Abstract microRNAs (miRNAs) are tiny non-coding evolutionary conserved RNAs that play a regulator... more Abstract microRNAs (miRNAs) are tiny non-coding evolutionary conserved RNAs that play a regulatory role in various cellular and physiological processes of plants. The regulation of miRNA target genes plays a crucial role in plant growth and environmental stress response. Identification of miRNAs in mango (Mangifera indica) is still unexplored, which is one of the most important commercial crop plants of the Anacardiaceae family. In the present study, computational approaches were used to identify miRNAs and their target genes using expressed sequence tags (ESTs) in mango. Functional annotations for the identified targets and assignment of gene ontology (GO) terms were performed. A total of 18 putative miRNAs were identified that belong to 12 diverse miRNA families. 44 potential target genes were predicted for 11 miRNAs. Functional annotation of targets suggested their key involvement in ripening, hormone, and transcription regulation. Overall, findings from this study will provide a broader insight into understanding the functions of miRNAs in M. indica.
Cancer is the uncontrolled growth of abnormal cells in the body. Cancerous cells are also called ... more Cancer is the uncontrolled growth of abnormal cells in the body. Cancerous cells are also called malignant cells, when it spread to other locations in the body via lymph or blood. The culprit gene found was WWP2, a WW domain containing E3 ubiquitin protein ligase2. It was proved to be a potential oncogene which attacks and breaks down a natural inhibitor (found to be PTEN) in the body which normally prevents cancer cells from spreading. So, it was evident that if this gene is blocked by right drugs, it can help checking the metastasis which occurs in the critical late stages of cancers. However, 3D structure of this protein is not yet available. Therefore, an attempt has been made to predict the structure of the protein. A three dimensional model was constructed using the comparative modeling approach and ab-initio methods to get its structural information. The model was validated using PROCHECK for its stereochemical quality. The stability of the protein was checked by performing the Molecular Dynamics simulation using GROMACS 4.0.6 software package and finally the virtual screening and docking was performed by using the ligands from ZINC database, to get the information about the possible inhibitors for the protein, so that it could be blocked by these inhibitors and its further activity could be checked.
Mycobacterium tuberculosis (MTB) is a pathogenic, acid fast bacterium of family Mycobacteriacea. ... more Mycobacterium tuberculosis (MTB) is a pathogenic, acid fast bacterium of family Mycobacteriacea. It is the most common causative agent of various cases of tuberculosis (TB). Tyrosine recombinase (abbreviated as Tyr or Y) or 4- hydroxyphenylalanine is one of the 22 amino acids that are used by cells to synthesize proteins. Homology modeling was performed by SWISS-MODEL, HHPred, ModWeb and Protein structure prediction server respectively. And 3D structures of modelled structures were visualized using the Rasmol tool. The structure were evaluated by Structure Analysis and Verification Servers (SAVES), uses PROCHECK, WHAT_IF, ERRAT, VERIFY 3D, and PROVE. The best model of Tyrosine recombinase was predicted by Protein structure prediction server. The energy minimization of the modelled structure of Tyrosine recombinase was done to improve the quality of the model using SPDBV tool and further evaluated by SAVES. The molecular dynamic simulation (MDS) study with GROMACS program used to check the stability of predicted 3D structure of Tyrosine recombinase. After doing molecular dynamic simulation it was found that the modelled structure was stable by graph. For avoiding unnecessary distribution of the protein, parameters set as 100 pico second time scale and 50000 steps. MDS results have shown the considerable stability to the modelled structure of Tyrosine recombinase. Docking of 3D structure was carried out by Patch dock.reaction) or DNA sequencing. The purity of DNA constitutes an essential step before applying molecular techniques. Although there exist a variety of protocols (1,2,3) but the current protocol is a modification of existing phenol chloroform method to gives surety of a ratio of A260/A280 more than 1.9 compared to earlier protocols.
