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Hodgins CL, Salama EM, Kumar R, Zhao Y, Roth SA, Cheung IZ, Chen J, Arganosa GC, Warkentin TD, Bhowmik P, Ham B, Ro D. Creating saponin-free yellow pea seeds by CRISPR/Cas9-enabled mutagenesis on β-amyrin synthase. Plant Direct 2024; 8:e563. [PMID: 38222934 PMCID: PMC10784647 DOI: 10.1002/pld3.563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/06/2023] [Accepted: 12/07/2023] [Indexed: 01/16/2024]
Abstract
Dry pea (Pisum sativum) seeds are valuable sources of plant protein, dietary fiber, and starch, but their uses in food products are restricted to some extent due to several off-flavor compounds. Saponins are glycosylated triterpenoids and are a major source of bitter, astringent, and metallic off-flavors in pea products. β-amyrin synthase (BAS) is the entry point enzyme for saponin biosynthesis in pea and therefore is an ideal target for knock-out using CRISPR/Cas9 genome editing to produce saponin deficient pea varieties. Here, in an elite yellow pea cultivar (CDC Inca), LC/MS analysis identified embryo tissue, not seed coat, as the main location of saponin storage in pea seeds. Differential expression analysis determined that PsBAS1 was preferentially expressed in embryo tissue relative to seed coat and was selected for CRISPR/Cas9 genome editing. The efficiency of CRISPR/Cas9 genome editing of PsBAS1 was systematically optimized in pea hairy roots. From these optimization procedures, the AtU6-26 promoter was found to be superior to the CaMV35S promoter for gRNA expression, and the use of 37°C was determined to increase the efficiency of CRISPR/Cas9 genome editing. These promoter and culture conditions were then applied to stable transformations. As a result, a bi-allelic mutation (deletion and inversion mutations) was generated in the PsBAS1 coding sequence in a T1 plant, and the segregated psbas1 plants from the T2 population showed a 99.8% reduction of saponins in their seeds. Interestingly, a small but statistically significant increase (~12%) in protein content with a slight decrease (~5%) in starch content was observed in the psbas1 mutants under phytotron growth conditions. This work demonstrated that flavor-improved traits can be readily introduced in any pea cultivar of interest using CRISPR/Cas9. Further field trials and sensory tests for improved flavor are necessary to assess the practical implications of the saponin-free pea seeds in food applications.
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Affiliation(s)
- Connor L. Hodgins
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
| | - Eman M. Salama
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
| | - Rahul Kumar
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
| | - Yang Zhao
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSaskatchewanCanada
| | - Susan A. Roth
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
| | - Irene Z. Cheung
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
| | - Jieyu Chen
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSaskatchewanCanada
| | - Gene C. Arganosa
- Department of Plant SciencesUniversity of SaskatchewanSaskatoonSaskatchewanCanada
| | - Thomas D. Warkentin
- Department of Plant SciencesUniversity of SaskatchewanSaskatoonSaskatchewanCanada
| | - Pankaj Bhowmik
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSaskatchewanCanada
| | - Byung‐Kook Ham
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSaskatchewanCanada
- Department of BiologyUniversity of SaskatchewanSaskatoonSaskatchewanCanada
| | - Dae‐Kyun Ro
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
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Asen ND, Aluko RE, Martynenko A, Utioh A, Bhowmik P. Yellow Field Pea Protein ( Pisum sativum L.): Extraction Technologies, Functionalities, and Applications. Foods 2023; 12:3978. [PMID: 37959097 PMCID: PMC10648759 DOI: 10.3390/foods12213978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
Yellow field peas (Pisum sativum L.) hold significant value for producers, researchers, and ingredient manufacturers due to their wealthy composition of protein, starch, and micronutrients. The protein quality in peas is influenced by both intrinsic factors like amino acid composition and spatial conformations and extrinsic factors including growth and processing conditions. The existing literature substantiates that the structural modulation and optimization of functional, organoleptic, and nutritional attributes of pea proteins can be obtained through a combination of chemical, physical, and enzymatic approaches, resulting in superior protein ingredients. This review underscores recent methodologies in pea protein extraction aimed at enhancing yield and functionality for diverse food systems and also delineates existing research gaps related to mitigating off-flavor issues in pea proteins. A comprehensive examination of conventional dry and wet methods is provided, in conjunction with environmentally friendly approaches like ultrafiltration and enzyme-assisted techniques. Additionally, the innovative application of hydrodynamic cavitation technology in protein extraction is explored, focusing on its prospective role in flavor amelioration. This overview offers a nuanced understanding of the advancements in pea protein extraction methods, catering to the interests of varied stakeholders in the field.
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Affiliation(s)
- Nancy D. Asen
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (N.D.A.); (R.E.A.)
| | - Rotimi E. Aluko
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; (N.D.A.); (R.E.A.)
