1
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McNulty MJ, Schwartz A, Delzio J, Karuppanan K, Jacobson A, Hart O, Dandekar A, Giritch A, Nandi S, Gleba Y, McDonald KA. Affinity Sedimentation and Magnetic Separation With Plant-Made Immunosorbent Nanoparticles for Therapeutic Protein Purification. Front Bioeng Biotechnol 2022; 10:865481. [PMID: 35573255 PMCID: PMC9092175 DOI: 10.3389/fbioe.2022.865481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/04/2022] [Indexed: 11/20/2022] Open
Abstract
The virus-based immunosorbent nanoparticle is a nascent technology being developed to serve as a simple and efficacious agent in biosensing and therapeutic antibody purification. There has been particular emphasis on the use of plant virions as immunosorbent nanoparticle chassis for their diverse morphologies and accessible, high yield manufacturing via plant cultivation. To date, studies in this area have focused on proof-of-concept immunosorbent functionality in biosensing and purification contexts. Here we consolidate a previously reported pro-vector system into a single Agrobacterium tumefaciens vector to investigate and expand the utility of virus-based immunosorbent nanoparticle technology for therapeutic protein purification. We demonstrate the use of this technology for Fc-fusion protein purification, characterize key nanomaterial properties including binding capacity, stability, reusability, and particle integrity, and present an optimized processing scheme with reduced complexity and increased purity. Furthermore, we present a coupling of virus-based immunosorbent nanoparticles with magnetic particles as a strategy to overcome limitations of the immunosorbent nanoparticle sedimentation-based affinity capture methodology. We report magnetic separation results which exceed the binding capacity reported for current industry standards by an order of magnitude.
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Affiliation(s)
- Matthew J. McNulty
- Department of Chemical Engineering, University of California, Davis, Davis, CA, United States
| | | | - Jesse Delzio
- Department of Chemical Engineering, University of California, Davis, Davis, CA, United States
| | - Kalimuthu Karuppanan
- Department of Chemical Engineering, University of California, Davis, Davis, CA, United States
| | - Aaron Jacobson
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Olivia Hart
- Department of Chemical Engineering, University of California, Davis, Davis, CA, United States
| | - Abhaya Dandekar
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | | | - Somen Nandi
- Department of Chemical Engineering, University of California, Davis, Davis, CA, United States
- Global HealthShare® Initiative, University of California, Davis, Davis, CA, United States
| | | | - Karen A. McDonald
- Department of Chemical Engineering, University of California, Davis, Davis, CA, United States
- Global HealthShare® Initiative, University of California, Davis, Davis, CA, United States
- *Correspondence: Karen A. McDonald,
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2
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Singh N, Barnych B, Morisseau C, Wagner KM, Wan D, Takeshita A, Pham H, Xu T, Dandekar A, Liu JY, Hammock BD. N-Benzyl-linoleamide, a Constituent of Lepidium meyenii (Maca), Is an Orally Bioavailable Soluble Epoxide Hydrolase Inhibitor That Alleviates Inflammatory Pain. J Nat Prod 2020; 83:3689-3697. [PMID: 33320645 PMCID: PMC7888481 DOI: 10.1021/acs.jnatprod.0c00938] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Lepidium meyenii (maca), a plant indigenous to the Peruvian Andes, recently has been utilized globally for claimed health or recreational benefits. The search for natural products that inhibit soluble epoxide hydrolase (sEH), with therapeutically relevant potencies and concentrations, led to the present study on bioactive amide secondary metabolites found in L. meyenii, the macamides. Based on known and suspected macamides, 19 possible macamides were synthesized and characterized. The majority of these amides displayed excellent inhibitory potency (IC50 ≈ 20-300 nM) toward the recombinant mouse, rat, and human sEH. Quantitative analysis of commercial maca products revealed that certain products contain known macamides (1-5, 8-12) at therapeutically relevant total concentrations (≥3.29 mg/g of root), while the inhibitory potency of L. meyenii extracts directly correlates with the sum of concentration/IC50 ratios of macamides present. Considering both its in vitro efficacy and high abundance in commercial products, N-benzyl-linoleamide (4) was identified as a particularly relevant macamide that can be utilized for in vivo studies. Following oral administration in the rat, compound 4 not only displayed acceptable pharmacokinetic characteristics but effectively reduced lipopolysaccharide-induced inflammatory pain. Inhibition of sEH by macamides provides a plausible biological mechanism of action to account for several beneficial effects previously observed with L. meyenii treatments.