Nematodes are responsible for causing severe diseases in plants, humans and other animals. Infect... more Nematodes are responsible for causing severe diseases in plants, humans and other animals. Infection is associated with the release of Excretory/Secretory (ES) proteins into host cytoplasm and interference with the host immune system which make them attractive targets for therapeutic use. The identification of ES proteins through bioinformatics approaches is cost- and time-effective and could be used for screening of potential targets for parasitic diseases for further experimental studies. Here, we identified and functionally annotated 93,949 ES proteins, in the genome of 73 nematodes using integration of various bioinformatics tools. 30.6% of ES proteins were found to be supported at RNA level. The predicted ES proteins, annotated by Gene Ontology terms, domains, metabolic pathways, proteases and enzyme class analysis were enriched in molecular functions of proteases, protease inhibitors, c-type lectin and hydrolases which are strongly associated with typical functions of ES proteins. We identified a total of 452 ES proteins from human and plant parasitic nematodes, homologues to DrugBank-approved targets and C. elegans RNA interference phenotype genes which could represent potential targets for parasite control and provide valuable resource for further experimental studies to understand host-pathogen interactions.
46-51Toxoplasma gondii is an obligate, intracellular, apicomplexan parasite that can infect a wid... more 46-51Toxoplasma gondii is an obligate, intracellular, apicomplexan parasite that can infect a wide range of warm-blooded animals including humans. In humans and other intermediate hosts, Toxoplasma develops into chronic infection that cannot be eliminated by host’s immune response or by currently used drugs. The ability of the parasite to convert to the bradyzoite stage and to live inside slow-growing cysts that can go unnoticed by the host immune system allows for the persistence of parasite throughout the life of the infected host. Little is known, however, about how bradyzoites manipulate their host cell. Large scale microarray experiments are becoming increasingly routine, particularly those which track a number of different cell lines through time. This time course information provides valuable insight into dynamics of various biological processes. The proper statistical analysis, however, requires the use of more sophisticated tools and complex statistical models. In the curre...
Current trends in Bioinformatics: An Insight, 2018
The main objective of animal genomics is to comprehend the genetic and molecular basis of all bio... more The main objective of animal genomics is to comprehend the genetic and molecular basis of all biological processes in animal. By understanding that, animals can be utilized as biological resources in the development of new breeds with improved quality and minimized costs. Animals with stress-resistant quality along with yield traits and reproductive traits are of major interest. This data, along with suitable technology, may help in designing predictive procedures for animal health and may also become part of future breeding decision management systems. Existing technologies generate a large amount of genomic data that requires proper processing, storage, and distribution. This data include sequence information as well as information on various markers, maps, functional discoveries, etc. In this chapter, we provide an insight on how different approaches, tools, and databases can be fruitfully utilized for the various animal breeding and genetics programs. Important objectives for animal bioinformatics comprises to encourage the submission of all sequence data into the public domain via various repositories; to make accessible the annotation of genes, proteins, and phenotypes; and to illustrate the relationships within the animal data and also between animal and other organisms.
Molecular modeling, dynamics studies and virtual screening of Fructose 1, 6 biphosphate aldolase-... more Molecular modeling, dynamics studies and virtual screening of Fructose 1, 6 biphosphate aldolase-II in community acquired- methicillin resistant
Genome-wide, a gene can be designated as indispensable for the survival of a cell or an organism,... more Genome-wide, a gene can be designated as indispensable for the survival of a cell or an organism, and its interruption can lead to the malfunctioning or death of the organism. Due to its essentiality for survival, these could be proposed as novel and promising candidates for broad-spectrum drug targets, if these are conserved across a genus. Identification of essential gene has been done in many organisms, and interestingly, most of them were pathogenic in nature. The genome-scale elucidation of essential genes plays an important role in development and complete genome availability. At large scale, gene-inactivation technologies such as targeted gene inactivation, genetic footprinting, and transposon-based mutagenesis are controlled by essential genes. In silico, numerous strategies and tools also have been developed, such as subtractive genomics, essentiality base mapping, and target identification using phylogenetic profiling. Bioinformatic approaches can also be used to analyze e...
