Genomic and Proteomic Databases: Foundations, Current Status and Future Applications

Navathe, Shamkant B.,Patil, Upen,Guan, Wei Korean Institute of Information Scientists and Eng 2007 Journal of Computing Science and Engineering Vol.1 No.1

In this paper we have provided an extensive survey of the databases and other resources related to the current research in bioinformatics and the issues that confront the database researcher in helping the biologists. Initially we give an overview of the concepts and principles that are fundamental in understanding the basis of the data that has been captured in these databases. We briefly trace the evolution of biological advances and point out the importance of capturing data about genes, the fundamental building blocks that encode the characteristics of life and proteins that are the essential ingredients for sustaining life. The study of genes and proteins is becoming extremely important and is being known as genomics and proteomics, respectively. Whereas there are numerous databases related to various subfields of biology, we have maintained a focus on genomic and proteomic databases which are the crucial stepping stones for other fields and are expected to play an important role in the future applications of biology and medicine. A detailed listing of these databases with information about their sizes, formats and current status is presented. Related databases like molecular pathways and interconnection network databases are mentioned, but their full coverage would be beyond the scope of a single paper. We comment on the peculiar nature of the data in biology that presents special problems in organizing and accessing these databases. We also discuss the capabilities needed for database development and information management in the bioinformatics arena with particular attention to ontology development. Two research case studies based on our own research are summarized dealing with the development of a new genome database called Mitomap and the creation of a framework for discovery of relationships among genes from the biomedical literature. The paper concludes with an overview of the applications that will be driven from these databases in medicine and healthcare. A glossary of important terms is provided at the end of the paper.

Genome‑wide mining of respiratory burst homologs and its expression in response to biotic and abiotic stresses in Triticum aestivum

Sudhir Navathe,Sakshi Singh,Vinay Kumar Singh,Ramesh Chand,Vinod Kumar Mishra,Arun Kumar Joshi 한국유전학회 2019 Genes & Genomics Vol.41 No.9

Background Membrane-bound NADPH oxidases (Nicotinamide adenine ainucleotide phosphate oxidase) also called respiratory burst oxidase homologs (Rboh) play an essential role in ROS production under normal as well as environmental stress conditions in plants. Objective To identify and study respiratory burst homologs (Rboh) from the wheat genome as well as characterize their role in various biological and molecular processes along with expression in response to biotic and abiotic stresses. Methods The Rboh homologs in the wheat genome were predicted based on data processing, alignment of sequences and phylogenetic analysis of sequences in numerous plant species and wheat. The conserved motifs were known followed by domain design study. The 3-D structure prediction and similarity modeling were administered for NADPH enzyme domain. Gene ontology and a functional study were done in addition to expression analysis of Triticum aestivum respiratory burst oxidase (TaRboh) gene family in response to biotic as well as abiotic stress. Results Phylogenetic analysis of Rboh gene family members among seven plant species including wheat, classified the family into four subfamilies. Rboh genes are mainly involved in various biological processes such as Response to oxidative stress, Superoxide anion generation, Hydrogen peroxide biosynthetic process. Among the molecular functions, calcium ion binding, peroxidase activity, oxidoreductase activity, superoxide-generating NADPH oxidase activity are essential. Enzyme annotation of the family and superfamily revealed that it encodes to five structural clusters and coding to enzymes NAD(P)H oxidase ( H2O2-forming) (EC:1.6.3.1), Ferric-chelate reductase (NADH) (EC: 1.16.1.7), Peroxidase (EC: 1.11.1.7), Ribose-phosphate diphosphokinase (EC: 2.7.6.1). The enzymes contain six membrane-spanning domains, two hemes, and conserved motifs associated with NADPH, EF-hand and FAD binding. The outcomes additionally reflect a distinct role of this enzyme in different molecular functions which are responsible for the stress signaling. Further, the transcripts of TaRboh found expressed in various plant parts such as stem, leaves, spike, seed, and roots. We also observed expression of these gene family members under drought/combination of drought + heat and important wheat pathogens such as Puccinia striformis, Blumeria graminis f.sp. tritici, Fusarium graminiarum, F. pseudograminiarum, and Zymoseptoria tritici. Conclusions The investigation demonstrated that identified respiratory burst homologs (Rboh) in T. aestivum were involved in pathogen activated ROS production and have regulatory functions in cell death and defense responses.

