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Madsen CK, Brearley CA, Harholt J, Brinch-Pedersen H. Optimized barley phytase gene expression by focused FIND-IT screening for mutations in cis-acting regulatory elements. Front Plant Sci 2024; 15:1372049. [PMID: 38495373 PMCID: PMC10940425 DOI: 10.3389/fpls.2024.1372049] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 02/12/2024] [Indexed: 03/19/2024]
Abstract
Introduction Induced modification of plant gene expression is of both fundamental and applied importance. Cis-acting regulatory elements (CREs) are major determinants of the spatiotemporal strength of gene expression. Yet, there are few examples where induced genetic variation in predetermined CREs has been exploited to improve or investigate crop plants. Methods The digital PCR based FIND-IT technology was applied to discover barley mutants with CRE variants in the promoter of the nutritional important barley grain phytase (PAPhy_a) gene. Results and discussion Mutants with higher or lower gene expression and ultimately higher or lower mature grain phytase activity (MGPA), respectively, were discovered. Field trials and inositol phosphate profiling during germination showed that PAPhy_a does not influence agronomic performance under the trial conditions but it does shorten the lag time of phosphate mobilization during germination. Higher endogenous MGPA is an improvement of grain quality for feed use as it improves the phosphate bioavailability for monogastric animals. Moreover, as the targeted CRE motifs of the PAPhy_a promoter are shared with a range of seed expressed genes like key cereal and legume storage genes, the current results demonstrates a concept for modulating individual gene expression levels of a range of seed genes.
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Affiliation(s)
| | - Charles Alistair Brearley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Jesper Harholt
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, Copenhagen, Denmark
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Riaz A, Kanwal F, Ahmad I, Ahmad S, Farooq A, Madsen CK, Brinch-Pedersen H, Bekalu ZE, Dai F, Zhang G, Alqudah AM. New Hope for Genome Editing in Cultivated Grasses: CRISPR Variants and Application. Front Genet 2022; 13:866121. [PMID: 35923689 PMCID: PMC9340155 DOI: 10.3389/fgene.2022.866121] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 06/23/2022] [Indexed: 12/24/2022] Open
Abstract
With the advent of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas) mediated genome editing, crop improvement has progressed significantly in recent years. In this genome editing tool, CRISPR-associated Cas nucleases are restricted to their target of DNA by their preferred protospacer adjacent motifs (PAMs). A number of CRISPR-Cas variants have been developed e.g. CRISPR-Cas9, -Cas12a and -Cas12b, with different PAM requirements. In this mini-review, we briefly explain the components of the CRISPR-based genome editing tool for crop improvement. Moreover, we intend to highlight the information on the latest development and breakthrough in CRISPR technology, with a focus on a comparison of major variants (CRISPR-Cas9, -Cas12a, and -Cas12b) to the newly developed CRISPR-SpRY that have nearly PAM-less genome editing ability. Additionally, we briefly explain the application of CRISPR technology in the improvement of cultivated grasses with regard to biotic and abiotic stress tolerance as well as improving the quality and yield.
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Affiliation(s)
- Asad Riaz
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Farah Kanwal
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Iqrar Ahmad
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Shakeel Ahmad
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Ayesha Farooq
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Claus Krogh Madsen
- Department of Agroecology, Research Center Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Henrik Brinch-Pedersen
- Department of Agroecology, Research Center Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Zelalem Eshetu Bekalu
- Department of Agroecology, Research Center Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Fei Dai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guoping Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- *Correspondence: Guoping Zhang, ; Ahmad M. Alqudah, ,
| | - Ahmad M. Alqudah
- Department of Agroecology, Research Center Flakkebjerg, Aarhus University, Slagelse, Denmark
- *Correspondence: Guoping Zhang, ; Ahmad M. Alqudah, ,
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Hanak T, Madsen CK, Brinch-Pedersen H. Genome Editing-accelerated Re-Domestication (GEaReD) - a new major direction in plant breeding. Biotechnol J 2022; 17:e2100545. [PMID: 35120401 DOI: 10.1002/biot.202100545] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/13/2022] [Accepted: 01/19/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND The effects of climate change, soil depletion, a growing world population putting pressure on food safety and security are major challenges for agriculture in the 21st century. The breeding success of the green revolution has decelerated and current programs can only offset the yield affecting factors. PURPOSE AND SCOPE New approaches are urgently needed and we propose "Genome Editing-accelerated Re-Domestication" (GEaReD) as a major new direction in plant breeding. By combining the upcoming technologies for phenotyping, omics, and artificial intelligence with the promising new CRISPR-toolkits, this approach is closer than ever. SUMMARY AND CONCLUSION Wild relatives of current crops are often adapted to harsh environments and have a high genetic diversity. Redomestication of wild barley or teosinte could generate new cultivars adapted to environmental changes. De novo domestication of perennial relatives such as Hordeum bulbosum could counter soil depletion and increase soil carbon. Recent research already proved the principle of redomestication in tomato and rice and therefore laid the foundation for GEaReD. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Tobias Hanak
