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vol. 12, no. 1, 2015 by Nazeer Ahmed

Rice is a staple food to almost one-third population of the world. The crop sustainability must t... more Rice is a staple food to almost one-third population of the world. The crop sustainability must therefore be considered
to keep pace with the growing world population. Microorganims are one of the key factors affecting crop productivity
and quality. Of particular interest is the plant rhiszosphere microbiome which has gained enormous attention in recent
years due to their role both as pathogen and plant growth promoting agents. Accordingly, the present study is aimed at
identification of bacteria isolated from soil samples collected from rice fields of district Jaffarabad, which belongs to
the major rice growing area of Pakistan. Six strains B9, B15, B34, B40, B52 and B53 were identified as genus Bacillus
whereas isolate B12 as genus Staphylococcus based on morphological and biochemical properties and 16S rRNA gene
sequence analysis. Isolates B9, B40 and B53 showed 99% similarity to Bacillus thuringiensis, Bacillus anthracis and
Bacillus endophyticus respectively. Conflicting results were observed for B15, B34 and B52 for sequence analysis
based on BLAST and SeqMatch alignment. The isolate B12 showed 99% similarity to Staphylococcus aureus. Our
findings indicate that instead of resorting rice bacterial populations through biochemical tests, the validation through
16S rRNA technique provides a more objective view.

Papers by Nazeer Ahmed

Methods in Molecular Biology, 2017

Plant cells respond to stresses and exogenous environmental stimuli. Production of altered levels... more Plant cells respond to stresses and exogenous environmental stimuli. Production of altered levels of reactive oxygen species (ROS) is one of a typical cellular responses against such stimuli. These responses are detectable through various techniques including luminol-based bioassays. Luminol-based bioassays provide an excellent opportunity for detection of ROS in plant leaf tissue when challenged with some exogenous stimuli like phytohormones, cytokinins, auxins, ABA, etc. The luminol-based protocol in point aims at measuring changes in the H2O2 levels of Arabidopsis leaf discs when exposed to phytohormone cytokinins. However, utility of the luminol-based ROS determination protocol is quite wide. We specifically optimized this protocol to quantify the effect of cytokinins on ROS production by Arabidopsis leaves.

Plant hormones are small signaling molecules that regulate almost every aspect of plant life cycl... more Plant hormones are small signaling molecules that regulate almost every aspect of plant life cycle. Plant pathogens alter hormonal balance of the host to cause disease. In response, host redefines hormone signaling networks to cope with the invading pathogen. Biotrophic pathogens are generally sensitive to salicylic acid mediated defense responses, whereas necrotrophic pathogens are deterred through jasmonate/ethylene pathways. Interaction between these pathways is regarded as central backbone of plant immunity. Classic hormones such as auxin, gibberellin, and cytokinin either promote salicylic acid or jasmonates mediated networks of immunity in plants. Here, we advocate a network biology perspective and emphasize the application of systems biology approaches for a comprehensive understanding of plantpathogen interactions.

Journal of Animal and Plant Sciences

Dengue viral infections pose threat to almost half of the world’s population health. The recent o... more Dengue viral infections pose threat to almost half of the world’s population health. The recent outbreak of dengue fever in Pakistan has invited attention of the scientific community to attempt devising ways and means and initiating programs controlling this menace. This work is also a step forward in the same direction. Utilizing different in-silico approaches like CLC Bio workbench, Protparam and Virus mploc comparative analysis of the full length genome and proteome of dengue virus serotypes was performed. All the four serotypes exhibited high level of similarities both at genome and proteome level. However, variations still existed though insignificant. Concerning prediction of sub-cellular localization of viral capsid, envelop and membrane glycoprotein in the host cell, all three proteins in four serotypes were shown to target endoplasmic reticulum. Endoplasmic reticulum hosting the viral structural proteins emerges as the pivot of the future studies aiming controlling dengue i...

Journal of Animal and Plant Sciences

Biologia (Lahore, Pakistan)

Four ascomycetous strains viz., Y371-Candida valdiviana, Y207-Saccharomyces kluyveri and two stra... more Four ascomycetous strains viz., Y371-Candida valdiviana, Y207-Saccharomyces kluyveri and two strains of Williopsis californica (Y2- and Y90), which appeared as sensitive in a previous research work (Mushtaq et al., 2010 & 2013) were used in this study to screen killer, sensitive and neutral phenotypes (Killer-Sensitive-Pattern, KSP) in 556 isolates of yeasts belonging to 89 species and 31 genera. Y207- S. kluyveri and Y371- C. valdiviana appeared most suitable strains to screen KSP in yeast species from all substrates as compared to Y90-W. californica which did not showed sensitivity against slime flux yeast isolates. Whereas, sensitive strain Y2-W. californica appeared sensitive against dairy and flowers’ nectar yeast isolates only. The phenomenon of killer activity appeared as strain character, however the ecological habitat was also found to play important role in determining the killer-sensitive pattern. The sensitive ascomycetous yeast strains Y207-S. kluyveri and Y2- W. califo...

