The Experts below are selected from a list of 176253 Experts worldwide ranked by ideXlab platform
Ashutosh Tiwari - One of the best experts on this subject based on the ideXlab platform.
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Studies on Bacterial Proteins Corona Interaction with Saponin Imprinted ZnO Nanohoneycombs and Their Toxic Responses.
ACS applied materials & interfaces, 2015Co-Authors: Deepali Sharma, Ashaduzzaman, Mohsen Golabi, Amritanshu Shriwastav, Krishna Bisetty, Ashutosh TiwariAbstract:Molecular imprinting generates robust, efficient, and highly mesoporous surfaces for biointeractions. Mechanistic interfacial interaction between the surface of core substrate and protein corona is crucial to understand the substantial microbial toxic responses at a nanoscale. In this study, we have focused on the mechanistic interactions between synthesized saponin imprinted zinc oxide nanohoneycombs (SIZnO NHs), average size 80–125 nm, surface area 20.27 m2/g, average pore density 0.23 pore/nm and number-average pore size 3.74 nm and Proteins corona of bacteria. The produced SIZnO NHs as potential antifungal and antiBacterial agents have been studied on Sclerotium rolfsii (S. rolfsii), Pythium debarynum (P. debarynum) and Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), respectively. SIZnO NHs exhibited the highest antiBacterial (∼50%) and antifungal (∼40%) activity against Gram-negative bacteria (E. coli) and fungus (P. debarynum), respectively at concentration of 0.1 mol. Scanning electr...
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Studies on Bacterial Proteins Corona Interaction with Saponin Imprinted ZnO Nanohoneycombs and Their Toxic Responses
2015Co-Authors: Deepali Sharma, Mohsen Golabi, Amritanshu Shriwastav, Krishna Bisetty, Md. Ashaduzzaman, Ashutosh TiwariAbstract:Molecular imprinting generates robust, efficient, and highly mesoporous surfaces for biointeractions. Mechanistic interfacial interaction between the surface of core substrate and protein corona is crucial to understand the substantial microbial toxic responses at a nanoscale. In this study, we have focused on the mechanistic interactions between synthesized saponin imprinted zinc oxide nanohoneycombs (SIZnO NHs), average size 80–125 nm, surface area 20.27 m2/g, average pore density 0.23 pore/nm and number-average pore size 3.74 nm and Proteins corona of bacteria. The produced SIZnO NHs as potential antifungal and antiBacterial agents have been studied on Sclerotium rolfsii (S. rolfsii), Pythium debarynum (P. debarynum) and Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), respectively. SIZnO NHs exhibited the highest antiBacterial (∼50%) and antifungal (∼40%) activity against Gram-negative bacteria (E. coli) and fungus (P. debarynum), respectively at concentration of 0.1 mol. Scanning electron spectroscopy (SEM) observation showed that the ZnO NHs ruptured the cell wall of bacteria and internalized into the cell. The molecular docking studies were carried out using binding Proteins present in the gram negative bacteria (lipopolysaccharide and lipocalin Blc) and gram positive bacteria (Staphylococcal Protein A, SpA). It was envisaged that the Proteins present in the Bacterial cell wall were found to interact and adsorb on the surface of SIZnO NHs thereby blocking the active sites of the Proteins used for cell wall synthesis. The binding affinity and interaction energies were higher in the case of binding Proteins present in gram negative bacteria as compared to that of gram positive bacteria. In addition, a kinetic mathematical model (KMM) was developed in MATLAB to predict the internalization in the Bacterial cellular uptake of the ZnO NHs for better understanding of their controlled toxicity. The results obtained from KMM exhibited a good agreement with the experimental data. Exploration of mechanistic interactions, as well as the formation of bioconjugate of Proteins and ZnO NHs would play a key role to interpret more complex biological systems in nature
Marie-claire Lett - One of the best experts on this subject based on the ideXlab platform.
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Monitoring the bactericidal effect of UV-A photocatalysis: A first approach through 1D and 2D protein electrophoresis
Catalysis Today, 2009Co-Authors: Florence Goulhen, Sébastien Josset, Nicolas Keller, Valérie Keller, Marie-claire LettAbstract:The bactericidal effect of UV-A photocatalysis is studied through the 1D and 2D protein electrophoresis biochemical approach over model and Bacterial Proteins, which shows that a majority of Proteins are heavily and non-specifically damaged. This suggests that the emergence of resistance to this treatment should be almost impossible.