- Richardson Centre for Food Technology and Research, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Alex Martynenko
- Department of Engineering, Dalhousie University, Agricultural Campus, P.O. Box 550, Truro, NS B2N 5E3, Canada;
| | - Alphonsus Utioh
- ACU Food Technology Services Inc., 64 Laverendrye Crescent, Portage la Prairie, MB R1N 1B2, Canada;
| | - Pankaj Bhowmik
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
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Bhowmik P, Yan W, Hodgins C, Polley B, Warkentin T, Nickerson M, Ro DK, Marsolais F, Domoney C, Shariati-Ievari S, Aliani M. CRISPR/Cas9-mediated lipoxygenase gene-editing in yellow pea leads to major changes in fatty acid and flavor profiles. Front Plant Sci 2023; 14:1246905. [PMID: 37810390 PMCID: PMC10552856 DOI: 10.3389/fpls.2023.1246905] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 08/23/2023] [Indexed: 10/10/2023]
Abstract
Introduction Although pulses are nutritious foods containing high amounts of protein, fiber and phytochemicals, their consumption and use in the food industry have been limited due to the formation of unappealing flavors/aromas described as beany, green, and grassy. Lipoxygenase (LOX) enzymes are prevalent among pulse seeds, and their activity can lead to the formation of specific volatile organic compounds (VOCs) from certain polyunsaturated fatty acids (PUFAs). As a widespread issue in legumes, including soybean, these VOCs have been linked to certain unappealing taste perception of foods containing processed pulse seeds. Methods To address this problem in pea and as proof of principle to promote the wider use of pulses, a Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) construct was designed to create null alleles (knockouts) of PsLOX2 which had been implicated in the generation of VOCs in peas. Results and discussion Successful CRISPR/Cas9-mediated LOX gene editing of stable transgenic pea lines (TGP) was confirmed by DNA sequencing of the wild type (WT) and TGP pslox2 mutant lines. These lines were also assessed for LOX activity, PUFA levels, and VOCs. Compared to WT peas, the TGP lines showed a significant reduction (p < 0.05) in LOX activity and in the concentration of key VOCs, including hexanal, 2-hexenal, heptanal, (E)-2-heptenal, (E,E)-2,4-heptadienal, 1-octen-3-ol, octanal, (E)-2-octenal (E,E)-2,4-nonadienal and furan-2-pentyl. The content of two essential PUFAs, linoleic and α-linolenic acids, the known substrates of LOX in plants, was higher in TGP flours, indicating the efficacy of the CRISPR-mediated gene editing in minimizing their oxidation and the further modification of PUFAs and their products. The collection of VOCs from the headspace of ground pea seeds, using a portable eNose also distinguished the TGP and WT lines. Multiple regression analysis showed that LOX activity correlated with the two VOCs, heptanal and (E,E)-2,4-heptadienal in pea flours. Partial Least Squares Regression (PLS-R) plot for selected PUFAs, VOCs, and sensor responses in WT and TGP lines showed distinct clusters for WT and TGP lines. Together this data demonstrates the utility of CRISPR mediated mutagenesis of PsLOX2 to quickly improve aroma and fatty acid (FA) profiles of pea seeds of an elite Canadian variety.
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Affiliation(s)
- Pankaj Bhowmik
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Wei Yan
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Connor Hodgins
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Brittany Polley
- Aquatic and Crop Resource Development Centre, National Research Council Canada, Saskatoon, SK, Canada
| | - Tom Warkentin
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Michael Nickerson
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Dae-Kyun Ro
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Frédéric Marsolais
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Claire Domoney
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Shiva Shariati-Ievari
- Division of Neurodegenerative Diseases (DND), St Boniface Hospital Research Center, Winnipeg, MB, Canada
| | - Michel Aliani
- Division of Neurodegenerative Diseases (DND), St Boniface Hospital Research Center, Winnipeg, MB, Canada
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB, Canada
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Pandey PK, Bhowmik P, Kagale S. Optimized methods for random and targeted mutagenesis in field pea ( Pisum sativum L.). Front Plant Sci 2022; 13:995542. [PMID: 36160971 PMCID: PMC9498975 DOI: 10.3389/fpls.2022.995542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Field pea is an important pulse crop for its dense nutritional profile and contribution to sustainable agricultural practices. Recently, it has received extensive attention as a potential leading source of plant-based proteins. However, the adoption of peas as a mainstream source of proteins is affected by a relatively moderate protein content, anti-nutritional factors and high levels of off-flavor components that reduce protein quality. Availability of genetic variation for desirable seed quality traits is the foundation for the sustainable development of pea varieties with improved protein content and quality. Mutagenesis has been an important tool in gene functional characterization studies and creating genetic variability for crop breeding. Large-scale mutagenesis of a crop using physical and chemical agents requires diligent selection of the mutagen and optimization of its dose to increase the frequency of mutations. In this study, we present detailed optimized protocols for physical and chemical mutagenesis of pea using gamma irradiation and ethyl methanesulfonate (EMS), respectively. Gamma radiation and EMS titration kill curves were established to identify optimal doses of the two mutagenic agents. Based on germination, survival rate and growth phenotypes, a gamma radiation dose of 225 Gy and EMS concentration of 5 mm were selected as optimal dosages for mutagenesis in field pea. The presented protocol has been modified from previously established mutagenesis protocols in other crop plants. Our results indicate that the optimal mutagen dosage is genotype dependent. CRISPR/Cas-based gene editing provides a precise and rapid method for targeted genetic manipulation in plants. With the recent success of gene editing in pea using CRISPR/Cas, this innovative technology is expected to become an integral component of the gene discovery and crop improvement toolkit in pea. Here, we describe an optimized methods for targeted mutagenesis of pea protoplasts, including mesophyll protoplast extraction, PEG-mediated transformation and gene editing of a LOX gene using CRISPR/Cas system. The general strategies and methods of mutagenesis described here provide an essential resource for mutation breeding and functional genomics studies in pea. These methods also provide a foundation for similar studies in other crops.
