Aarti Rana - Academia.edu (original) (raw)

Papers by Aarti Rana

Research paper thumbnail of Hybrid Additive Manufacturing

CRC Press eBooks, Jan 25, 2023

Research paper thumbnail of Epistemological Study of Urban Voids

ECS transactions, Apr 24, 2022

Research paper thumbnail of Evaluating complete surface-associated and secretory proteome of Leishmania donovani for discovering novel vaccines and diagnostic targets

Research paper thumbnail of An Analytical Study of Architecture Design Studios with Respect to Orientation and Facade Treatment

ECS Transactions

Building orientation is one of the most important design tools that can have a significant impact... more Building orientation is one of the most important design tools that can have a significant impact on the control of solar radiation and wind flow into a building. A country like Ethiopia has a predominantly hot and dry climate and hence receives an ample amount of sunlight throughout the year. The buildings need to be oriented to reduce the solar heat gain on the buildings and maximize the natural ventilation. The paper investigates the effect of orientation and facade treatment of the design studios on the thermal performance of students’ mental states and physical health. The design studio building is oriented in the east-west direction and located in Nekemte Campus of Wollega University, selected as the study area. The building orientation, facade treatment, window to wall ratio, and window size and level were studied and analyzed. The results from the data analysis clearly show that the east-west facing windows helps in thermal heat gain in the building, thereby increasing the i...

Research paper thumbnail of Enhancing Psychiatry Education through Podcasting: Learning from the Listener Experience

Academic Psychiatry, 2022

Objective Podcasts have recently been introduced into psychiatry education, despite limited evide... more Objective Podcasts have recently been introduced into psychiatry education, despite limited evidence evaluating podcasting in medical education. PsychEd is an educational, publicly available podcast targeting junior learners in psychiatry. This study characterized PsychEd’s listeners and the podcast’s role in their education. Methods The study involved a mixed-methods survey, followed by semi-structured phone interviews with respondents. There were 97 survey responders in total, of whom 9 participated in a telephone interview. Survey responses were coded as interval data and analyzed descriptively using statistical software. Interviews were transcribed and coded for emergent themes using a grounded theory model. Results PsychEd listeners represented an interprofessional audience, with 46 respondents (48%) being physicians or physicians in training, and 34 (35%) being allied mental health professionals. All respondents (100%) rated the podcast as “helpful” or “very helpful” for general knowledge. Listeners were attracted to PsychEd for the auditory learning format, the opportunity to review existing knowledge, the focus on core topics, the Canadian expertise, and the presentation of “clinical pearls.” Respondents highlighted valuable qualities of a psychiatry podcast: conversational, case-based, narrative approach, longer episodes (i.e., 30–60 minutes) as compared to other medical specialties, and a clinical focus. Furthermore, they identified podcasts as an opportunity for shared interprofessional curricula. Conclusion This study is the first to examine the motivations and experiences of listeners of a psychiatry educational podcast. The findings support existing literature on the benefits of podcasts in medical education. Future studies should explore the impact of podcasts on learning and behaviors.

Research paper thumbnail of Proteome wide identification of outer membrane proteins in pathogenic mycobacterial species a repertoire of candidate immunogens for translational medicine

Research paper thumbnail of Comparative proteome analysis reveals pathogen specific outer membrane proteins ofLeptospira

Proteins: Structure, Function, and Bioinformatics, 2018

Proteomes of pathogenic Leptospira interrogans and L. borgpetersenii and the saprophytic L. bifle... more Proteomes of pathogenic Leptospira interrogans and L. borgpetersenii and the saprophytic L. biflexa were filtered through computational tools to identify Outer Membrane Proteins (OMPs) that satisfy the required biophysical parameters for their presence on the outer membrane. A total of 133, 130 and 144 OMPs were identified in L. interrogans, L. borgpetersenii and L. biflexa respectively which forms approximately 4% of proteomes. A holistic analysis of transporting and pathogenic characteristics of OMPs together with Clusters of Orthologous Groups (COGs) among the OMPs and their distribution across three species was made and put forward a set of 21 candidate OMPs specific to pathogenic leptospires. It is also found that proteins homologous to the candidate OMPs were also present in other pathogenic species of leptospires. Six OMPs from L. interrogans and two from L. borgpetersenii observed to have similar COGs while those were not found in any intermediate or saprophytic forms. These OMPs appears to have role in infection and pathogenesis and useful for anti-leptospiral strategies.