Cancer is the uncontrolled growth of abnormal cells in the body. Cancerous cells are also called ... more Cancer is the uncontrolled growth of abnormal cells in the body. Cancerous cells are also called malignant cells, when it spread to other locations in the body via lymph or blood. The culprit gene found was WWP2, a WW domain containing E3 ubiquitin protein ligase2. It was proved to be a potential oncogene which attacks and breaks down a natural inhibitor (found to be PTEN) in the body which normally prevents cancer cells from spreading. So, it was evident that if this gene is blocked by right drugs, it can help checking the metastasis which occurs in the critical late stages of cancers. However, 3D structure of this protein is not yet available. Therefore, an attempt has been made to predict the structure of the protein. A three dimensional model was constructed using the comparative modeling approach and ab-initio methods to get its structural information. The model was validated using PROCHECK for its stereochemical quality. The stability of the protein was checked by performing t...
Hepatic copper levels differ among patients with Wilson disease (WD) and normal individuals depen... more Hepatic copper levels differ among patients with Wilson disease (WD) and normal individuals depending on the dietary intake, copper bioavailability, and genetic factors. Copper chloride (CuCl2) caused dose‐dependent reduction in cell viability of human teratocarcinoma (HepG2) cell line, measured using the 3‐(4,5‐dimethyl‐2‐thiazolyl)‐2,5‐diphenyl‐2H‐tetrazolium bromide (MTT) assay. Cells were exposed to different concentrations of CuCl2 in log doses and maximum cell viability reduction was recorded at 15 µg/mL. Toxic dose of CuCl2 is potent inducer of reactive oxygen species (ROS). Apoptosis as a pattern of cell death was confirmed through sub‐G1 fraction and morphological changes such as mitochondrial depolarization, endoplasmic reticulum and lysosomal destabilization, phosphatidylserine translocation, and DNA damage. Our transcriptional and translational results strongly support apoptotic cell death. Using the available data present in dbSNP and bioinformatics tools, three nonsyno...
Human Papilloma Virus (HPV) HPV type 16 E7 antigen is a known target in cervical cancer. We repor... more Human Papilloma Virus (HPV) HPV type 16 E7 antigen is a known target in cervical cancer. We report the predicted potential epitopes in the E7 antigen. We further describe the subsequent interaction of these linear epitope peptides with the human TMEM 50 A structural model using molecular docking. This data finds application in the development of components towards HPV associated disease prevention.
Abstract microRNAs (miRNAs) are tiny non-coding evolutionary conserved RNAs that play a regulator... more Abstract microRNAs (miRNAs) are tiny non-coding evolutionary conserved RNAs that play a regulatory role in various cellular and physiological processes of plants. The regulation of miRNA target genes plays a crucial role in plant growth and environmental stress response. Identification of miRNAs in mango (Mangifera indica) is still unexplored, which is one of the most important commercial crop plants of the Anacardiaceae family. In the present study, computational approaches were used to identify miRNAs and their target genes using expressed sequence tags (ESTs) in mango. Functional annotations for the identified targets and assignment of gene ontology (GO) terms were performed. A total of 18 putative miRNAs were identified that belong to 12 diverse miRNA families. 44 potential target genes were predicted for 11 miRNAs. Functional annotation of targets suggested their key involvement in ripening, hormone, and transcription regulation. Overall, findings from this study will provide a broader insight into understanding the functions of miRNAs in M. indica.
Cancer is the uncontrolled growth of abnormal cells in the body. Cancerous cells are also called ... more Cancer is the uncontrolled growth of abnormal cells in the body. Cancerous cells are also called malignant cells, when it spread to other locations in the body via lymph or blood. The culprit gene found was WWP2, a WW domain containing E3 ubiquitin protein ligase2. It was proved to be a potential oncogene which attacks and breaks down a natural inhibitor (found to be PTEN) in the body which normally prevents cancer cells from spreading. So, it was evident that if this gene is blocked by right drugs, it can help checking the metastasis which occurs in the critical late stages of cancers. However, 3D structure of this protein is not yet available. Therefore, an attempt has been made to predict the structure of the protein. A three dimensional model was constructed using the comparative modeling approach and ab-initio methods to get its structural information. The model was validated using PROCHECK for its stereochemical quality. The stability of the protein was checked by performing the Molecular Dynamics simulation using GROMACS 4.0.6 software package and finally the virtual screening and docking was performed by using the ligands from ZINC database, to get the information about the possible inhibitors for the protein, so that it could be blocked by these inhibitors and its further activity could be checked.