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Gao P, Quilichini TD, Yang H, Li Q, Nilsen KT, Qin L, Babic V, Liu L, Cram D, Pasha A, Esteban E, Condie J, Sidebottom C, Zhang Y, Huang Y, Zhang W, Bhowmik P, Kochian LV, Konkin D, Wei Y, Provart NJ, Kagale S, Smith M, Patterson N, Gillmor CS, Datla R, Xiang D. Evolutionary divergence in embryo and seed coat development of U's Triangle Brassica species illustrated by a spatiotemporal transcriptome atlas. New Phytol 2022; 233:30-51. [PMID: 34687557 DOI: 10.1111/nph.17759] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
The economically valuable Brassica species include the six related members of U's Triangle. Despite the agronomic and economic importance of these Brassicas, the impacts of evolution and relatively recent domestication events on the genetic landscape of seed development have not been comprehensively examined in these species. Here we present a 3D transcriptome atlas for the six species of U's Triangle, producing a unique resource that captures gene expression data for the major subcompartments of the seed, from the unfertilized ovule to the mature embryo and seed coat. This comprehensive dataset for seed development in tetraploid and ancestral diploid Brassicas provides new insights into evolutionary divergence and expression bias at the gene and subgenome levels during the domestication of these valued crop species. Comparisons of gene expression associated with regulatory networks and metabolic pathways operating in the embryo and seed coat during seed development reveal differences in storage reserve accumulation and fatty acid metabolism among the six Brassica species. This study illustrates the genetic underpinnings of seed traits and the selective pressures placed on seed production, providing an immense resource for continued investigation of Brassica polyploid biology, genomics and evolution.
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Affiliation(s)
- Peng Gao
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Teagen D Quilichini
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Hui Yang
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kirby T Nilsen
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, 2701 Grand Valley Road, Brandon, MB, R7C 1A1, Canada
| | - Li Qin
- College of Art & Science, University of Saskatchewan, 9 Campus Dr, Saskatoon, SK, S7N 5A5, Canada
| | - Vivijan Babic
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Li Liu
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Dustin Cram
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Asher Pasha
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Eddi Esteban
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Janet Condie
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Christine Sidebottom
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Yan Zhang
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Yi Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Wentao Zhang
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Pankaj Bhowmik
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Leon V Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - David Konkin
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Yangdou Wei
- College of Art & Science, University of Saskatchewan, 9 Campus Dr, Saskatoon, SK, S7N 5A5, Canada
| | - Nicholas J Provart
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Sateesh Kagale
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Mark Smith
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Nii Patterson
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - C Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV-IPN), Irapuato, Guanajuato, 36821, México
| | - Raju Datla
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Daoquan Xiang
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
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Abstract
Emerging threats of climate change require the rapid development of improved varieties with a higher tolerance to abiotic and biotic factors. Despite the success of traditional agricultural practices, novel techniques for precise manipulation of the crop's genome are needed. Doubled haploid (DH) methods have been used for decades in major crops to fix desired alleles in elite backgrounds in a short time. DH plants are also widely used for mapping of the quantitative trait loci (QTLs), marker-assisted selection (MAS), genomic selection (GS), and hybrid production. Recent discoveries of genes responsible for haploid induction (HI) allowed engineering this trait through gene editing (GE) in non-inducer varieties of different crops. Direct editing of gametes or haploid embryos increases GE efficiency by generating null homozygous plants following chromosome doubling. Increased understanding of the underlying genetic mechanisms responsible for spontaneous chromosome doubling in haploid plants may allow transferring this trait to different elite varieties. Overall, further improvement in the efficiency of the DH technology combined with the optimized GE could accelerate breeding efforts of the major crops.