- Department of Agroecology, Aarhus University, Crop Genetics and Biotechnology Forsøgsvej 1, Slagelse, 4200, Denmark
| | - Claus Krogh Madsen
- Department of Agroecology, Aarhus University, Crop Genetics and Biotechnology Forsøgsvej 1, Slagelse, 4200, Denmark
| | - Henrik Brinch-Pedersen
- Department of Agroecology, Aarhus University, Crop Genetics and Biotechnology Forsøgsvej 1, Slagelse, 4200, Denmark
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Bekalu ZE, Dionisio G, Madsen CK, Etzerodt T, Fomsgaard IS, Brinch-Pedersen H. Barley Nepenthesin-Like Aspartic Protease HvNEP-1 Degrades Fusarium Phytase, Impairs Toxin Production, and Suppresses the Fungal Growth. Front Plant Sci 2021; 12:702557. [PMID: 34394154 PMCID: PMC8358834 DOI: 10.3389/fpls.2021.702557] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Nepenthesins are categorized under the subfamily of the nepenthesin-like plant aspartic proteases (PAPs) that form a distinct group of atypical PAPs. This study describes the effect of nepenthesin 1 (HvNEP-1) protease from barley (Hordeum vulgare L.) on fungal histidine acid phosphatase (HAP) phytase activity. Signal peptide lacking HvNEP-1 was expressed in Pichia pastoris and biochemically characterized. Recombinant HvNEP-1 (rHvNEP-1) strongly inhibited the activity of Aspergillus and Fusarium phytases, which are enzymes that release inorganic phosphorous from phytic acid. Moreover, rHvNEP-1 suppressed in vitro fungal growth and strongly reduced the production of mycotoxin, 15-acetyldeoxynivalenol (15-ADON), from Fusarium graminearum. The quantitative PCR analysis of trichothecene biosynthesis genes (TRI) confirmed that rHvNEP-1 strongly repressed the expression of TRI4, TRI5, TRI6, and TRI12 in F. graminearum. The co-incubation of rHvNEP-1 with recombinant F. graminearum (rFgPHY1) and Fusarium culmorum (FcPHY1) phytases induced substantial degradation of both Fusarium phytases, indicating that HvNEP-1-mediated proteolysis of the fungal phytases contributes to the HvNEP-1-based suppression of Fusarium.
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Holme IB, Madsen CK, Wendt T, Brinch-Pedersen H. Horizontal Stacking of PAPhy_a Cisgenes in Barley Is a Potent Strategy for Increasing Mature Grain Phytase Activity. Front Plant Sci 2020; 11:592139. [PMID: 33193549 PMCID: PMC7644513 DOI: 10.3389/fpls.2020.592139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/05/2020] [Indexed: 06/11/2023]
Abstract
Mature grain phytase activity (MGPA) in the Triticea tribe cereals has evolved through gene duplications and neo-functionalization of the purple acid phosphatase phytase gene (PAPhy) in a common ancestor. Increased gene copy number of the PAPhy_a gene expressed during seed development has augmented the MGPA in cereals like rye and wheat. PAPhy_a phytase is highly stable and a potent enzyme in feed. However, barley only contains one HvPAPhy_a gene and the MGPA levels needs to be increased to substitute for the addition of microbial phytases to the feed. A substantial increase in MGPA for cisgenic barley was achieved with one extra homozygous HvPAPhy_a insert when the plants were grown in the greenhouse. In the current study, the stability of increased MGPA was confirmed in open field grown cisgenic barley. Furthermore, the gene dose response of phytase cisgenes from three different cisgenic barley plants were horizontally stacked. Cisgenic barley with 0, 1, 2, 3, 4, and 6 extra HvPAPhy_a inserts demonstrated a perfect positive linear correlation with the level of MGPA. The current study provides new insight into the potential of stacking of cisgenes in crops and suggests cisgene stacking as a versatile strategy for crop improvement.
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Madsen CK, Brinch-Pedersen H. Globoids and Phytase: The Mineral Storage and Release System in Seeds. Int J Mol Sci 2020; 21:ijms21207519. [PMID: 33053867 PMCID: PMC7589363 DOI: 10.3390/ijms21207519] [Citation(s) in RCA: 10] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 01/08/2023] Open
Abstract
Phytate and phytases in seeds are the subjects of numerous studies, dating back as far as the early 20th century. Most of these studies concern the anti-nutritional properties of phytate, and the prospect of alleviating the effects of phytate with phytase. As reasonable as this may be, it has led to a fragmentation of knowledge, which hampers the appreciation of the physiological system at hand. In this review, we integrate the existing knowledge on the chemistry and biosynthesis of phytate, the globoid cellular structure, and recent advances on plant phytases. We highlight that these components make up a system that serves to store and-in due time-release the seed's reserves of the mineral nutrients phosphorous, potassium, magnesium, and others, as well as inositol and protein. The central component of the system, the phytate anion, is inherently rich in phosphorous and inositol. The chemical properties of phytate enable it to sequester additional cationic nutrients. Compartmentalization and membrane transport processes regulate the buildup of phytate and its associated nutrients, resulting in globoid storage structures. We suggest, based on the current evidence, that the degradation of the globoid and the mobilization of the nutrients also depend on membrane transport processes, as well as the enzymatic action of phytase.