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Affiliation(s)
- Nalin Singh
- Department of Entomology and Nematology and UC Davis Comprehensive Cancer Center, University of California Davis, Davis, CA, 95616, United States
| | - Bogdan Barnych
- Department of Entomology and Nematology and UC Davis Comprehensive Cancer Center, University of California Davis, Davis, CA, 95616, United States
| | - Christophe Morisseau
- Department of Entomology and Nematology and UC Davis Comprehensive Cancer Center, University of California Davis, Davis, CA, 95616, United States
| | - Karen M. Wagner
- Department of Entomology and Nematology and UC Davis Comprehensive Cancer Center, University of California Davis, Davis, CA, 95616, United States
| | - Debin Wan
- Department of Entomology and Nematology and UC Davis Comprehensive Cancer Center, University of California Davis, Davis, CA, 95616, United States
| | - Ashley Takeshita
- Department of Entomology and Nematology and UC Davis Comprehensive Cancer Center, University of California Davis, Davis, CA, 95616, United States
| | - Hoang Pham
- Department of Entomology and Nematology and UC Davis Comprehensive Cancer Center, University of California Davis, Davis, CA, 95616, United States
| | - Ting Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, People’s Republic of China
| | - Abhaya Dandekar
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, United States
| | - Jun-Yan Liu
- Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, People’s Republic of China
| | - Bruce D. Hammock
- Department of Entomology and Nematology and UC Davis Comprehensive Cancer Center, University of California Davis, Davis, CA, 95616, United States
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3
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Marrano A, Britton M, Zaini PA, Zimin AV, Workman RE, Puiu D, Bianco L, Pierro EAD, Allen BJ, Chakraborty S, Troggio M, Leslie CA, Timp W, Dandekar A, Salzberg SL, Neale DB. High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome. Gigascience 2020; 9:giaa050. [PMID: 32432329 PMCID: PMC7238675 DOI: 10.1093/gigascience/giaa050] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 03/13/2020] [Accepted: 04/20/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The release of the first reference genome of walnut (Juglans regia L.) enabled many achievements in the characterization of walnut genetic and functional variation. However, it is highly fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to fully elucidate walnut biological processes. FINDINGS Here, we report the new chromosome-scale assembly of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the previous reference genome, the new assembly features an 84.4-fold increase in N50 size, with the 16 chromosomal pseudomolecules assembled and representing 95% of its total length. Using full-length transcripts from single-molecule real-time sequencing, we predicted 37,554 gene models, with a mean gene length higher than the previous gene annotations. Most of the new protein-coding genes (90%) present both start and stop codons, which represents a significant improvement compared with Chandler v1.0 (only 48%). We then tested the potential impact of the new chromosome-level genome on different areas of walnut research. By studying the proteome changes occurring during male flower development, we observed that the virtual proteome obtained from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic regions highly differentiated between Western and Eastern walnut cultivars. CONCLUSION Overall, Chandler v2.0 will serve as a valuable resource to better understand and explore walnut biology.
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Affiliation(s)
- Annarita Marrano
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Monica Britton
- Bioinformatics Core Facility, Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Paulo A Zaini
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, 3100 Wyman Park Dr., Baltimore, MD 21211, USA
| | - Rachael E Workman
- Department of Biomedical Engineering, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
| | - Daniela Puiu
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, 3100 Wyman Park Dr., Baltimore, MD 21211, USA
| | - Luca Bianco
- Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach, 1 38010 S. Michele all'Adige (TN) 38010, Italy
| | - Erica Adele Di Pierro
- Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach, 1 38010 S. Michele all'Adige (TN) 38010, Italy
| | - Brian J Allen
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Sandeep Chakraborty
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Michela Troggio
- Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach, 1 38010 S. Michele all'Adige (TN) 38010, Italy
| | - Charles A Leslie
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, 3100 Wyman Park Dr., Baltimore, MD 21211, USA
| | - Abhaya Dandekar
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Steven L Salzberg
- Department of Biomedical Engineering, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, 3100 Wyman Park Dr., Baltimore, MD 21211, USA
- Departments of Computer Science and Biostatistics, Johns Hopkins University, 3400 North Charles Street Baltimore, MD 21218, USA
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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4
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Marrano A, Britton M, Zaini PA, Zimin AV, Workman RE, Puiu D, Bianco L, Pierro EAD, Allen BJ, Chakraborty S, Troggio M, Leslie CA, Timp W, Dandekar A, Salzberg SL, Neale DB. High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome. Gigascience 2020. [PMID: 32432329 DOI: 10.1101/80979] [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] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND The release of the first reference genome of walnut (Juglans regia L.) enabled many achievements in the characterization of walnut genetic and functional variation. However, it is highly fragmented, preventing the integration of genetic, transcriptomic, and proteomic information to fully elucidate walnut biological processes. FINDINGS Here, we report the new chromosome-scale assembly of the walnut reference genome (Chandler v2.0) obtained by combining Oxford Nanopore long-read sequencing with chromosome conformation capture (Hi-C) technology. Relative to the previous reference genome, the new assembly features an 84.4-fold increase in N50 size, with the 16 chromosomal pseudomolecules assembled and representing 95% of its total length. Using full-length transcripts from single-molecule real-time sequencing, we predicted 37,554 gene models, with a mean gene length higher than the previous gene annotations. Most of the new protein-coding genes (90%) present both start and stop codons, which represents a significant improvement compared with Chandler v1.0 (only 48%). We then tested the potential impact of the new chromosome-level genome on different areas of walnut research. By studying the proteome changes occurring during male flower development, we observed that the virtual proteome obtained from Chandler v2.0 presents fewer artifacts than the previous reference genome, enabling the identification of a new potential pollen allergen in walnut. Also, the new chromosome-scale genome facilitates in-depth studies of intraspecies genetic diversity by revealing previously undetected autozygous regions in Chandler, likely resulting from inbreeding, and 195 genomic regions highly differentiated between Western and Eastern walnut cultivars. CONCLUSION Overall, Chandler v2.0 will serve as a valuable resource to better understand and explore walnut biology.