Mycobacterium tuberculosis (MTB) is a pathogenic, acid fast bacterium of family Mycobacteriacea. ... more Mycobacterium tuberculosis (MTB) is a pathogenic, acid fast bacterium of family Mycobacteriacea. It is the most common causative agent of various cases of tuberculosis (TB). Tyrosine recombinase (abbreviated as Tyr or Y) or 4- hydroxyphenylalanine is one of the 22 amino acids that are used by cells to synthesize proteins. Homology modeling was performed by SWISS-MODEL, HHPred, ModWeb and Protein structure prediction server respectively. And 3D structures of modelled structures were visualized using the Rasmol tool. The structure were evaluated by Structure Analysis and Verification Servers (SAVES), uses PROCHECK, WHAT_IF, ERRAT, VERIFY 3D, and PROVE. The best model of Tyrosine recombinase was predicted by Protein structure prediction server. The energy minimization of the modelled structure of Tyrosine recombinase was done to improve the quality of the model using SPDBV tool and further evaluated by SAVES. The molecular dynamic simulation (MDS) study with GROMACS program used to check the stability of predicted 3D structure of Tyrosine recombinase. After doing molecular dynamic simulation it was found that the modelled structure was stable by graph. For avoiding unnecessary distribution of the protein, parameters set as 100 pico second time scale and 50000 steps. MDS results have shown the considerable stability to the modelled structure of Tyrosine recombinase. Docking of 3D structure was carried out by Patch dock.reaction) or DNA sequencing. The purity of DNA constitutes an essential step before applying molecular techniques. Although there exist a variety of protocols (1,2,3) but the current protocol is a modification of existing phenol chloroform method to gives surety of a ratio of A260/A280 more than 1.9 compared to earlier protocols.
Nematodes are responsible for causing severe diseases in plants, humans and other animals. Infect... more Nematodes are responsible for causing severe diseases in plants, humans and other animals. Infection is associated with the release of Excretory/Secretory (ES) proteins into host cytoplasm and interference with the host immune system which make them attractive targets for therapeutic use. The identification of ES proteins through bioinformatics approaches is cost- and time-effective and could be used for screening of potential targets for parasitic diseases for further experimental studies. Here, we identified and functionally annotated 93,949 ES proteins, in the genome of 73 nematodes using integration of various bioinformatics tools. 30.6% of ES proteins were found to be supported at RNA level. The predicted ES proteins, annotated by Gene Ontology terms, domains, metabolic pathways, proteases and enzyme class analysis were enriched in molecular functions of proteases, protease inhibitors, c-type lectin and hydrolases which are strongly associated with typical functions of ES proteins. We identified a total of 452 ES proteins from human and plant parasitic nematodes, homologues to DrugBank-approved targets and C. elegans RNA interference phenotype genes which could represent potential targets for parasite control and provide valuable resource for further experimental studies to understand host-pathogen interactions.
46-51Toxoplasma gondii is an obligate, intracellular, apicomplexan parasite that can infect a wid... more 46-51Toxoplasma gondii is an obligate, intracellular, apicomplexan parasite that can infect a wide range of warm-blooded animals including humans. In humans and other intermediate hosts, Toxoplasma develops into chronic infection that cannot be eliminated by host’s immune response or by currently used drugs. The ability of the parasite to convert to the bradyzoite stage and to live inside slow-growing cysts that can go unnoticed by the host immune system allows for the persistence of parasite throughout the life of the infected host. Little is known, however, about how bradyzoites manipulate their host cell. Large scale microarray experiments are becoming increasingly routine, particularly those which track a number of different cell lines through time. This time course information provides valuable insight into dynamics of various biological processes. The proper statistical analysis, however, requires the use of more sophisticated tools and complex statistical models. In the curre...
