Sanjay Swarup - Academia.edu (original) (raw)

Papers by Sanjay Swarup

Plant Physiology, Dec 1, 1999

Polyclonal and monoclonal antibodies that recognize the 35-, 36-, and 37-kDa alternative oxidase ... more Polyclonal and monoclonal antibodies that recognize the 35-, 36-, and 37-kDa alternative oxidase proteins of Sauromatum guttatum (Schott) were used to isolate a cDNA clone, pAOSG81, from an S. guttatum cDNA expression library. A fusion protein with an apparent molecular mass of 48 kDa was expressed from a pUell9 derivative of pAOSG81 (pAOSG81-119) in Escherichia coli cells and was recognized by the monoclonal antibodies. When the in vitro translated and Abbreviation: IPTG, isopropyl-D-thiogalactopyranoside.

The pathogenicity gene, pthA, of Xanthomonas citri is required to elicit symptoms of Asiatic citr... more The pathogenicity gene, pthA, of Xanthomonas citri is required to elicit symptoms of Asiatic citrus canker disease; introduction of pthA into Xanthomonas strains that are mildly pathogenic or opportunistic on citrus confers the ability to induce cankers on citrus (S. Swarup, R. De Feyter, R. H. Brlansky, and D. W. Gabriel, Phytopathology 81:802-809, 1991). The structure and the function of pthA in other xanthomonads and in X. citri were further investigated. When pthA was introduced into strains of X. phaseoli and X. campestris pv. malvacearum (neither pathogenic to citrus), the transconjugants remained nonpathogenic to citrus and elicited a hypersensitive response (HR) on their respective hosts, bean and cotton. In X. c. pv. malvacearum, pthA conferred cultivar-specific avirulence. Structurally, pthA is highly similar to avrBs3 and avrBsP from X. c. pv. vesicatoria and to avrB4, avrb6, avrb7, avrBIn, avrB101, and avrB102 from X. c. pv. malvacearum. Surprisingly, marker-exchanged pthA::Tn5-gusA mutant B21.2 of X. citri specifically lost the ability to induce the nonhost HR on bean, but retained the ability to induce the nonhost HR on cotton. The loss of the ability of B21.2 to elicit an HR on bean was restored by introduction of cloned pthA, indicating that the genetics of the nonhost HR may be the same as that found in homologous interactions involving specific avr genes. In contrast with expectations of homologous HR reactions, however, elimination of pthA function (resulting in loss of HR) did not result in water-soaking or even moderate levels of growth in planta of X. citri on bean; the nonhost HR, therefore, may not be responsible for the "resistance" of bean to X. citri and may not limit the host range of X. citri on bean. The pleiotropic avirulence function of pthA and the heterologous HR of bean to X. citri are both evidently gratuitous.

Frequent fires in tropical Peat Swamp Forests (PSFs) that have been repurposed for forestry and a... more Frequent fires in tropical Peat Swamp Forests (PSFs) that have been repurposed for forestry and agriculture result in substantial emissions of locked carbon. Fire-affected PSFs emit double the amount of CH4 compared to intact ones over extended periods of time. CH4 production is largely driven by communities of microorganisms (microbiomes – archaea in particular), thus, our ability to reduce emissions hinges on (i) identifying those with the capacity to generate CH4, (ii) ecological processes that shape their composition and functioning, and (iii) environmental variables which drive them. Ecological processes are particularly important as they determine our ability to predict the trajectory of communities and their functioning. Trajectories of communities shaped by deterministic processes can be predicted based on environmental variables as opposed to those shaped by stochastic processes whose trajectories are difficult to predict. We fill this knowledge gap by sequencing and comparing the ecological processes shaping peat microbiomes from a fire-impacted PSF to an intact PSF that occur within the same peat dome in Brunei. The composition of archaeal communities were significantly different between the fire-impacted and intact PSFs and strongly stratified by depth. The largest difference was observed between communities from the surface (0-5 cm) and those from below the water table (95-100 cm). In the fire-impacted PSF, archaea doubled in abundance in the anoxic zone compared to the surface, while, no such change was detected in the intact PSF. Archaeal communities occurring in the anoxic layers of the fire-impacted PSF were dominated by methanogens from the class Methanomicrobia and Bathyarchaeia, both of which occur in high-methane flux habitats. We determined ecological processes shaping the assembly of these methanogenic populations using bin-based phylogenetic null models. This showed that methanogenic populations in the fire-impacted PSF were largely shaped by stochastic processes, whereas, similar populations, albeit at lower abundances, were shaped by deterministic processes in the intact PSF. Changes in pH and dissolved oxygen correlated strongly with differences in assembly processes. Our work shows that changes in the environment resulting from fires can set methanogenic communities on unpredictable trajectories, which in turn correlate strongly with both increased and non-homogeneous CH4 emissions. Altering these key environmental correlates could form the basis for developing nature-based solutions for reducing emissions from fire-impacted peatlands.