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Madsen CK, Brinch-Pedersen H. A novel wheat q' allele identified by forward genetic in silico TILLING. J Plant Physiol 2020; 251:153221. [PMID: 32590253 DOI: 10.1016/j.jplph.2020.153221] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/09/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
The major wheat domestication allele Q (encoding an APETALA2 like transcription factor) is responsible for the free threshing and square-headed spikes of modern wheat. Wild type q and null q' alleles cause a reversal to the speltoid phenotype. Q pleiotropically affects additional yield and quality traits so genetic variation in Q and its interaction partners remain important for crop improvement. Here we report the discovery of a novel q' allele that contribute to the molecular characterization of Q. This induced mutation cause an Ala→Thr substitution at a highly conserved position in the first of two APETALA2 like domains of the Q protein. The mutation correlates with a speltoid phenotype as expected for a loss of Q function. Thus, it is demonstrated that the first APETALA2 like domain is essential for Q function. The phenotype was discovered in a mutant from an in silico TILLING population and the causative mutation could be identified in the existing sequence data. This report therefore provides an example of a forward genetic application of in silico TILLING.
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Affiliation(s)
- Claus Krogh Madsen
- Section of Crop Genetics and Biotechnology, Department of Agroecology, Aarhus University. Forsøgsvej 1, 4200 Slagelse, Denmark.
| | - Henrik Brinch-Pedersen
- Section of Crop Genetics and Biotechnology, Department of Agroecology, Aarhus University. Forsøgsvej 1, 4200 Slagelse, Denmark
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Abstract
Phytases are pro-nutritional enzymes that hydrolyze phytate and make associated nutrients, such as phosphorous, iron, and zinc, bioavailable. Single-stomached animals and humans depend on phytase supplied through the diet or the action of phytase on the food before ingestion. As a result, phytases-or lack thereof-have a profound impact on agricultural ecosystems, resource management, animal health, and public health. Wheat, barley and their Triticeae relatives make exceptionally good natural sources of phytase. This review highlights advances in the understanding of the molecular basis of the phytase activity in wheat and barley, which has taken place over the past decade. It is shown how the phytase activity in the mature grains of wheat and barley can be ascribed to the PAPhy_a gene, which exists as a single gene in barley and in two or three homeologous copies in tetra- and hexaploid wheat, respectively. It is discussed how understanding the function and regulation of PAPhy_a may support the development of improved wheat and barley with even higher phytase activity.
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Affiliation(s)
- Claus Krogh Madsen
- Department of Molecular Biology and Genetics, Research Center Flakkebjerg, Aarhus University, 4200-Slagelse, Denmark.
| | - Henrik Brinch-Pedersen
- Department of Molecular Biology and Genetics, Research Center Flakkebjerg, Aarhus University, 4200-Slagelse, Denmark.
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Madsen CK, Brearley CA, Brinch-Pedersen H. Lab-scale preparation and QC of phytase assay substrate from rice bran. Anal Biochem 2019; 578:7-12. [PMID: 31054994 PMCID: PMC6587120 DOI: 10.1016/j.ab.2019.04.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/16/2019] [Accepted: 04/24/2019] [Indexed: 11/20/2022]
Abstract
Phytases are involved in the phosphate acquisition and remobilization in plants, microbes and animals. They have become important technical enzymes in the feed industry and are used to make phosphate, present in animal feed as phytate, available for monogastric animal nutrition. Phytases may also be beneficial to human nutrition because phytate is known to interfere with the uptake of important micronutrients. Accordingly, phytases attract considerable research attention and phytate substrate lacking contaminants that interfere with commonly used phosphate-release assays is essential for this field of science. A procedure to prepare suitable sodium phytate from rice bran is presented. Extracted phytate is precipitated with barium hydroxide and re-dissolved in methanol after washing steps and sulphuric acid treatment. Remaining impurities are precipitated before the dissolved phytate is recovered as the sodium salt by addition of sodium hydroxide. In order to make the substrate widely available for research communities, the procedure relies solely on basic laboratory equipment and materials. Methods for quality control and monitoring of the purified sodium phytate or commercial alternatives are also presented.
