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\n\n \n \n 2018\n \n \n (1)\n \n \n
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\n \n \n\n \n \n \n \n \n Functional characterization of 1-aminocyclopropane-1-carboxylic acid oxidase gene in Arabidopsis thaliana and its potential in providing flood tolerance.\n \n \n \n\n\n \n Ramadoss, N.; Gupta, D.; Vaidya, B.; Joshee, N.; and Basu, C.\n\n\n \n\n\n\n Biochemical and Biophysical Research Communications, 503(1). 2018.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n\n\n\n\n\n \n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{\n title = {Functional characterization of 1-aminocyclopropane-1-carboxylic acid oxidase gene in Arabidopsis thaliana and its potential in providing flood tolerance},\n type = {article},\n year = {2018},\n keywords = {ACC oxidase,Arabidopsis,Ethylene,Flood tolerance},\n volume = {503},\n id = {16b25f07-eeef-30cf-ba50-8769bd793127},\n created = {2019-03-22T15:15:44.977Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.977Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {© 2018 Elsevier Inc. Ethylene is a phytohormone that has gained importance through its role in stress tolerance and fruit ripening. In our study we evaluated the functional potential of the enzyme involved in ethylene biosynthesis of plants called ACC (aminocyclopropane-1-carboxylic acid) oxidase which converts precursor ACC to ethylene. Studies on ethylene have proven that it is effective in improving the flood tolerance in plants. Thus our goal was to understand the potential of ACC oxidase gene overexpression in providing flood tolerance in transgenic plants. ACC oxidase gene was PCR amplified and inserted into the pBINmgfp5-er vector, under the control of a constitutive Cauliflower Mosaic Virus promoter. GV101 strain of Agrobacterium tumefaciens containing recombinant pBINmgfp5-er vector (referred herein as pBIN-ACC) was used for plant transformation by the ‘floral dip’ method. The transformants were identified through kanamycin selection and grown till T3 (third transgenic) generation. The flood tolerance was assessed by placing both control and transgenic plants on deep plastic trays filled with tap water that covered the soil surface. Our result shows that wild-type Arabidopsis could not survive more than 20 days under flooding while the transgenic lines survived 35 days, suggesting development of flood tolerance with overexpression of ACC oxidase. Further molecular studies should be done to elucidate the role and pathways of ACC oxidase and other phytohormones involved in the development of flood adaptation.},\n bibtype = {article},\n author = {Ramadoss, N. and Gupta, D. and Vaidya, B.N. and Joshee, N. and Basu, C.},\n doi = {10.1016/j.bbrc.2018.06.036},\n journal = {Biochemical and Biophysical Research Communications},\n number = {1}\n}\n\n © 2018 Elsevier Inc. Ethylene is a phytohormone that has gained importance through its role in stress tolerance and fruit ripening. In our study we evaluated the functional potential of the enzyme involved in ethylene biosynthesis of plants called ACC (aminocyclopropane-1-carboxylic acid) oxidase which converts precursor ACC to ethylene. Studies on ethylene have proven that it is effective in improving the flood tolerance in plants. Thus our goal was to understand the potential of ACC oxidase gene overexpression in providing flood tolerance in transgenic plants. ACC oxidase gene was PCR amplified and inserted into the pBINmgfp5-er vector, under the control of a constitutive Cauliflower Mosaic Virus promoter. GV101 strain of Agrobacterium tumefaciens containing recombinant pBINmgfp5-er vector (referred herein as pBIN-ACC) was used for plant transformation by the ‘floral dip’ method. The transformants were identified through kanamycin selection and grown till T3 (third transgenic) generation. The flood tolerance was assessed by placing both control and transgenic plants on deep plastic trays filled with tap water that covered the soil surface. Our result shows that wild-type Arabidopsis could not survive more than 20 days under flooding while the transgenic lines survived 35 days, suggesting development of flood tolerance with overexpression of ACC oxidase. Further molecular studies should be done to elucidate the role and pathways of ACC oxidase and other phytohormones involved in the development of flood adaptation.\n
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\n\n \n \n 2017\n \n \n (1)\n \n \n
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\n \n \n\n \n \n \n \n \n RNA-seq analysis of the salt stress-induced transcripts in fast-growing bioenergy tree, Paulownia elongata.\n \n \n \n\n\n \n Chaires, M.; Gupta, D.; Joshee, N.; Cooper, K.; and Basu, C.\n\n\n \n\n\n\n Journal of Plant Interactions, 12(1). 2017.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{\n title = {RNA-seq analysis of the salt stress-induced transcripts in fast-growing bioenergy tree, Paulownia elongata},\n type = {article},\n year = {2017},\n keywords = {Paulownia elongata,RNA seq,Salt stress,qPCR},\n volume = {12},\n id = {1100e406-6cdc-30c7-9ed7-5bd0bd8178e9},\n created = {2019-03-22T15:15:45.017Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:45.017Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {© 2017 The Author(s). Paulowina elongata is a fast-growing tree species is grown in different climates and types of soils. Environmental adaptability as well as high-yielding biomass make the P. elongata species an ideal candidate for biofuel production. High soil salinity is known to inhibit plant growth dramatically or leads to plant death. The purpose of this study was to characterize the salt-induced changes in the transcriptome of P. elongata. Transcriptome differences in response to salt stress were determined by RNA sequencing (RNA-seq) using next generation sequencing and bioinformatics analysis. A total of 645 genes were found to have significant altered expression in response to salt stress. Expression levels of a selective subset of these genes were chosen and confirmed using quantitative real-time PCR. To the best of our knowledge, this is the first report of saltinduced transcriptome analysis in P. elongata. The current study indicates that differential expression of a select group of genes of P. elongata and their possible roles in pathways and mechanisms related to salt tolerance. Functional characterization of these genes will assist in future investigations of salt tolerance in P. elongata, which could be used to enhance biofuel production.},\n bibtype = {article},\n author = {Chaires, M. and Gupta, D. and Joshee, N. and Cooper, K.K. and Basu, C.},\n doi = {10.1080/17429145.2017.1298851},\n journal = {Journal of Plant Interactions},\n number = {1}\n}\n\n © 2017 The Author(s). Paulowina elongata is a fast-growing tree species is grown in different climates and types of soils. Environmental adaptability as well as high-yielding biomass make the P. elongata species an ideal candidate for biofuel production. High soil salinity is known to inhibit plant growth dramatically or leads to plant death. The purpose of this study was to characterize the salt-induced changes in the transcriptome of P. elongata. Transcriptome differences in response to salt stress were determined by RNA sequencing (RNA-seq) using next generation sequencing and bioinformatics analysis. A total of 645 genes were found to have significant altered expression in response to salt stress. Expression levels of a selective subset of these genes were chosen and confirmed using quantitative real-time PCR. To the best of our knowledge, this is the first report of saltinduced transcriptome analysis in P. elongata. The current study indicates that differential expression of a select group of genes of P. elongata and their possible roles in pathways and mechanisms related to salt tolerance. Functional characterization of these genes will assist in future investigations of salt tolerance in P. elongata, which could be used to enhance biofuel production.\n
\n\n\n\n
\n\n \n \n 2016\n \n \n (2)\n \n \n
\n \n \n \n
\n \n \n\n \n \n \n \n \n Transcriptional profiling.\n \n \n \n\n\n \n Zwenger, S.; and Basu, C.\n\n\n \n\n\n\n Volume 3 2016.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n
\n\n\n \n\n\n\n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n
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\n\n\n\n@book{\n title = {Transcriptional profiling},\n type = {book},\n year = {2016},\n source = {Principles and Practices of Plant Genomics},\n volume = {3},\n id = {1b994004-5f80-3cf3-96c4-1b81dee93dda},\n created = {2019-03-22T15:15:44.606Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.606Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n bibtype = {book},\n author = {Zwenger, S.R. and Basu, C.}\n}\n\n \n\n \n \n \n \n \n Leaf Proteome Analysis Reveals Prospective Drought and Heat Stress Response Mechanisms in Soybean.\n \n \n \n\n\n \n Das, A.; Eldakak, M.; Paudel, B.; Kim, D.; Hemmati, H.; Basu, C.; and Rohila, J.\n\n\n \n\n\n\n BioMed Research International, 2016. 2016.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n
\n\n\n\n\n\n \n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n
\n