Research paper thumbnail of The role of p38 MAPK pathway in p53 compromised state and telomere mediated DNA damage response

Mutation Research/Genetic Toxicology and Environmental Mutagenesis, 2018

The role of p38 MAPK pathway in p53 compromised state and telomere mediated DNA damage response, ... more The role of p38 MAPK pathway in p53 compromised state and telomere mediated DNA damage response, Mutation Research/Genetic Toxicology and Environmental Mutagenesis

Research paper thumbnail of System-wide coordinates of higher order functions in host-pathogen environment upon Mycobacterium tuberculosis infection

Scientific Reports, 2018

Molecular signatures and their interactions behind the successful establishment of infection of M... more Molecular signatures and their interactions behind the successful establishment of infection of Mycobacterium tuberculosis (Mtb) inside macrophage are largely unknown. In this work, we present an inter-system scale atlas of the gene expression signatures, their interactions and higher order gene functions of macrophage-Mtb environment at the time of infection. We have carried out large-scale meta-analysis of previously published gene expression microarray studies andhave identified a ranked list of differentially expressed genes and their higher order functions in intracellular Mtb as well as the infected macrophage. Comparative analysis of gene expression signatures of intracellular Mtb with the in vitro dormant Mtb at different hypoxic and oxidative stress conditions led to the identification of the large number of Mtb functional groups, namely operons, regulons and pathways that were common and unique to the intracellular environment and dormancy state. Some of the functions that...

Research paper thumbnail of Recent Trends in System-Scale Integrative Approaches for Discovering Protective Antigens Against Mycobacterial Pathogens

Frontiers in Genetics, 2018

Mycobacterial infections are one of the deadliest infectious diseases still posing a major health... more Mycobacterial infections are one of the deadliest infectious diseases still posing a major health burden worldwide. The battle against these pathogens needs to focus on novel approaches and key interventions. In recent times, availability of genome scale data has revolutionized the fields of computational biology and immunoproteomics. Here, we summarize the cutting-edge 'omics' technologies and innovative system scale strategies exploited to mine the available data. These may be targeted using highthroughput technologies to expedite the identification of novel antigenic candidates for the rational next generation vaccines and serodiagnostic development against mycobacterial pathogens for which traditional methods have been failing.

Research paper thumbnail of A multi-subunit based, thermodynamically stable model vaccine using combined immunoinformatics and protein structure based approach

Immunobiology, 2016

Immunizations with the conventional vaccines have failed to effectively inhibit the incidences an... more Immunizations with the conventional vaccines have failed to effectively inhibit the incidences and further dissemination of the infections. To address it, we have implemented protein structure based strategies to design an efficient multi-epitope subunit vaccine against Mycobacterium avium subsp. paratuberculosis (MAP). Previously reported immunodominant peptide epitope sequences from MAP1611 protein were conjugated together with a stretch of conserved amino acid residues of heparin-binding hemagglutinin, reported as a TLR4 agonist and was employed as an adjuvant to polarize the cellular responses toward host protective Th1 responses. These three types of component peptides were combined with the help of relevant linkers for efficient separation to improve and intensify the antigen processing and presentation. The primary structures of these multi peptides were 3-dimensional homology modeled to yield the final chimeric vaccine. Further, its conformational correctness and stability enhancement was assessed using molecular dynamics (MD) simulations. Finally, disulfide engineering in the most flexible regions of the molecule yielded three potential mutants, Y593C-E610C, Q631C-A634C and a double mutant Q631C-A634C/Y593C-E610C. The double mutant represents thermodynamically most stable version among them. It is potentially highly antigenic, soluble and non-allergen molecule interacting with the TLR receptor expressed on the immune cells. This vaccine contains both T-cell and several B-cell epitopes and an adjuvant which potentially possess protective cellular and humoral immune responses triggering properties. The presented vaccine strategy will be proven a promising pathogen specific candidate with wide therapeutic application against MAP which may be extended to other prevalent infections in future.