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Affiliation(s)
- Pankaj Bhowmik
- Aquatic and Crop Resource Development, National Research Council of Canada, Saskatoon, SK S7N 0W9, Canada;
| | - Andriy Bilichak
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, MB R6M 1Y5, Canada
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Liu K, Seegers S, Cao W, Wanasundara J, Chen J, Silva AE, Ross K, Franco AL, Vrijenhoek T, Bhowmik P, Li Y, Wu X, Bloomer S. An International Collaborative Study on Trypsin Inhibitor Assay for Legumes, Cereals, and Related Products. J AM OIL CHEM SOC 2021. [DOI: 10.1002/aocs.12459] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Keshun Liu
- National Small Grains and Potato Germplasm Research Unit United States Department of Agriculture, Agricultural Research Service 1691 S 2700 W Aberdeen ID 83210 USA
| | - Susan Seegers
- Bunge Creative Solution Center 16 Research Park Drive, St. Charles MO 63304 USA
| | - Wenming Cao
- Wilmar (Shanghai) R&D Center 118 Gaodong Road, Pudong New District, Shanghai 200137 China
| | - Janitha Wanasundara
- Saskatoon Research and Development Centre Agriculture and Agri‐Food Canada 107 Science Place, Saskatoon SK S7N 0X2 Canada
| | - Juxing Chen
- Novus International Inc. 20 Research Park Drive, St Charles MO 63304 USA
| | - Alessandro Esteves Silva
- CBO Laboratory 327 Arquiteto Clayton Alves Corrêa Avenue, Vale Verde, Valinhos SP 13279‐071 Brazil
| | - Kristopher Ross
- Eurofins Food Integrity and Innovation 3301 Kinsman Blvd., Madison WI 53704 USA
| | | | - Theo Vrijenhoek
- Nutreco Nederland BV – MasterLab Veerstraat 38, Boxmeer 5831 JN Netherlands
| | - Pankaj Bhowmik
- Aquatic and Crop Resource Development National Research Council of Canada 110 Gymnasium Place, Saskatoon SK S7N 0W9 Canada
| | - Yonghui Li
- Grain Science and Industry Kansas State University 1301 Mid Campus Dr., Manhattan KS 66506 USA
| | - Xin Wu
- American Oil Chemists' Society 2710 S. Boulder, Urbana IL 61802 USA
| | - Scott Bloomer
- American Oil Chemists' Society 2710 S. Boulder, Urbana IL 61802 USA
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Pantho MJH, Bhowmik P, Bobda C. Towards an Efficient CNN Inference Architecture Enabling In-Sensor Processing. Sensors (Basel) 2021; 21:s21061955. [PMID: 33802235 PMCID: PMC8001538 DOI: 10.3390/s21061955] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 11/16/2022]
Abstract
The astounding development of optical sensing imaging technology, coupled with the impressive improvements in machine learning algorithms, has increased our ability to understand and extract information from scenic events. In most cases, Convolution neural networks (CNNs) are largely adopted to infer knowledge due to their surprising success in automation, surveillance, and many other application domains. However, the convolution operations' overwhelming computation demand has somewhat limited their use in remote sensing edge devices. In these platforms, real-time processing remains a challenging task due to the tight constraints on resources and power. Here, the transfer and processing of non-relevant image pixels act as a bottleneck on the entire system. It is possible to overcome this bottleneck by exploiting the high bandwidth available at the sensor interface by designing a CNN inference architecture near the sensor. This paper presents an attention-based pixel processing architecture to facilitate the CNN inference near the image sensor. We propose an efficient computation method to reduce the dynamic power by decreasing the overall computation of the convolution operations. The proposed method reduces redundancies by using a hierarchical optimization approach. The approach minimizes power consumption for convolution operations by exploiting the Spatio-temporal redundancies found in the incoming feature maps and performs computations only on selected regions based on their relevance score. The proposed design addresses problems related to the mapping of computations onto an array of processing elements (PEs) and introduces a suitable network structure for communication. The PEs are highly optimized to provide low latency and power for CNN applications. While designing the model, we exploit the concepts of biological vision systems to reduce computation and energy. We prototype the model in a Virtex UltraScale+ FPGA and implement it in Application Specific Integrated Circuit (ASIC) using the TSMC 90nm technology library. The results suggest that the proposed architecture significantly reduces dynamic power consumption and achieves high-speed up surpassing existing embedded processors' computational capabilities.
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Bhowmik P, Pantho MJH, Bobda C. HARP: Hierarchical Attention Oriented Region-Based Processing for High-Performance Computation in Vision Sensor. Sensors (Basel) 2021; 21:1757. [PMID: 33806329 PMCID: PMC7961745 DOI: 10.3390/s21051757] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/23/2021] [Accepted: 03/01/2021] [Indexed: 11/17/2022]
Abstract
Cameras are widely adopted for high image quality with the rapid advancement of complementary metal-oxide-semiconductor (CMOS) image sensors while offloading vision applications' computation to the cloud. It raises concern for time-critical applications such as autonomous driving, surveillance, and defense systems since moving pixels from the sensor's focal plane are expensive. This paper presents a hardware architecture for smart cameras that understands the salient regions from an image frame and then performs high-level inference computation for sensor-level information creation instead of transporting raw pixels. A visual attention-oriented computational strategy helps to filter a significant amount of redundant spatiotemporal data collected at the focal plane. A computationally expensive learning model is then applied to the interesting regions of the image. The hierarchical processing in the pixels' data path demonstrates a bottom-up architecture with massive parallelism and gives high throughput by exploiting the large bandwidth available at the image source. We prototype the model in field-programmable gate array (FPGA) and application-specific integrated circuit (ASIC) for integrating with a pixel-parallel image sensor. The experiment results show that our approach achieves significant speedup while in certain conditions exhibits up to 45% more energy efficiency with the attention-oriented processing. Although there is an area overhead for inheriting attention-oriented processing, the achieved performance based on energy consumption, latency, and memory utilization overcomes that limitation.
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Affiliation(s)
| | | | - Christophe Bobda
- Electrical and Computer Engineering Department, University of Florida, Gainesville, FL 32603, USA; (P.B.); (M.J.H.P.)