Current protein & peptide science, Jan 30, 2015

The plant hormone auxin regulates a whole repertoire of plant growth and development. Many plant-... more The plant hormone auxin regulates a whole repertoire of plant growth and development. Many plant-associated microorganisms, by virtue of their auxin production capability, mediate phytostimulation effects on plants. Recent studies, however, demonstrate diverse mechanisms whereby plant pathogens manipulate auxin biosynthesis, signaling and transport pathways to promote host susceptibility. Auxin responses have been coupled to their antagonistic and synergistic interactions with salicylic acid and jasmonate mediated defenses, respectively. Here, we discuss that a better understanding of auxin crosstalk to plant immune networks would enable us to engineer crop plants with higher protection and low unintended yield losses.

Plant signaling & behavior, 2013

Crosstalk between auxin and cytokinin in plant growth and development has already been establishe... more Crosstalk between auxin and cytokinin in plant growth and development has already been established. However, their dynamics in plant immunity is still not well understood and requires systems biological approaches for analysis. Omics based public databases are exploited for the reconstruction, integration and analysis of Boolean models for hormonal interactions in plants. We established a meta-network by combining the plant immune regulatory network and the pathogen virulence specific network and used it as substrate for dynamic simulations on hormonal aspects of plant immunity. Our integrated analysis of this meta-network reveals antagonistic crosstalk between auxin and cytokinin in the Pst DC3000 and Arabidopsis interaction. Moreover, we discuss here the importance of Boolean models in unfolding inferences relevant to plant pathogen interactions.

The Plant Cell, 2012

Phytohormones signal and combine to maintain the physiological equilibrium in the plant. Pathogen... more Phytohormones signal and combine to maintain the physiological equilibrium in the plant. Pathogens enhance host susceptibility by modulating the hormonal balance of the plant cell. Unlike other plant hormones, the detailed role of cytokinin in plant immunity remains to be fully elucidated. Here, extensive data mining, including of pathogenicity factors, host regulatory proteins, enzymes of hormone biosynthesis, and signaling components, established an integrated signaling network of 105 nodes and 163 edges. Dynamic modeling and system analysis identified multiple cytokinin-mediated regulatory interactions in plant disease networks. This includes specific synergism between cytokinin and salicylic acid pathways and previously undiscovered aspects of antagonism between cytokinin and auxin in plant immunity. Predicted interactions and hormonal effects on plant immunity are confirmed in subsequent experiments with Pseudomonas syringae pv tomato DC3000 and Arabidopsis thaliana. Our dynamic simulation is instrumental in predicting system effects of individual components in complex hormone disease networks and synergism or antagonism between pathways.

Rice is a staple food to almost one-third population of the world. The crop sustainability must t... more Rice is a staple food to almost one-third population of the world. The crop sustainability must therefore be considered
to keep pace with the growing world population. Microorganims are one of the key factors affecting crop productivity
and quality. Of particular interest is the plant rhiszosphere microbiome which has gained enormous attention in recent
years due to their role both as pathogen and plant growth promoting agents. Accordingly, the present study is aimed at
identification of bacteria isolated from soil samples collected from rice fields of district Jaffarabad, which belongs to
the major rice growing area of Pakistan. Six strains B9, B15, B34, B40, B52 and B53 were identified as genus Bacillus
whereas isolate B12 as genus Staphylococcus based on morphological and biochemical properties and 16S rRNA gene
sequence analysis. Isolates B9, B40 and B53 showed 99% similarity to Bacillus thuringiensis, Bacillus anthracis and
Bacillus endophyticus respectively. Conflicting results were observed for B15, B34 and B52 for sequence analysis
based on BLAST and SeqMatch alignment. The isolate B12 showed 99% similarity to Staphylococcus aureus. Our
findings indicate that instead of resorting rice bacterial populations through biochemical tests, the validation through
16S rRNA technique provides a more objective view.

Methods in Molecular Biology, 2017

Plant cells respond to stresses and exogenous environmental stimuli. Production of altered levels... more Plant cells respond to stresses and exogenous environmental stimuli. Production of altered levels of reactive oxygen species (ROS) is one of a typical cellular responses against such stimuli. These responses are detectable through various techniques including luminol-based bioassays. Luminol-based bioassays provide an excellent opportunity for detection of ROS in plant leaf tissue when challenged with some exogenous stimuli like phytohormones, cytokinins, auxins, ABA, etc. The luminol-based protocol in point aims at measuring changes in the H2O2 levels of Arabidopsis leaf discs when exposed to phytohormone cytokinins. However, utility of the luminol-based ROS determination protocol is quite wide. We specifically optimized this protocol to quantify the effect of cytokinins on ROS production by Arabidopsis leaves.

Plant hormones are small signaling molecules that regulate almost every aspect of plant life cycl... more Plant hormones are small signaling molecules that regulate almost every aspect of plant life cycle. Plant pathogens alter hormonal balance of the host to cause disease. In response, host redefines hormone signaling networks to cope with the invading pathogen. Biotrophic pathogens are generally sensitive to salicylic acid mediated defense responses, whereas necrotrophic pathogens are deterred through jasmonate/ethylene pathways. Interaction between these pathways is regarded as central backbone of plant immunity. Classic hormones such as auxin, gibberellin, and cytokinin either promote salicylic acid or jasmonates mediated networks of immunity in plants. Here, we advocate a network biology perspective and emphasize the application of systems biology approaches for a comprehensive understanding of plantpathogen interactions.