Research paper thumbnail of Excavating the surface-associated and secretory proteome of Mycobacterium leprae for identifying vaccines and diagnostic markers relevant immunodominant epitopes

Pathogens and disease, Dec 1, 2016

For centuries, Mycobacterium leprae, etiological agent of leprosy, has been afflicting mankind re... more For centuries, Mycobacterium leprae, etiological agent of leprosy, has been afflicting mankind regardless of extensive use of live-attenuated vaccines and antibiotics. Surface-associated and secretory proteins (SASPs) are attractive targets against bacteria. We have integrated biological knowledge with computational approaches and present a proteome-wide identification of SASPs. We also performed computational assignment of immunodominant epitopes as coordinates of prospective antigenic candidates in most important class of SASPs, the outer membrane proteins (OMPs). Exploiting the known protein sequence and structural characteristics shared by the SASPs from bacteria, 17 lipoproteins, 11 secretory and 19 novel OMPs (including 4 essential proteins) were identified in M. leprae As OMPs represent the most exposed antigens on the cell surface, their immunoinformatics analysis showed that the identified 19 OMPs harbor T-cell MHC class I epitopes and class II epitopes against HLA-DR allel...

Research paper thumbnail of Terminal regions of β-catenin are critical for regulating its adhesion and transcription functions

Biochimica et biophysica acta, Sep 29, 2016

β-Catenin, the central molecule of canonical Wnt signaling pathway, has multiple binding partners... more β-Catenin, the central molecule of canonical Wnt signaling pathway, has multiple binding partners and performs many roles in the cell. Apart from being a transcriptional activator, β-catenin acts as a crucial effector component of cadherin/catenin complex to physically interact with actin cytoskeleton along with α-catenin and E-cadherin for regulating cell-cell adhesion. Here, we have generated a library of β-catenin point and deletion mutants to delineate regions within β-catenin that are important for α-catenin-β-catenin interaction, nuclear localization, and transcriptional activity of β-catenin. We observed a unique mechanism for nuclear localization of β-catenin and its mutants and show that N-terminal exon-3 region and C-terminal domain of β-catenin are critical for this activity of β-catenin. Furthermore, we show HepG2 cells have high β-catenin mediated transcriptional activity due to the presence of an interstitial deletion at the N-terminal region of β-catenin. Due to this ...

Research paper thumbnail of Co-relation between physico-mechanical and chemical properties of cement & resin capsules used in underground mines

Rock Engineering and Rock Mechanics: Structures in and on Rock Masses, 2014

Research paper thumbnail of A tug-of-war between the host and the pathogen generates strategic hotspots for the development of novel therapeutic interventions against infectious diseases

Virulence, 2015

Rub & Yusuf Akhter (2015) A tugof-war between the host and the pathogen generates strategic hotsp... more Rub & Yusuf Akhter (2015) A tugof-war between the host and the pathogen generates strategic hotspots for the development of novel therapeutic interventions against infectious diseases

Research paper thumbnail of Proteome-scale identification and characterization of mitochondria targeting proteins of Mycobacterium avium subspecies paratuberculosis: Potential virulence factors modulating host mitochondrial function

Mitochondrion, 2015

Mycobacterium avium subsp. paratuberculosis is the etiological agent of Johne&amp... more Mycobacterium avium subsp. paratuberculosis is the etiological agent of Johne's Disease among ruminants. During the course of infection, it expresses a number of proteins for its successful persistence inside the host that cause variety of physiological abnormalities in the host. Mitochondrion is one of the attractive targets for pathogenic bacteria. Employing a proteome-wide sequence and structural signature based approach we have identified 46 M. avium subsp. paratuberculosis proteins as potential targets for the host mitochondrial targeting. These may act as virulence factors modulating mitochondrial physiology for bacterial survival and immune evasion inside the host cells.

