation time or to reduce pathogen when being traded from a country to another. Gamma radiation is high-energy radiation emitted from certain radioactive isotopes as cobalt 60, these isotopes are potential sources of gamma radiation. Therefore, this research was conducted to find out the inactivation possibility of Hibiscus witches' broom (HibWB)-phytoplasma using gamma irradiation through tissue culture technique with clarify their effect on in vitro growth and survival rate.
The document discusses recombinant DNA technology. It begins by defining recombinant DNA as DNA molecules formed by joining DNA from two different species. It then discusses the key steps in recombinant DNA technology, including isolating DNA, cutting DNA with restriction enzymes, joining DNA together with DNA ligase, and amplifying the recombinant DNA by inserting it into a host cell. The document also covers applications of recombinant DNA technology such as producing insulin, vaccines, and monoclonal antibodies.
Gentic engineering for disease resistance in cropsChainika Gupta
Genetic engineering can be used to develop transgenic disease resistance in crops. First generation strategies introduced single antimicrobial genes, but second generation strategies manipulate entire signaling pathways for more durable resistance. Targets for second generation strategies include modifying defense signaling pathways using hormones, defense modulators like NPR1, transcription factors like WRKY, and R-genes. Other strategies express virulence factor detoxifiers, antimicrobial peptides/metabolites, phytoalexins, viral coat proteins or replicases, and antisense RNA to inhibit various plant pathogens. While promising, developing transgenic resistance also faces challenges like durability and effects on other pathogens.
Phytopathogen induced changes to plant methylomesroshni mohan
This document summarizes a seminar presentation on phytopathogen-induced changes to plant methylomes. It discusses various methods for profiling genome-wide DNA methylation in plants and provides examples of plant methylome changes induced by different pathogens, including bacteria, fungi, viruses, cyst nematodes, and rhizobium. It also describes a case study that analyzed differential DNA methylation and gene expression changes in Arabidopsis roots infected with the cyst nematode Heterodera schachtii using methylation profiling and RNA-sequencing. The study found H. schachtii preferentially induces hypomethylation and targets specific transposable elements and genes for differential methylation.
Transgenics, Environmental Concerns & Biosafety Issues Related To BT GeneVikas Verma
1. The document discusses Bacillus thuringiensis (Bt), a soil bacterium that produces Cry proteins toxic to insect pests. Genes coding for these Cry proteins have been inserted into crops like cotton, making them insect resistant.
2. The development of transgenic crops involves identifying genes for desired traits, copying the genes, transferring them to plant tissues, regenerating plants, and extensive safety testing before commercialization.
3. Major concerns regarding Bt crops include their potential effects on human health, development of insect resistance, gene transfer to wild plants, and impacts on biodiversity. Proper regulation and labeling are important to address these environmental and safety issues.
A mutation is a change in a DNA sequence that can be caused by errors during DNA replication, exposure to mutagens like radiation or chemicals, or infection by viruses. Mutations can be passed on to offspring or occur somatically in body cells. Some mutations can cause genetic disorders like sickle cell anemia, Down syndrome, or Edwards syndrome, while others may have no effect or even provide an advantage to survival. Mutants arise from mutations in existing genomes due to errors in DNA replication or repair.
Reverse vaccinology uses genomics and bioinformatics to identify antigens that could be used in vaccines, rather than relying on culturing pathogens. It sequences the genome of a pathogen and predicts potential antigens, allowing development of vaccines for pathogens that cannot be grown in culture. This approach was used to develop a vaccine for Neisseria meningitidis serogroup B, the first reverse vaccinology vaccine approved for use. Traditional vaccinology is limited by only being able to use antigens that are abundant during infection and that the pathogen can be cultured, whereas reverse vaccinology makes all antigens available for vaccine development.
Management of host plant resistance through immunizationAnshul Arya
it is a small presentation prepared for seminar purpose .immunization is a new technique very few people know about it even i did not get any slide prepared by it earlier even whatever i got was not purchased .so i prepared it for those who are interested to know about it without having problems to find the matter for it.
Antimicrobial Sensitivity Pattern of Pseudomonas fluorescens after Biofield T...Mahendra Kumar Trivedi
Objective of this study was to investigate the effect of biofield treatment on antimicrobial sensitivity patternof P. fluorescens. P. fluorescens cells were procured from MicroBioLogics in sealed packs bearing the AmericanType Culture Collection (ATCC 49838) number.