\n\n\n@article{\n title = {Leaf Proteome Analysis Reveals Prospective Drought and Heat Stress Response Mechanisms in Soybean},\n type = {article},\n year = {2016},\n volume = {2016},\n id = {7151c42a-b3c8-30cb-85de-536783126e60},\n created = {2019-03-22T15:15:45.067Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:45.067Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {© 2016 Aayudh Das et al. Drought and heat are among the major abiotic stresses that affect soybean crops worldwide. During the current investigation, the effect of drought, heat, and drought plus heat stresses was compared in the leaves of two soybean varieties, Surge and Davison, combining 2D-DIGE proteomic data with physiology and biochemical analyses. We demonstrated how 25 differentially expressed photosynthesis-related proteins affect RuBisCO regulation, electron transport, Calvin cycle, and carbon fixation during drought and heat stress. We also observed higher abundance of heat stress-induced EF-Tu protein in Surge. It is possible that EF-Tu might have activated heat tolerance mechanisms in the soybean. Higher level expressions of heat shock-related protein seem to be regulating the heat tolerance mechanisms. This study identifies the differential expression of various abiotic stress-responsive proteins that regulate various molecular processes and signaling cascades. One inevitable outcome from the biochemical and proteomics assays of this study is that increase of ROS levels during drought stress does not show significant changes at the phenotypic level in Davison and this seems to be due to a higher amount of carbonic anhydrase accumulation in the cell which aids the cell to become more resistant to cytotoxic concentrations of H2O2.},\n bibtype = {article},\n author = {Das, A. and Eldakak, M. and Paudel, B. and Kim, D.-W. and Hemmati, H. and Basu, C. and Rohila, J.S.},\n doi = {10.1155/2016/6021047},\n journal = {BioMed Research International}\n}\n\n © 2016 Aayudh Das et al. Drought and heat are among the major abiotic stresses that affect soybean crops worldwide. During the current investigation, the effect of drought, heat, and drought plus heat stresses was compared in the leaves of two soybean varieties, Surge and Davison, combining 2D-DIGE proteomic data with physiology and biochemical analyses. We demonstrated how 25 differentially expressed photosynthesis-related proteins affect RuBisCO regulation, electron transport, Calvin cycle, and carbon fixation during drought and heat stress. We also observed higher abundance of heat stress-induced EF-Tu protein in Surge. It is possible that EF-Tu might have activated heat tolerance mechanisms in the soybean. Higher level expressions of heat shock-related protein seem to be regulating the heat tolerance mechanisms. This study identifies the differential expression of various abiotic stress-responsive proteins that regulate various molecular processes and signaling cascades. One inevitable outcome from the biochemical and proteomics assays of this study is that increase of ROS levels during drought stress does not show significant changes at the phenotypic level in Davison and this seems to be due to a higher amount of carbonic anhydrase accumulation in the cell which aids the cell to become more resistant to cytotoxic concentrations of H2O2.\n
\n\n\n\n
\n\n \n \n 2015\n \n \n (5)\n \n \n
\n \n \n \n
\n \n \n\n \n \n \n \n \n Preface. PCR primer design.\n \n \n \n\n\n \n Basu, C.\n\n\n \n\n\n\n Methods in molecular biology (Clifton, N.J.), 1275. 2015.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n
\n\n\n \n\n\n\n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n
\n
\n\n\n\n@article{\n title = {Preface. PCR primer design},\n type = {article},\n year = {2015},\n volume = {1275},\n id = {dada0dd9-fd4f-3c40-b837-d7a66964e124},\n created = {2019-03-22T15:15:44.559Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.559Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n bibtype = {article},\n author = {Basu, C.},\n journal = {Methods in molecular biology (Clifton, N.J.)}\n}\n\n \n\n \n \n \n \n \n Transcriptional analyses of an ethanol inducible promoter in Escherichia coli and tobacco for production of cellulase and green fluorescent protein.\n \n \n \n\n\n \n Hemmati, H.; and Basu, C.\n\n\n \n\n\n\n Biotechnology and Biotechnological Equipment, 29(6). 2015.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n\n\n \n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n
\n\n\n@article{\n title = {Transcriptional analyses of an ethanol inducible promoter in Escherichia coli and tobacco for production of cellulase and green fluorescent protein},\n type = {article},\n year = {2015},\n keywords = {Biofuel,Cellulase,E. Coli,GFP,Inducible promoter},\n volume = {29},\n id = {555d0d73-23fa-3942-8b8e-e8888a244fa8},\n created = {2019-03-22T15:15:44.636Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.636Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {© 2015 The Author(s). Published by Taylor & Francis. Cellulase is a widely used enzyme for saccharification of plant cell walls for the production of biofuels. In our work, we tested an ethanol inducible native alcA promoter from Aspergillus nidulans in Escherichia coli (E. coli) and tobacco. The alcA promoter was fused with a cellulase gene and then the promoter was compared with other widely used promoters, namely, T5 and cauliflower mosaic virus (CaMV) 35S in E. coli. We also tested the activity of alcA promoter in tobacco by transiently expressing a green fluorescent protein gene under the control of alcA promoter. We concluded from our quantitative polymerase chain reaction (qPCR) results that when alcA promoter was expressed along with AlcR transcription factor, the alcA promoter was 11 times more active than the T5 promoter. The qPCR data suggested that there may be a direct correlation between AlcR concentrations and alcA activity, indicating a key role of the activator AlcR in the regulation of the alcA promoter. Our work on inducible promoter system for cellulase production may open new avenues of research in the field of biofuel development from living cells.},\n bibtype = {article},\n author = {Hemmati, H. and Basu, C.},\n doi = {10.1080/13102818.2015.1065711},\n journal = {Biotechnology and Biotechnological Equipment},\n number = {6}\n}\n\n © 2015 The Author(s). Published by Taylor & Francis. Cellulase is a widely used enzyme for saccharification of plant cell walls for the production of biofuels. In our work, we tested an ethanol inducible native alcA promoter from Aspergillus nidulans in Escherichia coli (E. coli) and tobacco. The alcA promoter was fused with a cellulase gene and then the promoter was compared with other widely used promoters, namely, T5 and cauliflower mosaic virus (CaMV) 35S in E. coli. We also tested the activity of alcA promoter in tobacco by transiently expressing a green fluorescent protein gene under the control of alcA promoter. We concluded from our quantitative polymerase chain reaction (qPCR) results that when alcA promoter was expressed along with AlcR transcription factor, the alcA promoter was 11 times more active than the T5 promoter. The qPCR data suggested that there may be a direct correlation between AlcR concentrations and alcA activity, indicating a key role of the activator AlcR in the regulation of the alcA promoter. Our work on inducible promoter system for cellulase production may open new avenues of research in the field of biofuel development from living cells.\n
\n\n\n\n \n\n \n \n \n \n \n Rapid and simple method of qPCR primer design.\n \n \n \n\n\n \n Thornton, B.; and Basu, C.\n\n\n \n\n\n\n Volume 1275 2015.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n\n\n \n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@book{\n title = {Rapid and simple method of qPCR primer design},\n type = {book},\n year = {2015},\n source = {Methods in Molecular Biology},\n keywords = {Free online software,Primer design,QPCR,Quantitative real-time polymerase chain reaction,Real-time PCR,SYBR Green primers},\n volume = {1275},\n id = {f314c507-b7c7-3910-a3f1-cb95ee4552a5},\n created = {2019-03-22T15:15:44.641Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.641Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {© Springer Science+Business Media New York 2015. Quantitative real-time polymerase chain reaction (qPCR) is a powerful tool for analysis and quantification of gene expression. It is advantageous compared to traditional gel-based method of PCR, as gene expression can be visualized “real-time” using a computer. In qPCR, a reporter dye system is used which intercalates with DNA’s region of interest and detects DNA amplification. Some of the popular reporter systems used in qPCR are the following: Molecular Beacon ®, SYBR Green ®, and Taqman ®. However, success of qPCR depends on the optimal primers used. Some of the considerations for primer design are the following: GC content, primer self-dimer, or secondary structure formation. Freely available software could be used for ideal qPCR primer design. Here we have shown how to use some freely available web-based software programs (such as Primerquest ®, Unafold ®, and Beacon designer ®) to design qPCR primers.},\n bibtype = {book},\n author = {Thornton, B. and Basu, C.},\n doi = {10.1007/978-1-4939-2365-6_13}\n}\n\n © Springer Science+Business Media New York 2015. Quantitative real-time polymerase chain reaction (qPCR) is a powerful tool for analysis and quantification of gene expression. It is advantageous compared to traditional gel-based method of PCR, as gene expression can be visualized “real-time” using a computer. In qPCR, a reporter dye system is used which intercalates with DNA’s region of interest and detects DNA amplification. Some of the popular reporter systems used in qPCR are the following: Molecular Beacon ®, SYBR Green ®, and Taqman ®. However, success of qPCR depends on the optimal primers used. Some of the considerations for primer design are the following: GC content, primer self-dimer, or secondary structure formation. Freely available software could be used for ideal qPCR primer design. Here we have shown how to use some freely available web-based software programs (such as Primerquest ®, Unafold ®, and Beacon designer ®) to design qPCR primers.\n
\n\n\n\n \n\n \n \n \n \n \n Molecular physiology of heat stress responses in plants.\n \n \n \n\n\n \n Hemmati, H.; Gupta, D.; and Basu, C.\n\n\n \n\n\n\n 2015.\n \n\n\n\n
