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Jadeja SP, LeBlanc A, O'Toole S, Austin RS, Bartlett D. The subsurface lesion in erosive tooth wear. J Dent 2023; 136:104652. [PMID: 37544352 PMCID: PMC10837081 DOI: 10.1016/j.jdent.2023.104652] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023] Open
Abstract
OBJECTIVES This study compared the surface change on natural and polished enamel exposed to a joint mechanical and chemical wear regimen. METHODS Human enamel samples were randomly assigned to natural (n = 30) or polished (n = 30) groups, subjected to erosion (n = 10, 0.3% citric acid, 5 min), abrasion (n = 10, 30 s), or a combination (n = 10). Wear in the form of step height was measured with a non-contact profilometer, and surface changes were inspected with SEM on selected sections. Data was normalised and underwent repeated measures MANOVA, accounting for substrate and erosive challenge as independent variables, with Bonferroni correction for significant post hoc interactions. RESULTS After four cycles, polished samples had mean step heights of 3.08 (0.40) μm after erosion and 4.08 (0.37) μm after erosion/abrasion. For natural samples, these measurements were 1.52 (0.22) μm and 3.62 (0.39) μm, respectively. Natural surfaces displayed less wear than polished surfaces under erosion-only conditions (p<0.0001), but the difference disappeared with added abrasion. SEM revealed a shallow subsurface layer for polished surfaces and natural ones undergoing only erosion. However, natural surfaces exposed to both erosion and abrasion showed deeper subsurface changes up to 50 µm. CONCLUSION Natural enamel, when exposed to erosion alone, showed less wear and minimal subsurface alterations. But with added abrasion, natural enamel surfaces saw increased wear and notable subsurface changes compared to polished ones. CLINICAL SIGNIFICANCE The pronounced subsurface lesions observed on eroded/abraded natural enamel surfaces highlight how combined wear challenges may accelerate tooth tissue loss.
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Affiliation(s)
- S P Jadeja
- Faculty of Dentistry, Oral and Clinical Sciences, Centre for Clinical, Oral and Translational Sciences, King's College London, London SE1 9RT, United Kingdom.
| | - A LeBlanc
- Faculty of Dentistry, Oral and Clinical Sciences, Centre for Clinical, Oral and Translational Sciences, King's College London, London SE1 9RT, United Kingdom
| | - S O'Toole
- Faculty of Dentistry, Oral and Clinical Sciences, Centre for Clinical, Oral and Translational Sciences, King's College London, London SE1 9RT, United Kingdom
| | - R S Austin
- Faculty of Dentistry, Oral and Clinical Sciences, Centre for Clinical, Oral and Translational Sciences, King's College London, London SE1 9RT, United Kingdom
| | - D Bartlett
- Faculty of Dentistry, Oral and Clinical Sciences, Centre for Clinical, Oral and Translational Sciences, King's College London, London SE1 9RT, United Kingdom
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Yang X, Hill KA, Austin RS, Tian L. Differential Gene Expression of Brachypodium distachyon Roots Colonized by Gluconacetobacter diazotrophicus and the Role of BdCESA8 in the Colonization. Mol Plant Microbe Interact 2021; 34:1143-1156. [PMID: 34709058 DOI: 10.1094/mpmi-06-20-0170-r] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Alternatives to synthetic nitrogen fertilizer are needed to reduce the costs of crop production and offset environmental damage. Nitrogen-fixing bacterium Gluconacetobacter diazotrophicus has been proposed as a possible biofertilizer for monocot crop production. However, the colonization of G. diazotrophicus in most monocot crops is limited and deep understanding of the response of host plants to G. diazotrophicus colonization is still lacking. In this study, the molecular response of the monocot plant model Brachypodium distachyon was studied during G. diazotrophicus root colonization. The gene expression profiles of B. distachyon root tissues colonized by G. diazotrophicus were generated via next-generation RNA sequencing, and investigated through gene ontology and metabolic pathway analysis. The RNA sequencing results indicated that Brachypodium is actively involved in G. diazotrophicus colonization via cell wall synthesis. Jasmonic acid, ethylene, gibberellin biosynthesis. nitrogen assimilation, and primary and secondary metabolite pathways are also modulated to accommodate and control the extent of G. diazotrophicus colonization. Cellulose synthesis is significantly downregulated during colonization. The loss of function mutant for Brachypodium cellulose synthase 8 (BdCESA8) showed decreased cellulose content in xylem and increased resistance to G. diazotrophicus colonization. This result suggested that the cellulose synthesis of the secondary cell wall is involved in G. diazotrophicus colonization. The results of this study provide insights for future research in regard to gene manipulation for efficient colonization of nitrogen-fixing bacteria in Brachypodium and monocot crops.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Xuan Yang
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada
| | - Kathleen A Hill
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada
| | - Ryan S Austin
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada
| | - Lining Tian
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada
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3