Current trends in Bioinformatics: An Insight, 2018
The main objective of animal genomics is to comprehend the genetic and molecular basis of all bio... more The main objective of animal genomics is to comprehend the genetic and molecular basis of all biological processes in animal. By understanding that, animals can be utilized as biological resources in the development of new breeds with improved quality and minimized costs. Animals with stress-resistant quality along with yield traits and reproductive traits are of major interest. This data, along with suitable technology, may help in designing predictive procedures for animal health and may also become part of future breeding decision management systems. Existing technologies generate a large amount of genomic data that requires proper processing, storage, and distribution. This data include sequence information as well as information on various markers, maps, functional discoveries, etc. In this chapter, we provide an insight on how different approaches, tools, and databases can be fruitfully utilized for the various animal breeding and genetics programs. Important objectives for animal bioinformatics comprises to encourage the submission of all sequence data into the public domain via various repositories; to make accessible the annotation of genes, proteins, and phenotypes; and to illustrate the relationships within the animal data and also between animal and other organisms.
Molecular modeling, dynamics studies and virtual screening of Fructose 1, 6 biphosphate aldolase-... more Molecular modeling, dynamics studies and virtual screening of Fructose 1, 6 biphosphate aldolase-II in community acquired- methicillin resistant
Genome-wide, a gene can be designated as indispensable for the survival of a cell or an organism,... more Genome-wide, a gene can be designated as indispensable for the survival of a cell or an organism, and its interruption can lead to the malfunctioning or death of the organism. Due to its essentiality for survival, these could be proposed as novel and promising candidates for broad-spectrum drug targets, if these are conserved across a genus. Identification of essential gene has been done in many organisms, and interestingly, most of them were pathogenic in nature. The genome-scale elucidation of essential genes plays an important role in development and complete genome availability. At large scale, gene-inactivation technologies such as targeted gene inactivation, genetic footprinting, and transposon-based mutagenesis are controlled by essential genes. In silico, numerous strategies and tools also have been developed, such as subtractive genomics, essentiality base mapping, and target identification using phylogenetic profiling. Bioinformatic approaches can also be used to analyze e...
Cancer is the uncontrolled growth of abnormal cells in the body. Cancerous cells are also called ... more Cancer is the uncontrolled growth of abnormal cells in the body. Cancerous cells are also called malignant cells, when it spread to other locations in the body via lymph or blood. The culprit gene found was WWP2, a WW domain containing E3 ubiquitin protein ligase2. It was proved to be a potential oncogene which attacks and breaks down a natural inhibitor (found to be PTEN) in the body which normally prevents cancer cells from spreading. So, it was evident that if this gene is blocked by right drugs, it can help checking the metastasis which occurs in the critical late stages of cancers. However, 3D structure of this protein is not yet available. Therefore, an attempt has been made to predict the structure of the protein. A three dimensional model was constructed using the comparative modeling approach and ab-initio methods to get its structural information. The model was validated using PROCHECK for its stereochemical quality. The stability of the protein was checked by performing t...
Hepatic copper levels differ among patients with Wilson disease (WD) and normal individuals depen... more Hepatic copper levels differ among patients with Wilson disease (WD) and normal individuals depending on the dietary intake, copper bioavailability, and genetic factors. Copper chloride (CuCl2) caused dose‐dependent reduction in cell viability of human teratocarcinoma (HepG2) cell line, measured using the 3‐(4,5‐dimethyl‐2‐thiazolyl)‐2,5‐diphenyl‐2H‐tetrazolium bromide (MTT) assay. Cells were exposed to different concentrations of CuCl2 in log doses and maximum cell viability reduction was recorded at 15 µg/mL. Toxic dose of CuCl2 is potent inducer of reactive oxygen species (ROS). Apoptosis as a pattern of cell death was confirmed through sub‐G1 fraction and morphological changes such as mitochondrial depolarization, endoplasmic reticulum and lysosomal destabilization, phosphatidylserine translocation, and DNA damage. Our transcriptional and translational results strongly support apoptotic cell death. Using the available data present in dbSNP and bioinformatics tools, three nonsyno...
Human Papilloma Virus (HPV) HPV type 16 E7 antigen is a known target in cervical cancer. We repor... more Human Papilloma Virus (HPV) HPV type 16 E7 antigen is a known target in cervical cancer. We report the predicted potential epitopes in the E7 antigen. We further describe the subsequent interaction of these linear epitope peptides with the human TMEM 50 A structural model using molecular docking. This data finds application in the development of components towards HPV associated disease prevention.
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Papers by Budhayash Gautam