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\n\n\n@book{\n title = {Molecular physiology of heat stress responses in plants},\n type = {book},\n year = {2015},\n source = {Elucidation of Abiotic Stress Signaling in Plants: Functional Genomics Perspectives, Volume 2},\n keywords = {Abiotic stress,Adaptation,Genetic transformations,Heat shock proteins,Heat stress response,Membrane fl uidity,Metabolites,Osmolytes,ROS scavenging system,Small non-coding RNA,Thermotolerance,Transcriptome},\n id = {01f4a8cb-155c-3d06-88ec-faaabb455a08},\n created = {2019-03-22T15:15:44.766Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.766Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {© Springer Science+Business Media New York 2015. Heat stress is one of the major abiotic stresses that plants encounter. Heat stress causes billions of dollars in losses of agricultural crops worldwide. Here, we summarize the molecular and whole genome responses due to heat stress in plants. It has been reported that there are cascades of biochemical reactions that lead to heat stress. In most cases, heat stress is coupled with drought stress response. With the advancements in genomic tools, we have more information on genes, which are upor down-regulated in plants due to heat stress. The heat-stressed plants may exhibit various physiological responses, including stomatal closure, suppressed photosynthesis, stunted growth, etc. Microarray and transcriptome sequencing gave us the tools to perform genome-wide expression profi ling in heat-stressed plants. Understanding how gene expression in heat-stressed plants works will help us to discover novel heat stress-tolerant genes. These genes could be overexpressed in crop plants to make transgenic heat-tolerant agricultural crops. Climate change and global warming are major concerns for us and production of thermotolerant plants could address the issue of global crop loss due to heat and drought stresses.},\n bibtype = {book},\n author = {Hemmati, H. and Gupta, D. and Basu, C.},\n doi = {10.1007/978-1-4939-2540-7_5}\n}\n\n © Springer Science+Business Media New York 2015. Heat stress is one of the major abiotic stresses that plants encounter. Heat stress causes billions of dollars in losses of agricultural crops worldwide. Here, we summarize the molecular and whole genome responses due to heat stress in plants. It has been reported that there are cascades of biochemical reactions that lead to heat stress. In most cases, heat stress is coupled with drought stress response. With the advancements in genomic tools, we have more information on genes, which are upor down-regulated in plants due to heat stress. The heat-stressed plants may exhibit various physiological responses, including stomatal closure, suppressed photosynthesis, stunted growth, etc. Microarray and transcriptome sequencing gave us the tools to perform genome-wide expression profi ling in heat-stressed plants. Understanding how gene expression in heat-stressed plants works will help us to discover novel heat stress-tolerant genes. These genes could be overexpressed in crop plants to make transgenic heat-tolerant agricultural crops. Climate change and global warming are major concerns for us and production of thermotolerant plants could address the issue of global crop loss due to heat and drought stresses.\n
\n\n\n\n \n\n \n \n \n \n \n 2-methyl-3-buten-2-ol (MBO) synthase expression in Nostoc punctiforme leads to over production of phytols.\n \n \n \n\n\n \n Gupta, D.; Ip, T.; Summers, M.; and Basu, C.\n\n\n \n\n\n\n Bioengineered Bugs, 6(1). 2015.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n
\n\n\n\n\n\n \n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n
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\n\n\n@article{\n title = {2-methyl-3-buten-2-ol (MBO) synthase expression in Nostoc punctiforme leads to over production of phytols},\n type = {article},\n year = {2015},\n volume = {6},\n id = {4e925c78-20ab-3755-9746-e0c6aab3b99d},\n created = {2019-03-22T15:15:44.892Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.892Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {© 2015 Taylor & Francis Group, LLC. Phytol is a diterpene alcohol of medicinal importance and it also has potential to be used as biofuel. We found over production of phytol in Nostoc punctiforme by expressing a 2-Methyl-3-buten-2-ol (MBO) synthase gene. MBO synthase catalyzes the conversion of dimethylallyl pyrophosphate (DMAPP) into MBO, a volatile hemiterpene alcohol, in Pinus sabiniana. The result of enhanced phytol production in N. punctiforme, instead of MBO, could be explained by one of the 2 models: either the presence of a native prenyltransferase enzyme with a broad substrate specificity, or appropriation of a MBO synthase metabolic intermediate by a native geranyl diphosphate (GDP) synthase. In this work, an expression vector with an indigenous petE promoter for gene expression in the cyanobacterium N. punctiforme was constructed and MBO synthase gene expression was successfully shown using reverse transcriptase (RT)-PCR and SDSPAGE. Gas chromatography – mass spectrophotometry (GC-MS) was performed to confirm phytol production from the transgenic N. punctiforme strains. We conclude that the expression of MBO synthase in N. punctiforme leads to overproduction of an economically important compound, phytol. This study provides insights about metabolic channeling of isoprenoids in cyanobacteria and also illustrates the challenges of bioengineering non-native hosts to produce economically important compounds.},\n bibtype = {article},\n author = {Gupta, D. and Ip, T. and Summers, M.L. and Basu, C.},\n doi = {10.4161/21655979.2014.979702},\n journal = {Bioengineered Bugs},\n number = {1}\n}\n\n © 2015 Taylor & Francis Group, LLC. Phytol is a diterpene alcohol of medicinal importance and it also has potential to be used as biofuel. We found over production of phytol in Nostoc punctiforme by expressing a 2-Methyl-3-buten-2-ol (MBO) synthase gene. MBO synthase catalyzes the conversion of dimethylallyl pyrophosphate (DMAPP) into MBO, a volatile hemiterpene alcohol, in Pinus sabiniana. The result of enhanced phytol production in N. punctiforme, instead of MBO, could be explained by one of the 2 models: either the presence of a native prenyltransferase enzyme with a broad substrate specificity, or appropriation of a MBO synthase metabolic intermediate by a native geranyl diphosphate (GDP) synthase. In this work, an expression vector with an indigenous petE promoter for gene expression in the cyanobacterium N. punctiforme was constructed and MBO synthase gene expression was successfully shown using reverse transcriptase (RT)-PCR and SDSPAGE. Gas chromatography – mass spectrophotometry (GC-MS) was performed to confirm phytol production from the transgenic N. punctiforme strains. We conclude that the expression of MBO synthase in N. punctiforme leads to overproduction of an economically important compound, phytol. This study provides insights about metabolic channeling of isoprenoids in cyanobacteria and also illustrates the challenges of bioengineering non-native hosts to produce economically important compounds.\n
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\n\n \n \n 2014\n \n \n (2)\n \n \n
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\n \n \n\n \n \n \n \n \n Engineering an isoprenoid pathway in Escherichia coli for production of 2-methyl-3-buten-2-ol: A potential biofuel.\n \n \n \n\n\n \n Gupta, D.; Summers, M.; and Basu, C.\n\n\n \n\n\n\n Molecular Biotechnology, 56(6). 2014.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n\n\n \n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{\n title = {Engineering an isoprenoid pathway in Escherichia coli for production of 2-methyl-3-buten-2-ol: A potential biofuel},\n type = {article},\n year = {2014},\n keywords = {2-Methyl-3-buten-2-ol,Biofuel,E. coli,Metabolic engineering},\n volume = {56},\n id = {198442be-b93f-336a-addd-6dccb90e6bba},\n created = {2019-03-22T15:15:44.773Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.773Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {2-Methyl-3-buten-2-ol (MBO) is a natural volatile 5-carbon alcohol produced by several pine species that have the potential to be used as biofuel. MBO has a high energy content making it superior to ethanol in terms of energy output, and due to its volatility and lower solubility in water, MBO is easier to recover than ethanol. Pine's MBO synthase enzyme utilizes the intermediate dimethylallyl pyrophosphate (DMAPP) produced by the methyl-erythritol-4- phosphate isoprenoid pathway for the production of MBO. In this study, we performed metabolic engineering of Escherichia coli to express an alternate mevalonate dependent pathway for production of DMAPP, along with a codon optimized Pinus sabiniana MBO synthase gene. This heterologous expressed pathway carried out the conversion of an acetyl CoA precursor to DMAPP leading to production of MBO. © 2013 Springer Science+Business Media.},\n bibtype = {article},\n author = {Gupta, D. and Summers, M.L. and Basu, C.},\n doi = {10.1007/s12033-013-9721-1},\n journal = {Molecular Biotechnology},\n number = {6}\n}\n\n 2-Methyl-3-buten-2-ol (MBO) is a natural volatile 5-carbon alcohol produced by several pine species that have the potential to be used as biofuel. MBO has a high energy content making it superior to ethanol in terms of energy output, and due to its volatility and lower solubility in water, MBO is easier to recover than ethanol. Pine's MBO synthase enzyme utilizes the intermediate dimethylallyl pyrophosphate (DMAPP) produced by the methyl-erythritol-4- phosphate isoprenoid pathway for the production of MBO. In this study, we performed metabolic engineering of Escherichia coli to express an alternate mevalonate dependent pathway for production of DMAPP, along with a codon optimized Pinus sabiniana MBO synthase gene. This heterologous expressed pathway carried out the conversion of an acetyl CoA precursor to DMAPP leading to production of MBO. © 2013 Springer Science+Business Media.\n
\n\n\n\n \n\n \n \n \n \n \n Biochemical analysis of ‘kerosene tree’ Hymenaea courbaril L. Under heat stress.\n \n \n \n\n\n \n Gupta, D.; Eldakak, M.; Rohila, J.; and Basu, C.\n\n\n \n\n\n\n Plant Signaling and Behavior, 9(10). 2014.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n\n\n\n\n\n \n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{\n title = {Biochemical analysis of ‘kerosene tree’ Hymenaea courbaril L. Under heat stress},\n type = {article},\n year = {2014},\n keywords = {Biofuel,Heat stress,Hymenaea,Protein,Sesquiterpene,Thermotolerance},\n volume = {9},\n id = {22b823e0-993d-3b1a-b0d2-99cf6656ecc2},\n created = {2019-03-22T15:15:44.902Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.902Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {© 2014 Taylor & Francis Group, LLC. Hymenaea courbaril or jatoba is a tropical tree known for its medically important secondary metabolites production. Considering climate change, the goal of this study was to investigate differential expression of proteins and lipids produced by this tree under heat stress conditions. Total lipid was extracted from heat stressed plant leaves and various sesquiterpenes produced by the tree under heat stress were identified. Gas chromatographic and mass spectrometric analysis were used to study lipid and volatile compounds produced by the plant. Several volatiles, isoprene, 2-methyl butanenitrile, b ocimene and a numbers of sesquiterpenes differentially produced by the plant under heat stress were identified. We propose these compounds were produced by the tree to cope up with heat stress. A protein gel electrophoresis (2-D DIGE) was performed to study differential expression of proteins in heat stressed plants. Several proteins were found to be expressed many folds different in heat stressed plants compared to the control. These proteins included heat shock proteins, histone proteins, oxygen evolving complex, and photosynthetic proteins, which, we believe, played key roles in imparting thermotolerance in Hymenaea tree. To the best of our knowledge, this is the first report of extensive molecular physiological study of Hymenaea trees under heat stress. This work will open avenues of further research on effects of heat stress in Hymenaea and the findings can be applied to understand how global warming can affect physiology of other plants.