Research paper thumbnail of Proteome-wide B and T cell epitope repertoires in outer membrane proteins of Mycobacterium avium subsp. paratuberculosis have vaccine and diagnostic relevance: a holistic approach

Journal of molecular recognition : JMR, Jan 26, 2015

Mycobacterium avium subsp. paratuberculosis (MAP) is an etiological agent of chronic inflammation... more Mycobacterium avium subsp. paratuberculosis (MAP) is an etiological agent of chronic inflammation of the intestine among ruminants and humans. Currently, there are no effective vaccines and sensitive diagnostic tests available for its control and detection. For this, it is of paramount importance to identify the MAP antigens, which may be immunologically recognized by the host immune system. To address this challenge, we performed identification of the immunogenic epitopes in the MAP outer membrane proteins (OMPs). We have previously identified 57 MAP proteins as OMPs [Rana A, Rub A, Akhter Y. 2014. Molecular BioSystems, 10:2329-2337] and have evaluated them for the epitope selection and analysis employing a computational approach. Thirty-five MAP OMPs are reported with nine-mer peptides showing high binding affinity to major histocompatibility complex (MHC) class I molecules and 28 MAP OMPs with 15-mer peptides of high binding affinity for MHC class II molecules. The presence of MH...

Research paper thumbnail of Efficacy of essential oils of aromatic plants as larvicide for the management of filarial vector Culex quinquefasciatus Say (Diptera: Culicidae) with special reference to Foeniculum vulgare

Asian Pacific Journal of Tropical Disease, 2012

Larvicide Foeniculum vulgare Tagetes patula Objective: To evaluate the larvicidal activity of ess... more Larvicide Foeniculum vulgare Tagetes patula Objective: To evaluate the larvicidal activity of essential oils derived from ten aromatic plants with special reference to Foeniculum vulgare (F. vulgare) against early fourth instar larvae of Culex quinquefasciatus (Cx. quinquefasciatus) Say (Diptera: Culicidae). Methods: Essential oils were extracted from plant materials through hydro distillation and efficacy was determined through bioassay method. Two of the effective oils were evaluated further for the determination of their LC 50 and LT 50 values based on Probit analysis.Essential oils of one plant was analyzed through TLC and HPLC. Results: Most of the essential oils caused 100% mortality within 120 min at 250 ppm. Oil of Tagetes patula (T. patula) and F. vulgare gave more than 90% mortality within 40 min. LC 50 values calculated after 60 min of treatment were (84.80 暲 7.65) and (24.69 暲 1.24) ppm for T. patula and F. vulgare respectively. At the same exposure period positive control temephos yielded (22.13暲2.39) ppm LC 50 value. At 50 ppm T. patula, F. vulgare and temephos exhibited LT 50 values (113.71 暲 10.29), (11.02 暲 3.31) and (38.15 暲 5.90) mins respectively. Presence of high quantity of trans anethole in the essential oils of F. vulgare was confirmed by TLC and HPLC results. Conclusions: Present study indicates that essential oils of spices/aromatic medicinal plants particularly F. vulgare and T. patula carry huge potential as a mosquito larvicide. This potential could be exploited for the development of safer and effective botanical mosquito larvicidal tool for the management of Cx. quinquefasciatus.

Research paper thumbnail of Evaluation of antifungal activity in essential oil of the Syzygium aromaticum (L.) by extraction, purification and analysis of its main component eugenol

Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology], 2011

Antifungal properties of some essential oils have been well documented. Clove oil is reported to ... more Antifungal properties of some essential oils have been well documented. Clove oil is reported to have strong antifungal activity against many fungal species. In this study we have evaluated antifungal potential of essential oil of Syzygium aromaticum (L.) against some common fungal pathogens of plants and animals namely, Fusarium moniliforme NCIM 1100, Fusarium oxysporum MTCC 284, Aspergillus sp., Mucor sp., Trichophyton rubrum and Microsporum gypseum. All fungal species were found to be inhibited by the oil when tested through agar well diffusion method. Minimum inhibitory concentration (MIC) was determined for all the species. Column chromatography was performed to separate the eugenol rich fraction from clove oil. Out of seven fractions maximum activity was obtained in column fraction II. TLC and HPLC data confirmed presence of considerable Eugenol in fraction II and clove oil. Microscopic study on effect of clove oil and column fraction II on spores of Mucor sp. and M. gypseum s...

Research paper thumbnail of Proteome-scale identification of outer membrane proteins in Mycobacterium avium subspecies paratuberculosis using a structure based combined hierarchical approach

Please note that technical editing may introduce minor changes to the text and/or graphics, which... more Please note that technical editing may introduce minor changes to the text and/or graphics, which may alter content. The journal's standard Terms & Conditions and the Ethical guidelines still apply. In no event shall the Royal Society of Chemistry be held responsible for any errors or omissions in this Accepted Manuscript or any consequences arising from the use of any information it contains.