Multi-drug resistant tuberculosis (MDR-TB) arises from inadequate or incomplete treatment that allows bacteria to develop resistance to multiple drugs. MDR-TB bacteria resist key first-line drugs like isoniazid and rifampin and require lengthy treatment with second-line drugs. The development of drug resistance threatens global TB control and highlights the need for improved diagnostics, treatment monitoring, and antibiotic stewardship to limit resistance.
The document discusses plant disease resistance genes (R-genes) and their importance in crop breeding for disease resistance. It contains the following key points:
1. R-genes encode receptors that recognize pathogen effector proteins and trigger plant immune responses. Most R-genes contain nucleotide binding and leucine-rich repeat domains.
2. Dozens of R-genes have been cloned from various plants using map-based cloning, transposon tagging, or a new method called MutRenSeq that enriches for R-gene sequences.
3. Introducing R-genes from wild crop relatives into domestic crops can provide natural and sustainable resistance to diseases while avoiding pesticide use and potential environmental damage.
Antimicrobial resistance, Dr Soumya Dey and Dr Tapas BaikarTapas Baikar
This document provides an overview of antimicrobial resistance (AMR). It defines AMR and discusses the types (natural vs acquired), mechanisms (mutation, gene transfer), and evolution of antibiotic resistance. Types of acquired resistance include mutation (single or multi-step) and gene transfer (conjugation, transformation, transduction). Common resistance mechanisms include drug tolerance, destruction, and impermeability. Examples are given of resistance mechanisms for antimalarial, antiretroviral, and antitubercular drugs. The global prevalence of multi-drug resistant tuberculosis and trends in AMR for various pathogens like E. coli, Salmonella, and Staphylococcus aureus in India are summarized. Interventions to address AMR include
This document summarizes research on the plant pathogenic bacterium Pseudomonas syringae and one of its virulence factors, HrpZ1. Key findings include:
1) HrpZ1 is a type III secreted protein that can form ion-conducting pores in lipid membranes and trigger plant immune responses. However, pore formation and immune activation are separate functions localized to different domains.
2) The C-terminal domain of HrpZ1 is necessary and sufficient for binding to plant membranes and stimulating immunity responses, but not for pore formation.
3) Insertional mutations in the C-terminal domain disrupt HrpZ1's ability to activate immunity, suggesting this domain contains motifs recognized by plant
Fungal biocontrol agents like Trichoderma spp. can induce systemic resistance in plants against pathogens through several mechanisms. They compete with pathogens for space and nutrients, produce antibiotics, or act as mycoparasites against other fungi. Trichoderma elicits plant defenses by inducing the expression of pathogenesis-related proteins and antioxidant enzymes. Case studies showed Trichoderma reduced disease severity in cotton, barley, and maize by triggering the plants' terpenoid defenses or increasing their tolerance to salt and drought stress. Fungal biocontrol is an environmentally sustainable alternative to chemicals for managing plant diseases.
Lecture 8 digital printing of textiles (condensed)Adane Nega
Digital printing of textiles allows for mass customization by printing designs directly from digital files without screens or plates. It provides benefits like quick design changes and short runs but adoption has been slow due to limitations in printing speed. Improvements are being made and digital printing is gaining acceptance for applications like sampling and short runs while conventional printing remains dominant for bulk production. In the future, further increases in printing speeds may allow digital printing to compete for more bulk production applications and even be used in a woven format like looms.
Lecture 5 dyeing of cotton with reactive dyesAdane Nega
The document discusses the discovery and development of reactive dyes for dyeing cotton fabrics. Reactive dyes were discovered in 1956 and allow for covalent bonding between dye molecules and cellulose fibers. They are classified as mono-functional or bi-functional depending on whether they contain one or two reactive groups. Common reactive groups include dichlorotriazine, monochlorotriazine, and vinyl sulphone. The document also describes different dyeing methods for reactive dyes such as batch, pad-batch, pad-dry, and pad-dry-bake and provides statistics on global cotton dyeing with reactive dyes.
Lecture 10 environment friendly dyeing of cottonAdane Nega
The document discusses various methods for making cotton dyeing more environmentally friendly. It focuses on reducing the amount of dyes, salts, and other chemicals released in effluents. Some key methods mentioned are using bifunctional reactive dyes for lower color effluents, low salt reactive dyes to reduce salt, replacing sodium hydrosulfite and sodium sulfide reducing agents, and dyeing at lower liquor ratios. The goal is to meet environmental standards while maintaining dye yield and fastness properties.