ACS food science & technology, Jul 25, 2022

Principles in Microbiome Engineering

Metagenome Assembled Genomes (MAG's) from three Asian green's grown in an urban farm in S... more Metagenome Assembled Genomes (MAG's) from three Asian green's grown in an urban farm in Singapore

Series on Advances in Bioinformatics and Computational Biology, 2005

Plant Cell Reports, 2004

We have developed a plant- Escherichia coli pASV shuttle vector from the essential elements of th... more We have developed a plant- Escherichia coli pASV shuttle vector from the essential elements of the Ageratum yellow vein virus (AYVV). The geminivirus vector contains the AYVV genome with the coat-protein deletion, the E. coli vector backbone of pUC19, a unique cloning site and gene expression cassettes for plant selection and reporter gene activity. The replication of pASV vectors was compared in Nicotiana benthamiana and N. tabacum BY2 cells, and the latter were found to be suitable for long-term maintenance of the vectors in culture. The vector DNA was detected at regular intervals by PCR, beta-glucuronidase expression analysis and plasmid rescue during a 4-month culture period. A novel methylation-based PCR assay was carried out to show de novo replication for pASV-derived vectors in 2-month-old tobacco BY2 cell lines. This is the first report of the extrachromosomal replication of monopartite begomovirus with stability and foreign gene expression in long-term cell cultures.

Molecular Plant-Microbe Interactions, 1992

The pathogenicity gene, pthA, of Xanthomonas citri is required to elicit symptoms of Asiatic citr... more The pathogenicity gene, pthA, of Xanthomonas citri is required to elicit symptoms of Asiatic citrus canker disease; introduction of pthA into Xanthomonas strains that are mildly pathogenic or opportunistic on citrus confers the ability to induce cankers on citrus (S. Swarup, R. De Feyter, R. H. Brlansky, and D. W. Gabriel, Phytopathology 81:802-809, 1991). The structure and the function of pthA in other xanthomonads and in X. citri were further investigated. When pthA was introduced into strains of X. phaseoli and X. campestris pv. malvacearum (neither pathogenic to citrus), the transconjugants remained nonpathogenic to citrus and elicited a hypersensitive response (HR) on their respective hosts, bean and cotton. In X. c. pv. malvacearum, pthA conferred cultivar-specific avirulence. Structurally, pthA is highly similar to avrBs3 and avrBsP from X. c. pv. vesicatoria and to avrB4, avrb6, avrb7, avrBIn, avrB101, and avrB102 from X. c. pv. malvacearum. Surprisingly, marker-exchanged pthA::Tn5-gusA mutant B21.2 of X. citri specifically lost the ability to induce the nonhost HR on bean, but retained the ability to induce the nonhost HR on cotton. The loss of the ability of B21.2 to elicit an HR on bean was restored by introduction of cloned pthA, indicating that the genetics of the nonhost HR may be the same as that found in homologous interactions involving specific avr genes. In contrast with expectations of homologous HR reactions, however, elimination of pthA function (resulting in loss of HR) did not result in water-soaking or even moderate levels of growth in planta of X. citri on bean; the nonhost HR, therefore, may not be responsible for the "resistance" of bean to X. citri and may not limit the host range of X. citri on bean. The pleiotropic avirulence function of pthA and the heterologous HR of bean to X. citri are both evidently gratuitous.

The emerging field of rhizosphere metabolomics involves analysis of entire metabolite complement ... more The emerging field of rhizosphere metabolomics involves analysis of entire metabolite complement (metabolome), in an unbiased way to understand complex physiological, pathological, symbiotic and other relationships among the inhabitants of the rhizosphere. Metabolomic studies of the rhizosphere are quite challenging since the rhizosphere is a complex as well as a dynamic microenvironment. Metabolite composition in the rhizosphere is primarily governed by the nature of root exudates, secretions from rhizobacteria, fungi and other soil organisms. Conversely, the nature of these root exudates also directly or indirectly affects microbial growth in the rhizosphere. While some compounds enhance growth, others have antimicrobial activities. Apart from the diverse roles of compounds present, the complexity of the rhizosphere also stems from competition among rhizosphere microbes. Some of them are growth-promoting, while others are pathogenic. These effects are not only confined to the micr...