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Monitoring the bactericidal effect of UV-A photocatalysis: A first approach through 1D and 2D protein electrophoresis
Catalysis Today, 2009Co-Authors: Florence Goulhen-chollet, Sébastien Josset, Nicolas Keller, Valérie Keller, Marie-claire LettAbstract:International audienceThe bactericidal effect of UV-A photocatalysis is studied through the 1D and 2D protein electrophoresis biochemical approach over model and Bacterial Proteins, which shows that a majority of Proteins are heavily and non-specifically damaged. This suggests that the emergence of resistance to this treatment should be almost impossible
Deepali Sharma - One of the best experts on this subject based on the ideXlab platform.
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Studies on Bacterial Proteins Corona Interaction with Saponin Imprinted ZnO Nanohoneycombs and Their Toxic Responses.
ACS applied materials & interfaces, 2015Co-Authors: Deepali Sharma, Ashaduzzaman, Mohsen Golabi, Amritanshu Shriwastav, Krishna Bisetty, Ashutosh TiwariAbstract:Molecular imprinting generates robust, efficient, and highly mesoporous surfaces for biointeractions. Mechanistic interfacial interaction between the surface of core substrate and protein corona is crucial to understand the substantial microbial toxic responses at a nanoscale. In this study, we have focused on the mechanistic interactions between synthesized saponin imprinted zinc oxide nanohoneycombs (SIZnO NHs), average size 80–125 nm, surface area 20.27 m2/g, average pore density 0.23 pore/nm and number-average pore size 3.74 nm and Proteins corona of bacteria. The produced SIZnO NHs as potential antifungal and antiBacterial agents have been studied on Sclerotium rolfsii (S. rolfsii), Pythium debarynum (P. debarynum) and Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), respectively. SIZnO NHs exhibited the highest antiBacterial (∼50%) and antifungal (∼40%) activity against Gram-negative bacteria (E. coli) and fungus (P. debarynum), respectively at concentration of 0.1 mol. Scanning electr...
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Studies on Bacterial Proteins Corona Interaction with Saponin Imprinted ZnO Nanohoneycombs and Their Toxic Responses
2015Co-Authors: Deepali Sharma, Mohsen Golabi, Amritanshu Shriwastav, Krishna Bisetty, Md. Ashaduzzaman, Ashutosh TiwariAbstract:Molecular imprinting generates robust, efficient, and highly mesoporous surfaces for biointeractions. Mechanistic interfacial interaction between the surface of core substrate and protein corona is crucial to understand the substantial microbial toxic responses at a nanoscale. In this study, we have focused on the mechanistic interactions between synthesized saponin imprinted zinc oxide nanohoneycombs (SIZnO NHs), average size 80–125 nm, surface area 20.27 m2/g, average pore density 0.23 pore/nm and number-average pore size 3.74 nm and Proteins corona of bacteria. The produced SIZnO NHs as potential antifungal and antiBacterial agents have been studied on Sclerotium rolfsii (S. rolfsii), Pythium debarynum (P. debarynum) and Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), respectively. SIZnO NHs exhibited the highest antiBacterial (∼50%) and antifungal (∼40%) activity against Gram-negative bacteria (E. coli) and fungus (P. debarynum), respectively at concentration of 0.1 mol. Scanning electron spectroscopy (SEM) observation showed that the ZnO NHs ruptured the cell wall of bacteria and internalized into the cell. The molecular docking studies were carried out using binding Proteins present in the gram negative bacteria (lipopolysaccharide and lipocalin Blc) and gram positive bacteria (Staphylococcal Protein A, SpA). It was envisaged that the Proteins present in the Bacterial cell wall were found to interact and adsorb on the surface of SIZnO NHs thereby blocking the active sites of the Proteins used for cell wall synthesis. The binding affinity and interaction energies were higher in the case of binding Proteins present in gram negative bacteria as compared to that of gram positive bacteria. In addition, a kinetic mathematical model (KMM) was developed in MATLAB to predict the internalization in the Bacterial cellular uptake of the ZnO NHs for better understanding of their controlled toxicity. The results obtained from KMM exhibited a good agreement with the experimental data. Exploration of mechanistic interactions, as well as the formation of bioconjugate of Proteins and ZnO NHs would play a key role to interpret more complex biological systems in nature
Kuo-chen Chou - One of the best experts on this subject based on the ideXlab platform.