This document discusses sustainable and eco-friendly textile sourcing and production. It covers topics like sourcing from China, Africa, and India; sustainable dyeing methods; questions for eco designers; and resources for recycled and organic materials. Key sustainable textile companies mentioned include Indego Africa, Joy of Life, Kishor Imports, Lenzing, and AirDye. Digital printing is highlighted as a water-free dyeing method.
The document discusses organic and naturally colored cotton production around the world. It provides details on the history and development of organic cotton cultivation in various countries like India, Peru, Australia, and its usage in textile and apparel production. It also summarizes the work of Sally Fox in breeding varieties of naturally colored cotton and establishing companies for producing fabrics and clothing from these cotton varieties.
The document discusses eco-friendly textiles and organic cotton cultivation. It notes that conventional cotton production relies heavily on pesticides and fertilizers that harm the environment and human health. Organic cotton is identified as a more sustainable alternative that maintains soil health and uses natural pest control methods instead of chemicals. The document outlines the benefits of organic cotton cultivation for the environment and farmers.
Eco fibres and ecofriendly textiles ms univ. 21.2.04 finalAdane Nega
The document discusses eco-friendly textiles and organic cotton cultivation. It notes that conventional cotton production relies heavily on pesticides and fertilizers that harm the environment and human health. Organic cotton cultivation avoids the use of chemicals and promotes sustainable agriculture. Some of the benefits of organic cotton include reduced costs, management of pesticide resistance, and environmental friendliness. India is a major cotton producer but organic cotton currently makes up a very small percentage of production. Several organizations promote organic cotton farming in India.
Environmental friendly processing of textile fibresmona verma
This document discusses eco-friendly and organic cotton processing using enzymes. It begins with introductions to cotton production in India and the advantages and disadvantages of cotton. It then defines what makes materials eco-friendly and describes organic cotton certification standards. The rest of the document focuses on using enzymes for cotton processing, their properties, mechanisms, and specific uses for desizing and other treatments to make processing more environmentally sustainable.
Presentation on Green Marketing and eco-friendly products|Can marketing reall...Kartik Mehta
Green marketing involves developing and promoting products and services in an environmentally friendly way. It can help build a company's image and satisfy customer demand for sustainable options. However, there are also challenges to green marketing, such as higher costs and lack of consumer awareness. Authentic green marketing that avoids greenwashing can help drive long-term growth while addressing environmental issues.
Fulfillment an E-Archiving System for MENA CountriesIJSRED
This document describes an in silico analysis of Clostridium perfringens type D epsilon toxin to identify B cell epitopes and select optimal multiepitope fragments for vaccine development. The epsilon toxin sequence was obtained from databases and analyzed using various algorithms to predict linear and discontinuous epitopes. Three overlapping fragments were selected based on predicted epitope scores. Fragment 3 had the highest score for linear epitopes while Fragment 1 scored highest for discontinuous epitopes. Additional experimental validation is still needed to confirm the predicted epitopes and evaluate the fragments' potential as vaccine candidates.
Chlorogenic acid may be a potent inhibitor of dimeric SARS-CoV-2 main proteas...LucyPi1
Abstract Background: Since the emergence of coronavirus disease 2019 to date, there is no available approved drug or definitive treatment for coronavirus disease 2019 viral infection, and the identification of novel hits against therapeutic targets has become a global emergency. Echinacea purpurea is a traditional herb utilized to treat cough, fever, sore throat, respiratory tract infection, and so on as an immune stimulant. In this study, in silico molecular docking approach was used to screen phytocompounds from E. purpurea against severe acute respiratory syndrome coronavirus 2 main protease 3C-like protease (3CLpro) and severe acute respiratory syndrome coronavirus main peptidase (96% sequence similarity) to blunt the viral gene expression and viral replication. Methods: Initially, we screened phytocompounds for their druggability and ADMET property. Furthermore, x-ray crystallographic structures of main proteases 3CLpro and main peptidase having Protein Data Bank ID 6LU7 and 2GTB were used as protein targets for the identification of potential drug candidates. We performed docking using AutoDock Vina by PyRx 0.8 software. BIOVIA Discovery Studio Visualizer v2019 was used to analyze ligand-protein complex. The probable protein targets of the selected compound were predicted by BindingDB (P ≥ 0.7). STRING and Kyoto Encyclopedia of Genes and Genomes pathways are utilized to identify the molecular pathways modulated by the predicted targets (FDR ≤ 0.05), and the network interaction between compounds and protein pathways was constricted by Cytoscape 3.6.1. Results: Among all the compounds, chlorogenic acid showed druggable characteristics and scored the lowest binding energy with main protease and main peptidase via interacting with active site 1 domain amino acid residues. Interestingly, chlorogenic acid interacted with Phe140 main protease 3CLpro, which is potentially involved in the dimerization. Enrichment analysis identified chlorogenic acid to modulate insulin resistance, necroptosis, interleukin-17, tumor necrosis factor signaling pathway, legionellosis, T helper 17 cell differentiation, advanced glycation end products and receptor for advanced glycation end products, mitogen-activated protein kinase, Ras, estrogen, vascular endothelial growth factor, B-cell receptor, nuclear factor kappa B, Rap1, hypoxia inducible factor-1, phosphatidylinositide 3-kinase-Akt, insulin, mechanistic target of rapamycin, p53, retinoic acid inducible gene I like receptor, and ErbB signaling pathways. Conclusion: Chlorogenic acid may act as a potent main protease 3CLpro inhibitor and may also inhibit the severe acute respiratory syndrome coronavirus 2 dimerization, viral gene expression, and replication within the lung epithelium. Chlorogenic acid may go a long way in finding one of the multipronged solutions to tackle coronavirus disease 2019 viral infection in the future.