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Adhikary D, Kulkarni M, El-Mezawy A, Mobini S, Elhiti M, Gjuric R, Ray A, Polowick P, Slaski JJ, Jones MP, Bhowmik P. Medical Cannabis and Industrial Hemp Tissue Culture: Present Status and Future Potential. Front Plant Sci 2021; 12:627240. [PMID: 33747008 PMCID: PMC7968383 DOI: 10.3389/fpls.2021.627240] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/04/2021] [Indexed: 05/22/2023]
Abstract
In recent years high-THC (psychoactive) and low-THC (industrial hemp) type cannabis (Cannabis sativa L.) have gained immense attention in medical, food, and a plethora of other consumer product markets. Among the planting materials used for cultivation, tissue culture clones provide various advantages such as economies of scale, production of disease-free and true-to-type plants for reducing the risk of GMP-EuGMP level medical cannabis production, as well as the development and application of various technologies for genetic improvement. Various tissue culture methods have the potential application with cannabis for research, breeding, and novel trait development, as well as commercial mass propagation. Although tissue culture techniques for plant regeneration and micropropagation have been reported for different cannabis genotypes and explant sources, there are significant variations in the response of cultures and the morphogenic pathway. Methods for many high-yielding elite strains are still rudimentary, and protocols are not established. With a recent focus on sequencing and genomics in cannabis, genetic transformation systems are applied to medical cannabis and hemp for functional gene annotation via traditional and transient transformation methods to create novel phenotypes by gene expression modulation and to validate gene function. This review presents the current status of research focusing on different aspects of tissue culture, including micropropagation, transformation, and the regeneration of medicinal cannabis and industrial hemp transformants. Potential future tissue culture research strategies helping elite cannabis breeding and propagation are also presented.
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Affiliation(s)
- Dinesh Adhikary
- Department of Agricultural, Food, & Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | - Manoj Kulkarni
- Canadian Cannabis Breeding Consortium, Edmonton, AB, Canada
| | | | - Saied Mobini
- Canadian Cannabis Breeding Consortium, Edmonton, AB, Canada
| | | | - Rale Gjuric
- Farmers Business Network Inc., Winnipeg, MB, Canada
| | - Anamika Ray
- Canadian Cannabis Breeding Consortium, Edmonton, AB, Canada
| | | | | | - Maxwell P. Jones
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
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11
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Cho JY, Bhowmik P, Polowick PL, Dodard SG, El-Bakkari M, Nowak G, Fenniri H, Hemraz UD. Cellular Delivery of Plasmid DNA into Wheat Microspores Using Rosette Nanotubes. ACS Omega 2020; 5:24422-24433. [PMID: 33015458 PMCID: PMC7528298 DOI: 10.1021/acsomega.0c02830] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
Plant genetic engineering offers promising solutions to the increasing demand for efficient, sustainable, and high-yielding crop production as well as changing environmental conditions. The main challenge for gene delivery in plants is the presence of a cell wall that limits the transportation of genes within the cells. Microspores are plant cells that are, under the right conditions, capable of generating embryos, leading to the formation of haploid plants. Here, we designed cationic and fluorescent rosette nanotubes (RNTs) that penetrate the cell walls of viable wheat microspores under mild conditions and in the absence of an external force. These nanomaterials can capture plasmid DNA to form RNT-DNA complexes and transport their DNA cargo into live microspores. The nanomaterials and the complexes formed were nontoxic to the microspores.
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Affiliation(s)
- Jae-Young Cho
- Nanotechnology Research Centre, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
| | - Pankaj Bhowmik
- Aquatic and Crop Resource Development, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Patricia L Polowick
- Aquatic and Crop Resource Development, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Sabine G Dodard
- Aquatic and Crop Resource Development, National Research Council of Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada
| | - Mounir El-Bakkari
- Nanotechnology Research Centre, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
| | - Goska Nowak
- Aquatic and Crop Resource Development, National Research Council of Canada, 110 Gymnasium Place, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Hicham Fenniri
- Nanotechnology Research Centre, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
- Departments of Chemical, Biomedical Engineering, Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Usha D Hemraz
- Aquatic and Crop Resource Development, National Research Council of Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada
- Nanotechnology Research Centre, National Research Council of Canada, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
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12
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Abstract
CRISPR/Cas9-based genome editing technology has the potential to revolutionize agriculture, but many plant species and/or genotypes are recalcitrant to conventional transformation methods. Additionally, the long generation time of crop plants poses a significant obstacle to effective application of gene editing technology, as it takes a long time to produce modified homozygous genotypes. The haploid single-celled microspores are an attractive target for gene editing experiments, as they enable generation of homozygous doubled haploid mutants in one generation. Here, we describe optimized methods for genome editing of haploid wheat microspores and production of doubled haploid plants by microspore culture.
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Affiliation(s)
| | | | | | - Sateesh Kagale
- National Research Council Canada, Saskatoon, SK, Canada.
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13
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Cram D, Kulkarni M, Buchwaldt M, Rajagopalan N, Bhowmik P, Rozwadowski K, Parkin IAP, Sharpe AG, Kagale S. WheatCRISPR: a web-based guide RNA design tool for CRISPR/Cas9-mediated genome editing in wheat. BMC Plant Biol 2019; 19:474. [PMID: 31694550 PMCID: PMC6836449 DOI: 10.1186/s12870-019-2097-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/23/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND CRISPR/Cas9 gene editing has become a revolutionary technique for crop improvement as it can facilitate fast and efficient genetic changes without the retention of transgene components in the final plant line. Lack of robust bioinformatics tools to facilitate the design of highly specific functional guide RNAs (gRNAs) and prediction of off-target sites in wheat is currently an obstacle to effective application of CRISPR technology to wheat improvement. DESCRIPTION We have developed a web-based bioinformatics tool to design specific gRNAs for genome editing and transcriptional regulation of gene expression in wheat. A collaborative study between the Broad Institute and Microsoft Research used large-scale empirical evidence to devise algorithms (Doech et al., 2016, Nature Biotechnology 34, 184-191) for predicting the on-target activity and off-target potential of CRISPR/SpCas9 (Streptococcus pyogenes Cas9). We applied these prediction models to determine on-target specificity and potential off-target activity for individual gRNAs targeting specific loci in the wheat genome. The genome-wide gRNA mappings and the corresponding Doench scores predictive of the on-target and off-target activities were used to create a gRNA database which was used as a data source for the web application termed WheatCRISPR. CONCLUSION The WheatCRISPR tool allows researchers to browse all possible gRNAs targeting a gene or sequence of interest and select effective gRNAs based on their predicted high on-target and low off-target activity scores, as well as other characteristics such as position within the targeted gene. It is publicly available at https://crispr.bioinfo.nrc.ca/WheatCrispr/ .