},\n bibtype = {article},\n author = {Gupta, D. and Eldakak, M. and Rohila, J.S. and Basu, C.},\n doi = {10.4161/15592316.2014.972851},\n journal = {Plant Signaling and Behavior},\n number = {10}\n}\n\n © 2014 Taylor & Francis Group, LLC. Hymenaea courbaril or jatoba is a tropical tree known for its medically important secondary metabolites production. Considering climate change, the goal of this study was to investigate differential expression of proteins and lipids produced by this tree under heat stress conditions. Total lipid was extracted from heat stressed plant leaves and various sesquiterpenes produced by the tree under heat stress were identified. Gas chromatographic and mass spectrometric analysis were used to study lipid and volatile compounds produced by the plant. Several volatiles, isoprene, 2-methyl butanenitrile, b ocimene and a numbers of sesquiterpenes differentially produced by the plant under heat stress were identified. We propose these compounds were produced by the tree to cope up with heat stress. A protein gel electrophoresis (2-D DIGE) was performed to study differential expression of proteins in heat stressed plants. Several proteins were found to be expressed many folds different in heat stressed plants compared to the control. These proteins included heat shock proteins, histone proteins, oxygen evolving complex, and photosynthetic proteins, which, we believe, played key roles in imparting thermotolerance in Hymenaea tree. To the best of our knowledge, this is the first report of extensive molecular physiological study of Hymenaea trees under heat stress. This work will open avenues of further research on effects of heat stress in Hymenaea and the findings can be applied to understand how global warming can affect physiology of other plants.\n
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\n\n \n \n 2011\n \n \n (3)\n \n \n
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\n \n \n\n \n \n \n \n \n Real-time PCR (qPCR) primer design using free online software.\n \n \n \n\n\n \n Thornton, B.; and Basu, C.\n\n\n \n\n\n\n Biochemistry and Molecular Biology Education, 39(2). 2011.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n\n\n \n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{\n title = {Real-time PCR (qPCR) primer design using free online software},\n type = {article},\n year = {2011},\n keywords = {Primer design,Primer3,Real-time PCR,SYBR® Green},\n volume = {39},\n id = {499455f8-9640-3de2-8a6a-f4d077e70752},\n created = {2019-03-22T15:15:44.681Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.681Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {Real-time PCR (quantitative PCR or qPCR) has become the preferred method for validating results obtained from assays which measure gene expression profiles. The process uses reverse transcription polymerase chain reaction (RT-PCR), coupled with fluorescent chemistry, to measure variations in transcriptome levels between samples. The four most commonly used fluorescent chemistries are SYBR® Green dyes and TaqMan®, Molecular Beacon or Scorpion probes. SYBR® Green is very simple to use and cost efficient. As SYBR® Green dye binds to any double-stranded DNA product, its success depends greatly on proper primer design. Many types of online primer design software are available, which can be used free of charge to design desirable SYBR® Green-based qPCR primers. This laboratory exercise is intended for those who have a fundamental background in PCR. It addresses the basic fluorescent chemistries of real-time PCR, the basic rules and pitfalls of primer design, and provides a step-by-step protocol for designing SYBR® Green-based primers with free, online software. Copyright © 2010 Wiley Periodicals, Inc.},\n bibtype = {article},\n author = {Thornton, B. and Basu, C.},\n doi = {10.1002/bmb.20461},\n journal = {Biochemistry and Molecular Biology Education},\n number = {2}\n}\n\n Real-time PCR (quantitative PCR or qPCR) has become the preferred method for validating results obtained from assays which measure gene expression profiles. The process uses reverse transcription polymerase chain reaction (RT-PCR), coupled with fluorescent chemistry, to measure variations in transcriptome levels between samples. The four most commonly used fluorescent chemistries are SYBR® Green dyes and TaqMan®, Molecular Beacon or Scorpion probes. SYBR® Green is very simple to use and cost efficient. As SYBR® Green dye binds to any double-stranded DNA product, its success depends greatly on proper primer design. Many types of online primer design software are available, which can be used free of charge to design desirable SYBR® Green-based qPCR primers. This laboratory exercise is intended for those who have a fundamental background in PCR. It addresses the basic fluorescent chemistries of real-time PCR, the basic rules and pitfalls of primer design, and provides a step-by-step protocol for designing SYBR® Green-based primers with free, online software. Copyright © 2010 Wiley Periodicals, Inc.\n
\n\n\n\n \n\n \n \n \n \n \n Gene expression in response to cryoprotectant and liquid nitrogen exposure in Arabidopsis shoot tips.\n \n \n \n\n\n \n Volk, G.; Henk, A.; and Basu, C.\n\n\n \n\n\n\n Volume 908 2011.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n\n\n \n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@book{\n title = {Gene expression in response to cryoprotectant and liquid nitrogen exposure in Arabidopsis shoot tips},\n type = {book},\n year = {2011},\n source = {Acta Horticulturae},\n keywords = {Cryopreservation,Microarray,PVS3,Vitrification},\n volume = {908},\n id = {7374894d-7b98-3d8f-b3bf-92d58ea69763},\n created = {2019-03-22T15:15:44.806Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.806Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {Arabidopsis thaliana is an ideal model system to study plant cryopreservation at the molecular level. We have developed reliable cryopreservation methods for Arabidopsis shoot tips using the cryoprotectant Plant Vitrification Solution 3. We have made use of the fully sequenced Arabidopsis genome and readily available microarray slides representing 29,000 genes to compare the gene expression patterns among dissected control shoot tips, cryoprotectant-treated shoot tips, liquid nitrogen-treated shoot tips, and post-exposure recovering shoot tips. Genes upregulated during recovery after PVS3 and liquid nitrogen exposure encode proteins involved in response to stimuli such as cold, heat, water deprivation, and oxidative stress. Further investigation of the identified genes may reveal common genetic responses to cryoprotectants as well as suites of genes whose expression correlates with enhanced survival after cryoexposure.},\n bibtype = {book},\n author = {Volk, G.M. and Henk, A. and Basu, C.},\n doi = {10.17660/ActaHortic.2011.908.4}\n}\n\n Arabidopsis thaliana is an ideal model system to study plant cryopreservation at the molecular level. We have developed reliable cryopreservation methods for Arabidopsis shoot tips using the cryoprotectant Plant Vitrification Solution 3. We have made use of the fully sequenced Arabidopsis genome and readily available microarray slides representing 29,000 genes to compare the gene expression patterns among dissected control shoot tips, cryoprotectant-treated shoot tips, liquid nitrogen-treated shoot tips, and post-exposure recovering shoot tips. Genes upregulated during recovery after PVS3 and liquid nitrogen exposure encode proteins involved in response to stimuli such as cold, heat, water deprivation, and oxidative stress. Further investigation of the identified genes may reveal common genetic responses to cryoprotectants as well as suites of genes whose expression correlates with enhanced survival after cryoexposure.\n
\n\n\n\n \n\n \n \n \n \n \n The production of the sesquiterpene β-caryophyllene in a transgenic strain of the cyanobacterium Synechocystis.\n \n \n \n\n\n \n Reinsvold, R.; Jinkerson, R.; Radakovits, R.; Posewitz, M.; and Basu, C.\n\n\n \n\n\n\n Journal of Plant Physiology, 168(8). 2011.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n\n\n\n\n\n \n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{\n title = {The production of the sesquiterpene β-caryophyllene in a transgenic strain of the cyanobacterium Synechocystis},\n type = {article},\n year = {2011},\n keywords = {Beta caryophyllene,Biofuel,Cyanobacterium,Sesquiterpene},\n volume = {168},\n id = {d97ebda2-1092-3edd-87e5-d345e0d9f789},\n created = {2019-03-22T15:15:45.024Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:45.024Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {The plant secondary metabolite, β-caryophyllene, is a ubiquitous component of many plant resins that has traditionally been used in the cosmetics industry to provide a woody, spicy aroma to cosmetics and perfumes. Clinical studies have shown it to be potentially effective as an antibiotic, anesthetic, and anti-inflammatory agent. Additionally, there is significant interest in engineering phototrophic microorganisms with sesquiterpene synthase genes for the production of biofuels. Currently, the isolation of β-caryophyllene relies on purification methods from oleoresins extracted from large amounts of plant material. An engineered cyanobacterium platform that produces β-caryophyllene may provide a more sustainable and controllable means of production. To this end, the β-caryophyllene synthase gene (QHS1) from Artemisia annua was stably inserted, via double homologous recombination, into the genome of the cyanobacterium Synechocystis sp. strain PCC6803. Gene insertion into Synechocystis was confirmed through PCR assays and sequencing reactions. Transcription and expression of QHS1 were confirmed using RT-PCR, and synthesis of β-caryophyllene was confirmed in the transgenic strain using GC-FID and GC-MS analysis. © 2010 Elsevier GmbH.},\n bibtype = {article},\n author = {Reinsvold, R.E. and Jinkerson, R.E. and Radakovits, R. and Posewitz, M.C. and Basu, C.},\n doi = {10.1016/j.jplph.2010.11.006},\n journal = {Journal of Plant Physiology},\n number = {8}\n}\n\n The plant secondary metabolite, β-caryophyllene, is a ubiquitous component of many plant resins that has traditionally been used in the cosmetics industry to provide a woody, spicy aroma to cosmetics and perfumes. Clinical studies have shown it to be potentially effective as an antibiotic, anesthetic, and anti-inflammatory agent. Additionally, there is significant interest in engineering phototrophic microorganisms with sesquiterpene synthase genes for the production of biofuels. Currently, the isolation of β-caryophyllene relies on purification methods from oleoresins extracted from large amounts of plant material. An engineered cyanobacterium platform that produces β-caryophyllene may provide a more sustainable and controllable means of production. To this end, the β-caryophyllene synthase gene (QHS1) from Artemisia annua was stably inserted, via double homologous recombination, into the genome of the cyanobacterium Synechocystis sp. strain PCC6803. Gene insertion into Synechocystis was confirmed through PCR assays and sequencing reactions. Transcription and expression of QHS1 were confirmed using RT-PCR, and synthesis of β-caryophyllene was confirmed in the transgenic strain using GC-FID and GC-MS analysis. © 2010 Elsevier GmbH.\n