Research paper thumbnail of Hybrid Additive Manufacturing

CRC Press eBooks, Jan 25, 2023

Research paper thumbnail of Epistemological Study of Urban Voids

ECS transactions, Apr 24, 2022

Research paper thumbnail of Evaluating complete surface-associated and secretory proteome of Leishmania donovani for discovering novel vaccines and diagnostic targets

Research paper thumbnail of An Analytical Study of Architecture Design Studios with Respect to Orientation and Facade Treatment

ECS Transactions

Building orientation is one of the most important design tools that can have a significant impact... more Building orientation is one of the most important design tools that can have a significant impact on the control of solar radiation and wind flow into a building. A country like Ethiopia has a predominantly hot and dry climate and hence receives an ample amount of sunlight throughout the year. The buildings need to be oriented to reduce the solar heat gain on the buildings and maximize the natural ventilation. The paper investigates the effect of orientation and facade treatment of the design studios on the thermal performance of students’ mental states and physical health. The design studio building is oriented in the east-west direction and located in Nekemte Campus of Wollega University, selected as the study area. The building orientation, facade treatment, window to wall ratio, and window size and level were studied and analyzed. The results from the data analysis clearly show that the east-west facing windows helps in thermal heat gain in the building, thereby increasing the i...

Research paper thumbnail of Enhancing Psychiatry Education through Podcasting: Learning from the Listener Experience

Academic Psychiatry, 2022

Objective Podcasts have recently been introduced into psychiatry education, despite limited evide... more Objective Podcasts have recently been introduced into psychiatry education, despite limited evidence evaluating podcasting in medical education. PsychEd is an educational, publicly available podcast targeting junior learners in psychiatry. This study characterized PsychEd’s listeners and the podcast’s role in their education. Methods The study involved a mixed-methods survey, followed by semi-structured phone interviews with respondents. There were 97 survey responders in total, of whom 9 participated in a telephone interview. Survey responses were coded as interval data and analyzed descriptively using statistical software. Interviews were transcribed and coded for emergent themes using a grounded theory model. Results PsychEd listeners represented an interprofessional audience, with 46 respondents (48%) being physicians or physicians in training, and 34 (35%) being allied mental health professionals. All respondents (100%) rated the podcast as “helpful” or “very helpful” for general knowledge. Listeners were attracted to PsychEd for the auditory learning format, the opportunity to review existing knowledge, the focus on core topics, the Canadian expertise, and the presentation of “clinical pearls.” Respondents highlighted valuable qualities of a psychiatry podcast: conversational, case-based, narrative approach, longer episodes (i.e., 30–60 minutes) as compared to other medical specialties, and a clinical focus. Furthermore, they identified podcasts as an opportunity for shared interprofessional curricula. Conclusion This study is the first to examine the motivations and experiences of listeners of a psychiatry educational podcast. The findings support existing literature on the benefits of podcasts in medical education. Future studies should explore the impact of podcasts on learning and behaviors.

Research paper thumbnail of Proteome wide identification of outer membrane proteins in pathogenic mycobacterial species a repertoire of candidate immunogens for translational medicine

Research paper thumbnail of Comparative proteome analysis reveals pathogen specific outer membrane proteins ofLeptospira

Proteins: Structure, Function, and Bioinformatics, 2018

Proteomes of pathogenic Leptospira interrogans and L. borgpetersenii and the saprophytic L. bifle... more Proteomes of pathogenic Leptospira interrogans and L. borgpetersenii and the saprophytic L. biflexa were filtered through computational tools to identify Outer Membrane Proteins (OMPs) that satisfy the required biophysical parameters for their presence on the outer membrane. A total of 133, 130 and 144 OMPs were identified in L. interrogans, L. borgpetersenii and L. biflexa respectively which forms approximately 4% of proteomes. A holistic analysis of transporting and pathogenic characteristics of OMPs together with Clusters of Orthologous Groups (COGs) among the OMPs and their distribution across three species was made and put forward a set of 21 candidate OMPs specific to pathogenic leptospires. It is also found that proteins homologous to the candidate OMPs were also present in other pathogenic species of leptospires. Six OMPs from L. interrogans and two from L. borgpetersenii observed to have similar COGs while those were not found in any intermediate or saprophytic forms. These OMPs appears to have role in infection and pathogenesis and useful for anti-leptospiral strategies.