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Saatian B, Austin RS, Tian G, Chen C, Nguyen V, Kohalmi SE, Geelen D, Cui Y. Analysis of a novel mutant allele of GSL8 reveals its key roles in cytokinesis and symplastic trafficking in Arabidopsis. BMC Plant Biol 2018; 18:295. [PMID: 30466394 PMCID: PMC6249969 DOI: 10.1186/s12870-018-1515-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [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: 10/16/2017] [Accepted: 10/31/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Plant cell walls are mainly composed of polysaccharides such as cellulose and callose. Callose exists at a very low level in the cell wall; however, it plays critical roles at different stages of plant development as well as in defence against unfavorable conditions. Callose is accumulated at the cell plate, at plasmodesmata and in male and female gametophytes. Despite the important roles of callose in plants, the mechanisms of its synthesis and regulatory properties are not well understood. RESULTS CALLOSE SYNTHASE (CALS) genes, also known as GLUCAN SYNTHASE-LIKE (GSL), comprise a family of 12 members in Arabidopsis thaliana. Here, we describe a new allele of GSL8 (named essp8) that exhibits pleiotropic seedling defects. Reduction of callose deposition at the cell plates and plasmodesmata in essp8 leads to ectopic endomitosis and an increase in the size exclusion limit of plasmodesmata during early seedling development. Movement of two non-cell-autonomous factors, SHORT ROOT and microRNA165/6, both required for root radial patterning during embryonic root development, are dysregulated in the primary root of essp8. This observation provides evidence for a molecular mechanism explaining the gsl8 root phenotype. We demonstrated that GSL8 interacts with PLASMODESMATA-LOCALIZED PROTEIN 5, a β-1,3-glucanase, and GSL10. We propose that they all might be part of a putative callose synthase complex, allowing a concerted regulation of callose deposition at plasmodesmata. CONCLUSION Analysis of a novel mutant allele of GSL8 reveals that GSL8 is a key player in early seedling development in Arabidopsis. GSL8 is required for maintaining the basic ploidy level and regulating the symplastic trafficking. Callose deposition at plasmodesmata is highly regulated and occurs through interaction of different components, likely to be incorporated into a callose biosynthesis complex. We are providing new evidence supporting an earlier hypothesis that GSL8 might have regulatory roles apart from its enzymatic function in plasmodesmata regulation.
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Affiliation(s)
- Behnaz Saatian
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON Canada
- Department of Biology, Western University, 1391 Sandford St, London, ON N5V 4T3 Canada
| | - Ryan S. Austin
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON Canada
- Department of Biology, Western University, 1391 Sandford St, London, ON N5V 4T3 Canada
| | - Gang Tian
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON Canada
| | - Chen Chen
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON Canada
- Department of Biology, Western University, 1391 Sandford St, London, ON N5V 4T3 Canada
| | - Vi Nguyen
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON Canada
| | - Susanne E. Kohalmi
- Department of Biology, Western University, 1391 Sandford St, London, ON N5V 4T3 Canada
| | - Danny Geelen
- In Vitro Biology and Horticulture, Department of Plant Production, University of Ghent, 9000 Ghent, Belgium
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON Canada
- Department of Biology, Western University, 1391 Sandford St, London, ON N5V 4T3 Canada
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Duwadi K, Austin RS, Mainali HR, Bett K, Marsolais F, Dhaubhadel S. Slow darkening of pinto bean seed coat is associated with significant metabolite and transcript differences related to proanthocyanidin biosynthesis. BMC Genomics 2018; 19:260. [PMID: 29661146 PMCID: PMC5903001 DOI: 10.1186/s12864-018-4550-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 02/14/2018] [Indexed: 11/29/2022] Open
Abstract
Background Postharvest seed coat darkening in pinto bean is an undesirable trait resulting in a loss in the economic value of the crop. The extent of darkening varies between the bean cultivars and their storage conditions. Results Metabolite analysis revealed that the majority of flavonoids including proanthocyanidin monomer catechin accumulated at higher level in a regular darkening (RD) pinto line CDC Pintium than in a slow darkening (SD) line 1533–15. A transcriptome analysis was conducted to compare gene expression between CDC Pintium and 1533–15 and identify the gene (s) that may play a role in slow darkening processes in 1533–15 pinto. RNAseq against total RNA from RD and SD cultivars found several phenylpropanoid genes, metabolite transporter genes and genes involved in gene regulation or modification to be differentially expressed between CDC Pintium and 1533–15. Conclusion RNAseq analysis and metabolite data of seed coat tissue from CDC Pintium and 1533–15 revealed that the whole proanthocyanidin biosynthetic pathway was downregulated in 1533–15. Additionally, genes that encode for putative transporter proteins were also downregulated in 1533–15 suggesting both synthesis and accumulation of proanthocyanidin is reduced in SD pintos. Electronic supplementary material The online version of this article (10.1186/s12864-018-4550-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kishor Duwadi
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Ryan S Austin
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada.,Department of Biology, University of Western Ontario, London, ON, Canada
| | - Hemanta R Mainali
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Kirstin Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Frédéric Marsolais
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada.,Department of Biology, University of Western Ontario, London, ON, Canada
| | - Sangeeta Dhaubhadel
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada. .,Department of Biology, University of Western Ontario, London, ON, Canada.