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Computational identification of Brassica napus pollen specific protein Bnm1 as an allergen
1. International Journal on Bioinformatics & Biosciences (IJBB) Vol.3, No.2, June 2013
DOI: 10.5121/ijbb.2013.3205 45
Computational identification of Brassica napus
pollen specific protein Bnm1 as an allergen
Md. Rezaul Islama,*
, Ahsan Habib Polashb
, M Sadman Sakiba
, Chinmoy Sahac
,
Atiqur Rahmana
a
Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka-1000,
Bangladesh
b
Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology,
University of Dhaka, Dhaka-1000, Bangladesh
c
Postgraduate School of Molecular Medicine, Erasmus MC, Rotterdam, The Netherlands.
E-mail address: rezaul.nayeem@gmail.com
Abstract
Bnm1 is a pollen specific protein from Brassica napus (oilseed rape) and it is specifically expressed in the
bi-cellular and tri-cellular stages of pollen development. Since the incidence of pollinosis due to oilseed
rape (Brassica napus) is increasing day by day, keeping pace with its high cultivation rate, the search for
its allergens is a demand of time to develop effective immune therapy. In the present study, different
computational tools were adopted to predict the potential of Bnm1 as a candidate allergen. Physico-
chemical properties of Bnm1 showed its molecular weight (~20kD) and theoretical pI (5.27) along with
other properties to be fallen between the ranges essential for a protein to be an allergen. Keeping in mind
the capability of allergen to induce both humoral and cell mediated immune response, we checked both the
potential B cell and T cell epitope candidates of Bnm1 using different immune-informatics tools housed at
IEDB analysis resource. For B cell epitope prediction, potential antigenic sites on the protein surface were
predicted by both propensity scale and machine learning method followed by their mapping on Bnm1 3D
structure predicted from homology modeling. In case of T cell epitope prediction, interaction of the core
sequence with seven abundant MHC-II alleles (DRB1*0101, DRB1*0301, DRB1*0401, DRB1*0701,
DRB1*1101, DRB1*1301 and DRB1*1501) within an IC50 range (IC50<25) was the basis. We observed
multiple epitope interactions with DRB1*0101 allele, implying that this interactions might evoke a strong
TH2 response ensuring an increased production of IgE response. Based on our prediction we hereby claim
that the Bnm1 is a potential allergen having capability to induce both humoral and cell mediated allergic
responses. However, in vitro analysis was out of our scope and therefore it should have to be performed to
validate the potency of Bnm1 as an allergen.
Key words: Bnm1, Brassica napus, allergen, pollinosis, in silico, epitope
1. Introduction
Allergens are mostly small proteins or protein bound small substances having a molecular weight
ranging from 15 to 40 kD [1]. These proteins or protein associated substances not only can induce
IgE antibody mediated immune response but also can induce other antibody responses like IgA,
IgM, and IgG [2]. Moreover, they can elicit T cell response in the human body system which is
mostly Th2 cell mediated [3, 4]. The sources of these allergens can be different food items,
foreign serums, insect venoms, pollens, insect products etc. [5]. Most of the allergens have
biological function but little is known about their functional relevance to allergenicity. The
functional property of allergen like enzyme activity may contribute to the induction of
allergenicity [6]. Pollen allergy (pollinosis) has brought a large attention to the scientific
2. International Journal on Bioinformatics & Biosciences (IJBB) Vol.3, No.2, June 2013
46
community around the world and the rate of pollinosis is increasing day by day [7, 8]. Among
the symptoms of immediate response upon exposure to pollen allergens are allergic rhinitis,
asthma and hay-fever [9-11] etc. Individuals who are hypersensitive to pollen often show allergic
like symptoms.