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Affiliation(s)
- Claus Krogh Madsen
- Institute of Molecular Biology and Genetics, Aarhus University, Forsogsvej 1, 4200, Slagelse, Denmark.
| | - Charles Alistair Brearley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Henrik Brinch-Pedersen
- Institute of Molecular Biology and Genetics, Aarhus University, Forsogsvej 1, 4200, Slagelse, Denmark
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Nørgaard JV, Malla N, Dionisio G, Madsen CK, Pettersson D, Lærke HN, Hjortshøj RL, Brinch-Pedersen H. Exogenous xylanase or protease for pigs fed barley cultivars with high or low enzyme inhibitors. Anim Feed Sci Technol 2019. [DOI: 10.1016/j.anifeedsci.2018.12.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Krogh Madsen C, Pettersson D, Hjortshøj R, Katholm A, Brinch-Pedersen H. Superior Growth Rates in Broilers Fed Wheat with Low In Vitro Feed-Xylanase Inhibition. J Agric Food Chem 2018; 66:4044-4050. [PMID: 29575893 DOI: 10.1021/acs.jafc.8b00208] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Grain-batch variation in xylanase-inhibitor levels may account for variations in the efficacy of feed xylanase supplementation. This would make inhibition an important quality parameter in the routine analysis of feedstuffs. Two analytical procedures for testing feedstuffs against specific xylanases were researched: the high-throughput viscosity-pressure assay (ViPr) and the extraction-free remazol-brilliant-blue-beechwood-xylan (RBBX) assay. Thirty-two wheat cultivars were analyzed for inhibition of a commercial xylanase, Ronozyme WX. Four cultivars were selected for a feeding experiment in which the growth of 1440 broilers from ages 7-33 days was monitored. The treatments resulted up to 7 % difference (day 14) in broiler weight . The cultivar choice had an effect throughout the experiment ( p < 0.05). The performance ranking of the treatments corresponded better to xylanase inhibition than to crude-protein content or nonstarch-polysaccharide content. Wheat-grain xylanase-inhibitor content is therefore a highly relevant quality parameter when broiler diets are supplemented with feed xylanase.
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Affiliation(s)
- Claus Krogh Madsen
- Department of Molecular Biology and Genetics, Research Center Flakkebjerg , Aarhus University , 4200 Slagelse , Denmark
| | | | | | | | - Henrik Brinch-Pedersen
- Department of Molecular Biology and Genetics, Research Center Flakkebjerg , Aarhus University , 4200 Slagelse , Denmark
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Bekalu ZE, Madsen CK, Dionisio G, Brinch-Pedersen H. Aspergillus ficuum phytase activity is inhibited by cereal grain components. PLoS One 2017; 12:e0176838. [PMID: 28472144 PMCID: PMC5417552 DOI: 10.1371/journal.pone.0176838] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/18/2017] [Indexed: 11/19/2022] Open
Abstract
In the current study, we report for the first time that grain components of barley, rice, wheat and maize can inhibit the activity of Aspergillus ficuum phytase. The phytase inhibition is dose dependent and varies significantly between cereal species, between cultivars of barley and cultivars of wheat and between Fusarium graminearum infected and non-infected wheat grains. The highest endpoint level of phytase activity inhibition was 90%, observed with grain protein extracts (GPE) from F. graminearum infected wheat. Wheat GPE from grains infected with F. graminearum inhibits phytase activity significantly more than GPE from non-infected grains. For four barley cultivars studied, the IC50 value ranged from 0.978 ± 0.271 to 3.616 ± 0.087 mg×ml-1. For two non-infected wheat cultivars investigated, the IC50 values were varying from 2.478 ± 0.114 to 3.038 ± 0.097 mg×ml-1. The maize and rice cultivars tested gaveIC50 values on 0.983 ± 0.205 and 1.972 ± 0.019 mg×ml-1, respectively. After purifying the inhibitor from barley grains via Superdex G200, an approximately 30–35 kDa protein was identified. No clear trend for the mechanism of inhibition could be identified via Michaelis-Menten kinetics and Lineweaver-Burk plots. However, testing of the purified phytase inhibitor together with the A. ficuum phytase and the specific protease inhibitors pepstatin A, E64, EDTA and PMSF revealed that pepstatin A repealed the phytase inhibition. This indicates that the observed inhibition of A. ficuum phytase by cereal grain extracts is caused by protease activity of the aspartic proteinase type.