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Chen C, Li C, Wang Y, Renaud J, Tian G, Kambhampati S, Saatian B, Nguyen V, Hannoufa A, Marsolais F, Yuan ZC, Yu K, Austin RS, Liu J, Kohalmi SE, Wu K, Huang S, Cui Y. Cytosolic acetyl-CoA promotes histone acetylation predominantly at H3K27 in Arabidopsis. Nat Plants 2017; 3:814-824. [PMID: 28947800 DOI: 10.1038/s41477-017-0023-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 08/31/2017] [Indexed: 05/23/2023]
Abstract
Acetyl-coenzyme A (acetyl-CoA) is a central metabolite and the acetyl source for protein acetylation, particularly histone acetylation that promotes gene expression. However, the effect of acetyl-CoA levels on histone acetylation status in plants remains unknown. Here, we show that malfunctioned cytosolic acetyl-CoA carboxylase1 (ACC1) in Arabidopsis leads to elevated levels of acetyl-CoA and promotes histone hyperacetylation predominantly at lysine 27 of histone H3 (H3K27). The increase of H3K27 acetylation (H3K27ac) is dependent on adenosine triphosphate (ATP)-citrate lyase which cleaves citrate to acetyl-CoA in the cytoplasm, and requires histone acetyltransferase GCN5. A comprehensive analysis of the transcriptome and metabolome in combination with the genome-wide H3K27ac profiles of acc1 mutants demonstrate the dynamic changes in H3K27ac, gene transcripts and metabolites occurring in the cell by the increased levels of acetyl-CoA. This study suggests that H3K27ac is an important link between cytosolic acetyl-CoA level and gene expression in response to the dynamic metabolic environments in plants.
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Affiliation(s)
- Chen Chen
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada
- Department of Biology, Western University, London, Ontario, N6A 5B7, Canada
| | - Chenlong Li
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying Wang
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada
| | - Justin Renaud
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada
| | - Gang Tian
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada
| | - Shrikaar Kambhampati
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada
- Department of Biology, Western University, London, Ontario, N6A 5B7, Canada
| | - Behnaz Saatian
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada
- Department of Biology, Western University, London, Ontario, N6A 5B7, Canada
| | - Vi Nguyen
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada
- Department of Biology, Western University, London, Ontario, N6A 5B7, Canada
| | - Frédéric Marsolais
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada
- Department of Biology, Western University, London, Ontario, N6A 5B7, Canada
| | - Ze-Chun Yuan
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada
| | - Kangfu Yu
- Agriculture and Agri-Food Canada, Harrow Research and Development Centre, Harrow, Ontario, N0R 1G0, Canada
| | - Ryan S Austin
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada
- Department of Biology, Western University, London, Ontario, N6A 5B7, Canada
| | - Jun Liu
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada
- Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Susanne E Kohalmi
- Department of Biology, Western University, London, Ontario, N6A 5B7, Canada
| | - Keqiang Wu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, 106, Taiwan
| | - Shangzhi Huang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada.
- Department of Biology, Western University, London, Ontario, N6A 5B7, Canada.