Brassica napus (oilseed rape), belonging to cruciferae family, is one of the most cultivated crop
plants around the world. The importance of this plant as a source of oil and medicinal
components is reviewed elsewhere. Cultivation rate of oilseed rape around the globe has been
increasing over the last 10 years resulting in about 31.5 Mha of lands used to cultivate in 2010
[12] The recent introduction of genetically engineered oil seed has geared the cultivation rate
even more [13, 14].
With the pace of the cultivation rate of this plant an alarming concern for allergenicity is
generated, since pollen from oilseed rape have been reported as potential allergen. In the most
abundant regions, most patients with hay-fever blame the blooming of Brassica napus for their
symptoms during its flowering season [15]. During this flowering season the microscopic male
cells of the plant make round or oval structural grain which is programmed to transport along the
wind to help in the process of pollination. Pollens of Brassica napus guided by the wind are
spreaded everywhere around the cultivated land and people mostly farmers having exposed to it
suffer from hay-fever, allergic rhinitis like seasonal diseases [15]
Although some of the high molecular mass proteins in oilseed rape pollen have been identified as
allergens [16-20], a quest for other allergens is going on in different laboratories. In modern
biology, in silico approaches have made it possible to give a straightforward time and money
saving way to find out the solution of many biological problems like vaccine design [21],
prediction of deleterious effects of mutations [22] and many more. It can also predict potential
allergens from a given whole proteome.
Bnm1 is a pollen specific protein in Brassica napus and it is specifically expressed in the
bicellular and tricellular stages of pollen development [23]. In the present study we have
attempted to analyze the potentials of Bnm1 to be an allergen using different computational tools
and immune-informatics databases. To our knowledge, this is the first immune-informatics
approach to examine the potency of Bnm1 from oilseed rape to be an allergen.
2. Materials and Methods:
2.1 Protein Sequence retrieval
Bnm1 (pollen specific protein) protein sequence (P93760) for Brassica napus was retrieved from
the UniProt database (http://www.uniprot.org/). This protein sequence was the basis to perform
different computational predictions from linear amino acid residues.
2.2 Prediction of physico-chemical properties
Different physico-chemical properties for Bnm1 protein was predicted from its linear amino acid
sequence. ProtParam tool was employed to predict various physical and chemical properties for
Bnm1 protein including the molecular weight, theoretical pI, atomic composition, amino acid
composition, instability index, extinction coefficient, grand average of hydropathicity (GRAVY),
estimated half-life, and aliphatic index [24].
2.3 Potential antigenic sites prediction
Antigenicity of the protein was predicted by determination of hydrophobic-hydrophilic region
and thereby determining the regions of protein, exposed to outer surface and can react to B cell.
To predict the potential antigenic sites two prediction methods called Kolaskar-Tongaonkar
antigenicity and Parker’s hydrophilicity were assigned followed by determination of antigenic
propensity and hydrophilicity respectively from the plots generated [25, 26].
3. International Journal on Bioinformatics & Biosciences (IJBB) Vol.3, No.2, June 2013
47
2.4 Potential B cell epitope prediction:
All the regions exposed to outer surface are not potent site to react with B cell, that’s why B cell
epitopes are needed to be predicted. A machine learning tool BepiPred housed at IEDB analysis
tools was assigned to predict B cell epitope [27]. This tool uses a combinatorial algorithm
comprising both hidden markov model and antigenic propensity and thus was used to cross check
the predicted result from Parker’s hydrophilicity and Kolaskar-Tongaonkar antigenicity
prediction method [25, 26].