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Affiliation(s)
- Annarita Marrano
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Monica Britton
- Bioinformatics Core Facility, Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Paulo A Zaini
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, 3100 Wyman Park Dr., Baltimore, MD 21211, USA
| | - Rachael E Workman
- Department of Biomedical Engineering, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
| | - Daniela Puiu
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, 3100 Wyman Park Dr., Baltimore, MD 21211, USA
| | - Luca Bianco
- Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach, 1 38010 S. Michele all'Adige (TN) 38010, Italy
| | - Erica Adele Di Pierro
- Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach, 1 38010 S. Michele all'Adige (TN) 38010, Italy
| | - Brian J Allen
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Sandeep Chakraborty
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Michela Troggio
- Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach, 1 38010 S. Michele all'Adige (TN) 38010, Italy
| | - Charles A Leslie
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, 3100 Wyman Park Dr., Baltimore, MD 21211, USA
| | - Abhaya Dandekar
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Steven L Salzberg
- Department of Biomedical Engineering, Johns Hopkins University, 720 Rutland Avenue, Baltimore, MD 21205, USA
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, 3100 Wyman Park Dr., Baltimore, MD 21211, USA
- Departments of Computer Science and Biostatistics, Johns Hopkins University, 3400 North Charles Street Baltimore, MD 21218, USA
| | - David B Neale
- Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
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5
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Arias MC, Lockwood A, Ali M, Veras K, Olivares J, Bentley S, Dandekar A. Effects of a hospital-based pilot education program on breastfeeding
knowledge in Santiago, Dominican Republic. Ann Glob Health 2016. [DOI: 10.1016/j.aogh.2016.04.615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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6
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Bjornson M, Dandekar A, Dehesh K. Determinants of timing and amplitude in the plant general stress response. J Integr Plant Biol 2016; 58:119-26. [PMID: 26108530 DOI: 10.1111/jipb.12373] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 06/22/2015] [Indexed: 05/06/2023]
Abstract
Plants have evolved intricate signaling cascades to rapidly and effectively respond to biotic and abiotic challenges. The precise timing of these responses enables optimal resource reallocation to maintain the balance between stress adaptation and growth. Thus, an in-depth understanding of the immediate and long-term mechanisms regulating resource allocation is critical in deciphering how plants withstand environmental challenges. To date however, understanding of this tradeoff has focused on the amplitude of long-term responses, rather than the timing of rapid stress responses. This review presents current knowledge on kinetics of secondary messengers involved in regulation of rapid and general stress responses, followed by rapid stress responsive transduction machinery, and finally the transcriptional response of a functional general stress responsive cis-element. Within this context we discuss the role of timing of initial peak activation and later oscillating peak responses, and explore hormonal and stress signaling crosstalk confounding greater understanding of these cascades.
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Affiliation(s)
- Marta Bjornson
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Department of Plant Biology, University of California, Davis, CA 95616, USA
| | - Abhaya Dandekar
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Katayoon Dehesh
- Department of Plant Biology, University of California, Davis, CA 95616, USA
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7
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Bjornson M, Song X, Dandekar A, Franz A, Drakakaki G, Dehesh K. A Chemical Genetic Screening Procedure for Arabidopsis thaliana Seedlings. Bio Protoc 2015; 5:e1519. [PMID: 27446980 DOI: 10.21769/bioprotoc.1519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Unbiased screening approaches are powerful tools enabling identification of novel players in biological processes. Chemical genetic screening refers to the technique of using a reporter response, such as expression of luciferase driven by a promoter of interest, to discover small molecules that affect a given process when applied to plants. These chemicals then act as tools for identification of regulatory components that could not otherwise be detected by forward genetic screens due to gene family redundancy or mutant lethality. This protocol describes a chemical genetic screen using Arabidopsis thaliana seedlings, which has led to recognition of novel players in the plant general stress response.