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Dastmalchi M, Chapman P, Yu J, Austin RS, Dhaubhadel S. Transcriptomic evidence for the control of soybean root isoflavonoid content by regulation of overlapping phenylpropanoid pathways. BMC Genomics 2017; 18:70. [PMID: 28077078 PMCID: PMC5225596 DOI: 10.1186/s12864-016-3463-y] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 12/22/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Isoflavonoids are a class of specialized metabolites found predominantly in legumes. They play a role in signaling for symbiosis with nitrogen-fixing bacteria and inhibiting pathogen infection. RESULTS A transcriptomic approach using soybean cultivars with high (Conrad and AC Colombe) and low (AC Glengarry and Pagoda) root isoflavonoid content was used to find elements that underlie this variation. Two genes, encoding the flavonoid-metabolizing enzymes, flavonoid 3'-hydroxylase (GmF3'H) and dihydroflavonol 4-reductase (GmDFR), had lower expression levels in high isoflavonoid cultivars. These enzymes compete with isoflavonoid biosynthetic enzymes for the important branch-point substrate naringenin and its derivatives. Differentially expressed genes, between the two sets of cultivars, encode transcription factors, transporters and enzymatic families of interest, such as oxidoreductases, hydrolases and transferases. In addition, genes annotated with stress and disease response were upregulated in high isoflavonoid cultivars. CONCLUSIONS Coordinated regulation of genes involved in flavonoid metabolism could redirect flux into the isoflavonoid branch of the phenylpropanoid pathway, by reducing competition for the flavanone substrate. These candidate genes could help identify mechanisms to overcome the endogenous bottleneck to isoflavonoid production, facilitate biosynthesis in heterologous systems, and enhance crop resistance against pathogenic infections.
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Affiliation(s)
- Mehran Dastmalchi
- Department of Biology, University of Western Ontario, London, ON, Canada
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Patrick Chapman
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Jaeju Yu
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Ryan S Austin
- Department of Biology, University of Western Ontario, London, ON, Canada
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Sangeeta Dhaubhadel
- Department of Biology, University of Western Ontario, London, ON, Canada.
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada.
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Hossain MS, Shrestha A, Zhong S, Miri M, Austin RS, Sato S, Ross L, Huebert T, Tromas A, Torres-Jerez I, Tang Y, Udvardi M, Murray JD, Szczyglowski K. Lotus japonicus NF-YA1 Plays an Essential Role During Nodule Differentiation and Targets Members of the SHI/STY Gene Family. Mol Plant Microbe Interact 2016; 29:950-964. [PMID: 27929718 DOI: 10.1094/mpmi-10-16-0206-r] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Legume plants engage in intimate relationships with rhizobial bacteria to form nitrogen-fixing nodules, root-derived organs that accommodate the microsymbiont. Members of the Nuclear Factor Y (NF-Y) gene family, which have undergone significant expansion and functional diversification during plant evolution, are essential for this symbiotic liaison. Acting in a partially redundant manner, NF-Y proteins were shown, previously, to regulate bacterial infection, including selection of a superior rhizobial strain, and to mediate nodule structure formation. However, the exact mechanism by which these transcriptional factors exert their symbiotic functions has remained elusive. By carrying out detailed functional analyses of Lotus japonicus mutants, we demonstrate that LjNF-YA1 becomes indispensable downstream from the initial cortical cell divisions but prior to nodule differentiation, including cell enlargement and vascular bundle formation. Three affiliates of the SHORT INTERNODES/STYLISH transcription factor gene family, called STY1, STY2, and STY3, are demonstrated to be among likely direct targets of LjNF-YA1, and our results point to their involvement in nodule formation.
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Affiliation(s)
- Md Shakhawat Hossain
- 1 Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3 Canada
| | - Arina Shrestha
- 1 Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3 Canada
- 2 Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7 Canada
| | - Sihui Zhong
- 1 Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3 Canada
| | - Mandana Miri
- 1 Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3 Canada
- 2 Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7 Canada
| | - Ryan S Austin
- 1 Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3 Canada
- 2 Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7 Canada
| | - Shusei Sato
- 3 Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Sendai, 980-8577, Japan; and
| | - Loretta Ross
- 1 Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3 Canada
| | - Terry Huebert
- 1 Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3 Canada
| | - Alexandre Tromas
- 1 Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3 Canada
| | - Ivone Torres-Jerez
- 4 Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, U.S.A
| | - Yuhong Tang
- 4 Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, U.S.A
| | - Michael Udvardi
- 4 Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, U.S.A
| | - Jeremy D Murray
- 4 Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, U.S.A
| | - Krzysztof Szczyglowski
- 1 Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3 Canada
- 2 Department of Biology, University of Western Ontario, London, Ontario, N6A 5B7 Canada
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Austin RS, Hiu S, Waese J, Ierullo M, Pasha A, Wang TT, Fan J, Foong C, Breit R, Desveaux D, Moses A, Provart NJ. New BAR tools for mining expression data and exploring Cis-elements in Arabidopsis thaliana. Plant J 2016; 88:490-504. [PMID: 27401965 DOI: 10.1111/tpj.13261] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [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: 04/14/2016] [Revised: 06/23/2016] [Accepted: 07/01/2016] [Indexed: 05/21/2023]
Abstract
Identifying sets of genes that are specifically expressed in certain tissues or in response to an environmental stimulus is useful for designing reporter constructs, generating gene expression markers, or for understanding gene regulatory networks. We have developed an easy-to-use online tool for defining a desired expression profile (a modification of our Expression Angler program), which can then be used to identify genes exhibiting patterns of expression that match this profile as closely as possible. Further, we have developed another online tool, Cistome, for predicting or exploring cis-elements in the promoters of sets of co-expressed genes identified by such a method, or by other methods. We present two use cases for these tools, which are freely available on the Bio-Analytic Resource at http://BAR.utoronto.ca.