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Affiliation(s)
- Zelalem Eshetu Bekalu
- Department of Molecular Biology and Genetics, Research Center Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Claus Krogh Madsen
- Department of Molecular Biology and Genetics, Research Center Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Giuseppe Dionisio
- Department of Molecular Biology and Genetics, Research Center Flakkebjerg, Aarhus University, Slagelse, Denmark
| | - Henrik Brinch-Pedersen
- Department of Molecular Biology and Genetics, Research Center Flakkebjerg, Aarhus University, Slagelse, Denmark
- * E-mail:
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Holme IB, Dionisio G, Madsen CK, Brinch‐Pedersen H. Barley HvPAPhy_a as transgene provides high and stable phytase activities in mature barley straw and in grains. Plant Biotechnol J 2017; 15:415-422. [PMID: 27633382 PMCID: PMC5362685 DOI: 10.1111/pbi.12636] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 05/11/2016] [Revised: 09/01/2016] [Accepted: 09/12/2016] [Indexed: 05/31/2023]
Abstract
The phytase purple acid phosphatase (HvPAPhy_a) expressed during barley seed development was evaluated as transgene for overexpression in barley. The phytase was expressed constitutively driven by the cauliflower mosaic virus 35S-promoter, and the phytase activity was measured in the mature grains, the green leaves and in the dry mature vegetative plant parts left after harvest of the grains. The T2 -generation of HvPAPhy_a transformed barley showed phytase activity increases up to 19-fold (29 000 phytase units (FTU) per kg in mature grains). Moreover, also in green leaves and mature dry straw, phytase activities were increased significantly by 110-fold (52 000 FTU/kg) and 57-fold (51 000 FTU/kg), respectively. The HvPAPhy_a-transformed barley plants with high phytase activities possess triple potential utilities for the improvement of phosphate bioavailability. First of all, the utilization of the mature grains as feed to increase the release of bio-available phosphate and minerals bound to the phytate of the grains; secondly, the utilization of the powdered straw either directly or phytase extracted hereof as a supplement to high phytate feed or food; and finally, the use of the stubble to be ploughed into the soil for mobilizing phytate-bound phosphate for plant growth.
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Affiliation(s)
- Inger Bæksted Holme
- Department of Molecular Biology and GeneticsFaculty of Science and TechnologyResearch Centre FlakkebjergAarhus UniversitySlagelseDenmark
| | - Giuseppe Dionisio
- Department of Molecular Biology and GeneticsFaculty of Science and TechnologyResearch Centre FlakkebjergAarhus UniversitySlagelseDenmark
| | - Claus Krogh Madsen
- Department of Molecular Biology and GeneticsFaculty of Science and TechnologyResearch Centre FlakkebjergAarhus UniversitySlagelseDenmark
| | - Henrik Brinch‐Pedersen
- Department of Molecular Biology and GeneticsFaculty of Science and TechnologyResearch Centre FlakkebjergAarhus UniversitySlagelseDenmark
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Madsen CK, Vismans G, Brinch-Pedersen H. The PARS sequence increase the efficiency of stable Pichia pastoris transformation. J Microbiol Methods 2016; 129:1-7. [PMID: 27444547 DOI: 10.1016/j.mimet.2016.07.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/12/2016] [Accepted: 07/16/2016] [Indexed: 10/21/2022]
Abstract
The methylotrophic yeast Pichia pastoris is a popular host for recombinant expression of proteins. Plasmids containing the Pichia autonomously replicating sequence (PARS) transform P. pastoris with higher efficiency than linear DNA equipped with termini designed for homologous recombination. Moreover, PARS containing constructs provide higher protein yields. Unfortunately, these autonomous plasmids are inherently unstable and the preferred method of P. pastoris transformation is therefore stable integration in the genome by homologous recombination. In the present study we report that a novel combination of PARS and linearization of plasmids for P. pastoris transformation serves to significantly increase the transformation efficiency. Moreover, it is demonstrated that the constructs do not re-circularize but integrate stably into the P. pastoris genome.
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Affiliation(s)
- Claus Krogh Madsen
- Department of Molecular Biology and Genetics, Section for Crop Genetics and Biotechnology, Aarhus University, Forsogsvej 1, 4200 Slagelse, Denmark.