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\n \n \n\n \n \n \n \n \n Plant genomics in the 21st century.\n \n \n \n\n\n \n Basu, C.\n\n\n \n\n\n\n Current Genomics, 11(1). 2010.\n \n\n\n\n
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\n\n\n\n@article{\n title = {Plant genomics in the 21st century},\n type = {article},\n year = {2010},\n volume = {11},\n id = {a6a37805-ba7b-3f5d-89e8-b3f7d2e1871a},\n created = {2019-03-22T15:15:44.560Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.560Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n bibtype = {article},\n author = {Basu, C.},\n journal = {Current Genomics},\n number = {1}\n}\n\n \n\n \n \n \n \n \n Analysis and functional annotation of expressed sequence tags from the diesel tree (Copaifera officinalis).\n \n \n \n\n\n \n Zwenger, S.; Reinsvold, R.; and Basu, C.\n\n\n \n\n\n\n Plant Biotechnology, 27(5). 2010.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n\n\n \n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{\n title = {Analysis and functional annotation of expressed sequence tags from the diesel tree (Copaifera officinalis)},\n type = {article},\n year = {2010},\n keywords = {Biofuel,Copaifera,Diesel tree,EST library,Heat stress},\n volume = {27},\n id = {fb1c6001-bcf3-3229-8090-cf9933894129},\n created = {2019-03-22T15:15:44.810Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.810Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {Copaiba (Copaifera officinalis) is a tropical plant that is also known as the 'diesel tree', previously noted for production of diesel-like oleoresin. The advancements in molecular tools such as expressed sequence tag (EST) library construction provide a novel opportunity for insight into the physiology of this tree. We generated a small set of ESTs for a young copaiba, sequencing and annotating a total of 613 unigenes. Of these, 84% showed similarity to the National Center for Biotechnology Information (NCBI) database. Annotation showed 70% of unigenes had at least one associated Gene Ontology (GO) term. We found a majority of ESTs to be associated with heat response genes. Based on these data, this EST library of C. officinalis represents a small but important step in helping to understand the general physiology and heatresponse expression patterns. Additionally, this small collection of EST offers a modest starting point in helping to understand this enigmatic tropical plant. © 2010 The Japanese Society for Plant Cell and Molecular Biology.},\n bibtype = {article},\n author = {Zwenger, S.R. and Reinsvold, R.E. and Basu, C.},\n doi = {10.5511/plantbiotechnology.10.0628a},\n journal = {Plant Biotechnology},\n number = {5}\n}\n\n Copaiba (Copaifera officinalis) is a tropical plant that is also known as the 'diesel tree', previously noted for production of diesel-like oleoresin. The advancements in molecular tools such as expressed sequence tag (EST) library construction provide a novel opportunity for insight into the physiology of this tree. We generated a small set of ESTs for a young copaiba, sequencing and annotating a total of 613 unigenes. Of these, 84% showed similarity to the National Center for Biotechnology Information (NCBI) database. Annotation showed 70% of unigenes had at least one associated Gene Ontology (GO) term. We found a majority of ESTs to be associated with heat response genes. Based on these data, this EST library of C. officinalis represents a small but important step in helping to understand the general physiology and heatresponse expression patterns. Additionally, this small collection of EST offers a modest starting point in helping to understand this enigmatic tropical plant. © 2010 The Japanese Society for Plant Cell and Molecular Biology.\n
\n\n\n\n \n\n \n \n \n \n \n Does an expressed sequence tag (EST) library of Salsola iberica (tumbleweed) help to understand plant responses to environmental stresses?.\n \n \n \n\n\n \n Zwenger, S.; Alsaggaf, R.; and Basu, C.\n\n\n \n\n\n\n Plant Signaling and Behavior, 5(11). 2010.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n\n\n \n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{\n title = {Does an expressed sequence tag (EST) library of Salsola iberica (tumbleweed) help to understand plant responses to environmental stresses?},\n type = {article},\n year = {2010},\n keywords = {Expressed sequence tag,Gene ontology,Salsola iberica,Weed,Weediness},\n volume = {5},\n id = {902aaf30-3786-3886-a2c4-91e07281552c},\n created = {2019-03-22T15:15:44.845Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.845Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {Weeds play an important role in agriculture and molecular techniques are useful to help understand traits that contribute to weediness and weeds' interactions with the environment. A total of 377 expressed sequence tags (ESTs) from a modest library were arranged into 227 unique fragments and 61 contigs, which consisted of two or more ESTs. From blastx results, we mapped and annotated unigenes using the gene ontology vocabulary according to biological process, cellular component and molecular function. These were then compared to a reference set of Arabidopsis thaliana sequences for statistically significant over- or underrepresented genes. The sequences were also compared against multiple protein databases for similarity of functional domains. Overall, the S. iberica sequences showed high similarity to response to stress, which included salt-induced proteins, betaine aldehydehyde dehydrogenase and calcium binding proteins. Only a modest number of transcripts were sequenced; however, the results presented here demonstrate the metabolic versatility of S. iberica in sub-optimal conditions that are likely to contribute to its cosmopolitan distribution. Here we propose that an EST library of an economically important weed species could be used to understand the weed's interactions with the environment. © 2010 Landes Bioscience.},\n bibtype = {article},\n author = {Zwenger, S.R. and Alsaggaf, R. and Basu, C.},\n doi = {10.4161/psb.5.11.12837},\n journal = {Plant Signaling and Behavior},\n number = {11}\n}\n\n Weeds play an important role in agriculture and molecular techniques are useful to help understand traits that contribute to weediness and weeds' interactions with the environment. A total of 377 expressed sequence tags (ESTs) from a modest library were arranged into 227 unique fragments and 61 contigs, which consisted of two or more ESTs. From blastx results, we mapped and annotated unigenes using the gene ontology vocabulary according to biological process, cellular component and molecular function. These were then compared to a reference set of Arabidopsis thaliana sequences for statistically significant over- or underrepresented genes. The sequences were also compared against multiple protein databases for similarity of functional domains. Overall, the S. iberica sequences showed high similarity to response to stress, which included salt-induced proteins, betaine aldehydehyde dehydrogenase and calcium binding proteins. Only a modest number of transcripts were sequenced; however, the results presented here demonstrate the metabolic versatility of S. iberica in sub-optimal conditions that are likely to contribute to its cosmopolitan distribution. Here we propose that an EST library of an economically important weed species could be used to understand the weed's interactions with the environment. © 2010 Landes Bioscience.\n
\n\n\n\n \n\n \n \n \n \n \n Efficient atmospheric cleansing of oxidized organic trace gases by vegetation.\n \n \n \n\n\n \n Karl, T.; Harley, P.; Emmons, L.; Thornton, B.; Guenther, A.; Basu, C.; Turnipseed, A.; and Jardine, K.\n\n\n \n\n\n\n Science, 330(6005). 2010.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n
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\n\n\n@article{\n title = {Efficient atmospheric cleansing of oxidized organic trace gases by vegetation},\n type = {article},\n year = {2010},\n volume = {330},\n id = {02798d33-2cbc-32cb-9b37-691d17c90bef},\n created = {2019-03-22T15:15:45.120Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:45.120Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {The biosphere is the major source and sink of nonmethane volatile organic compounds (VOCs) in the atmosphere. Gas-phase chemical reactions initiate the removal of these compounds from the atmosphere, which ultimately proceeds via deposition at the surface or direct oxidation to carbon monoxide or carbon dioxide. We performed ecosystem-scale flux measurements that show that the removal of oxygenated VOC via dry deposition is substantially larger than is currently assumed for deciduous ecosystems. Laboratory experiments indicate efficient enzymatic conversion and potential up-regulation of various stress-related genes, leading to enhanced uptake rates as a response to ozone and methyl vinyl ketone exposure or mechanical wounding. A revised scheme for the uptake of oxygenated VOCs, incorporated into a global chemistry-transport model, predicts appreciable regional changes in annual dry deposition fluxes.},\n bibtype = {article},\n author = {Karl, T. and Harley, P. and Emmons, L. and Thornton, B. and Guenther, A. and Basu, C. and Turnipseed, A. and Jardine, K.},\n doi = {10.1126/science.1192534},\n journal = {Science},\n number = {6005}\n}\n\n The biosphere is the major source and sink of nonmethane volatile organic compounds (VOCs) in the atmosphere. Gas-phase chemical reactions initiate the removal of these compounds from the atmosphere, which ultimately proceeds via deposition at the surface or direct oxidation to carbon monoxide or carbon dioxide. We performed ecosystem-scale flux measurements that show that the removal of oxygenated VOC via dry deposition is substantially larger than is currently assumed for deciduous ecosystems. Laboratory experiments indicate efficient enzymatic conversion and potential up-regulation of various stress-related genes, leading to enhanced uptake rates as a response to ozone and methyl vinyl ketone exposure or mechanical wounding. A revised scheme for the uptake of oxygenated VOCs, incorporated into a global chemistry-transport model, predicts appreciable regional changes in annual dry deposition fluxes.\n