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Affiliation(s)
- Ryan S Austin
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Shu Hiu
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Jamie Waese
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Matthew Ierullo
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Ting Ting Wang
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Jim Fan
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Curtis Foong
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Robert Breit
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Darrell Desveaux
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Alan Moses
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Nicholas J Provart
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
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Gao R, Austin RS, Amyot L, Hannoufa A. Comparative transcriptome investigation of global gene expression changes caused by miR156 overexpression in Medicago sativa. BMC Genomics 2016; 17:658. [PMID: 27542359 PMCID: PMC4992203 DOI: 10.1186/s12864-016-3014-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 08/12/2016] [Indexed: 11/24/2022] Open
Abstract
Background Medicago sativa (alfalfa) is a low-input forage and potential bioenergy crop, and improving its yield and quality has always been a focus of the alfalfa breeding industry. Transgenic alfalfa plants overexpressing a precursor of alfalfa microRNA156 (MsmiR156) were recently generated by our group. These plants (miR156OE) showed enhanced biomass yield, reduced internodal length, increased shoot branching and trichome density, and a delay in flowering time. Transcripts of three SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) genes (MsSPL6, MsSPL12, and MsSPL13) were found to be targeted for cleavage by MsmiR156 in alfalfa. Results To further illustrate the molecular mechanisms underlying the effects of miR156 in alfalfa, two miR156OE genotypes (A11a and A17) were subjected to Next Generation RNA Sequencing with Illumina HiSeq. More than 1.11 billion clean reads were obtained from our available sequenced samples. A total of 160,472 transcripts were generated using Trinity de novo assembly and 4,985 significantly differentially expressed genes were detected in miR156OE plants A11a and A17 using the Medicago truncatula genome as reference. A total of 17 genes (including upregulated, downregulated, and unchanged) were selected for quantitative real-time PCR (qRT-PCR) validation, which showed that gene expression levels were largely consistent between qRT-PCR and RNA-Seq data. In addition to the established SPL genes MsSPL6, MsSPL12 and MsSPL13, four new SPLs; MsSPL2, MsSPL3, MsSPL4 and MsSPL9 were also down-regulated significantly in both miR156OE plants. These seven SPL genes belong to genes phylogeny clades VI, IV, VIII, V and VII, which have been reported to be targeted by miR156 in Arabidopsis thaliana. The gene ontology terms characterized electron transporter, starch synthase activity, sucrose transport, sucrose-phosphate synthase activity, chitin binding, sexual reproduction, flavonoid biosynthesis and lignin catabolism correlate well to the phenotypes of miR156OE alfalfa plants. Conclusions This is the first report of changes in global gene expression in response to miR156 overexpression in alfalfa. The discovered miR156-targeted SPL genes belonging to different clades indicate miR156 plays fundamental and multifunctional roles in regulating alfalfa plant development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3014-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ruimin Gao
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Ryan S Austin
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada.,Department of Biology, University of Western Ontario, 151 Richmond Street, London, ON, N6A 5B7, Canada
| | - Lisa Amyot
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada. .,Department of Biology, University of Western Ontario, 151 Richmond Street, London, ON, N6A 5B7, Canada.
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Sar Sancakli H, Austin RS, Al-Saqabi F, Moazzez R, Bartlett D. The influence of varnish and high fluoride on erosion and abrasion in a laboratory investigation. Aust Dent J 2015; 60:38-42. [PMID: 25721276 DOI: 10.1111/adj.12271] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2014] [Indexed: 11/26/2022]
Abstract
BACKGROUND The aim of this study was to investigate the potential of concentrated fluoride varnishes to reduce enamel loss from repeated cycles of citric acid erosion and toothbrush abrasion in vitro. METHODS Polished human enamel samples were exposed to fluoride varnishes: Bifluorid10® (NaF&CaF2- 45,200 ppmF), Duraphat® (NaF 22,600 ppmF), Fluor-Protector® (difluorsilane 1000 ppmF) and a control coating of copal ether varnish (0 ppmF) group and a deionized water group. For each group of 16 samples, nine cycles of erosion and nine cycles of erosion-abrasion [1 cycle=erosion (0.3% citric acid, pH 3.2, 5 min)+artificial saliva (1 h, pH 7.0)+abrasion (120 linear strokes in artificial saliva from Oral B medium soft brushes 300 g loading]. The change in the enamel surface was evaluated using optical profilometry. RESULTS Duraphat® and Bifluorid10® applications had a median (IQR) step height of 4.21 um (1.59) and 5.01 um (1.02). This was statistically significantly less than Fluor-Protector® 6.83 um (1.25), copal ether 7.22 um (1.97) and water 7.39 um (1.96) (p<0.001). For erosion-abrasion, both Duraphat® and Bifluorid® had statistically lower step heights than the other products (p<0.01). CONCLUSIONS The action of fluoride in a range of single-application topical varnishes was effective in reducing enamel wear from erosion and erosion-abrasion in this laboratory study.
