Mohan Babu - Academia.edu (original) (raw)
Papers by Mohan Babu
Journal of General Virology, 2008
Methods in Molecular Biology, 2011
Cellular processes are carried out through a series of molecular interactions. Various experiment... more Cellular processes are carried out through a series of molecular interactions. Various experimental approaches can be used to investigate these functional relationships on a large-scale. Recently, the power of investigating biological systems from the perspective of genetic (gene-gene, or epistatic) interactions has been evidenced by the ability to elucidate novel functional relationships. Examples of functionally related genes include genes that buffer each other's function or impinge on the same biological process. Genetic interactions have traditionally been investigated in bacteria by combining pairs of mutations (for example, gene deletions) and assessing deviation of the phenotype of each double mutant from an expected neutral (or no interaction) phenotype. Fitness is a particularly convenient phenotype to measure: when the double mutant grows faster or slower than expected, the two mutated genes are said to show alleviating or aggravating interactions, respectively. The most commonly used neutral model assumes that the fitness of the double mutant is equal to the product of individual single mutant fitness. A striking genetic interaction is exemplified by the loss of two nonessential genes that buffer each other in performing an essential biological function: deleting only one of these genes produces no detectable fitness defect; however, loss of both genes simultaneously results in systems failure, leading to synthetic sickness or lethality. Systematic large-scale genetic interaction screens have been used to generate functional maps for model eukaryotic organisms, such as yeast, to describe the functional organization of gene products into pathways and protein complexes within a cell. They also reveal the modular arrangement and cross-talk of pathways and complexes within broader functional neighborhoods (Dixon et al. Annu Rev Genet 43:601-625, 2009). Here, we present a high-throughput quantitative Escherichia coli synthetic genetic array (eSGA) screening procedure, which we developed to systematically infer genetic interactions by scoring growth defects among large numbers of double mutants in a classic gram-negative bacterium. The eSGA method exploits the rapid colony growth, ease of genetic manipulation, and natural efficient genetic exchange via conjugation of laboratory E. coli strains. Replica pinning is used to grow and mate arrayed sets of single-gene mutant strains as well as to select double mutants en mass. Strain fitness, which is used as the eSGA readout, is quantified by the digital imaging of the plates and subsequent measuring and comparing single and double mutant colony sizes. While eSGA can be used to screen select mutants to probe the functions of individual genes; using eSGA more broadly to collect genetic interaction data for many combinations of genes can help reconstruct a functional interaction network to reveal novel links and components of biological pathways as well as unexpected connections between pathways. A variety of bacterial systems can be investigated, wherein the genes impinge on a essential biological process (e.g., cell wall assembly, ribosome biogenesis, chromosome replication) that are of interest from the perspective of drug development (Babu et al. Mol Biosyst 12:1439-1455, 2009). We also show how genetic interactions generated by high-throughput eSGA screens can be validated by manual small-scale genetic crosses and by genetic complementation and gene rescue experiments.
Virus Research, 2008
A naturally occurring Rsv4 resistance-breaking isolate (L-RB) and a closely related non-resistanc... more A naturally occurring Rsv4 resistance-breaking isolate (L-RB) and a closely related non-resistance-breaking isolate (L) of Soybean mosaic virus (SMV) were identified in soybean fields in London, Ontario, Canada. The viral genomes of L and L-RB were completely sequenced. Each isolate has a 9585-nucleotide genome with a single open reading frame encoding a polyprotein of approximately 350 kDa. L-RB and L have a very high sequence similarity (99.6%) at both the nucleotide and amino acid levels. Phylogenetic analysis showed that the two isolates belong to the G2 pathotype. Pathogenicity predictions of all virus/soybean combinations, based on the phylogenetic profile, were confirmed by pathogenicity tests using L and L-RB isolates and soybeans carrying different resistance genes, with an exception that L-RB infected a soybean cultivar carrying Rsv4 resistance. The temporal and spatial proximity of L and L-RB and their high sequence similarity suggest L-RB was likely derived from the SMV-L quasispecies. Recombination analysis did not reveal the evidence of genetic recombination for the emergence of L-RB. Mutations introduced by virus-encoded RNA-dependent RNA polymerase during viral genome replication and selection pressure probably contributed to the occurrence of L-RB.
FEMS Microbiology Reviews, 2009
FEMS Microbiology Reviews, 2005
Bioresource Technology, 2011
Biodiesel as an eco-friendly fuel is gaining much acceptance in recent years. This communication ... more Biodiesel as an eco-friendly fuel is gaining much acceptance in recent years. This communication provides an overview on the possibility of using mixed microalgae existing in ecological water-bodies for harnessing biodiesel. Microalgal cultures from five water-bodies are cultivated in domestic wastewater in open-ponds and the harvested algal-biomass was processed through acid-catalyzed transesterification. Experiments evidenced the potential of using mixed microalgae for harnessing biodiesel. Presence of palmitic acid (C16:0) in higher fraction and physical properties of algal oil correlated well with the biodiesel properties. Functional characteristics of water-bodies showed to influence both species diversity and lipid accumulation. Microalgae from stagnant water-bodies receiving domestic discharges documented higher lipid accumulation. Algal-oil showed to consist 33 types of saturated and unsaturated fatty acids having wide food and fuel characteristics. Simultaneous wastewater treatment was also noticed due to the syntrophic association in the water-body microenvironment. Diversity studies visualized the composition of algae species known to accumulate higher lipids.