Genomic and Proteomic Databases

Shamkant B. Navathe,Upen Patil,Wei Guan 한국정보과학회 2007 Journal of Computing Science and Engineering Vol.1 No.1

In this paper we have provided an extensive survey of the databases and other resources related to the current research in bioinformatics and the issues that confront the database researcher in helping the biologists. Initially we give an overview of the concepts and principles that are fundamental in understanding the basis of the data that has been captured in these databases. We briefly trace the evolution of biological advances and point out the importance of capturing data about genes, the fundamental building blocks that encode the characteristics of life and proteins that are the essential ingredients for sustaining life. The study of genes and proteins is becoming extremely important and is being known as genomics and proteomics, respectively. Whereas there are numerous databases related to various subfields of biology, we have maintained a focus on genomic and proteomic databases which are the crucial stepping stones for other fields and are expected to play an important role in the future applications of biology and medicine. A detailed listing of these databases with information about their sizes, formats and current status is presented. Related databases like molecular pathways and interconnection network databases are mentioned, but their full coverage would be beyond the scope of a single paper. We comment on the peculiar nature of the data in biology that presents special problems in organizing and accessing these databases. We also discuss the capabilities needed for database development and information management in the bioinformatics arena with particular attention to ontology development. Two research case studies based on our own research are summarized dealing with the development of a new genome database called Mitomap and the creation of a framework for discovery of relationships among genes from the biomedical literature. The paper concludes with an overview of the applications that will be driven from these databases in medicine and healthcare. A glossary of important terms is provided at the end of the paper.

(${\beta}$-Galactoside Prodrugs of Doxorubicin for Application in Antibody Directed Enzyme Prodrug Therapy/prodrug Mono Therapy

Devalapally, Harikrishna,Navath, Raghavendra Swamy,Yenamandra, Venkateshwarlu,Akkinepally, RaghuRam Rao,Devarakonda, Rama Krishna 대한약학회 2007 Archives of Pharmacal Research Vol.30 No.6

Anthracycline antibiotics, particularly doxorubicin and daunorubicin, have been used extensively in the treatment of human malignancies. However cardiotoxicity and multidrug resistance are significant problems that limit the clinical efficacy of such agents. Rational design to avoid these side effects includes strategies such as drug targeting and prodrug synthesis. Described here are the synthesis and preliminary biological evaluation of the enzymatically activated two new prodrugs (6 & 11) of doxorubicin. These prodrugs were designed as potential candidates for selective chemotherapy in ADEPT or PMT strategies. They are constituted of a galactose moiety, a spacer and the cytotoxic drug and they differ by the type of spacer. The prodrugs were stable in a buffer, and the in vitro studies showed good detoxification and hydrolysis kinetics. As prodrug 11 was readily hydrolyzed, this could be a valuable candidate for further development.

Hydrogen Peroxide Prompted Lignification Affects Pathogenicity of Hemi-biotrophic Pathogen Bipolaris sorokiniana to Wheat

Poudel, Ajit,Navathe, Sudhir,Chand, Ramesh,Mishra, Vinod K.,Singh, Pawan K.,Joshi, Arun K. The Korean Society of Plant Pathology 2019 Plant Pathology Journal Vol.35 No.4