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Affiliation(s)
- H Sar Sancakli
- Department of Restorative Dentistry, Faculty of Dentistry, Istanbul University, Istanbul, Turkey
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11
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Milly H, Austin RS, Thompson I, Banerjee A. In Vitro Effect of Air-abrasion Operating Parameters on Dynamic Cutting Characteristics of Alumina and Bio-active Glass Powders. Oper Dent 2014; 39:81-9. [DOI: 10.2341/12-466-l] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
SUMMARY
Minimally invasive dentistry advocates the maintenance of all repairable tooth structures during operative caries management in combination with remineralization strategies. This study evaluated the effect of air-abrasion operating parameters on its cutting efficiency/pattern using bio-active glass (BAG) powder and alumina powder as a control in order to develop its use as a minimally invasive operative technique. The cutting efficiency/pattern assessment on an enamel analogue, Macor, was preceded by studying the powder flow rate (PFR) of two different commercial intraoral air-abrasion units with differing powder-air admix systems. The parameters tested included air pressure, powder flow rate, nozzle-substrate distance, nozzle angle, shrouding the air stream with a curtain of water, and the chemistry of abrasive powder. The abraded troughs were scanned and analyzed using confocal white light profilometry and MountainsMap surface analysis software. Data were analyzed statistically using one-way and repeated-measures analysis of variance tests (p=0.05). The air-abrasion unit using a vibration mechanism to admix the abrasive powder with the air stream exhibited a constant PFR regardless of the set air pressure. Significant differences in cutting efficiency were observed according to the tested parameters (p<0.05). Alumina powder removed significantly more material than did BAG powder. Using low air pressure and suitable consideration of the effect of air-abrasion parameters on cutting efficiency/patterns can improve the ultraconservative cutting characteristics of BAG air-abrasion, thereby allowing an introduction of this technology for the controlled cleaning/removal of enamel, where it is indicated clinically.
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Affiliation(s)
- H Milly
- Hussam Milly, BDS, DipOS, MSc, Biomaterials, Biomimetics & Biophotonics Research Group, King's College London Dental Institute at Guy's Hospital, King's Health Partners, London, United Kingdom
| | - RS Austin
- Rupert S Austin, BDS, PhD, Unit of Prosthodontics, King's College London Dental Institute at Guy's Hospital, King's Health Partners, London, United Kingdom
| | - I Thompson
- Ian Thompson, B.Eng, PhD, Biomaterials, Biomimetics & Biophotonics Research Group, King's College London Dental Institute at Guy's Hospital, King's Health Partners, London, United Kingdom
| | - A Banerjee
- Avijit Banerjee, BDS, MSc, PhD, FDS (Rest Dent) FDS RCS (Eng) FHEA, Unit of Conservative Dentistry , Biomaterials, Biomimetics & Biophotonics Research Group, King's College London Dental Institute at Guy's Hospital, King's Health Partners, London, United Kingdom
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12
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Moazzez RV, Austin RS, Rojas-Serrano M, Carpenter G, Cotroneo E, Proctor G, Zaidel L, Bartlett DW. Comparison of the possible protective effect of the salivary pellicle of individuals with and without erosion. Caries Res 2013; 48:57-62. [PMID: 24217151 DOI: 10.1159/000352042] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 05/14/2013] [Indexed: 11/19/2022] Open
Abstract
The acquired pellicle adheres to tooth surfaces and has been suggested to provide differing degrees of protection against acidic erosion. This study investigated whether pellicle formed on enamel blocks in patients suffering dietary dental erosion modified the effect of an in vitro simulated dietary challenge, in comparison with pellicle formed on enamel blocks in healthy subjects and to no-pellicle enamel samples. Sixty subjects recruited from dental erosion clinics were compared to healthy age-matched controls. Subjects wore a custom-made maxillary splint holding human enamel blocks for 1 h during which the acquired enamel pellicle was formed. Enamel blocks were removed from the splints and a simulated dietary erosive challenge of 10 min was performed. In addition the challenge was performed on 30 enamel samples without pellicle. Profilometry showed no statistical difference between samples from the erosion subjects with a mean step height of 1.74 µm (SD 0.88) and median roughness (Sa) of 0.39 µm (interquartile range, IQR 0.3-0.56) and the controls with 1.34 µm (SD 0.66) and 0.33 µm (IQR 0.27-0.38), respectively. The control samples without pellicle had Sa of 0.44 µm (IQR 0.36-0.69) and these differences were statistically significant compared to those from the healthy subjects (p = 0.002). Mean (SD) microhardness reduction with a 100-gram load for the erosion group was 113.5 (10) KHN, for healthy subjects was 93 (15.4) KHN and for the enamel samples without pellicle 139.6 (21.8) KHN and all groups were statistically different. The microhardness and roughness data suggested the pellicle influenced erosion under these study conditions.