2.5 Prediction of 3D structure of Bnm1 and mapping of B cell epitopes on the
structure
For 3-D structure prediction we followed a template based Bnm1 protein structure modeling
using RaptorX (http://raptorx.uchicago.edu/) server which makes several alignments of the target
protein sequence with different protein templates having sparse protein sequence to predict the ab
initio model of protein, which is essential to have a better structure prediction [28]. Based on the
alignment score top ten ranked alignments were predicted by probabilistic-consistency algorithm
and a novel nonlinear scoring function. We chose the structure of Bnm1 which showed maximum
alignment score between the Bnm1 protein and its target template (RCSB PDB ID 1x8z, chain
A). Energy minimization of the structure was performed by Swiss PDB viewer tool [29]. To
validate the structure a Ramachandran plot was generated using ProCheck program [30] which
measures the stereo-chemical properties of the protein structure.
2.6 Potential T cell epitope prediction
To check whether the Bnm1 protein can elicit T cell response, we predicted potential T cell
epitopes using “Peptide binding to MHC class II molecules” program under “MHCII binding
prediction” tool in IEDB analysis resource. For our prediction we followed NetMHCIIpan
prediction method choosing the seven abundant HLA class II alleles DRB1*0101, DRB1*0301,
DRB1*0401, DRB1*0701, DRB1*1101, DRB1*1301 and DRB1*1501 from the selection panel
[31, 32]. Later, from the predicted T cell epitopes only those epitopes having IC50 score less than
25 were selected as potential T cell epitope candidates since epitopes having IC50 value < 25
shows higher binding affinity with MHC alleles [33].
3. Results and Discussion
3.1 Physico-chemical properties predicts similar characteristics of Bnm1 like
conventional allergen
Physico-chemical properties of an intact protein sometimes can predict the allergenic potential of
a protein [34]. Bnm1 consists of 182 amino acids and the molecular weight was predicted to be
approximately 20 kD (Table 1). The total amino acid distribution along the Bnm1 protein (Figure
1) shows that there is no tryptophan residue present and among the 20 amino acids six amino acid
residues e.g. Ala, Asp, Leu, Ser, Thr and Val comprise almost 60% of total composition of Bnm1
protein (Figure 1). Since all of these highly abundant residues have acidic pI (minimum 2.77 for
Asp to maximum 6.0 for Ala) range, this suggests the protein’s theoretical pI to be acidic which is
a combinatorial score of all the pI scores for all the amino acid residues present in Bnm1 protein.
4. International Journal on Bioinformatics & Biosciences (IJBB) Vol.3, No.2, June 2013
48
Table 1 Detail of physico-chemical properties for Bnm1 protein from oilseed rape
Properties score
Number of amino acids 182
Molecular weight 19651.2
Theoretical pI 5.27
Total number of negatively charged residues
(Asp + Glu)
24
Total number of positively charged residues
(Arg + Lys)
17
Total number of atoms 2759
Ext. coefficient(M-1
cm-1)
7575
The estimated half-life
30 hours
The instability index (II) 40.27
Aliphatic index
88.63
Grand average of hydropathicity (GRAVY) -0.128
ProtParam prediction shows that the protein is acidic (pI 5.27) and net negatively charged as total
number of negatively charged residues outnumber the total number of positively charged residues
(Table 1), hence it may preferentially be processed by dendritic cells [34]. Based on the half lives
of the individual N-terminal amino acid residues, the predicted overall half life of the Bnm1 [35,
36] was quite a high as 30 hours. The predicted instability index of the Bnm1 indicates that this
protein is slightly unstable. The grand average of hydropathicity predicted from the Bnm1 linear
protein sequence was predicted as negative and hence most of the amino acid residues in Bnm1
protein are likely to be present on the surface of the folded Bnm1 protein.
5. International Journal on Bioinformatics & Biosciences (IJBB) Vol.3, No.2, June 2013
49
Figure 1 Amino acid composition of Bnm1 Among the all amino acids present in Bnm1, Alanine (Ala) is
~16.5% of total composition and thus outnumbers the other amino acid. Cysteine (Cys) is of least
percentage present in Bnm1 protien. Note there is no tryptophan residue in its total composition.
3.2 Potential antigenic sites are on the surface of the Bnm1 protein
To show allergenic response the whole protein does not need to be antigenic; rather there are
some antigenic determinants which are called epitope accounts for the immunogenic reactions. It
is hypothesized that the antigenic epitope must reside in the outer layer or the hydrophilic region
of the protein so that it can interact with others. So simply hydrophobic or hydrophilic profile of a
protein sometimes can predict a protein’s potential as an allergen from the linear amino acid
sequence [37]. For prediction of Bnm1 allergenicity, Kolaskar and Tongaonkar prediction method
was employed which functions on the basis of physico-chemical properties of amino acids in
proteins and abundances in experimentally known epitopes [25]. In Kolaskar scale X axis
represents amino acid residues whereas Y axis represents anigenic propensity of the protein.