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a multi label classifier for predicting the subcellular localization of gram negative Bacterial Proteins with both single and multiple sites
PLOS ONE, 2011Co-Authors: Xuan Xiao, Kuo-chen ChouAbstract:Prediction of protein subcellular localization is a challenging problem, particularly when the system concerned contains both singleplex and multiplex Proteins. In this paper, by introducing the “multi-label scale” and hybridizing the information of gene ontology with the sequential evolution information, a novel predictor called iLoc-Gneg is developed for predicting the subcellular localization of Gram-positive Bacterial Proteins with both single-location and multiple-location sites. For facilitating comparison, the same stringent benchmark dataset used to estimate the accuracy of Gneg-mPLoc was adopted to demonstrate the power of iLoc-Gneg. The dataset contains 1,392 Gram-negative Bacterial Proteins classified into the following eight locations: (1) cytoplasm, (2) extracellular, (3) fimbrium, (4) flagellum, (5) inner membrane, (6) nucleoid, (7) outer membrane, and (8) periplasm. Of the 1,392 Proteins, 1,328 are each with only one subcellular location and the other 64 are each with two subcellular locations, but none of the Proteins included has pairwise sequence identity to any other in a same subset (subcellular location). It was observed that the overall success rate by jackknife test on such a stringent benchmark dataset by iLoc-Gneg was over 91%, which is about 6% higher than that by Gneg-mPLoc. As a user-friendly web-server, iLoc-Gneg is freely accessible to the public at http://icpr.jci.edu.cn/bioinfo/iLoc-Gneg. Meanwhile, a step-by-step guide is provided on how to use the web-server to get the desired results. Furthermore, for the user's convenience, the iLoc-Gneg web-server also has the function to accept the batch job submission, which is not available in the existing version of Gneg-mPLoc web-server. It is anticipated that iLoc-Gneg may become a useful high throughput tool for Molecular Cell Biology, Proteomics, System Biology, and Drug Development.
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gneg mploc a top down strategy to enhance the quality of predicting subcellular localization of gram negative Bacterial Proteins
Journal of Theoretical Biology, 2010Co-Authors: Hong-bin Shen, Kuo-chen ChouAbstract:Abstract By incorporating the information of gene ontology, functional domain, and sequential evolution, a new predictor called Gneg-mPLoc was developed. It can be used to identify Gram-negative Bacterial Proteins among the following eight locations: (1) cytoplasm, (2) extracellular, (3) fimbrium, (4) flagellum, (5) inner membrane, (6) nucleoid, (7) outer membrane, and (8) periplasm. It can also be used to deal with the case when a query protein may simultaneously exist in more than one location. Compared with the original predictor called Gneg-PLoc, the new predictor is much more powerful and flexible. For a newly constructed stringent benchmark dataset in which none of Proteins included has ≥25% pairwise sequence identity to any other in a same subset (location), the overall jackknife success rate achieved by Gneg-mPLoc was 85.5%, which was more than 14% higher than the corresponding rate by the Gneg-PLoc. As a user friendly web-server, Gneg-mPLoc is freely accessible at http://www.csbio.sjtu.edu.cn/bioinf/Gneg-multi/ .
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Gpos-PLoc: an ensemble classifier for predicting subcellular localization of Gram-positive Bacterial Proteins.
Protein engineering design & selection : PEDS, 2007Co-Authors: Hong-bin Shen, Kuo-chen ChouAbstract:A statistical analysis indicated that, of the 35,016 Gram-positive Bacterial Proteins from the recent Swiss-Prot database, approximately 57% of these entries are without subcellular location annotations. In the gene ontology database, the corresponding percentage is approximately 67%, meaning the percentage of Proteins without subcellular component annotations is even higher. With the avalanche of gene products generated in the post-genomic era, the number of such location-unknown entries will continuously increase. It is highly desired to develop an automated method for timely and accurately identifying their subcellular localization because the information thus obtained is very useful for both basic research and drug discovery practice. In view of this, an ensemble classifier called 'Gpos-PLoc' was developed for predicting Gram-positive protein subcellular localization. The new predictor is featured by fusing many basic classifiers, each of which was engineered according to the optimized evidence-theoretic K-nearest neighbors rule. As a demonstration, tests were performed on Gram-positive Proteins among the following five subcellular location sites: (1) cell wall, (2) cytoplasm, (3) extracell, (4) periplasm and (5) plasma membrane. To eliminate redundancy and homology bias, only those Proteins which have 80% for both jackknife cross-validation test and independent dataset test, implying that Gpos-PLoc might become a very useful vehicle for expediting the analysis of Gram-positive Bacterial Proteins. Gpos-PLoc is freely accessible to public as a web-server at http://202.120.37.186/bioinf/Gpos/. To support the need of many investigators in the relevant areas, a downloadable file is provided at the same website to list the results identified by Gpos-PLoc for 31,898 Gram-positive Bacterial protein entries in Swiss-Prot database that either have no subcellular location annotation or are annotated with uncertain terms such as 'probable', 'potential', 'perhaps' and 'by similarity'. Such large-scale results will be updated once a year to include the new entries of Gram-positive Bacterial Proteins and reflect the continuous development of Gpos-PLoc.