Advances in Agroecology, 2011

Water Science and Technology, May 1, 2012

Microbial loads in freshwater systems have important implications in biogeochemical cycling in ur... more Microbial loads in freshwater systems have important implications in biogeochemical cycling in urban environments. Immersed surfaces in freshwaters provide surfaces for bacterial attachment and growth. Microorganisms that adhere initially to these surfaces play a critical role in biofilm formation and sustenance. Currently, there is little understanding on the type of organisms that initially adhere to different surfaces in urban canals. In this study, water from an urban stormwater canal was employed to allow bacteria to attach to different surfaces in a flowcell apparatus and understand the differences and changes in bacterial community structure. Bacterial communities were highly diverse on different surfaces as indicated by Jaccard's indices of 0.14-0.56. Bacteria on aluminium were the most diverse and on Plexiglas the least. Bacterial communities were highly dynamic in the early attachment phase and it changed by 59% between 3 and 6 h on aluminium. Specificity of attachment to surfaces was observed for some bacteria. Judicious use of materials in urban aquatic environment would help mitigate microbial load in urban waters.

Frontiers in Robotics and AI

Using a team of robots for estimating scalar environmental fields is an emerging approach. The ai... more Using a team of robots for estimating scalar environmental fields is an emerging approach. The aim of such an approach is to reduce the mission time for collecting informative data as compared to a single robot. However, increasing the number of robots requires coordination and efficient use of the mission time to provide a good approximation of the scalar field. We suggest an online multi-robot framework m-AdaPP to handle this coordination. We test our framework for estimating a scalar environmental field with no prior information and benchmark the performance via field experiments against conventional approaches such as lawn mower patterns. We demonstrated that our framework is capable of handling a team of robots for estimating a scalar field and outperforms conventional approaches used for approximating water quality parameters. The suggested framework can be used for estimating other scalar functions such as air temperature or vegetative index using land or aerial robots as wel...

Soil Biology, 2008

... Sanjay Swarup Small Molecule Biology Laboratory, Department of Biological Sciences, National ... more ... Sanjay Swarup Small Molecule Biology Laboratory, Department of Biological Sciences, National University of Singapore, Singapore 117543 e-mail: sanjay@nus.edu.sg Page 2. ... However, “metabolomics” is a preferred term for unbiased metabolite analyses (Bhalla et al. 2005). ...

EGU General Assembly Conference Abstracts, Apr 1, 2019

Plant Physiology, Dec 1, 1999

Polyclonal and monoclonal antibodies that recognize the 35-, 36-, and 37-kDa alternative oxidase ... more Polyclonal and monoclonal antibodies that recognize the 35-, 36-, and 37-kDa alternative oxidase proteins of Sauromatum guttatum (Schott) were used to isolate a cDNA clone, pAOSG81, from an S. guttatum cDNA expression library. A fusion protein with an apparent molecular mass of 48 kDa was expressed from a pUell9 derivative of pAOSG81 (pAOSG81-119) in Escherichia coli cells and was recognized by the monoclonal antibodies. When the in vitro translated and Abbreviation: IPTG, isopropyl-D-thiogalactopyranoside.

The pathogenicity gene, pthA, of Xanthomonas citri is required to elicit symptoms of Asiatic citr... more The pathogenicity gene, pthA, of Xanthomonas citri is required to elicit symptoms of Asiatic citrus canker disease; introduction of pthA into Xanthomonas strains that are mildly pathogenic or opportunistic on citrus confers the ability to induce cankers on citrus (S. Swarup, R. De Feyter, R. H. Brlansky, and D. W. Gabriel, Phytopathology 81:802-809, 1991). The structure and the function of pthA in other xanthomonads and in X. citri were further investigated. When pthA was introduced into strains of X. phaseoli and X. campestris pv. malvacearum (neither pathogenic to citrus), the transconjugants remained nonpathogenic to citrus and elicited a hypersensitive response (HR) on their respective hosts, bean and cotton. In X. c. pv. malvacearum, pthA conferred cultivar-specific avirulence. Structurally, pthA is highly similar to avrBs3 and avrBsP from X. c. pv. vesicatoria and to avrB4, avrb6, avrb7, avrBIn, avrB101, and avrB102 from X. c. pv. malvacearum. Surprisingly, marker-exchanged pthA::Tn5-gusA mutant B21.2 of X. citri specifically lost the ability to induce the nonhost HR on bean, but retained the ability to induce the nonhost HR on cotton. The loss of the ability of B21.2 to elicit an HR on bean was restored by introduction of cloned pthA, indicating that the genetics of the nonhost HR may be the same as that found in homologous interactions involving specific avr genes. In contrast with expectations of homologous HR reactions, however, elimination of pthA function (resulting in loss of HR) did not result in water-soaking or even moderate levels of growth in planta of X. citri on bean; the nonhost HR, therefore, may not be responsible for the "resistance" of bean to X. citri and may not limit the host range of X. citri on bean. The pleiotropic avirulence function of pthA and the heterologous HR of bean to X. citri are both evidently gratuitous.