Journal of Animal and Plant Sciences

Dengue viral infections pose threat to almost half of the world’s population health. The recent o... more Dengue viral infections pose threat to almost half of the world’s population health. The recent outbreak of dengue fever in Pakistan has invited attention of the scientific community to attempt devising ways and means and initiating programs controlling this menace. This work is also a step forward in the same direction. Utilizing different in-silico approaches like CLC Bio workbench, Protparam and Virus mploc comparative analysis of the full length genome and proteome of dengue virus serotypes was performed. All the four serotypes exhibited high level of similarities both at genome and proteome level. However, variations still existed though insignificant. Concerning prediction of sub-cellular localization of viral capsid, envelop and membrane glycoprotein in the host cell, all three proteins in four serotypes were shown to target endoplasmic reticulum. Endoplasmic reticulum hosting the viral structural proteins emerges as the pivot of the future studies aiming controlling dengue i...

Journal of Animal and Plant Sciences

Biologia (Lahore, Pakistan)

Four ascomycetous strains viz., Y371-Candida valdiviana, Y207-Saccharomyces kluyveri and two stra... more Four ascomycetous strains viz., Y371-Candida valdiviana, Y207-Saccharomyces kluyveri and two strains of Williopsis californica (Y2- and Y90), which appeared as sensitive in a previous research work (Mushtaq et al., 2010 & 2013) were used in this study to screen killer, sensitive and neutral phenotypes (Killer-Sensitive-Pattern, KSP) in 556 isolates of yeasts belonging to 89 species and 31 genera. Y207- S. kluyveri and Y371- C. valdiviana appeared most suitable strains to screen KSP in yeast species from all substrates as compared to Y90-W. californica which did not showed sensitivity against slime flux yeast isolates. Whereas, sensitive strain Y2-W. californica appeared sensitive against dairy and flowers’ nectar yeast isolates only. The phenomenon of killer activity appeared as strain character, however the ecological habitat was also found to play important role in determining the killer-sensitive pattern. The sensitive ascomycetous yeast strains Y207-S. kluyveri and Y2- W. califo...

Current protein & peptide science, Jan 30, 2015

The plant hormone auxin regulates a whole repertoire of plant growth and development. Many plant-... more The plant hormone auxin regulates a whole repertoire of plant growth and development. Many plant-associated microorganisms, by virtue of their auxin production capability, mediate phytostimulation effects on plants. Recent studies, however, demonstrate diverse mechanisms whereby plant pathogens manipulate auxin biosynthesis, signaling and transport pathways to promote host susceptibility. Auxin responses have been coupled to their antagonistic and synergistic interactions with salicylic acid and jasmonate mediated defenses, respectively. Here, we discuss that a better understanding of auxin crosstalk to plant immune networks would enable us to engineer crop plants with higher protection and low unintended yield losses.

Plant signaling & behavior, 2013

Crosstalk between auxin and cytokinin in plant growth and development has already been establishe... more Crosstalk between auxin and cytokinin in plant growth and development has already been established. However, their dynamics in plant immunity is still not well understood and requires systems biological approaches for analysis. Omics based public databases are exploited for the reconstruction, integration and analysis of Boolean models for hormonal interactions in plants. We established a meta-network by combining the plant immune regulatory network and the pathogen virulence specific network and used it as substrate for dynamic simulations on hormonal aspects of plant immunity. Our integrated analysis of this meta-network reveals antagonistic crosstalk between auxin and cytokinin in the Pst DC3000 and Arabidopsis interaction. Moreover, we discuss here the importance of Boolean models in unfolding inferences relevant to plant pathogen interactions.

The Plant Cell, 2012

Phytohormones signal and combine to maintain the physiological equilibrium in the plant. Pathogen... more Phytohormones signal and combine to maintain the physiological equilibrium in the plant. Pathogens enhance host susceptibility by modulating the hormonal balance of the plant cell. Unlike other plant hormones, the detailed role of cytokinin in plant immunity remains to be fully elucidated. Here, extensive data mining, including of pathogenicity factors, host regulatory proteins, enzymes of hormone biosynthesis, and signaling components, established an integrated signaling network of 105 nodes and 163 edges. Dynamic modeling and system analysis identified multiple cytokinin-mediated regulatory interactions in plant disease networks. This includes specific synergism between cytokinin and salicylic acid pathways and previously undiscovered aspects of antagonism between cytokinin and auxin in plant immunity. Predicted interactions and hormonal effects on plant immunity are confirmed in subsequent experiments with Pseudomonas syringae pv tomato DC3000 and Arabidopsis thaliana. Our dynamic simulation is instrumental in predicting system effects of individual components in complex hormone disease networks and synergism or antagonism between pathways.