Research paper thumbnail of The role of p38 MAPK pathway in p53 compromised state and telomere mediated DNA damage response

Mutation Research/Genetic Toxicology and Environmental Mutagenesis, 2018

The role of p38 MAPK pathway in p53 compromised state and telomere mediated DNA damage response, ... more The role of p38 MAPK pathway in p53 compromised state and telomere mediated DNA damage response, Mutation Research/Genetic Toxicology and Environmental Mutagenesis

Research paper thumbnail of System-wide coordinates of higher order functions in host-pathogen environment upon Mycobacterium tuberculosis infection

Scientific Reports, 2018

Molecular signatures and their interactions behind the successful establishment of infection of M... more Molecular signatures and their interactions behind the successful establishment of infection of Mycobacterium tuberculosis (Mtb) inside macrophage are largely unknown. In this work, we present an inter-system scale atlas of the gene expression signatures, their interactions and higher order gene functions of macrophage-Mtb environment at the time of infection. We have carried out large-scale meta-analysis of previously published gene expression microarray studies andhave identified a ranked list of differentially expressed genes and their higher order functions in intracellular Mtb as well as the infected macrophage. Comparative analysis of gene expression signatures of intracellular Mtb with the in vitro dormant Mtb at different hypoxic and oxidative stress conditions led to the identification of the large number of Mtb functional groups, namely operons, regulons and pathways that were common and unique to the intracellular environment and dormancy state. Some of the functions that...

Research paper thumbnail of Recent Trends in System-Scale Integrative Approaches for Discovering Protective Antigens Against Mycobacterial Pathogens

Frontiers in Genetics, 2018

Mycobacterial infections are one of the deadliest infectious diseases still posing a major health... more Mycobacterial infections are one of the deadliest infectious diseases still posing a major health burden worldwide. The battle against these pathogens needs to focus on novel approaches and key interventions. In recent times, availability of genome scale data has revolutionized the fields of computational biology and immunoproteomics. Here, we summarize the cutting-edge 'omics' technologies and innovative system scale strategies exploited to mine the available data. These may be targeted using highthroughput technologies to expedite the identification of novel antigenic candidates for the rational next generation vaccines and serodiagnostic development against mycobacterial pathogens for which traditional methods have been failing.

Research paper thumbnail of A multi-subunit based, thermodynamically stable model vaccine using combined immunoinformatics and protein structure based approach

Immunobiology, 2016

Immunizations with the conventional vaccines have failed to effectively inhibit the incidences an... more Immunizations with the conventional vaccines have failed to effectively inhibit the incidences and further dissemination of the infections. To address it, we have implemented protein structure based strategies to design an efficient multi-epitope subunit vaccine against Mycobacterium avium subsp. paratuberculosis (MAP). Previously reported immunodominant peptide epitope sequences from MAP1611 protein were conjugated together with a stretch of conserved amino acid residues of heparin-binding hemagglutinin, reported as a TLR4 agonist and was employed as an adjuvant to polarize the cellular responses toward host protective Th1 responses. These three types of component peptides were combined with the help of relevant linkers for efficient separation to improve and intensify the antigen processing and presentation. The primary structures of these multi peptides were 3-dimensional homology modeled to yield the final chimeric vaccine. Further, its conformational correctness and stability enhancement was assessed using molecular dynamics (MD) simulations. Finally, disulfide engineering in the most flexible regions of the molecule yielded three potential mutants, Y593C-E610C, Q631C-A634C and a double mutant Q631C-A634C/Y593C-E610C. The double mutant represents thermodynamically most stable version among them. It is potentially highly antigenic, soluble and non-allergen molecule interacting with the TLR receptor expressed on the immune cells. This vaccine contains both T-cell and several B-cell epitopes and an adjuvant which potentially possess protective cellular and humoral immune responses triggering properties. The presented vaccine strategy will be proven a promising pathogen specific candidate with wide therapeutic application against MAP which may be extended to other prevalent infections in future.