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Affiliation(s)
- Marta Bjornson
- Department of Plant Sciences, University of California, Davis, USA; Department of Plant Sciences, University of California, Davis, USA
| | - Xingshun Song
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Abhaya Dandekar
- Department of Plant Sciences, University of California, Davis, USA
| | - Annaliese Franz
- Department of Chemistry, University of California, Davis, USA
| | | | - Katayoon Dehesh
- Department of Plant Sciences, University of California, Davis, USA
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8
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Pardington P, Chaudhary A, Norvell M, Gupta G, Dandekar A, Gouran H, Uratsu S, Aguero C, Feldstein P, Bruening G, Civerolo E, Hao G, Duan Y, Stover E. Pathogen clearance by engineering of novel innate immune defense (INM3P.414). The Journal of Immunology 2015. [DOI: 10.4049/jimmunol.194.supp.127.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Pathogens circumvent host immune defense to propagate their lifecycle. We have been studying the mechanisms of pathogen-induced host cell death to develop a robust strategy for pathogen clearance. The strategy involves designing and developing a protein chimera with one domain for recognizing conserved pathogen membrane elements and another for lysing the pathogen membrane. This dualistic synergy of recognition and lysis permits rapid pathogen clearance thereby preventing host cell death and disease development. This strategy has been successfully applied to counteract bacterial infections and diseases in grape, citrus, and tobacco. We have engineered a chimera consisting of protease (recognition domain) and cecropin (lysis domain) to prevent Pierce’s disease, a deadly disease in grape caused by Xylella fastidiosa. We have shown that transgenic plants expressing the chimera of protease and cecropin effectively clear Xylella fastidiosa from sites of colonization. We have also designed a protein chimera of thionin (with both recognition and lysis domains) and a synthetic lytic peptide. We have shown that this same chimera prevents citrus canker which is caused by Xanthamonas axonopodis citri and wildfire disease in tobacco which is caused by Pseudomonas syringe pv. tobaci. This protein engineering strategy appears to be an effective therapy against a broad spectrum of plant pathogens. A similar approach is now being evaluated against multiple human pathogens.
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Affiliation(s)
- Paige Pardington
- 2Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, NM
| | - Anu Chaudhary
- 3Microbiology, University of Washington, Los Alamos, NM
| | - Meghan Norvell
- 4Business and Technology Development, nanoMR, Albuquerque, NM
| | | | - Abhaya Dandekar
- 5Plant Sciences, University of California at Davis, Davis, CA
| | | | - Sandra Uratsu
- 5Plant Sciences, University of California at Davis, Davis, CA
| | - Cecilia Aguero
- 5Plant Sciences, University of California at Davis, Davis, CA
| | - Paul Feldstein
- 5Plant Sciences, University of California at Davis, Davis, CA
| | - George Bruening
- 5Plant Sciences, University of California at Davis, Davis, CA
| | | | - Guixia Hao
- 8Subtropical Insects and Horticulture, U.S. Horticultural Research Laboratory, Fort Pierce, FL
| | - YongPing Duan
- 9Plant Pathology, U.S. Horticultural Research Laboratory, Fort Pierce, FL
| | - Ed Stover
- 10Horticulture and Genetics, USDA-ARS; U.S. Horticultural Research Laboratory, Fort Pierce, FL
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9
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Abstract
Alpha helices (AH) are peptide fragments characterized by regular patterns of hydrogen bonding between the carbonyl oxygen and amino nitrogen of residues regularly spaced in sequence, resulting in spiral conformations. Their preponderance in protein structures underlines their importance. Interestingly, AHs are present in most anti-microbial peptides, although they might remain in random-coil conformations depending on the solvent dielectric. For example, the cecropin component of the chimeric anti-microbial protein designed previously by our group comprises of two AHs linked by a short stretch of random coil. These anti-microbial peptides are often amphipathic (quantified by a hydrophobic moment), aligning hydrophobic residues on one surface and charged residues on the others. In the current work, we reproduce previously described computational methods to compute the hydrophobic moment of AHs - and provide open access to the source code (PAGAL). We simultaneously generated input files for TikZ (a package for creating high resolution graphics programmatically) to obtain the Edmundson wheel and showing the direction and magnitude of the hydrophobic moment, and Pymol scripts to generate color coded protein surfaces. Additionally, we have observed an empirical structural property of AHs: the distance between the Cα atoms of the ith and (i+4)th residue is equal to the distance between the carbonyl oxygens of the ith and (i+4)th residue. We validated this using 100 non-homologous high resolution structures from the PISCES database. The source code and manual is available at http://github.com/sanchak/pagal and on http://dx.doi.org/10.5281/zenodo.11136.
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Affiliation(s)
- Sandeep Chakraborty
- Plant Sciences Department, University of California, Davis, 95616, USA ; Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Basuthkar Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400 005, India
| | - Abhaya Dandekar
- Plant Sciences Department, University of California, Davis, 95616, USA
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10
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Chakraborty S, Rao BJ, Asgeirsson B, Dandekar A. Characterizing alpha helical properties of Ebola viral proteins as potential targets for inhibition of alpha-helix mediated protein-protein interactions. F1000Res 2014; 3:251. [PMID: 25717367 PMCID: PMC4329671 DOI: 10.12688/f1000research.5573.3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/26/2015] [Indexed: 01/28/2023] Open
Abstract
Ebola, considered till recently as a rare and endemic disease, has dramatically transformed into a potentially global humanitarian crisis. The genome of Ebola, a member of the Filoviridae family, encodes seven proteins. Based on the recently implemented software (PAGAL) for analyzing the hydrophobicity and amphipathicity properties of alpha helices (AH) in proteins, we characterize the helices in the Ebola proteome. We demonstrate that AHs with characteristically unique features are involved in critical interactions with the host proteins. For example, the Ebola virus membrane fusion subunit, GP2, from the envelope glycoprotein ectodomain has an AH with a large hydrophobic moment. The neutralizing antibody (KZ52) derived from a human survivor of the 1995 Kikwit outbreak recognizes a protein epitope on this AH, emphasizing the critical nature of this secondary structure in the virulence of the Ebola virus. Our method ensures a comprehensive list of such `hotspots'. These helices probably are or can be the target of molecules designed to inhibit AH mediated protein-protein interactions. Further, by comparing the AHs in proteins of the related Marburg viruses, we are able to elicit subtle changes in the proteins that might render them ineffective to previously successful drugs. Such differences are difficult to identify by a simple sequence or structural alignment. Thus, analyzing AHs in the small Ebola proteome can aid rational design aimed at countering the `largest Ebola epidemic, affecting multiple countries in West Africa' (
http://www.cdc.gov/vhf/ebola/outbreaks/2014-west-africa/index.html).