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Affiliation(s)
- R V Moazzez
- Salivary Research Unit, King's College London Dental Institute, London, UK
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13
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Wu D, Austin RS, Zhou S, Brown D. The root transcriptome for North American ginseng assembled and profiled across seasonal development. BMC Genomics 2013; 14:564. [PMID: 23957709 PMCID: PMC3751939 DOI: 10.1186/1471-2164-14-564] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 08/06/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ginseng including North American ginseng (Panax quinquefolius L.) is one of the most widely used medicinal plants. Its success is thought to be due to a diverse collection of ginsenosides that serve as its major bioactive compounds. However, few genomic resources exist and the details concerning its various biosynthetic pathways remain poorly understood. As the root is the primary tissue harvested commercially for ginsenosides, next generation sequencing was applied to the characterization and assembly of the root transcriptome throughout seasonal development. Transcripts showing homology to ginsenoside biosynthesis enzymes were profiled in greater detail. RESULTS RNA extracts from root samples from seven development stages of North American ginseng were subjected to 454 sequencing, filtered for quality and used in the de novo assembly of a collective root reference transcriptome consisting of 41,623 transcripts. Annotation efforts using a number of public databases resulted in detailed annotation information for 34,801 (84%) transcripts. In addition, 3,955 genes were assigned to metabolic pathways using the Kyoto Encyclopedia of Genes and Genomes. Among our results, we found all of the known enzymes involved in the ginsenoside backbone biosynthesis and used co-expression analysis to identify a number of candidate sequences involved in the latter stages ginsenoside biosynthesis pathway. Transcript profiles suggest ginsenoside biosynthesis occurs at distinct stages of development. CONCLUSIONS The assembly generated provides a comprehensive annotated reference for future transcriptomic study of North American ginseng. A collection of putative ginsenoside biosynthesis genes were identified and candidate genes predicted from the lesser understood downstream stages of biosynthesis. Transcript expression profiles across seasonal development suggest a primary dammarane-type ginsenoside biosynthesis occurs just prior to plant senescence, with secondary ginsenoside production occurring throughout development. Data from the study provide a valuable resource for conducting future ginsenoside biosynthesis research in this important medicinal plant.
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Affiliation(s)
- Di Wu
- Western University, 1151 Richmond St, London, ON, Canada
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Schreiber KJ, Austin RS, Gong Y, Zhang J, Fung P, Wang PW, Guttman DS, Desveaux D. Forward chemical genetic screens in Arabidopsis identify genes that influence sensitivity to the phytotoxic compound sulfamethoxazole. BMC Plant Biol 2012; 12:226. [PMID: 23176361 PMCID: PMC3541222 DOI: 10.1186/1471-2229-12-226] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [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: 04/23/2012] [Accepted: 11/22/2012] [Indexed: 05/20/2023]
Abstract
BACKGROUND The sulfanilamide family comprises a clinically important group of antimicrobial compounds which also display bioactivity in plants. While there is evidence that sulfanilamides inhibit folate biosynthesis in both bacteria and plants, the complete network of plant responses to these compounds remains to be characterized. As such, we initiated two forward genetic screens in Arabidopsis in order to identify mutants that exhibit altered sensitivity to sulfanilamide compounds. These screens were based on the growth phenotype of seedlings germinated in the presence of the compound sulfamethoxazole (Smex). RESULTS We identified a mutant with reduced sensitivity to Smex, and subsequent mapping indicated that a gene encoding 5-oxoprolinase was responsible for this phenotype. A mutation causing enhanced sensitivity to Smex was mapped to a gene lacking any functional annotation. CONCLUSIONS The genes identified through our forward genetic screens represent novel mediators of Arabidopsis responses to sulfanilamides and suggest that these responses extend beyond the perturbation of folate biosynthesis.