Research paper thumbnail of Excavating the surface-associated and secretory proteome of Mycobacterium leprae for identifying vaccines and diagnostic markers relevant immunodominant epitopes

Pathogens and disease, Dec 1, 2016

For centuries, Mycobacterium leprae, etiological agent of leprosy, has been afflicting mankind re... more For centuries, Mycobacterium leprae, etiological agent of leprosy, has been afflicting mankind regardless of extensive use of live-attenuated vaccines and antibiotics. Surface-associated and secretory proteins (SASPs) are attractive targets against bacteria. We have integrated biological knowledge with computational approaches and present a proteome-wide identification of SASPs. We also performed computational assignment of immunodominant epitopes as coordinates of prospective antigenic candidates in most important class of SASPs, the outer membrane proteins (OMPs). Exploiting the known protein sequence and structural characteristics shared by the SASPs from bacteria, 17 lipoproteins, 11 secretory and 19 novel OMPs (including 4 essential proteins) were identified in M. leprae As OMPs represent the most exposed antigens on the cell surface, their immunoinformatics analysis showed that the identified 19 OMPs harbor T-cell MHC class I epitopes and class II epitopes against HLA-DR allel...

Research paper thumbnail of Terminal regions of β-catenin are critical for regulating its adhesion and transcription functions

Biochimica et biophysica acta, Sep 29, 2016

β-Catenin, the central molecule of canonical Wnt signaling pathway, has multiple binding partners... more β-Catenin, the central molecule of canonical Wnt signaling pathway, has multiple binding partners and performs many roles in the cell. Apart from being a transcriptional activator, β-catenin acts as a crucial effector component of cadherin/catenin complex to physically interact with actin cytoskeleton along with α-catenin and E-cadherin for regulating cell-cell adhesion. Here, we have generated a library of β-catenin point and deletion mutants to delineate regions within β-catenin that are important for α-catenin-β-catenin interaction, nuclear localization, and transcriptional activity of β-catenin. We observed a unique mechanism for nuclear localization of β-catenin and its mutants and show that N-terminal exon-3 region and C-terminal domain of β-catenin are critical for this activity of β-catenin. Furthermore, we show HepG2 cells have high β-catenin mediated transcriptional activity due to the presence of an interstitial deletion at the N-terminal region of β-catenin. Due to this ...

Research paper thumbnail of Co-relation between physico-mechanical and chemical properties of cement & resin capsules used in underground mines

Rock Engineering and Rock Mechanics: Structures in and on Rock Masses, 2014

Research paper thumbnail of A tug-of-war between the host and the pathogen generates strategic hotspots for the development of novel therapeutic interventions against infectious diseases

Virulence, 2015

Rub & Yusuf Akhter (2015) A tugof-war between the host and the pathogen generates strategic hotsp... more Rub & Yusuf Akhter (2015) A tugof-war between the host and the pathogen generates strategic hotspots for the development of novel therapeutic interventions against infectious diseases

Research paper thumbnail of Proteome-scale identification and characterization of mitochondria targeting proteins of Mycobacterium avium subspecies paratuberculosis: Potential virulence factors modulating host mitochondrial function

Mitochondrion, 2015

Mycobacterium avium subsp. paratuberculosis is the etiological agent of Johne&amp... more Mycobacterium avium subsp. paratuberculosis is the etiological agent of Johne's Disease among ruminants. During the course of infection, it expresses a number of proteins for its successful persistence inside the host that cause variety of physiological abnormalities in the host. Mitochondrion is one of the attractive targets for pathogenic bacteria. Employing a proteome-wide sequence and structural signature based approach we have identified 46 M. avium subsp. paratuberculosis proteins as potential targets for the host mitochondrial targeting. These may act as virulence factors modulating mitochondrial physiology for bacterial survival and immune evasion inside the host cells.

Research paper thumbnail of Proteome-wide B and T cell epitope repertoires in outer membrane proteins of Mycobacterium avium subsp. paratuberculosis have vaccine and diagnostic relevance: a holistic approach

Journal of molecular recognition : JMR, Jan 26, 2015

Mycobacterium avium subsp. paratuberculosis (MAP) is an etiological agent of chronic inflammation... more Mycobacterium avium subsp. paratuberculosis (MAP) is an etiological agent of chronic inflammation of the intestine among ruminants and humans. Currently, there are no effective vaccines and sensitive diagnostic tests available for its control and detection. For this, it is of paramount importance to identify the MAP antigens, which may be immunologically recognized by the host immune system. To address this challenge, we performed identification of the immunogenic epitopes in the MAP outer membrane proteins (OMPs). We have previously identified 57 MAP proteins as OMPs [Rana A, Rub A, Akhter Y. 2014. Molecular BioSystems, 10:2329-2337] and have evaluated them for the epitope selection and analysis employing a computational approach. Thirty-five MAP OMPs are reported with nine-mer peptides showing high binding affinity to major histocompatibility complex (MHC) class I molecules and 28 MAP OMPs with 15-mer peptides of high binding affinity for MHC class II molecules. The presence of MH...