Bioresource Technology, 2012
Biophysical Journal, 2009
Journal of General Virology, 2008
Methods in Molecular Biology, 2011
Cellular processes are carried out through a series of molecular interactions. Various experiment... more Cellular processes are carried out through a series of molecular interactions. Various experimental approaches can be used to investigate these functional relationships on a large-scale. Recently, the power of investigating biological systems from the perspective of genetic (gene-gene, or epistatic) interactions has been evidenced by the ability to elucidate novel functional relationships. Examples of functionally related genes include genes that buffer each other's function or impinge on the same biological process. Genetic interactions have traditionally been investigated in bacteria by combining pairs of mutations (for example, gene deletions) and assessing deviation of the phenotype of each double mutant from an expected neutral (or no interaction) phenotype. Fitness is a particularly convenient phenotype to measure: when the double mutant grows faster or slower than expected, the two mutated genes are said to show alleviating or aggravating interactions, respectively. The most commonly used neutral model assumes that the fitness of the double mutant is equal to the product of individual single mutant fitness. A striking genetic interaction is exemplified by the loss of two nonessential genes that buffer each other in performing an essential biological function: deleting only one of these genes produces no detectable fitness defect; however, loss of both genes simultaneously results in systems failure, leading to synthetic sickness or lethality. Systematic large-scale genetic interaction screens have been used to generate functional maps for model eukaryotic organisms, such as yeast, to describe the functional organization of gene products into pathways and protein complexes within a cell. They also reveal the modular arrangement and cross-talk of pathways and complexes within broader functional neighborhoods (Dixon et al. Annu Rev Genet 43:601-625, 2009). Here, we present a high-throughput quantitative Escherichia coli synthetic genetic array (eSGA) screening procedure, which we developed to systematically infer genetic interactions by scoring growth defects among large numbers of double mutants in a classic gram-negative bacterium. The eSGA method exploits the rapid colony growth, ease of genetic manipulation, and natural efficient genetic exchange via conjugation of laboratory E. coli strains. Replica pinning is used to grow and mate arrayed sets of single-gene mutant strains as well as to select double mutants en mass. Strain fitness, which is used as the eSGA readout, is quantified by the digital imaging of the plates and subsequent measuring and comparing single and double mutant colony sizes. While eSGA can be used to screen select mutants to probe the functions of individual genes; using eSGA more broadly to collect genetic interaction data for many combinations of genes can help reconstruct a functional interaction network to reveal novel links and components of biological pathways as well as unexpected connections between pathways. A variety of bacterial systems can be investigated, wherein the genes impinge on a essential biological process (e.g., cell wall assembly, ribosome biogenesis, chromosome replication) that are of interest from the perspective of drug development (Babu et al. Mol Biosyst 12:1439-1455, 2009). We also show how genetic interactions generated by high-throughput eSGA screens can be validated by manual small-scale genetic crosses and by genetic complementation and gene rescue experiments.
Virus Research, 2008
A naturally occurring Rsv4 resistance-breaking isolate (L-RB) and a closely related non-resistanc... more A naturally occurring Rsv4 resistance-breaking isolate (L-RB) and a closely related non-resistance-breaking isolate (L) of Soybean mosaic virus (SMV) were identified in soybean fields in London, Ontario, Canada. The viral genomes of L and L-RB were completely sequenced. Each isolate has a 9585-nucleotide genome with a single open reading frame encoding a polyprotein of approximately 350 kDa. L-RB and L have a very high sequence similarity (99.6%) at both the nucleotide and amino acid levels. Phylogenetic analysis showed that the two isolates belong to the G2 pathotype. Pathogenicity predictions of all virus/soybean combinations, based on the phylogenetic profile, were confirmed by pathogenicity tests using L and L-RB isolates and soybeans carrying different resistance genes, with an exception that L-RB infected a soybean cultivar carrying Rsv4 resistance. The temporal and spatial proximity of L and L-RB and their high sequence similarity suggest L-RB was likely derived from the SMV-L quasispecies. Recombination analysis did not reveal the evidence of genetic recombination for the emergence of L-RB. Mutations introduced by virus-encoded RNA-dependent RNA polymerase during viral genome replication and selection pressure probably contributed to the occurrence of L-RB.
FEMS Microbiology Reviews, 2009
FEMS Microbiology Reviews, 2005
Bioresource Technology, 2011
Biodiesel as an eco-friendly fuel is gaining much acceptance in recent years. This communication ... more Biodiesel as an eco-friendly fuel is gaining much acceptance in recent years. This communication provides an overview on the possibility of using mixed microalgae existing in ecological water-bodies for harnessing biodiesel. Microalgal cultures from five water-bodies are cultivated in domestic wastewater in open-ponds and the harvested algal-biomass was processed through acid-catalyzed transesterification. Experiments evidenced the potential of using mixed microalgae for harnessing biodiesel. Presence of palmitic acid (C16:0) in higher fraction and physical properties of algal oil correlated well with the biodiesel properties. Functional characteristics of water-bodies showed to influence both species diversity and lipid accumulation. Microalgae from stagnant water-bodies receiving domestic discharges documented higher lipid accumulation. Algal-oil showed to consist 33 types of saturated and unsaturated fatty acids having wide food and fuel characteristics. Simultaneous wastewater treatment was also noticed due to the syntrophic association in the water-body microenvironment. Diversity studies visualized the composition of algae species known to accumulate higher lipids.
Bioresource Technology, 2012
Biophysical Journal, 2009