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Affiliation(s)
- Dustin Cram
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Manoj Kulkarni
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Miles Buchwaldt
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | | | - Pankaj Bhowmik
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Kevin Rozwadowski
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | - Isobel A. P. Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | - Andrew G. Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
- Global Institute for Food Security, University of Saskatchewan, 110 Gymnasium Place, Saskatoon, SK S7N 4J8 Canada
| | - Sateesh Kagale
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
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14
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Rajagopalan N, Kagale S, Bhowmik P, Song H. A Two-Step Method for Obtaining Highly Pure Cas9 Nuclease for Genome Editing, Biophysical, and Structural Studies. Methods Protoc 2018; 1:mps1020017. [PMID: 31164560 PMCID: PMC6526429 DOI: 10.3390/mps1020017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 05/22/2018] [Accepted: 05/22/2018] [Indexed: 11/20/2022] Open
Abstract
Cas9 is a site-specific RNA-guided endonuclease (RGEN) that can be used for precise genome editing in various cell types from multiple species. Ribonucleoprotein (RNP) complexes, which contains the Cas9 protein in complex with a guide RNA, are sufficient for the precise editing of genomes in various cells. This DNA-free method is more specific in editing the target sites and there is no integration of foreign DNA into the genome. Also, there are ongoing studies into the interactions of Cas9 protein with modified guide RNAs, as well as structure-activity studies of Cas9 protein and its variants. All these investigations require highly pure Cas9 protein. A single-step metal affinity enrichment yielding impure Cas9 is the most common method of purification described. This is sufficient for many gene editing applications of this protein. However, to obtain Cas9 of higher purity, which might be essential for biophysical characterization, chemical modifications, and structural investigations, laborious multi-step protocols are employed. Here, we describe a two-step Cas9 purification protocol that uses metal affinity enrichment followed by cation exchange chromatography. This simple method can yield a milligram of highly pure Cas9 protein per liter of culture in a single day.
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Affiliation(s)
| | - Sateesh Kagale
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada.
| | - Pankaj Bhowmik
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada.
| | - Halim Song
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada.
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15
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Bhowmik P, Ellison E, Polley B, Bollina V, Kulkarni M, Ghanbarnia K, Song H, Gao C, Voytas DF, Kagale S. Targeted mutagenesis in wheat microspores using CRISPR/Cas9. Sci Rep 2018; 8:6502. [PMID: 29695804 PMCID: PMC5916876 DOI: 10.1038/s41598-018-24690-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/09/2018] [Indexed: 12/26/2022] Open
Abstract
CRISPR/Cas9 genome editing is a transformative technology that will facilitate the development of crops to meet future demands. However, application of gene editing is hindered by the long life cycle of many crop species and because desired genotypes generally require multiple generations to achieve. Single-celled microspores are haploid cells that can develop into double haploid plants and have been widely used as a breeding tool to generate homozygous plants within a generation. In this study, we combined the CRISPR/Cas9 system with microspore technology and developed an optimized haploid mutagenesis system to induce genetic modifications in the wheat genome. We investigated a number of factors that may affect the delivery of CRISPR/Cas9 reagents into microspores and found that electroporation of a minimum of 75,000 cells using 10–20 µg DNA and a pulsing voltage of 500 V is optimal for microspore transfection using the Neon transfection system. Using multiple Cas9 and sgRNA constructs, we present evidence for the seamless introduction of targeted modifications in an exogenous DsRed gene and two endogenous wheat genes, including TaLox2 and TaUbiL1. This study demonstrates the value and feasibility of combining microspore technology and CRISPR/Cas9-based gene editing for trait discovery and improvement in plants.
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Affiliation(s)
- Pankaj Bhowmik
- Canadian Wheat Improvement Flagship Program, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada.
| | - Evan Ellison
- Department of Genetics, Cell Biology, and Development, Center for Genome Engineering, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Brittany Polley
- Canadian Wheat Improvement Flagship Program, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Venkatesh Bollina
- Canadian Wheat Improvement Flagship Program, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Manoj Kulkarni
- Canadian Wheat Improvement Flagship Program, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Kaveh Ghanbarnia
- Canadian Wheat Improvement Flagship Program, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Halim Song
- Canadian Wheat Improvement Flagship Program, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Daniel F Voytas
- Department of Genetics, Cell Biology, and Development, Center for Genome Engineering, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Sateesh Kagale
- Canadian Wheat Improvement Flagship Program, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada.