Frequent fires in tropical Peat Swamp Forests (PSFs) that have been repurposed for forestry and a... more Frequent fires in tropical Peat Swamp Forests (PSFs) that have been repurposed for forestry and agriculture result in substantial emissions of locked carbon. Fire-affected PSFs emit double the amount of CH4 compared to intact ones over extended periods of time. CH4 production is largely driven by communities of microorganisms (microbiomes – archaea in particular), thus, our ability to reduce emissions hinges on (i) identifying those with the capacity to generate CH4, (ii) ecological processes that shape their composition and functioning, and (iii) environmental variables which drive them. Ecological processes are particularly important as they determine our ability to predict the trajectory of communities and their functioning. Trajectories of communities shaped by deterministic processes can be predicted based on environmental variables as opposed to those shaped by stochastic processes whose trajectories are difficult to predict. We fill this knowledge gap by sequencing and comparing the ecological processes shaping peat microbiomes from a fire-impacted PSF to an intact PSF that occur within the same peat dome in Brunei. The composition of archaeal communities were significantly different between the fire-impacted and intact PSFs and strongly stratified by depth. The largest difference was observed between communities from the surface (0-5 cm) and those from below the water table (95-100 cm). In the fire-impacted PSF, archaea doubled in abundance in the anoxic zone compared to the surface, while, no such change was detected in the intact PSF. Archaeal communities occurring in the anoxic layers of the fire-impacted PSF were dominated by methanogens from the class Methanomicrobia and Bathyarchaeia, both of which occur in high-methane flux habitats. We determined ecological processes shaping the assembly of these methanogenic populations using bin-based phylogenetic null models. This showed that methanogenic populations in the fire-impacted PSF were largely shaped by stochastic processes, whereas, similar populations, albeit at lower abundances, were shaped by deterministic processes in the intact PSF. Changes in pH and dissolved oxygen correlated strongly with differences in assembly processes. Our work shows that changes in the environment resulting from fires can set methanogenic communities on unpredictable trajectories, which in turn correlate strongly with both increased and non-homogeneous CH4 emissions. Altering these key environmental correlates could form the basis for developing nature-based solutions for reducing emissions from fire-impacted peatlands.

ACS food science & technology, Jul 25, 2022

Principles in Microbiome Engineering

Metagenome Assembled Genomes (MAG's) from three Asian green's grown in an urban farm in S... more Metagenome Assembled Genomes (MAG's) from three Asian green's grown in an urban farm in Singapore

Series on Advances in Bioinformatics and Computational Biology, 2005

Plant Cell Reports, 2004

We have developed a plant- Escherichia coli pASV shuttle vector from the essential elements of th... more We have developed a plant- Escherichia coli pASV shuttle vector from the essential elements of the Ageratum yellow vein virus (AYVV). The geminivirus vector contains the AYVV genome with the coat-protein deletion, the E. coli vector backbone of pUC19, a unique cloning site and gene expression cassettes for plant selection and reporter gene activity. The replication of pASV vectors was compared in Nicotiana benthamiana and N. tabacum BY2 cells, and the latter were found to be suitable for long-term maintenance of the vectors in culture. The vector DNA was detected at regular intervals by PCR, beta-glucuronidase expression analysis and plasmid rescue during a 4-month culture period. A novel methylation-based PCR assay was carried out to show de novo replication for pASV-derived vectors in 2-month-old tobacco BY2 cell lines. This is the first report of the extrachromosomal replication of monopartite begomovirus with stability and foreign gene expression in long-term cell cultures.