Mohsen Golabi - One of the best experts on this subject based on the ideXlab platform.
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Studies on Bacterial Proteins Corona Interaction with Saponin Imprinted ZnO Nanohoneycombs and Their Toxic Responses.
ACS applied materials & interfaces, 2015Co-Authors: Deepali Sharma, Ashaduzzaman, Mohsen Golabi, Amritanshu Shriwastav, Krishna Bisetty, Ashutosh TiwariAbstract:Molecular imprinting generates robust, efficient, and highly mesoporous surfaces for biointeractions. Mechanistic interfacial interaction between the surface of core substrate and protein corona is crucial to understand the substantial microbial toxic responses at a nanoscale. In this study, we have focused on the mechanistic interactions between synthesized saponin imprinted zinc oxide nanohoneycombs (SIZnO NHs), average size 80–125 nm, surface area 20.27 m2/g, average pore density 0.23 pore/nm and number-average pore size 3.74 nm and Proteins corona of bacteria. The produced SIZnO NHs as potential antifungal and antiBacterial agents have been studied on Sclerotium rolfsii (S. rolfsii), Pythium debarynum (P. debarynum) and Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), respectively. SIZnO NHs exhibited the highest antiBacterial (∼50%) and antifungal (∼40%) activity against Gram-negative bacteria (E. coli) and fungus (P. debarynum), respectively at concentration of 0.1 mol. Scanning electr...
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Studies on Bacterial Proteins Corona Interaction with Saponin Imprinted ZnO Nanohoneycombs and Their Toxic Responses
2015Co-Authors: Deepali Sharma, Mohsen Golabi, Amritanshu Shriwastav, Krishna Bisetty, Md. Ashaduzzaman, Ashutosh TiwariAbstract:Molecular imprinting generates robust, efficient, and highly mesoporous surfaces for biointeractions. Mechanistic interfacial interaction between the surface of core substrate and protein corona is crucial to understand the substantial microbial toxic responses at a nanoscale. In this study, we have focused on the mechanistic interactions between synthesized saponin imprinted zinc oxide nanohoneycombs (SIZnO NHs), average size 80–125 nm, surface area 20.27 m2/g, average pore density 0.23 pore/nm and number-average pore size 3.74 nm and Proteins corona of bacteria. The produced SIZnO NHs as potential antifungal and antiBacterial agents have been studied on Sclerotium rolfsii (S. rolfsii), Pythium debarynum (P. debarynum) and Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), respectively. SIZnO NHs exhibited the highest antiBacterial (∼50%) and antifungal (∼40%) activity against Gram-negative bacteria (E. coli) and fungus (P. debarynum), respectively at concentration of 0.1 mol. Scanning electron spectroscopy (SEM) observation showed that the ZnO NHs ruptured the cell wall of bacteria and internalized into the cell. The molecular docking studies were carried out using binding Proteins present in the gram negative bacteria (lipopolysaccharide and lipocalin Blc) and gram positive bacteria (Staphylococcal Protein A, SpA). It was envisaged that the Proteins present in the Bacterial cell wall were found to interact and adsorb on the surface of SIZnO NHs thereby blocking the active sites of the Proteins used for cell wall synthesis. The binding affinity and interaction energies were higher in the case of binding Proteins present in gram negative bacteria as compared to that of gram positive bacteria. In addition, a kinetic mathematical model (KMM) was developed in MATLAB to predict the internalization in the Bacterial cellular uptake of the ZnO NHs for better understanding of their controlled toxicity. The results obtained from KMM exhibited a good agreement with the experimental data. Exploration of mechanistic interactions, as well as the formation of bioconjugate of Proteins and ZnO NHs would play a key role to interpret more complex biological systems in nature