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16
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Bhowmik P, Ellison E, Polley B, Bollina V, Kulkarni M, Ghanbarnia K, Song H, Gao C, Voytas DF, Kagale S. Targeted mutagenesis in wheat microspores using CRISPR/Cas9. Sci Rep 2018. [PMID: 29695804 DOI: 10.1038/s41598-018-24690-8v] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
CRISPR/Cas9 genome editing is a transformative technology that will facilitate the development of crops to meet future demands. However, application of gene editing is hindered by the long life cycle of many crop species and because desired genotypes generally require multiple generations to achieve. Single-celled microspores are haploid cells that can develop into double haploid plants and have been widely used as a breeding tool to generate homozygous plants within a generation. In this study, we combined the CRISPR/Cas9 system with microspore technology and developed an optimized haploid mutagenesis system to induce genetic modifications in the wheat genome. We investigated a number of factors that may affect the delivery of CRISPR/Cas9 reagents into microspores and found that electroporation of a minimum of 75,000 cells using 10-20 µg DNA and a pulsing voltage of 500 V is optimal for microspore transfection using the Neon transfection system. Using multiple Cas9 and sgRNA constructs, we present evidence for the seamless introduction of targeted modifications in an exogenous DsRed gene and two endogenous wheat genes, including TaLox2 and TaUbiL1. This study demonstrates the value and feasibility of combining microspore technology and CRISPR/Cas9-based gene editing for trait discovery and improvement in plants.
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Affiliation(s)
- Pankaj Bhowmik
- Canadian Wheat Improvement Flagship Program, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada.
| | - Evan Ellison
- Department of Genetics, Cell Biology, and Development, Center for Genome Engineering, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Brittany Polley
- Canadian Wheat Improvement Flagship Program, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Venkatesh Bollina
- Canadian Wheat Improvement Flagship Program, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Manoj Kulkarni
- Canadian Wheat Improvement Flagship Program, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Kaveh Ghanbarnia
- Canadian Wheat Improvement Flagship Program, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Halim Song
- Canadian Wheat Improvement Flagship Program, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Daniel F Voytas
- Department of Genetics, Cell Biology, and Development, Center for Genome Engineering, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Sateesh Kagale
- Canadian Wheat Improvement Flagship Program, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada.
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17
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Haque E, Taniguchi H, Hassan MM, Bhowmik P, Karim MR, Śmiech M, Zhao K, Rahman M, Islam T. Application of CRISPR/Cas9 Genome Editing Technology for the Improvement of Crops Cultivated in Tropical Climates: Recent Progress, Prospects, and Challenges. Front Plant Sci 2018; 9:617. [PMID: 29868073 PMCID: PMC5952327 DOI: 10.3389/fpls.2018.00617] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/18/2018] [Indexed: 05/19/2023]
Abstract
The world population is expected to increase from 7.3 to 9.7 billion by 2050. Pest outbreak and increased abiotic stresses due to climate change pose a high risk to tropical crop production. Although conventional breeding techniques have significantly increased crop production and yield, new approaches are required to further improve crop production in order to meet the global growing demand for food. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 (CRISPR-associated protein9) genome editing technology has shown great promise for quickly addressing emerging challenges in agriculture. It can be used to precisely modify genome sequence of any organism including plants to achieve the desired trait. Compared to other genome editing tools such as zinc finger nucleases (ZFNs) and transcriptional activator-like effector nucleases (TALENs), CRISPR/Cas9 is faster, cheaper, precise and highly efficient in editing genomes even at the multiplex level. Application of CRISPR/Cas9 technology in editing the plant genome is emerging rapidly. The CRISPR/Cas9 is becoming a user-friendly tool for development of non-transgenic genome edited crop plants to counteract harmful effects from climate change and ensure future food security of increasing population in tropical countries. This review updates current knowledge and potentials of CRISPR/Cas9 for improvement of crops cultivated in tropical climates to gain resiliency against emerging pests and abiotic stresses.
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Affiliation(s)
- Effi Haque
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Hiroaki Taniguchi
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, Poland
| | - Md. Mahmudul Hassan
- Division of Genetics, Genomics and Development School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Patuakhali, Bangladesh
| | - Pankaj Bhowmik
- National Research Council of Canada, Saskatoon, SK, Canada
| | - M. Rezaul Karim
- Department of Biotechnology and Genetic Engineering Jahangirnagar University Savar, Dhaka, Bangladesh
| | - Magdalena Śmiech
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, Poland
| | - Kaijun Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mahfuzur Rahman
- Extension Service, West Virginia University, Morgantown, WV, United States
| | - Tofazzal Islam
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
- Extension Service, West Virginia University, Morgantown, WV, United States
- *Correspondence: Tofazzal Islam
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18
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Bhowmik P, Das S, Konar A, Nandi D, Chakraborty A. Emotion clustering from stimulated electroencephalographic signals using a Duffing oscillator. ACTA ACUST UNITED AC 2010. [DOI: 10.1504/ijcih.2010.034131] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Saha A, Chaudhury AN, Bhowmik P, Chatterjee R. Awareness of cervical cancer among female students of premier colleges in Kolkata, India. Asian Pac J Cancer Prev 2010; 11:1085-1090. [PMID: 21133629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
Abstract
In the absence of any nationwide cervical screening program, cancer of cervix remains a major public health problem for India. We here assessed knowledge levels of female college students about cervical cancer, its risk factors, the human papillomavirus (HPV) etiologic agent and Pap (Papanicolaou) smear testing for screening. We conducted a questionnaire survey of the students (N=630), aged 17 to 24 years, in Kolkata, India. Only 20% correctly identified cervix cancer as the most prevalent female cancer in India, while 43% were aware of the ages of occurrence. Though 41% thought sexual activity to be associated with cervical cancer, its risk factors, like, smoking, having multiple sex partners, cervical infections, early onset of sexual intercourse, multiple parity were recognized by 29%, 3%, 4%, 13% and 15%, respectively. The terms Pap test and HPV had been heard by 11% and 15 % of the students, respectively, and 75% of the students desired to have protective vaccination. Bivariate analysis revealed that educational stream, standard of the college and family size were significantly associated with knowledge levels. Additionally, multivariate regression analysis indicated city students were more knowledgeable than those from outside the city. It is imperative that women gather adequate knowledge on cervical cancer for the success of any program to control the disease. Wide and effective spreading of awareness about the disease among women must form an integral part of public health policy of government.