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Affiliation(s)
- Sandeep Chakraborty
- Plant Sciences Department, University of California, Davis, 95616, USA ; Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, 400 005, India
| | - Basuthkar J Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, 400 005, India
| | - Bjarni Asgeirsson
- Science Institute, Department of Biochemistry, University of Iceland, Dunhaga 3, IS-107 Reykjavik, Iceland
| | - Abhaya Dandekar
- Plant Sciences Department, University of California, Davis, 95616, USA
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11
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Chakraborty S, Rao BJ, Asgeirsson B, Dandekar A. Characterizing alpha helical properties of Ebola viral proteins as potential targets for inhibition of alpha-helix mediated protein-protein interactions. F1000Res 2014; 3:251. [PMID: 25717367 PMCID: PMC4329671 DOI: 10.12688/f1000research.5573.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/26/2015] [Indexed: 08/06/2023] Open
Abstract
Ebola, considered till recently as a rare and endemic disease, has dramatically transformed into a potentially global humanitarian crisis. The genome of Ebola, a member of the Filoviridae family, encodes seven proteins. Based on the recently implemented software (PAGAL) for analyzing the hydrophobicity and amphipathicity properties of alpha helices (AH) in proteins, we characterize the helices in the Ebola proteome. We demonstrate that AHs with characteristically unique features are involved in critical interactions with the host proteins. For example, the Ebola virus membrane fusion subunit, GP2, from the envelope glycoprotein ectodomain has an AH with a large hydrophobic moment. The neutralizing antibody (KZ52) derived from a human survivor of the 1995 Kikwit outbreak recognizes a protein epitope on this AH, emphasizing the critical nature of this secondary structure in the virulence of the Ebola virus. Our method ensures a comprehensive list of such `hotspots'. These helices probably are or can be the target of molecules designed to inhibit AH mediated protein-protein interactions. Further, by comparing the AHs in proteins of the related Marburg viruses, we are able to elicit subtle changes in the proteins that might render them ineffective to previously successful drugs. Such differences are difficult to identify by a simple sequence or structural alignment. Thus, analyzing AHs in the small Ebola proteome can aid rational design aimed at countering the `largest Ebola epidemic, affecting multiple countries in West Africa' ( http://www.cdc.gov/vhf/ebola/outbreaks/2014-west-africa/index.html).
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Affiliation(s)
- Sandeep Chakraborty
- Plant Sciences Department, University of California, Davis, 95616, USA
- Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, 400 005, India
| | - Basuthkar J. Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, 400 005, India
| | - Bjarni Asgeirsson
- Science Institute, Department of Biochemistry, University of Iceland, Dunhaga 3, IS-107 Reykjavik, Iceland
| | - Abhaya Dandekar
- Plant Sciences Department, University of California, Davis, 95616, USA
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Gouran H, Chakraborty S, Rao BJ, Asgeirsson B, Dandekar A. Directed evolution induces tributyrin hydrolysis in a virulence factor of Xylella fastidiosa using a duplicated gene as a template. F1000Res 2014; 3:215. [PMID: 25717364 PMCID: PMC4329599 DOI: 10.12688/f1000research.5147.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/26/2014] [Indexed: 01/22/2023] Open
Abstract
Duplication of genes is one of the preferred ways for natural selection to add advantageous functionality to the genome without having to reinvent the wheel with respect to catalytic efficiency and protein stability. The duplicated secretory virulence factors of Xylella fastidiosa (LesA, LesB and LesC), implicated in Pierce's disease of grape and citrus variegated chlorosis of citrus species, epitomizes the positive selection pressures exerted on advantageous genes in such pathogens. A deeper insight into the evolution of these lipases/esterases is essential to develop resistance mechanisms in transgenic plants. Directed evolution, an attempt to accelerate the evolutionary steps in the laboratory, is inherently simple when targeted for loss of function. A bigger challenge is to specify mutations that endow a new function, such as a lost functionality in a duplicated gene. Previously, we have proposed a method for enumerating candidates for mutations intended to transfer the functionality of one protein into another related protein based on the spatial and electrostatic properties of the active site residues (DECAAF). In the current work, we present in vivo validation of DECAAF by inducing tributyrin hydrolysis in LesB based on the active site similarity to LesA. The structures of these proteins have been modeled using RaptorX based on the closely related LipA protein from Xanthomonas oryzae. These mutations replicate the spatial and electrostatic conformation of LesA in the modeled structure of the mutant LesB as well, providing in silico validation before proceeding to the laborious in vivo work. Such focused mutations allows one to dissect the relevance of the duplicated genes in finer detail as compared to gene knockouts, since they do not interfere with other moonlighting functions, protein expression levels or protein-protein interaction.