| | - Gilles Vismans
- Wageningen University, 6708PB Wageningen, The Netherlands
| | - Henrik Brinch-Pedersen
- Department of Molecular Biology and Genetics, Section for Crop Genetics and Biotechnology, Aarhus University, Forsogsvej 1, 4200 Slagelse, Denmark
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Kronbak R, Ingvardsen CR, Madsen CK, Gregersen PL. A novel approach to the generation of seamless constructs for plant transformation. Plant Methods 2014; 10:10. [PMID: 24855486 PMCID: PMC4030040 DOI: 10.1186/1746-4811-10-10] [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] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/01/2014] [Indexed: 06/03/2023]
Abstract
BACKGROUND When creating plant transformation vectors, full control of nucleotides flanking the insert in the final construct may be desirable. Modern ligase-independent methods for DNA-recombination are based on linearization by classical type II restriction endonucleases (REs) alone or in combination with nicking enzymes leaving residual nucleotides behind in the final construct. We here explore the use of type IIS and type IIB REs for vector linearization that combined with sequence and ligase-independent cloning (SLIC) overcomes this problem and promotes seamless gene-insertion in vectors. Providing the basis for a collection of biolistic plant transformation vectors ready to be cloned with different genes-of-interest, we present two vectors, where promoter and terminator are joined by a spacer. During spacer-removal linearization (SRL), type IIS and type IIB REs remove their own recognition sequences from the vector leaving no undesired, short sequences behind. RESULTS We designed two plant transformation vectors prepared for SRL in combination with SLIC, pAUrumII and pAUrumIII, harboring a spacer with recognition sites for a type IIS and IIB RE, respectively. The gene for a green fluorescent protein, gfp, was successfully cloned into both vectors; traces of pAUrumIII, however, contaminated the transformation due to incomplete linearization, an issue not encountered with the type IIS linearized pAUrumII. Both constructs, pAUrumII-gfp and pAUrumIII-gfp, were functional, when tested in vitro on wheat and barley endosperm cells for transient gfp expression. CONCLUSIONS All nucleotides flanking an insert in a biolistic plant transformation vector can be customized by means of SRL in combination with SLIC. Especially type IIS REs promote an efficient cloning result. Based on our findings, we believe that the SRL system can be useful in a series of plant transformation vectors, favoring the presence of functional sequences for optimal expression over redundant cloning-site remnants.
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Affiliation(s)
- Remy Kronbak
- Science and Technology, Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark
| | - Christina Rønn Ingvardsen
- Science and Technology, Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark
| | - Claus Krogh Madsen
- Science and Technology, Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark
| | - Per Langkjær Gregersen
- Science and Technology, Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark
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Madsen CK, Dionisio G, Holme IB, Holm PB, Brinch-Pedersen H. High mature grain phytase activity in the Triticeae has evolved by duplication followed by neofunctionalization of the purple acid phosphatase phytase (PAPhy) gene. J Exp Bot 2013; 64:3111-23. [PMID: 23918958 PMCID: PMC3733140 DOI: 10.1093/jxb/ert116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The phytase activity in food and feedstuffs is an important nutritional parameter. Members of the Triticeae tribe accumulate purple acid phosphatase phytases (PAPhy) during grain filling. This accumulation elevates mature grain phytase activities (MGPA) up to levels between ~650 FTU/kg for barley and 6000 FTU/kg for rye. This is notably more than other cereals. For instance, rice, maize, and oat have MGPAs below 100 FTU/kg. The cloning and characterization of the PAPhy gene complement from wheat, barley, rye, einkorn, and Aegilops tauschii is reported here. The Triticeae PAPhy genes generally consist of a set of paralogues, PAPhy_a and PAPhy_b, and have been mapped to Triticeae chromosomes 5 and 3, respectively. The promoters share a conserved core but the PAPhy_a promoter have acquired a novel cis-acting regulatory element for expression during grain filling while the PAPhy_b promoter has maintained the archaic function and drives expression during germination. Brachypodium is the only sequenced Poaceae sharing the PAPhy duplication. As for the Triticeae, the duplication is reflected in a high MGPA of ~4200 FTU/kg in Brachypodium. The sequence conservation of the paralogous loci on Brachypodium chromosomes 1 and 2 does not extend beyond the PAPhy gene. The results indicate that a single-gene segmental duplication may have enabled the evolution of high MGPA by creating functional redundancy of the parent PAPhy gene. This implies that similar MGPA levels may be out of reach in breeding programs for some Poaceae, e.g. maize and rice, whereas Triticeae breeders should focus on PAPhy_a.
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Affiliation(s)
- Claus Krogh Madsen
- Aarhus University, Faculty of Science and Technology, Dept. of Molecular Biology and Genetics, Research Centre Flakkebjerg, DK-4200 Slagelse, Denmark
| | - Giuseppe Dionisio
- Aarhus University, Faculty of Science and Technology, Dept. of Molecular Biology and Genetics, Research Centre Flakkebjerg, DK-4200 Slagelse, Denmark
| | - Inger Bæksted Holme
- Aarhus University, Faculty of Science and Technology, Dept. of Molecular Biology and Genetics, Research Centre Flakkebjerg, DK-4200 Slagelse, Denmark
| | - Preben Bach Holm
- Aarhus University, Faculty of Science and Technology, Dept. of Molecular Biology and Genetics, Research Centre Flakkebjerg, DK-4200 Slagelse, Denmark
| | - Henrik Brinch-Pedersen
- Aarhus University, Faculty of Science and Technology, Dept. of Molecular Biology and Genetics, Research Centre Flakkebjerg, DK-4200 Slagelse, Denmark
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Adams DB, Snider WT, Madsen CK. NLFM waveform generation using tunable integrated optical ring resonators: simulation and proof of concept experiment. Opt Express 2010; 18:12537-12542. [PMID: 20588379 DOI: 10.1364/oe.18.012537] [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: 05/29/2023]
Abstract
The NLFM waveform resulting from a tunable integrated optical ring resonator is simulated. The metrics of interest are the first sidelobe levels and FWHM times of the autocorrelation, as these directly relate to the long-range performance and fine range resolution of a LADAR system, and should ideally be as small as possible. Through simulation, the maximum sidelobe level of the autocorrelation of an NLFM waveform generated by a series of tunable integrated optical ring resonators is shown to be -20 to -30 dB or lower. A proof of concept experiment employing an off-the-shelf thermally tunable silicon-nitride optical ring resonator is shown to generate NLFM chirped waveforms with a bandwidth of 28 kHz.