Figure 2 Kolaskar and Tongaonkar antigneicity graphical plot. The protein sequences those satisfied the set
threshold value (antigenic propensity threshold 1.00) are predicted to be potential antigenic site against which
antibodies can elicit the response.
6. International Journal on Bioinformatics & Biosciences (IJBB) Vol.3, No.2, June 2013
50
Table 2 Potential antigenic peptide sequences predicted from kolaskar and Togaonkar
antigenicity plot
number Start
position
End
position
Peptide sequence Peptide
length
1 4 40 FSVLSTFAAAAITLQLLLVPASASPHM
KYIDAICDRS
37
2 43 50 QDYCVKTL 8
3 56 76 TAAPIGLNPLAEVMALTIAHA 21
4 80 86 AAFAET 7
5 96 107 YHKAYLAWADL 12
6 109 117 SANLKLKQS 9
7 119 126 DTAHYDVR 8
8 136 142 EGLVASK 7
9 160 170 LLDLAASAADA 11
For Bnm1 the average antigenic propensity of the bnm1 protein is 1.037 so all residues having a
value greater that 1.037 are potential antigenic determinant (Figure 2). Nine peptides are found to
satisfy the threshold (1.00) value set prior to analysis and thus are potential antigenic sites of the
protein and they have the potential to evoke B cell response. The detail of the individual peptide
is summarized in Table 2 .The peptide regions ranging from 4 to 39 amino acid residue having
“FSVLSTFAAAAITLQLLLVPASASPHMKYIDAICDR” sequence and 55 to 75 amino acid
residue having “PTAAPIGLNPLAEVMALTIAH” sequence are predicted to have the highest
antigenic propensity score and both in total comprise about 38% portion as allergenic sites of all
the sites in Bnm1 protein.
Figure 3 Parker hydrophilicity plot In Parker hydrophilicity prediction scale X axis represents the
hydrophilicity score whereas the Y axis represents the sequence position. The average score of
hydrophilicity is 1.887 and thus the peptide regions having hydrophilicity score above the average score are
hydrophilic and are likely to be present on the surface of the Bnm1 protein. Nine potential hydrophilic
regions predicted here are highlighted as yellow color region whereas the green shaded regions could not
satisfy the minimum hydrophilicity score and thus are likely to be present within the core of Bnm1 protein.
Hydrophilic regions of the protein are likely to be exposed to outer surface and are most likely to
evoke B cell response. To predict the hydrophilic region of the Bnm1, we assigned Parker
hydrophilicity prediction [26] method and the predicted hydrophilicity plot shows the hydrophilic
regions of Bnm1 protein shaded in yellow color (Figure 3).
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51
Since the single-scale amino acid propensity profiles cannot always predict B cell epitope
location reliably as even the best Antigen Prediction method could yield marginally better score
than the ROC (receiver operating characteristics) plot [38] so we also performed a machine
learning process, BepiPred to predict the antigenic sites that can increase the prediction success
which is reviewed elsewhere [39, 40].
3.3 potential B cell epitopes overlap the antigenic sites of Bnm1
Peptides exposed to the outer surface of the protein do not mean that they will react with B cell.
To predict the B cell epitopes we employed BepiPred tool which is a antibody epitope prediction
program that combines both hidden Markov model and antigenic propensity scale method making
the prediction more reliable [27]. BepiPred predicted seven potential B cell epitopes highlighted
as yellow marked region for Bnm1 protein sequences (Figure 4) and the maximum score
predicted is 2.034. The predicted epitopes fit exactly in the hydrophilic regions predicted from
Parker hydrophilicity plot and thus are likely to be exposed on the surface of the protein. A detail
of individual B cell epitopes is summarized in Table 3.
Figure 4 Potential B cell epitopes predicted from BepiPred tool The amino acid sequences having a
score above the threshold (0.350) are predicted to be potential B cell epitopes and are highlighted as yellow
color. The maximum score predicted here is 2.034
Table 3 Predicted B cell epitope sequences and their position along with their length.