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\n\n \n \n 2009\n \n \n (3)\n \n \n
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\n \n \n\n \n \n \n \n \n An Introduction to Molecular Genetic and Genomic Techniques.\n \n \n \n\n\n \n Basu, C.; and Zwenger, S.\n\n\n \n\n\n\n 2009.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n\n@book{\n title = {An Introduction to Molecular Genetic and Genomic Techniques},\n type = {book},\n year = {2009},\n source = {Weedy and Invasive Plant Genomics},\n keywords = {Amplified fragment length polymorphism (AFLP),Inter simple sequence repeats (ISSR),Map-based cloning and functional genomics,Map-based cloning and molecular markers,Microarray technology and weed biology physiology,Molecular genetic and genomic techniques,Molecular tools and understanding genetic basis of,Quantitative trait loci (QTL) and allelopathic eff,Random amplification of polymorphic DNA (RAPD),Weediness traits and Arabidopsis},\n id = {cfb89aa7-b535-3761-96fa-8c1a7c8fd28f},\n created = {2019-03-22T15:15:44.674Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.674Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n bibtype = {book},\n author = {Basu, C. and Zwenger, S.R.},\n doi = {10.1002/9780813806198.ch2}\n}\n\n \n\n \n \n \n \n \n Comparative analyses of plant transcription factor databases.\n \n \n \n\n\n \n Ramirez, S.; and Basu, C.\n\n\n \n\n\n\n Current Genomics, 10(1). 2009.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n
\n\n\n \n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{\n title = {Comparative analyses of plant transcription factor databases},\n type = {article},\n year = {2009},\n keywords = {Bioinformatics,Plant transcription factor databases},\n volume = {10},\n id = {a27cf91d-0a4c-3004-96f1-54553a257fa1},\n created = {2019-03-22T15:15:44.723Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.723Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {Transcription factors (TFs) are proteinaceous complex, which bind to the promoter regions in the DNA and affect transcription initiation. Plant TFs control gene expressions and genes control many physiological processes, which in turn trigger cascades of biochemical reactions in plant cells. The databases available for plant TFs are somewhat abundant but all convey different information and in different formats. Some of the publicly available plant TF databases may be narrow, while others are broad in scopes. For example, some of the best TF databases are ones that are very specific with just one plant species, but there are also other databases that contain a total of up to 20 different plant species. In this review plant TF databases ranging from a single species to many will be assessed and described. The comparative analyses of all the databases and their advantages and disadvantages are also discussed. © 2009 Bentham Science Publishers Ltd.},\n bibtype = {article},\n author = {Ramirez, S.R. and Basu, C.},\n doi = {10.2174/138920209787581253},\n journal = {Current Genomics},\n number = {1}\n}\n\n Transcription factors (TFs) are proteinaceous complex, which bind to the promoter regions in the DNA and affect transcription initiation. Plant TFs control gene expressions and genes control many physiological processes, which in turn trigger cascades of biochemical reactions in plant cells. The databases available for plant TFs are somewhat abundant but all convey different information and in different formats. Some of the publicly available plant TF databases may be narrow, while others are broad in scopes. For example, some of the best TF databases are ones that are very specific with just one plant species, but there are also other databases that contain a total of up to 20 different plant species. In this review plant TF databases ranging from a single species to many will be assessed and described. The comparative analyses of all the databases and their advantages and disadvantages are also discussed. © 2009 Bentham Science Publishers Ltd.\n
\n\n\n\n \n\n \n \n \n \n \n Optimization of a digoxigenin-based immunoassay system for gene detection in Arabidopsis thaliana.\n \n \n \n\n\n \n Hart, S.; and Basu, C.\n\n\n \n\n\n\n Journal of Biomolecular Techniques, 20(2). 2009.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{\n title = {Optimization of a digoxigenin-based immunoassay system for gene detection in Arabidopsis thaliana},\n type = {article},\n year = {2009},\n keywords = {Arabidopsis thaliana,Digoxigenin,Gene detection,Nonradioactive},\n volume = {20},\n id = {a9aeb868-10d5-3f16-bb4e-25cbc01fa82b},\n created = {2019-03-22T15:15:44.723Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.723Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {Digoxigenin is derived from a plant steroid hormone digoxin found in the plants Digitalis sp. Digoxigenin has been used successfully in labeling nucleic acids. In this experiment we optimized minimum probe requirement for a nonradioactive digoxigenin-based gene detection system in the model plant Arabidopsis thaliana. We showed that 1 μL of labeled probe was sufficient to hybridize onto 1-10 μg of target plasmid DNA. We also examined the sensitivity of labeled probe and showed that 2 μL of labeled probe was not able to hybridize with 1 μg of target DNA, although 2 μL of labeled probe was able to detect target DNA ranging from 2 to 10 μg. To test the efficacy of our optimization protocol, we used 1 μL of labeled plasmid DNA pU16893 harboring an Arabidopsis housekeeping gene elongation factor-1 and showed that the elongation factor-1 gene could be detected in Arabidopsis genome under various environmental conditions. This paper describes a nonradioactive in situ hybridization technique to detect nucleic acids in plants. © 2009 ABRF.},\n bibtype = {article},\n author = {Hart, S.M. and Basu, C.},\n journal = {Journal of Biomolecular Techniques},\n number = {2}\n}\n\n Digoxigenin is derived from a plant steroid hormone digoxin found in the plants Digitalis sp. Digoxigenin has been used successfully in labeling nucleic acids. In this experiment we optimized minimum probe requirement for a nonradioactive digoxigenin-based gene detection system in the model plant Arabidopsis thaliana. We showed that 1 μL of labeled probe was sufficient to hybridize onto 1-10 μg of target plasmid DNA. We also examined the sensitivity of labeled probe and showed that 2 μL of labeled probe was not able to hybridize with 1 μg of target DNA, although 2 μL of labeled probe was able to detect target DNA ranging from 2 to 10 μg. To test the efficacy of our optimization protocol, we used 1 μL of labeled plasmid DNA pU16893 harboring an Arabidopsis housekeeping gene elongation factor-1 and showed that the elongation factor-1 gene could be detected in Arabidopsis genome under various environmental conditions. This paper describes a nonradioactive in situ hybridization technique to detect nucleic acids in plants. © 2009 ABRF.\n
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\n\n \n \n 2008\n \n \n (1)\n \n \n
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\n \n \n\n \n \n \n \n \n Gene amplification from cryopreserved Arabidopsis thaliana shoot tips.\n \n \n \n\n\n \n Basu, C.\n\n\n \n\n\n\n Current Issues in Molecular Biology, 10(1). 2008.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n
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\n\n\n@article{\n title = {Gene amplification from cryopreserved Arabidopsis thaliana shoot tips},\n type = {article},\n year = {2008},\n volume = {10},\n id = {cfccd263-68bd-380d-b31e-d6a400a4a4ae},\n created = {2019-03-22T15:15:44.602Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.602Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {Cryopreservation is a way to store elite quality plant germplasms. The exact mechanism of stress tolerance during cryopreservation is unknown. Unavavailability of a detailed protocol for understanding the moelcular genetics of plant cryostress is a major obstacle in plant cryobiology research. This paper describes the methods of extraction of total RNA from cryogenically stored plant tissues accompanied by successful amplication of cDNAs by reverse transcriptase PCR. The whole process can be completed in two to three days. Through this protocol, several genes were indentified which were differentially expressed during cryostress. This protocol will help researchers to pursue further research in the field of molecular genetics of plant cryostress. Interesting genes identified via these processes can be cloned and plants can be transfomred for the purpose of trait enhancement and modification.},\n bibtype = {article},\n author = {Basu, C.},\n journal = {Current Issues in Molecular Biology},\n number = {1}\n}\n\n Cryopreservation is a way to store elite quality plant germplasms. The exact mechanism of stress tolerance during cryopreservation is unknown. Unavavailability of a detailed protocol for understanding the moelcular genetics of plant cryostress is a major obstacle in plant cryobiology research. This paper describes the methods of extraction of total RNA from cryogenically stored plant tissues accompanied by successful amplication of cDNAs by reverse transcriptase PCR. The whole process can be completed in two to three days. Through this protocol, several genes were indentified which were differentially expressed during cryostress. This protocol will help researchers to pursue further research in the field of molecular genetics of plant cryostress. Interesting genes identified via these processes can be cloned and plants can be transfomred for the purpose of trait enhancement and modification.\n
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\n\n \n \n 2007\n \n \n (1)\n \n \n
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\n \n \n\n \n \n \n \n \n Transformation and segregation of GFP fluorescence and glyphosate resistance in horseweed (Conyza canadensis) hybrids.\n \n \n \n\n\n \n Halfhill, M.; Good, L.; Basu, C.; Burris, J.; Main, C.; Mueller, T.; and Stewart Jr., C.\n\n\n \n\n\n\n Plant Cell Reports, 26(3). 2007.\n \n\n\n\n