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Affiliation(s)
- Hossein Gouran
- Plant Sciences Department, University of California, Davis, CA, 95616, USA
| | - Sandeep Chakraborty
- Plant Sciences Department, University of California, Davis, CA, 95616, USA
- Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, 400 005, India
| | - Basuthkar J. Rao
- Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, 400 005, India
| | - Bjarni Asgeirsson
- Science Institute, Department of Biochemistry, University of Iceland, Dunhaga 3, IS-107 Reykjavik, Iceland
| | - Abhaya Dandekar
- Plant Sciences Department, University of California, Davis, CA, 95616, USA
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Gupta G, Dandekar A, Gouran H, Aguero C, Bruening G, A. Feldstein P, Nascimento R, Goulart L, Norvell M, Pardington P, Chaudhary A, Civerolo E. Pathogen clearance by engineering novel host innate immunity (P1251). The Journal of Immunology 2013. [DOI: 10.4049/jimmunol.190.supp.56.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
A few years ago, we introduced a concept that a protein chimera of pathogen recognition and lysis domains would be able to rapidly clear a broad-spectrum of pathogens [Crit Rev Immunol 2007;27(3):233-245]. For a wide variety of viral, bacterial, and fungal pathogens, appropriate recognition and lysis domains can be chosen from the host innate immune repertoire. A chimera of the recognition and lysis domains would be designed with the aid of a flexible linker to ensure synergy of the two functions and therefore, the rapid clearance of the targeted pathogen. In this work, we demonstrate the design of such a chimera and the efficacy of this chimera in clearing a plant pathogen Xylella fastidiosa (Xf) that causes diseases in multiple plants of economic importance. The most notable ones are Pierce’s disease (PD) in grape and variegated chlorosis (CVC) in citrus. Specifically, we show the construction of the transgenic grapevines expressing a protein chimera of recognition and lysis domains specific for Xf. This chimera clears Xf from the xylem (the site of colonization) and blocks the development of PD [Proc Natl Acad Sci U S A. 2012;109(10):3721-3725]. The same chimera can be applied to block CVC. Finally, we indicate how such chimeras of recognition and lysis domains can be developed to target multiple human pathogens.
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Affiliation(s)
- Goutam Gupta
- 1Biosciences, Los Alamos National Laboratory, Los Alamos, NM
| | | | | | | | | | | | | | - Luiz Goulart
- 5Medical Microbiology and Immunology, UC Davis, Davis, CA
| | - Meghan Norvell
- 1Biosciences, Los Alamos National Laboratory, Los Alamos, NM
| | | | - Anu Chaudhary
- 1Biosciences, Los Alamos National Laboratory, Los Alamos, NM
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Drakakaki G, Dandekar A. Protein secretion: how many secretory routes does a plant cell have? Plant Sci 2013; 203-204:74-8. [PMID: 23415330 DOI: 10.1016/j.plantsci.2012.12.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 12/18/2012] [Accepted: 12/26/2012] [Indexed: 05/19/2023]
Abstract
Conventional protein secretion is mediated by the endomembrane system. Secreted proteins are inserted into the endomembrane system through a N-terminal signal peptide and follow the endoplasmic reticulum to the Golgi trafficking pathway en route to the plasma membrane or the extracellular apoplastic space. In mammalian and yeast cells, unconventional secretion has been identified and relatively well studied. Also in plants, evidence of unconventional secretion mechanisms is accumulating. The ever-increasing number of leaderless proteins identified in proteomic studies indicates the importance of unconventional protein secretion in plants. Novel approaches, such as chemical genomics and vesicle proteomics might be able to provide new insights into unconventional protein secretion in plants.
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Affiliation(s)
- Georgia Drakakaki
- Department of Plant Sciences, University of California, Davis 95616, USA
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Kumar P, Uratsu S, Dandekar A, Falk BW. Tomato bushy stunt virus recombination guided by introduced microRNA target sequences. J Virol 2009; 83:10472-9. [PMID: 19640975 PMCID: PMC2753150 DOI: 10.1128/jvi.00665-09] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2009] [Accepted: 07/24/2009] [Indexed: 01/24/2023] Open
Abstract
Previously we described Tomato bushy stunt virus (TBSV) vectors, which retained their capsid protein gene and were engineered with magnesium chelatase (ChlH) and phytoene desaturase (PDS) gene sequences from Nicotiana benthamiana. Upon plant infection, these vectors eventually lost the inserted sequences, presumably as a result of recombination. Here, we modified the same vectors to also contain the plant miR171 or miR159 target sequences immediately 3' of the silencing inserts. We inoculated N. benthamiana plants and sequenced recombinant RNAs recovered from noninoculated upper leaves. We found that while some of the recombinant RNAs retained the microRNA (miRNA) target sites, most retained only the 3' 10 and 13 nucleotides of the two original plant miRNA target sequences, indicating in planta miRNA-guided RNA-induced silencing complex cleavage of the recombinant TBSV RNAs. In addition, recovered RNAs also contained various fragments of the original sequence (ChlH and PDS) upstream of the miRNA cleavage site, suggesting that the 3' portion of the miRNA-cleaved TBSV RNAs served as a template for negative-strand RNA synthesis by the TBSV RNA-dependent RNA polymerase (RdRp), followed by template switching by the RdRp and continued RNA synthesis resulting in loss of nonessential nucleotides.