Number
Start
position
End
position
Epitope sequence
Length of
epitope
1 25 29 SASPH 5
2 39 44 RSHDQD 6
3 50 61 LTTNPPTAAPIG 12
4 85 94 ETGKADQTFT 10
5 115 133 KQSPDTAHYDVRSSTDQMK 19
6 140 149 ASKNDQASTT 10
7 166 178 SAADAVDDDDENI 13
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52
3.4 Mapping of the B cell epitopes in the modeled structure confirms their presence
on the surface of Bnm1
The predicted 3-D structure of Bnm1(Figure 5) was visualized using Pymol molecular
visualization system [41]. Ramachandran plot generated to validate the predicted structure
(Figure 5) shows the amino acid distribution in different regions of the plot. A detail
Figure 5 3D structure and its validation using Ramachandran plot for Bnm1 protein (A) Cartoon
representation of the predicted structure of Bnm1 protein. This image has been developed using pymol
molecular visualization system (B) amino acid residues are distributed in Ramachandran plot. All the
amino acid residues lie in the allowed residues in distribution plot making the prediction reliable.
of the distribution of amino acids in different regions is summarized in Table 4. Once the
structure was found to be reliable, this 3D structure was chosen as the template to map the
Table 4 Distribution of different amino acid residues in Ramachandran plot
Region of distribution of amino acid
residues
Percentage of distribution
Most favored regions 92.9
Additional allowed regions 7.1
Generously allowed regions 0.0
Disallowed regions 0.0
predicted B cell epitopes in Bnm1 protein (Figure 6). The yellow balls (Figure 6) represent the
predicted B cell epitopes and all of these yellow colored regions are on the surface of the protein.
So what we observed from the primary structure of Bnm1 is consistent in its 3D structure.
9. International Journal on Bioinformatics & Biosciences (IJBB) Vol.3, No.2, June 2013
53
Figure 6 Mapping of B cell epitopes on 3D structure of Bnm1 All the B cell epitopes predicted from
BepiPred prediction tool are mapped on the surface of the Bnm1 protein structure where B cell epitopes are
highlighted as yellow color and on the other hand the rest of the portion of Bnm1 protein is highlighted as
pink color.
3.5 Predicted potential T cell epitopes of Bnm1 shows multiple interactions with
DRB1* 0101
We also checked whether Bnm1 can induce T cell response since some allergens can induce both
humoral and cell mediated immune response to exert immune-inflammation [42-44]. MHC class
II epitope prediction was performed for the highly abundant selected alleles e.g. DRB1*0101,
DRB1*0301, DRB1*0401, DRB1*0701, DRB1*1101, DRB1*1301 and DRB1*1501 [31]. The
prediction tool retrieved 29 potential candidate T cell epitopes for HLA-DRB1*01:01 allele but
only 4 for HLA-DRB1*03:01 allele (Supplementary file 1). There is no allele interaction
predicted for DRB1*04:01, DRB1*07:01, DRB1*11:01, DRB1*13:01 and DRB1*15:01 within
chosen IC50 range (IC50<25.0). IgE production in response to particular allergens is associated
with certain MHC class II alleles, suggesting that particular MHC-peptide interactions might
evoke a strong TH2 response and several ragweed pollen allergens induce IgE responses which is
associated with haplotypes having HLA-II DRB1*1501 allele [45]. Our result suggests that Bnm1
protein may induce production of IgE response which is largely associated with HLA-
DRB1*01:01 allele.
4. Conclusion
To design an effective immune therapy against the allergic response to oilseed rape pollens it is
highly needed to know about the array of allergens in its pollen. Our computational approaches
strongly suggest that Bnm1, the pollen specific protein, is likely to be an allergen. However, In
vitro analyses are warranted to validate the allergenicity of Bnm1.
Acknowledgement
We would like to thank Md. Tariqul Tareq for reviewing the manuscript critically.
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Supplementary Files:
Supplementary Table 1 Predicted T cell candidate epitopes having IC50 < 25.0 score
Allele name Start
Position
End
position
Core sequence Peptide sequence IC50
score
HLA-DRB1*01:01 19 27 LLLVPASAS TLQLLLVPASASPHM 4.8
HLA-DRB1*01:01 19 27 LLLVPASAS LQLLLVPASASPHMK 5.0
HLA-DRB1*01:01 17 25 LQLLLVPAS ITLQLLLVPASASPH 5.4
HLA-DRB1*01:01 19 27 LLLVPASAS QLLLVPASASPHMKY 6.4
HLA-DRB1*01:01 17 25 LQLLLVPAS AITLQLLLVPASASP 6.5
HLA-DRB1*01:01 17 25 LQLLLVPAS AAITLQLLLVPASAS 7.4
HLA-DRB1*03:01 103 111 VVADLKSAN YLAVVADLKSANLK
L
7.7