Research paper thumbnail of Efficacy of essential oils of aromatic plants as larvicide for the management of filarial vector Culex quinquefasciatus Say (Diptera: Culicidae) with special reference to Foeniculum vulgare

Asian Pacific Journal of Tropical Disease, 2012

Larvicide Foeniculum vulgare Tagetes patula Objective: To evaluate the larvicidal activity of ess... more Larvicide Foeniculum vulgare Tagetes patula Objective: To evaluate the larvicidal activity of essential oils derived from ten aromatic plants with special reference to Foeniculum vulgare (F. vulgare) against early fourth instar larvae of Culex quinquefasciatus (Cx. quinquefasciatus) Say (Diptera: Culicidae). Methods: Essential oils were extracted from plant materials through hydro distillation and efficacy was determined through bioassay method. Two of the effective oils were evaluated further for the determination of their LC 50 and LT 50 values based on Probit analysis.Essential oils of one plant was analyzed through TLC and HPLC. Results: Most of the essential oils caused 100% mortality within 120 min at 250 ppm. Oil of Tagetes patula (T. patula) and F. vulgare gave more than 90% mortality within 40 min. LC 50 values calculated after 60 min of treatment were (84.80 暲 7.65) and (24.69 暲 1.24) ppm for T. patula and F. vulgare respectively. At the same exposure period positive control temephos yielded (22.13暲2.39) ppm LC 50 value. At 50 ppm T. patula, F. vulgare and temephos exhibited LT 50 values (113.71 暲 10.29), (11.02 暲 3.31) and (38.15 暲 5.90) mins respectively. Presence of high quantity of trans anethole in the essential oils of F. vulgare was confirmed by TLC and HPLC results. Conclusions: Present study indicates that essential oils of spices/aromatic medicinal plants particularly F. vulgare and T. patula carry huge potential as a mosquito larvicide. This potential could be exploited for the development of safer and effective botanical mosquito larvicidal tool for the management of Cx. quinquefasciatus.

Research paper thumbnail of Evaluation of antifungal activity in essential oil of the Syzygium aromaticum (L.) by extraction, purification and analysis of its main component eugenol

Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology], 2011

Antifungal properties of some essential oils have been well documented. Clove oil is reported to ... more Antifungal properties of some essential oils have been well documented. Clove oil is reported to have strong antifungal activity against many fungal species. In this study we have evaluated antifungal potential of essential oil of Syzygium aromaticum (L.) against some common fungal pathogens of plants and animals namely, Fusarium moniliforme NCIM 1100, Fusarium oxysporum MTCC 284, Aspergillus sp., Mucor sp., Trichophyton rubrum and Microsporum gypseum. All fungal species were found to be inhibited by the oil when tested through agar well diffusion method. Minimum inhibitory concentration (MIC) was determined for all the species. Column chromatography was performed to separate the eugenol rich fraction from clove oil. Out of seven fractions maximum activity was obtained in column fraction II. TLC and HPLC data confirmed presence of considerable Eugenol in fraction II and clove oil. Microscopic study on effect of clove oil and column fraction II on spores of Mucor sp. and M. gypseum s...

Research paper thumbnail of Proteome-scale identification of outer membrane proteins in Mycobacterium avium subspecies paratuberculosis using a structure based combined hierarchical approach

Please note that technical editing may introduce minor changes to the text and/or graphics, which... more Please note that technical editing may introduce minor changes to the text and/or graphics, which may alter content. The journal's standard Terms & Conditions and the Ethical guidelines still apply. In no event shall the Royal Society of Chemistry be held responsible for any errors or omissions in this Accepted Manuscript or any consequences arising from the use of any information it contains.