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Affiliation(s)
- Pavan Kumar
- Plant Biology Graduate Group, University of California, Davis, Davis, CA 95616, USA
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Getachew G, Pittroff W, Putnam D, Dandekar A, Goyal S, DePeters E. The influence of addition of gallic acid, tannic acid, or quebracho tannins to alfalfa hay on in vitro rumen fermentation and microbial protein synthesis. Anim Feed Sci Technol 2008. [DOI: 10.1016/j.anifeedsci.2007.03.011] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Peng BZ, Dandekar A, Sun CY, Luo H, Ma QL, Pang WX, Chen GJ. Hydrate Film Growth on the Surface of a Gas Bubble Suspended in Water. J Phys Chem B 2007; 111:12485-93. [PMID: 17929860 DOI: 10.1021/jp074606m] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- B. Z. Peng
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, China, and Department of Petroleum Engineering, University of Alaska Fairbanks, Fairbanks, Alaska 99775
| | - A. Dandekar
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, China, and Department of Petroleum Engineering, University of Alaska Fairbanks, Fairbanks, Alaska 99775
| | - C. Y. Sun
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, China, and Department of Petroleum Engineering, University of Alaska Fairbanks, Fairbanks, Alaska 99775
| | - H. Luo
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, China, and Department of Petroleum Engineering, University of Alaska Fairbanks, Fairbanks, Alaska 99775
| | - Q. L. Ma
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, China, and Department of Petroleum Engineering, University of Alaska Fairbanks, Fairbanks, Alaska 99775
| | - W. X. Pang
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, China, and Department of Petroleum Engineering, University of Alaska Fairbanks, Fairbanks, Alaska 99775
| | - G. J. Chen
- State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing 102249, China, and Department of Petroleum Engineering, University of Alaska Fairbanks, Fairbanks, Alaska 99775
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Pignatta D, Kumar P, Turina M, Dandekar A, Falk BW. Quantitative analysis of efficient endogenous gene silencing in Nicotiana benthamiana plants using tomato bushy stunt virus vectors that retain the capsid protein gene. Mol Plant Microbe Interact 2007; 20:609-18. [PMID: 17555269 DOI: 10.1094/mpmi-20-6-0609] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Tomato bushy stunt virus (TBSV) coat protein (CP) replacement vectors have been used previously to silence transgenes (e.g., the green fluorescent protein gene) but have not been effective for silencing endogenous plant genes. New TBSV vectors which retained the CP gene were developed by engineering an XhoI restriction site in three positions (3f, CEB, and CEA) of the pTBSV-100 infectious clone. Magnesium chelatase (ChlH) and phytoene desaturase (PDS) were chosen as targets for endogenous gene silencing. Initial experiments using CP replacement vectors with a 230-bp sense or antisense ChlH insert gave a silencing phenotype prominent only in the first new leaves above those inoculated. No silencing phenotype was apparent beyond these leaves whereas, for PDS, no silencing phenotype was observed. When plants were inoculated with the XhoI insert vectors containing ChlH and PDS sequences, plants showed a silencing phenotype extensively throughout the challenged plant, indicating an improved ability for virus movement and silencing in Nicotiana benthamiana host plants. Silencing efficiencies were quantified using realtime reverse-transcription polymerase chain reaction, indicating specific silencing effects of each individual silencing vector. Only one recombinant vector (pPD-3f5), where the XhoI insert was at the 3' end of the CP gene, failed to give effective silencing. Here, we show that our new CP-retaining TBSV vectors (CEA-CEB) form typical TBSV virions, retain silencing inserts of variable lengths (110 to 260 nucleotides), and can systemically silence endogenous genes in N. benthamiana.