Spot blotch caused by Bipolaris sorokiniana has spread to more than 9 million ha of wheat in the warm, humid areas of the Eastern Gangetic Plains (EGP) of South Asia and is a disease of major concern in other similar wheat growing regions worldwide. Differential lignin content in resistant and susceptible genotypes and its association with free radicals such as hydrogen peroxide ($H_2O_2$), superoxide ($O_2{^-}$) and hydroxyl radical ($OH^-$) were studied after inoculation under field conditions for two consecutive years. $H_2O_2$ significantly influenced lignin content in flag leaves, whereas there was a negative correlation among lignin and $H_2O_2$ to the Area Under Disease Progress Curve (AUDPC). The production of $H_2O_2$ was higher in the resistant genotypes than susceptible ones. The $O_2{^-}$ and $OH^-$ positively correlated with AUDPC but negatively with lignin content. This study illustrates that $H_2O_2$ has a vital role in prompting lignification and thereby resistance to spot blotch in wheat. We used cluster analysis to separate the resistant and susceptible genotypes by phenotypic and biochemical traits. $H_2O_2$ associated lignin production significantly reduced the number of appressoria and penetration pegs. We visualized the effect of lignin in disease resistance using differential histochemical staining of tissue from resistant and susceptible genotypes, which shows the variable accumulation of hydrogen peroxide and lignin around penetration sites.

β-Galactoside Prodrugs of Doxorubicin for Application in Antibody Directed Enzyme Prodrug Therapy/Prodrug MonoTherapy

HariKrishna Devalapally,Raghavendra Swamy Navath,Venkateshwarlu Yenamandra,RaghuRam Rao Akkinepally,Rama Krishna Devarakonda 대한약학회 2007 Archives of Pharmacal Research Vol.30 No.6

Anthracycline antibiotics, particularly doxorubicin and daunorubicin, have been used extensively in the treatment of human malignancies. However cardiotoxicity and multidrug resistance are significant problems that limit the clinical efficacy of such agents. Rational design to avoid these side effects includes strategies such as drug targeting and prodrug synthesis. Described here are the synthesis and preliminary biological evaluation of the enzymatically activated two new prodrugs (6 & 11) of doxorubicin. These prodrugs were designed as potential candidates for selective chemotherapy in ADEPT or PMT strategies. They are constituted of a galactose moiety, a spacer and the cytotoxic drug and they differ by the type of spacer. The prodrugs were stable in a buffer, and the in vitro studies showed good detoxification and hydrolysis kinetics. As prodrug 11 was readily hydrolyzed, this could be a valuable candidate for further development.

Hydrogen Peroxide Prompted Lignification Affects Pathogenicity of Hemi-biotrophic Pathogen Bipolaris sorokiniana to Wheat

Ajit Poudel,Sudhir Navathe,Ramesh Chand,Vinod K. Mishra,Pawan K. Singh,Arun K. Joshi 한국식물병리학회 2019 Plant Pathology Journal Vol.35 No.4

Spot blotch caused by Bipolaris sorokiniana has spread to more than 9 million ha of wheat in the warm, humid areas of the Eastern Gangetic Plains (EGP) of South Asia and is a disease of major concern in other similar wheat growing regions worldwide. Differential lignin content in resistant and susceptible genotypes and its association with free radicals such as hydrogen peroxide (H2O2), superoxide (O2 -) and hydroxyl radical (OH-) were studied after inoculation under field conditions for two consecutive years. H2O2 significantly influenced lignin content in flag leaves, whereas there was a negative correlation among lignin and H2O2 to the Area Under Disease Progress Curve (AUDPC). The production of H2O2 was higher in the resistant genotypes than susceptible ones. The O2 - and OH- positively correlated with AUDPC but negatively with lignin content. This study illustrates that H2O2 has a vital role in prompting lignification and thereby resistance to spot blotch in wheat. We used cluster analysis to separate the resistant and susceptible genotypes by phenotypic and biochemical traits. H2O2 associated lignin production significantly reduced the number of appressoria and penetration pegs. We visualized the effect of lignin in disease resistance using differential histochemical staining of tissue from resistant and susceptible genotypes, which shows the variable accumulation of hydrogen peroxide and lignin around penetration sites.