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Affiliation(s)
- D B Adams
- Texas A and M University, 3128 TAMU, College Station, 77843 Texas, USA.
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18
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Acharya BR, Madsen CK, Baldwin KW, MacHarrie RA, Rogers JA, Möller L, Huang CC, Pindak R. In-line liquid-crystal microcell polarimeter for high-speed polarization analysis. Opt Lett 2003; 28:1096-1098. [PMID: 12879919 DOI: 10.1364/ol.28.001096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We report a type of high-speed microcell polarimeter that utilizes microelectrodes, liquid-crystal films, and ultrathin high-contrast polarizers, all integrated between the tips of two optical fibers. When combined with optimized nematic liquid-crystal materials, this compact (2.5 cm x 0.5 cm x 0.5 cm) device offers excellent optical properties and continuous, high-speed operation at > 2 kHz with moderately low operating voltages. It requires no bulk optical elements, and it shows excellent performance when implemented for the measurement of degree of polarization in 10-Gbit/s test systems. Polarimeters based on this design have promising potential applications in polarization analysis for high-speed optical communication systems.
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Affiliation(s)
- Bharat R Acharya
- Bell Laboratories, Lucent Technologies, Murray Hill, New Jersey 07974, USA
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19
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Abstract
By use of a near-field scanning optical microscope (NSOM) in collection mode, the intensity distribution along a 2 x 2 multimode interference coupler was directly imaged as a function of wavelength. Although calculations can predict the general trend of wavelength dependence and the approximate positions of multiple images in the coupler, the accuracy is poor because of uncertainties in the waveguide width. We show that direct imaging using a NSOM bypasses calculational uncertainties and proves to be a powerful technique for studying these waveguide devices.
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Affiliation(s)
- A L Campillo
- Bell Laboratories, Lucent Technologies, Murray Hill, New Jersey 07974, USA
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20
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Madsen CK, Oswald P. Optical filter architecture for approximating any 2 X 2 unitary matrix. Opt Lett 2003; 28:534-536. [PMID: 12696607 DOI: 10.1364/ol.28.000534] [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: 05/24/2023]
Abstract
A new optical filter architecture and a new design methodology are presented for approximating any frequency-dependent 2 x 2 unitary matrix that consists of two coupled phase and amplitude responses. Design examples are provided for the compensation of polarization mode dispersion (PMD) by approximating the inverse of a synthesized fiber's Jones matrix. Compensation of the channel PMD over the signal bandwidth is demonstrated, as required for demultiplexing channels in a polarization-multiplexed system.
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Affiliation(s)
- C K Madsen
- Lucent Technologies, Bell Laboratories, Room 1D350, Murray Hill, New Jersey 07974, USA.
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21
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Leick L, Madsen CK. Dispersion compensation of a 1x N passive optical router with low loss, a flat passband, and low cross talk. Opt Lett 2002; 27:1318-1320. [PMID: 18026436 DOI: 10.1364/ol.27.001318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A 1xN interferometer-based router with single-stage all-pass filters in the arms has low loss, a flat passband, and low cross talk. However, we show that the router has substantial cubic dispersion over the channel passband, which is identical from channel to channel. For a 1x4 router with a free spectral range of 100 GHz, the average dispersion slope over a 60% passband is -8x10(3)ps/nm(2), and thus a cascade of four routers incurs a significant system power penalty. A three-stage all-pass filter placed on the input arm reduces the dispersion of all channels by a factor of 16. The router is quite insensitive to variations in the all-pass filter design parameters.
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22
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Abstract
Polarization mode dispersion (PMD) compensation is addressed by decomposition of a fiber's Jones matrix into amplitude and phase responses, which are then compensated for separately. Cubic and higher-order phase compensation substantially reduce the cumulative probability at a given system penalty over first-order PMD compensation, as demonstrated for a 40-Gbit/s non-return-to-zero signal and a fiber PMD with a differential group delay of 20 ps (rms). Single-stage all-pass filters provide tunable compensation that is comparable to that obtained with a variable-delay line, and multistage all-pass filters are well suited for higher-order phase compensation.