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Affiliation(s)
- Daniela Pignatta
- Dipartimento di Scienze e Tecnologie Agroambientali, Bologna, Italy
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Pang W, Chen G, Dandekar A, Sun C, Zhang C. Experimental study on the scale-up effect of gas storage in the form of hydrate in a quiescent reactor. Chem Eng Sci 2007. [DOI: 10.1016/j.ces.2007.01.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Horn R, Lecouls AC, Callahan A, Dandekar A, Garay L, McCord P, Howad W, Chan H, Verde I, Main D, Jung S, Georgi L, Forrest S, Mook J, Zhebentyayeva T, Yu Y, Kim HR, Jesudurai C, Sosinski B, Arús P, Baird V, Parfitt D, Reighard G, Scorza R, Tomkins J, Wing R, Abbott AG. Candidate gene database and transcript map for peach, a model species for fruit trees. Theor Appl Genet 2005; 110:1419-28. [PMID: 15846479 DOI: 10.1007/s00122-005-1968-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2004] [Accepted: 11/15/2004] [Indexed: 05/03/2023]
Abstract
Peach (Prunus persica) is a model species for the Rosaceae, which includes a number of economically important fruit tree species. To develop an extensive Prunus expressed sequence tag (EST) database for identifying and cloning the genes important to fruit and tree development, we generated 9,984 high-quality ESTs from a peach cDNA library of developing fruit mesocarp. After assembly and annotation, a putative peach unigene set consisting of 3,842 ESTs was defined. Gene ontology (GO) classification was assigned based on the annotation of the single "best hit" match against the Swiss-Prot database. No significant homology could be found in the GenBank nr databases for 24.3% of the sequences. Using core markers from the general Prunus genetic map, we anchored bacterial artificial chromosome (BAC) clones on the genetic map, thereby providing a framework for the construction of a physical and transcript map. A transcript map was developed by hybridizing 1,236 ESTs from the putative peach unigene set and an additional 68 peach cDNA clones against the peach BAC library. Hybridizing ESTs to genetically anchored BACs immediately localized 11.2% of the ESTs on the genetic map. ESTs showed a clustering of expressed genes in defined regions of the linkage groups. [The data were built into a regularly updated Genome Database for Rosaceae (GDR), available at (http://www.genome.clemson.edu/gdr/).].
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Affiliation(s)
- Renate Horn
- Department of Genetics, Biochemistry and Life Science Studies, Clemson University, Clemson, SC 29634, USA
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Ovbiagele B, Saver JL, Fredieu A, Suzuki S, McNair N, Dandekar A, Razinia T, Kidwell CS. PROTECT: A coordinated stroke treatment program to prevent recurrent thromboembolic events. Neurology 2004; 63:1217-22. [PMID: 15477541 DOI: 10.1212/01.wnl.0000140493.83607.f1] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To assess the impact of the Preventing Recurrence of Thromboembolic Events through Coordinated Treatment (PROTECT) Program on achievement of its eight secondary prevention goals at the time of discharge. METHODS Achievement rates for the eight program goals at time of discharge were compared in all patients discharged from a university hospital-based stroke service with a diagnosis of ischemic stroke or TIA during a 1-year period after implementation of the PROTECT Program vs rates obtained from a comparable group of patients admitted to the same service during the preceding year. RESULTS Demographic and medical features were comparable in the baseline and intervention cohorts for all patients with cerebral ischemia presumed due to large-vessel atherosclerosis or small-vessel disease (baseline year n = 117, intervention n = 130). Implementation rates in patients without specific contraindications increased for all four medication goals: 97 to 100% for antithrombotic agents, 68 to 97% for statins, 42 to 90% for angiotensin-converting enzyme inhibitors/angiotensin receptor blockers, and 14 to 70% for diuretics. Although data were not collected on baseline lifestyle instruction rates, instruction in the program's four lifestyle interventions was achieved by discharge in 100% of the intervention cohort. CONCLUSION Implementation of this single-center, systems-based, in-hospital program to initiate secondary stroke prevention therapies was associated with a substantial increase in treatment utilization at the time of hospital discharge.
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Affiliation(s)
- B Ovbiagele
- Stroke Center and Department of Neurology, UCLA Medical Center, Los Angeles, CA, USA.
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Teuber S, Peterson W, Uratsu S, Dandekar A, Roux K, Sathe S. Identification and cloning of Jug r 4, a major food allergen from english walnut belonging to the legumin group. J Allergy Clin Immunol 2003. [DOI: 10.1016/s0091-6749(03)80879-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Brown PH, Bellaloui N, Hu H, Dandekar A. Transgenically enhanced sorbitol synthesis facilitates phloem boron transport and increases tolerance of tobacco to boron deficiency. Plant Physiol 1999; 119:17-20. [PMID: 9880341 PMCID: PMC32216 DOI: 10.1104/pp.119.1.17] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/1998] [Accepted: 09/08/1998] [Indexed: 05/18/2023]
Abstract
The mobility of elements within plants contributes to a plant species' tolerance of nutrient deficiencies in the soil. The genetic manipulation of within-plant nutrient movement may therefore provide a means to enhance plant growth under conditions of variable soil nutrient availability. In these experiments tobacco (Nicotiana tabacum) was engineered to synthesize sorbitol, and the resultant effect on phloem mobility of boron (B) was determined. In contrast to wild-type tobacco, transgenic tobacco plants containing sorbitol exhibit a marked increase in within-plant B mobility and a resultant increase in plant growth and yield when grown with limited or interrupted soil B supply. Growth of transgenic tobacco could be maintained by reutilization of B present in mature tissues or from B supplied as a foliar application to mature leaves. In contrast, B present in mature leaves of control tobacco lines could not be used to provide the B requirements for new plant growth. 10B-labeling experiments verified that B is phloem mobile in transgenic tobacco but is immobile in control lines. These results demonstrate that the transgenic enhancement of within-plant nutrient mobility is a viable approach to improve plant tolerance of nutrient stress.
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Affiliation(s)
- PH Brown
- Department of Pomology, University of California, Davis, California 95616, USA
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