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Affiliation(s)
- A Saha
- Department of Statistics, All India Institute of Hygiene & Public Health, Kolkatta, India
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20
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Abstract
In this Account we highlight the experimental evidence in favor of our view that carbon nanotubes should be considered as a new macromolecular form of carbon with unique properties and with great potential for practical applications. We show that carbon nanotubes may take on properties that are normally associated with molecular species, such as solubility in organic solvents, solution-based chemical transformations, chromatography, and spectroscopy. It is already clear that the nascent field of nanotube chemistry will rival that of the fullerenes.
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Affiliation(s)
- S Niyogi
- Center for Nanoscale Science and Engineering, Department of Chemistry, University of California, Riverside, California 92521-0403, USA
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21
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Zhao B, Hu H, Niyogi S, Itkis ME, Hamon MA, Bhowmik P, Meier MS, Haddon RC. Chromatographic purification and properties of soluble single-walled carbon nanotubes. J Am Chem Soc 2001; 123:11673-7. [PMID: 11716724 DOI: 10.1021/ja010488j] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report an improved chromatographic purification of soluble single-walled carbon nanotubes (s-SWNTs) using gel permeation chromatography. Three fractions are separated by gel permeation chromatography, and the first fraction contains 74% of the s-SWNTs as detected by atomic force microscopy and UV and near-infrared spectroscopy.
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Affiliation(s)
- B Zhao
- Departments of Chemistry and Chemical and Environmental Engineering, University of California, Riverside, California 92521-0403, USA
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22
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Abstract
OBJECTIVE To observe the effect of endurance training on novice users of an arm-propelled three-wheeled chair (APTWC), powered by asynchronous arm crank propulsion, in actual locomotive conditions. STUDY DESIGN A continuous endurance training programme was administered by instructing subjects to propel themselves at free chosen speed (FCS) for 15 minutes, twice daily. Data were collected at two-week intervals consecutively and this was continued until the maximum beneficial effect was achieved. SETTING The study was conducted in outdoor settings similar to those the users encountered in their everyday life. SUBJECTS Twelve male paraplegics (below T10), age 30.5 +/- 8.59 years, weight 41.75 kg (+/- 5.76) recommended to use the APTWC as an ambulatory device. INTERVENTION The propulsion speed (metres per minute), peak heart rate (beats per minute) and oxygen uptake (litres per minute) were measured in consecutive sessions at two-week intervals. Physiological cost index (beats m(-1)), oxygen consumption (ml kg(-1) min(-1)) and oxygen cost (ml kg(-1) m(-1)) were derived to assess fitness level. RESULTS Significant changes were observed in the variables following endurance training for 12 weeks. The propulsion speed increased considerably and the cardiorespiratory parameters were found to be reduced. One-way analysis of variance was done for each parameter separately for seven sets of readings taken to assess the overall change over the study period of 12 weeks. The F-ratios were found to be significant (p < 0.01) in each case, except for body weight and oxygen uptake. The pairwise comparison of the biweekly results of the parameters which showed an overall significant change over the study period revealed that after the first two weeks there was considerable change (p < 0.01) for all the parameters. The trend was upward for speed and downward for the other cardiovascular stress parameters. These trends continued until the 10th week showing significant change, after which the values become stable as was revealed by thestatistical tests (p > 0.05). The percentage difference in the mean values from the initial stage (before training) to the 12th week ranged from 10.44% in the case of heart rate to 69.70% in the case of propulsion speed. CONCLUSION Self-ambulation at free chosen speed regularly for 10-12 weeks provides efficiency and improves fitness status required for wheelchairs driven by an asynchronous arm crank propulsion technique and no special exercise programme is required.
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Affiliation(s)
- G Mukherjee
- Department of Occupational Health, All India Institute of Hygiene and Public and Public Health, Calcutta
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Niyogi S, Hu H, Hamon MA, Bhowmik P, Zhao B, Rozenzhak SM, Chen J, Itkis ME, Meier MS, Haddon RC. Chromatographic purification of soluble single-walled carbon nanotubes (s-SWNTS). J Am Chem Soc 2001; 123:733-4. [PMID: 11456587 DOI: 10.1021/ja0024439] [Citation(s) in RCA: 158] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- S Niyogi
- Departments of Chemistry and Physics and Advanced Carbon Materials Center University of Kentucky, Lexington, Kentucky 40506-0055, USA
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24
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Ghosh S, Saha AK, Bhowmik P. Ellis-van Creveld syndrome. J Indian Med Assoc 1992; 90:71. [PMID: 1634791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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