Molecular Plant-Microbe Interactions, 1992

The pathogenicity gene, pthA, of Xanthomonas citri is required to elicit symptoms of Asiatic citr... more The pathogenicity gene, pthA, of Xanthomonas citri is required to elicit symptoms of Asiatic citrus canker disease; introduction of pthA into Xanthomonas strains that are mildly pathogenic or opportunistic on citrus confers the ability to induce cankers on citrus (S. Swarup, R. De Feyter, R. H. Brlansky, and D. W. Gabriel, Phytopathology 81:802-809, 1991). The structure and the function of pthA in other xanthomonads and in X. citri were further investigated. When pthA was introduced into strains of X. phaseoli and X. campestris pv. malvacearum (neither pathogenic to citrus), the transconjugants remained nonpathogenic to citrus and elicited a hypersensitive response (HR) on their respective hosts, bean and cotton. In X. c. pv. malvacearum, pthA conferred cultivar-specific avirulence. Structurally, pthA is highly similar to avrBs3 and avrBsP from X. c. pv. vesicatoria and to avrB4, avrb6, avrb7, avrBIn, avrB101, and avrB102 from X. c. pv. malvacearum. Surprisingly, marker-exchanged pthA::Tn5-gusA mutant B21.2 of X. citri specifically lost the ability to induce the nonhost HR on bean, but retained the ability to induce the nonhost HR on cotton. The loss of the ability of B21.2 to elicit an HR on bean was restored by introduction of cloned pthA, indicating that the genetics of the nonhost HR may be the same as that found in homologous interactions involving specific avr genes. In contrast with expectations of homologous HR reactions, however, elimination of pthA function (resulting in loss of HR) did not result in water-soaking or even moderate levels of growth in planta of X. citri on bean; the nonhost HR, therefore, may not be responsible for the "resistance" of bean to X. citri and may not limit the host range of X. citri on bean. The pleiotropic avirulence function of pthA and the heterologous HR of bean to X. citri are both evidently gratuitous.

The emerging field of rhizosphere metabolomics involves analysis of entire metabolite complement ... more The emerging field of rhizosphere metabolomics involves analysis of entire metabolite complement (metabolome), in an unbiased way to understand complex physiological, pathological, symbiotic and other relationships among the inhabitants of the rhizosphere. Metabolomic studies of the rhizosphere are quite challenging since the rhizosphere is a complex as well as a dynamic microenvironment. Metabolite composition in the rhizosphere is primarily governed by the nature of root exudates, secretions from rhizobacteria, fungi and other soil organisms. Conversely, the nature of these root exudates also directly or indirectly affects microbial growth in the rhizosphere. While some compounds enhance growth, others have antimicrobial activities. Apart from the diverse roles of compounds present, the complexity of the rhizosphere also stems from competition among rhizosphere microbes. Some of them are growth-promoting, while others are pathogenic. These effects are not only confined to the micr...

Advances in Agroecology, 2011

Water Science and Technology, May 1, 2012

Microbial loads in freshwater systems have important implications in biogeochemical cycling in ur... more Microbial loads in freshwater systems have important implications in biogeochemical cycling in urban environments. Immersed surfaces in freshwaters provide surfaces for bacterial attachment and growth. Microorganisms that adhere initially to these surfaces play a critical role in biofilm formation and sustenance. Currently, there is little understanding on the type of organisms that initially adhere to different surfaces in urban canals. In this study, water from an urban stormwater canal was employed to allow bacteria to attach to different surfaces in a flowcell apparatus and understand the differences and changes in bacterial community structure. Bacterial communities were highly diverse on different surfaces as indicated by Jaccard's indices of 0.14-0.56. Bacteria on aluminium were the most diverse and on Plexiglas the least. Bacterial communities were highly dynamic in the early attachment phase and it changed by 59% between 3 and 6 h on aluminium. Specificity of attachment to surfaces was observed for some bacteria. Judicious use of materials in urban aquatic environment would help mitigate microbial load in urban waters.

Frontiers in Robotics and AI

Using a team of robots for estimating scalar environmental fields is an emerging approach. The ai... more Using a team of robots for estimating scalar environmental fields is an emerging approach. The aim of such an approach is to reduce the mission time for collecting informative data as compared to a single robot. However, increasing the number of robots requires coordination and efficient use of the mission time to provide a good approximation of the scalar field. We suggest an online multi-robot framework m-AdaPP to handle this coordination. We test our framework for estimating a scalar environmental field with no prior information and benchmark the performance via field experiments against conventional approaches such as lawn mower patterns. We demonstrated that our framework is capable of handling a team of robots for estimating a scalar field and outperforms conventional approaches used for approximating water quality parameters. The suggested framework can be used for estimating other scalar functions such as air temperature or vegetative index using land or aerial robots as wel...

Soil Biology, 2008

... Sanjay Swarup Small Molecule Biology Laboratory, Department of Biological Sciences, National ... more ... Sanjay Swarup Small Molecule Biology Laboratory, Department of Biological Sciences, National University of Singapore, Singapore 117543 e-mail: sanjay@nus.edu.sg Page 2. ... However, “metabolomics” is a preferred term for unbiased metabolite analyses (Bhalla et al. 2005). ...

EGU General Assembly Conference Abstracts, Apr 1, 2019