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\n\n\n@article{\n title = {Transformation and segregation of GFP fluorescence and glyphosate resistance in horseweed (Conyza canadensis) hybrids},\n type = {article},\n year = {2007},\n keywords = {Herbicide resistance,Hybridization,In vitro assay,Tissue culture,Transgenic,Weeds},\n volume = {26},\n id = {2ac79443-d6f9-38d5-8927-d08fd700c242},\n created = {2019-03-22T15:15:45.108Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:45.108Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {The goal of this research was to generate a breeding population of horseweed segregating for glyphosate resistance. In order to generate a marker to select between hybrids of glyphosate resistant (GR) and glyphosate susceptible (GS) horseweed, a GR horseweed accession from western Tennessee was transformed with a green fluorescent protein (GFP) transgene. The GFP marker allowed for the simple and accurate determination of GR hybrid plants by visual observation. GR plants were shown to be transgenic via the green fluorescence under UV light, and resistant to glyphosate when sprayed with the field-use-rate 0.84 kg acid equivalent ha-1 of glyphosate (i.e. Roundup TM) herbicide. An in vitro screen for glyphosate resistance in seedlings was developed, and a 5 μM glyphosate concentration was found to reduce dry weight in GS seedlings but not in GR seedlings. The GR plants containing GFP were then hand-crossed with GS plants from eastern Tennessee under greenhouse conditions, with GS plants acting as the pollen acceptor. Resulting seed was collected and germinated for GFP fluorescence screening. Seedlings that exhibited the transgenic GFP phenotype were selected as F 1 hybrids between GR and GS horseweed. Thirty GS × GR hybrids were produced on the basis of a green-fluorescent GFP phenotype of GR plants. GS × GFP/GR F1 hybrids produced F2 seeds, and F 2 plants were shown to segregate for GFP fluorescence and glyphosate resistance independently. Both traits segregated at a Mendelian 3:1 ratio, indicating a single gene is responsible for each phenotype. © 2006 Springer-Verlag.},\n bibtype = {article},\n author = {Halfhill, M.D. and Good, L.L. and Basu, C. and Burris, J. and Main, C.L. and Mueller, T.C. and Stewart Jr., C.N.},\n doi = {10.1007/s00299-006-0219-1},\n journal = {Plant Cell Reports},\n number = {3}\n}\n\n The goal of this research was to generate a breeding population of horseweed segregating for glyphosate resistance. In order to generate a marker to select between hybrids of glyphosate resistant (GR) and glyphosate susceptible (GS) horseweed, a GR horseweed accession from western Tennessee was transformed with a green fluorescent protein (GFP) transgene. The GFP marker allowed for the simple and accurate determination of GR hybrid plants by visual observation. GR plants were shown to be transgenic via the green fluorescence under UV light, and resistant to glyphosate when sprayed with the field-use-rate 0.84 kg acid equivalent ha-1 of glyphosate (i.e. Roundup TM) herbicide. An in vitro screen for glyphosate resistance in seedlings was developed, and a 5 μM glyphosate concentration was found to reduce dry weight in GS seedlings but not in GR seedlings. The GR plants containing GFP were then hand-crossed with GS plants from eastern Tennessee under greenhouse conditions, with GS plants acting as the pollen acceptor. Resulting seed was collected and germinated for GFP fluorescence screening. Seedlings that exhibited the transgenic GFP phenotype were selected as F 1 hybrids between GR and GS horseweed. Thirty GS × GR hybrids were produced on the basis of a green-fluorescent GFP phenotype of GR plants. GS × GFP/GR F1 hybrids produced F2 seeds, and F 2 plants were shown to segregate for GFP fluorescence and glyphosate resistance independently. Both traits segregated at a Mendelian 3:1 ratio, indicating a single gene is responsible for each phenotype. © 2006 Springer-Verlag.\n
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\n\n \n \n 2005\n \n \n (1)\n \n \n
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\n \n \n\n \n \n \n \n \n Pathogenicity of Xanthomonas translucens from annual bluegrass on golf course putting greens.\n \n \n \n\n\n \n Mitkowski, N.; Browning, M.; Basu, C.; Jordan, K.; and Jackson, N.\n\n\n \n\n\n\n Plant Disease, 89(5). 2005.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n
\n\n\n\n\n\n \n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n
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\n\n\n@article{\n title = {Pathogenicity of Xanthomonas translucens from annual bluegrass on golf course putting greens},\n type = {article},\n year = {2005},\n volume = {89},\n id = {bcfc5e77-e2c9-372f-add0-643abaf2bcee},\n created = {2019-03-22T15:15:45.062Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:45.062Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {Bacterial wilt of Poa annua has been seen increasingly in the Northeast and mid-Atlantic United States in the past few years. The disease causes severe injury to putting greens and can kill large stands of turfgrass. For some time, however, both the bacterial origin of the disease and the causal agent were in doubt. In order to investigate the identity of the causal agent, isolation of the pathogen was undertaken and pathogenicity was confirmed using Koch's postulates on P. annua. Additional pathogenicity trials then were undertaken to determine the host range of the causal bacterium. Ability of the bacterium to cause disease was restricted to P. annua van annua and P. attenuata. However, the bacterium was able to survive asymptomatically in vascular systems of P. annua var. reptans and P. trivialis. Experiments to determine the optimal growth temperature of the organism demonstrated that the bacterial growth peaked between 30 and 35°C. Fatty acid analysis suggested that the bacterium might be a species of Xanthomonas but was inconclusive. Ribosomal RNA analysis demonstrated significant similarity to the American Type Culture Collection isolate of Xanthomonas translucens pv. poae at 99.8%. Comparison of the host range to previously reported data agrees with our molecular findings and indicates that the likely casual organism of bacterial wilt of annual bluegrass is X. translucens pv. poae. © 2005 The American Phytopathological Society.},\n bibtype = {article},\n author = {Mitkowski, N.A. and Browning, M. and Basu, C. and Jordan, K. and Jackson, N.},\n doi = {10.1094/PD-89-0469},\n journal = {Plant Disease},\n number = {5}\n}\n\n Bacterial wilt of Poa annua has been seen increasingly in the Northeast and mid-Atlantic United States in the past few years. The disease causes severe injury to putting greens and can kill large stands of turfgrass. For some time, however, both the bacterial origin of the disease and the causal agent were in doubt. In order to investigate the identity of the causal agent, isolation of the pathogen was undertaken and pathogenicity was confirmed using Koch's postulates on P. annua. Additional pathogenicity trials then were undertaken to determine the host range of the causal bacterium. Ability of the bacterium to cause disease was restricted to P. annua van annua and P. attenuata. However, the bacterium was able to survive asymptomatically in vascular systems of P. annua var. reptans and P. trivialis. Experiments to determine the optimal growth temperature of the organism demonstrated that the bacterial growth peaked between 30 and 35°C. Fatty acid analysis suggested that the bacterium might be a species of Xanthomonas but was inconclusive. Ribosomal RNA analysis demonstrated significant similarity to the American Type Culture Collection isolate of Xanthomonas translucens pv. poae at 99.8%. Comparison of the host range to previously reported data agrees with our molecular findings and indicates that the likely casual organism of bacterial wilt of annual bluegrass is X. translucens pv. poae. © 2005 The American Phytopathological Society.\n
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\n\n \n \n 2004\n \n \n (2)\n \n \n
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\n \n \n\n \n \n \n \n \n Use of β-glucuronidase reporter gene for gene expression analysis in turfgrasses.\n \n \n \n\n\n \n Basu, C.; Kausch, A.; and Chandlee, J.\n\n\n \n\n\n\n Biochemical and Biophysical Research Communications, 320(1). 2004.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n
\n\n\n \n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{\n title = {Use of β-glucuronidase reporter gene for gene expression analysis in turfgrasses},\n type = {article},\n year = {2004},\n keywords = {Biotechnology,Turfgrass transformation,β-Glucuronidase},\n volume = {320},\n id = {1e361f2d-cf90-374c-8029-9f3f53f2d53d},\n created = {2019-03-22T15:15:44.853Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.853Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {The β-glucuronidase (GUS) gene has been successfully used as a reporter gene in innumerable number of plant species. The functional GUS gene produces blue coloration in plants upon integration into the plant genome. Because of the ease it provides to analyze the gene expression (as no expensive equipment is needed), GUS gene is surely plant biotechnologist's first choice as a reporter gene. The turfgrass family contains the world's most economically important horticultural crops. There is a world-wide drive for genetic modification of grasses due to its huge economic importance. GUS gene can be transiently or stably expressed in grasses for the purpose of promoter analysis and to study tissue-specific and developmental gene expression. This paper summarizes the use of GUS gene for transient and stable expression studies in various turfgrass species. © 2004 Elsevier Inc. All rights reserved.},\n bibtype = {article},\n author = {Basu, C. and Kausch, A.P. and Chandlee, J.M.},\n doi = {10.1016/j.bbrc.2004.05.128},\n journal = {Biochemical and Biophysical Research Communications},\n number = {1}\n}\n\n The β-glucuronidase (GUS) gene has been successfully used as a reporter gene in innumerable number of plant species. The functional GUS gene produces blue coloration in plants upon integration into the plant genome. Because of the ease it provides to analyze the gene expression (as no expensive equipment is needed), GUS gene is surely plant biotechnologist's first choice as a reporter gene. The turfgrass family contains the world's most economically important horticultural crops. There is a world-wide drive for genetic modification of grasses due to its huge economic importance. GUS gene can be transiently or stably expressed in grasses for the purpose of promoter analysis and to study tissue-specific and developmental gene expression. This paper summarizes the use of GUS gene for transient and stable expression studies in various turfgrass species. © 2004 Elsevier Inc. All rights reserved.\n