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Madsen CK, Lenz G, Bruce AJ, Capuzzo MA, Gomez LT, Nielsen TN, Brener I. Multistage dispersion compensator using ring resonators. Opt Lett 1999; 24:1555-1557. [PMID: 18079861 DOI: 10.1364/ol.24.001555] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A compact, multichannel dispersion-compensating filter is demonstrated with D=-4200 ps/nm, a +/-5-ps group delay ripple, <3-dB loss, and a 4.5-GHz passband width out of a 12.5-GHz free spectral range. We show that multistage designs can achieve a substantial increase in passband width and peak dispersion for a given group-delay ripple compared with single-stage designs. The dispersion-compensation effectiveness was demonstrated in a 320-km, seven-channel nonlinear system simulation for OC48 signals.
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Affiliation(s)
- C K Madsen
- Bell Laboratories, Lucent Technologies, Room 1D148, 600 Mountain Avenue, Murray Hill, New Jersey 07974, USA
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Abstract
This study examined pre-internship fears of music therapy majors. Additional analysis included comparison of pre-internship fears of music therapy majors with pre-internship fears of music education majors. Subjects for this study were music therapy/music education majors at a large southeastern university (N = 61; N = 32) who were surveyed during the year prior to their internship. Utilizing identical procedures, each subject was asked to list the 3 greatest fears that they had concerning their internship. Two independent evaluators then classified the perceived fears based on a taxonomic structure developed during the initial study on pre-internship fears of music education majors. Reliability for the classification of pre-internship music therapy fears was.97. Ranking reported fears revealed a hierarchy of pre-internship fears and provided comparisons between the two populations. Analysis of data indicated that the music therapy interns listed "general preparation/being prepared" as their primary fear followed by issues relating to "failure/not cut out for therapy." The next most frequently noted fears related to concerns about "internship placement" and concerns about the "physical environment" (money, moving, housing, etc.). Music therapy subject responses were also examined in relationship to the responses of music education subjects. Subject responses revealed a very low fear concerning "discipline" for the music therapy majors, yet this category was the highest listed by the music education seniors. "Failure/not being cut out for teaching/therapy" was expressed as a concern with the next highest frequency by the education majors and was rated quite high by the therapy majors. Fears about the "physical environment including money, moving, etc." were quite high for the music therapy majors, yet these fears received very low ratings by the music education students. In addition, fears related to the "supervising teacher/placement" and "students not learning/clients not responding" also registered somewhat differentiated responses with therapy majors evidencing more concern when compared to the music educators.
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Affiliation(s)
- CK Madsen
- Center for Music Research, The Florida State University
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25
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Madsen CK, Zhao JH. Increasing the free spectral range of silica waveguide rings for filter applications. Opt Lett 1998; 23:186-188. [PMID: 18084454 DOI: 10.1364/ol.23.000186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Ring resonators are promising building blocks for developing compact optical filters with arbitrary functions; however, a major challenge for planar waveguide filter implementations is to overcome the limited free spectral range (FSR) for a given core-to-cladding refractive-index difference (D) while maintaining low loss and a large range of coupling ratios. The loss and coupling of rings operating in the whispering-gallery-mode regime were investigated by use of Ge-doped silica waveguides with a low refractive-index difference (D=0.75%) . A FSR of 12 GHz with a loss of 0.36 dB/cm was demonstrated with coupling ratios of 30% (41% optimum).
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Abstract
Narrow-band planar waveguide filters are sensitive to fabrication errors that make it difficult to realize multistage filters successfully and maintain tight center wavelength tolerances unless a tuning technique is available. An analysis algorithm combined with waveguide heaters has been successfully used to demonstrate that fabrication errors can be compensated in an autoregressive (AR) lattice architecture that makes it possible to concatenate conveniently multiple stages and to achieve higher-order filter functions. Compensation of fabrication errors on filter functions for a second- and third-order AR lattice filter is presented, and issues related to the application of the analysis algorithm are discussed. In combination with postfabrication tuning of the coupling ratios, the analysis algorithm will allow complete control of the filter function after fabrication.
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Affiliation(s)
- C K Madsen
- Department of Electrical and Computer Engineering, Rutgers University, Piscataway, New Jersey 08854, USA
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Abstract
Rural black, economically impoverished Head Start children, whose normal diets were deficient in nutritional requirements, were not consuming the nutritional breakfasts of, to them, unfamiliar foods provided by the county school system. This study investigated a positive simple method to increase the amount of food consumed and thereby ensure proper nutrition. Teachers dispensed sugar-coated cereal and small candies paired with praise contingent on eating behaviors and rewarded children who finished the entire meal with additional treats and praise. Substantial increases were produced in the proportion of meals consumed and in the number of children observed engaged in eating behaviors. These simple traditional behavioral procedures are readily available for any staff working with economically impoverished children as one method of increasing their sampling and consumption of unfamiliar nutritious foods.
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