\n\n\n\n \n\n \n \n \n \n \n Weed genomics: New tools to understand weed biology.\n \n \n \n\n\n \n Basu, C.; Halfhill, M.; Mueller, T.; and Stewart Jr., C.\n\n\n \n\n\n\n Trends in Plant Science, 9(8). 2004.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n
\n\n\n\n\n\n \n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n
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\n\n\n@article{\n title = {Weed genomics: New tools to understand weed biology},\n type = {article},\n year = {2004},\n volume = {9},\n id = {e114b4da-b20b-376e-9888-cd6b56b34788},\n created = {2019-03-22T15:15:44.935Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.935Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {In spite of the large yield losses that weeds inflict on crops, we know little about the genomics of economically important weed species. Comparative genomics between plant model species and weeds, map-based approaches, genomic sequencing and functional genomics can play vital roles in understanding and dissecting weedy traits of agronomically important weed species that damage crops. Weed genomics research should increase our understanding of the evolution of herbicide resistance and of the basic genetics underlying traits that make weeds a successful group of plants. Here, we propose specific weed candidates as genomic models, including economically important plants that have evolved herbicide resistance on several occasions and weeds with good comparative genomic qualities that can be anchored to the genomics of Arabidopsis and Oryza sativa.},\n bibtype = {article},\n author = {Basu, C. and Halfhill, M.D. and Mueller, T.C. and Stewart Jr., C.N.},\n doi = {10.1016/j.tplants.2004.06.003},\n journal = {Trends in Plant Science},\n number = {8}\n}\n\n In spite of the large yield losses that weeds inflict on crops, we know little about the genomics of economically important weed species. Comparative genomics between plant model species and weeds, map-based approaches, genomic sequencing and functional genomics can play vital roles in understanding and dissecting weedy traits of agronomically important weed species that damage crops. Weed genomics research should increase our understanding of the evolution of herbicide resistance and of the basic genetics underlying traits that make weeds a successful group of plants. Here, we propose specific weed candidates as genomic models, including economically important plants that have evolved herbicide resistance on several occasions and weeds with good comparative genomic qualities that can be anchored to the genomics of Arabidopsis and Oryza sativa.\n
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\n\n\n\n\n \n \n 2003\n \n \n (2)\n \n \n
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\n \n \n\n \n \n \n \n \n Promoter analysis in transient assays using a GUS reporter gene construct in creeping bentgrass (Agrostis palustris).\n \n \n \n\n\n \n Basu, C.; Kausch, A.; Luo, H.; and Chandlee, J.\n\n\n \n\n\n\n Journal of Plant Physiology, 160(10). 2003.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n\n\n \n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{\n title = {Promoter analysis in transient assays using a GUS reporter gene construct in creeping bentgrass (Agrostis palustris)},\n type = {article},\n year = {2003},\n keywords = {GUS,Microprojectile bombardment,Promoter analysis,Turfgrass transformation},\n volume = {160},\n id = {d7e18bd3-1f71-3038-be0e-884118285351},\n created = {2019-03-22T15:15:44.940Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.940Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {Transient expression profiles for several chimeric β-glucuronidase (GUS) gene constructs were determined in tissues (young leaves, mature leaves and roots) of creeping bentgrass (Agrostis palustris, cv. Penn A4) following microprojectile bombardment. The constructs analyzed consisted of the uidA (GUS) reporter gene driven by four different promoters (ubiquitin 3-potato, ubiquitin corn, ubiquitin rice and CaMV 35S). The total number of GUS hits (or transient expression units; TEUs) were determined manually under a dissecting scope after histochemical staining for GUS. Results suggest that the ubiquitin rice promoter is most active in cells of turfgrass, regardless of the developmental stage or tissue-type. The ubiquitin corn promoter was the next best. Of the four promoter used, except for ubiquitin 3-potato, reporter gene activity was dramatically higher in mature leaves compared to young leaves. The relative efficiency of each promoter was about the same in roots and leaves. We have also analyzed uidA (GUS) reporter gene activity following microprojectile bombardment in transient expression assays with callus from two cultivars (Providence or Penn A4) of creeping bentgrass. Differences in the frequency of GUS positive hits were observed between cultivars up to 72 hours post-bombardment. However, this difference between cultivars disappeared after 72 hours post-bombardment. This information describing promoter functionality in bentgrass will be important when designing gene constructs for trait modification and when choosing appropriate cultivars for improvement through gene transfer experiments. This is the first in depth report on organ-specific and developmental gene expression profiles for transgenes in a turfgrass species.},\n bibtype = {article},\n author = {Basu, C. and Kausch, A.P. and Luo, H. and Chandlee, J.M.},\n doi = {10.1078/0176-1617-01104},\n journal = {Journal of Plant Physiology},\n number = {10}\n}\n\n Transient expression profiles for several chimeric β-glucuronidase (GUS) gene constructs were determined in tissues (young leaves, mature leaves and roots) of creeping bentgrass (Agrostis palustris, cv. Penn A4) following microprojectile bombardment. The constructs analyzed consisted of the uidA (GUS) reporter gene driven by four different promoters (ubiquitin 3-potato, ubiquitin corn, ubiquitin rice and CaMV 35S). The total number of GUS hits (or transient expression units; TEUs) were determined manually under a dissecting scope after histochemical staining for GUS. Results suggest that the ubiquitin rice promoter is most active in cells of turfgrass, regardless of the developmental stage or tissue-type. The ubiquitin corn promoter was the next best. Of the four promoter used, except for ubiquitin 3-potato, reporter gene activity was dramatically higher in mature leaves compared to young leaves. The relative efficiency of each promoter was about the same in roots and leaves. We have also analyzed uidA (GUS) reporter gene activity following microprojectile bombardment in transient expression assays with callus from two cultivars (Providence or Penn A4) of creeping bentgrass. Differences in the frequency of GUS positive hits were observed between cultivars up to 72 hours post-bombardment. However, this difference between cultivars disappeared after 72 hours post-bombardment. This information describing promoter functionality in bentgrass will be important when designing gene constructs for trait modification and when choosing appropriate cultivars for improvement through gene transfer experiments. This is the first in depth report on organ-specific and developmental gene expression profiles for transgenes in a turfgrass species.\n
\n\n\n\n \n\n \n \n \n \n \n Transient reporter gene (GUS) expression in creeping bentgrass (Agrostis palustris) is affected by in vivo nucleolytic activity.\n \n \n \n\n\n \n Basu, C.; Luo, H.; Kausch, A.; and Chandlee, J.\n\n\n \n\n\n\n Biotechnology Letters, 25(12). 2003.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n\n\n\n\n\n \n\n\n\n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
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\n\n\n@article{\n title = {Transient reporter gene (GUS) expression in creeping bentgrass (Agrostis palustris) is affected by in vivo nucleolytic activity},\n type = {article},\n year = {2003},\n keywords = {Creeping bentgrass,Microprojectile bombardment,Nuclease,β-glucuronidase},\n volume = {25},\n id = {40b5ac76-5ba9-3a1f-98c8-8b9cc58e0e15},\n created = {2019-03-22T15:15:44.971Z},\n file_attached = {false},\n profile_id = {d153cf7c-e30a-3e6e-8a50-cd731bb5fe6e},\n last_modified = {2019-03-22T15:15:44.971Z},\n read = {false},\n starred = {false},\n authored = {true},\n confirmed = {false},\n hidden = {false},\n private_publication = {false},\n abstract = {Leaf and callus tissues of a creeping bentgrass cultivar (Penn A4) had high nuclease activities that degraded exogenously added plasmid DNA. When callus tissue was incubated for 24 h with heparin, spermidine, aurintricarboxylic acid or polyethylene glycol, only heparin and spermidine were effective as in vitro nuclease inhibitors, protecting exogenously added plasmid DNA from degradation. When β-glucuronidase (GUS) reporter gene activity was evaluated in heparin-treated (0.6%), 14-month old callus following microprojectile bombardment, GUS activity increased 1000-fold compared to equivalent aged untreated Penn A4 callus. Similar enhancement from heparin pretreatment (0.6% or 1.2%) was not observed in 6-month old callus. This is likely due to much higher activities of nuclease in the younger callus.},\n bibtype = {article},\n author = {Basu, C. and Luo, H. and Kausch, A.P. and Chandlee, J.M.},\n doi = {10.1023/A:1024050720199},\n journal = {Biotechnology Letters},\n number = {12}\n}\n\n Leaf and callus tissues of a creeping bentgrass cultivar (Penn A4) had high nuclease activities that degraded exogenously added plasmid DNA. When callus tissue was incubated for 24 h with heparin, spermidine, aurintricarboxylic acid or polyethylene glycol, only heparin and spermidine were effective as in vitro nuclease inhibitors, protecting exogenously added plasmid DNA from degradation. When β-glucuronidase (GUS) reporter gene activity was evaluated in heparin-treated (0.6%), 14-month old callus following microprojectile bombardment, GUS activity increased 1000-fold compared to equivalent aged untreated Penn A4 callus. Similar enhancement from heparin pretreatment (0.6% or 1.2%) was not observed in 6-month old callus. This is likely due to much higher activities of nuclease in the younger callus.\n
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