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Affiliation(s)
- Karl J Schreiber
- Current address: Department of Plant & Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA
| | - Ryan S Austin
- Current address: Southern Crop Protection and Food Research Centre, Agriculture & Agri-Food Canada, London, ON, N5V 4T3, Canada
| | - Yunchen Gong
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Jianfeng Zhang
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Pauline Fung
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Pauline W Wang
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - David S Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Darrell Desveaux
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
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15
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Liao D, Pajak A, Karcz SR, Chapman BP, Sharpe AG, Austin RS, Datla R, Dhaubhadel S, Marsolais F. Transcripts of sulphur metabolic genes are co-ordinately regulated in developing seeds of common bean lacking phaseolin and major lectins. J Exp Bot 2012; 63:6283-95. [PMID: 23066144 PMCID: PMC3481216 DOI: 10.1093/jxb/ers280] [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: 05/08/2023]
Abstract
The lack of phaseolin and phytohaemagglutinin in common bean (dry bean, Phaseolus vulgaris) is associated with an increase in total cysteine and methionine concentrations by 70% and 10%, respectively, mainly at the expense of an abundant non-protein amino acid, S-methyl-cysteine. Transcripts were profiled between two genetically related lines differing for this trait at four stages of seed development using a high density microarray designed for common bean. Transcripts of multiple sulphur-rich proteins were elevated, several previously identified by proteomics, including legumin, basic 7S globulin, albumin-2, defensin, albumin-1, the Bowman-Birk type proteinase inhibitor, the double-headed trypsin inhibitor, and the Kunitz trypsin inhibitor. A co-ordinated regulation of transcripts coding for sulphate transporters, sulphate assimilatory enzymes, serine acetyltransferases, cystathionine β-lyase, homocysteine S-methyltransferase and methionine gamma-lyase was associated with changes in cysteine and methionine concentrations. Differential gene expression of sulphur-rich proteins preceded that of sulphur metabolic enzymes, suggesting a regulation by demand from the protein sink. Up-regulation of SERAT1;1 and -1;2 expression revealed an activation of cytosolic O-acetylserine biosynthesis. Down-regulation of SERAT2;1 suggested that cysteine and S-methyl-cysteine biosynthesis may be spatially separated in different subcellular compartments. Analysis of free amino acid profiles indicated that enhanced cysteine biosynthesis was correlated with a depletion of O-acetylserine. These results contribute to our understanding of the regulation of sulphur metabolism in developing seed in response to a change in the composition of endogenous proteins.
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Affiliation(s)
- Dengqun Liao
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
| | - Agnieszka Pajak
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
| | - Steven R. Karcz
- Agriculture and Agri-Food Canada, Bioproducts and Bioprocesses, Saskatoon Research Centre, 107 Science Place, Saskatoon, Saskatchewan S7N 0X2, Canada
| | - B. Patrick Chapman
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
| | - Andrew G. Sharpe
- National Research Council Canada, Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Ryan S. Austin
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
| | - Raju Datla
- National Research Council Canada, Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Sangeeta Dhaubhadel
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Frédéric Marsolais
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, Ontario N6A 5B7, Canada
- * To whom correspondence should be addressed. E-mail:
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Austin RS, Vidaurre D, Stamatiou G, Breit R, Provart NJ, Bonetta D, Zhang J, Fung P, Gong Y, Wang PW, McCourt P, Guttman DS. Next-generation mapping of Arabidopsis genes. Plant J 2011; 67:715-25. [PMID: 21518053 DOI: 10.1111/j.1365-313x.2011.04619.x] [Citation(s) in RCA: 192] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Next-generation genomic sequencing technologies have made it possible to directly map mutations responsible for phenotypes of interest via direct sequencing. However, most mapping strategies proposed to date require some prior genetic analysis, which can be very time-consuming even in genetically tractable organisms. Here we present a de novo method for rapidly and robustly mapping the physical location of EMS mutations by sequencing a small pooled F₂ population. This method, called Next Generation Mapping (NGM), uses a chastity statistic to quantify the relative contribution of the parental mutant and mapping lines to each SNP in the pooled F₂ population. It then uses this information to objectively localize the candidate mutation based on its exclusive segregation with the mutant parental line. A user-friendly, web-based tool for performing NGM analysis is available at http://bar.utoronto.ca/NGM. We used NGM to identify three genes involved in cell-wall biology in Arabidopsis thaliana, and, in a power analysis, demonstrate success in test mappings using as few as ten F₂ lines and a single channel of Illumina Genome Analyzer data. This strategy can easily be applied to other model organisms, and we expect that it will also have utility in crops and any other eukaryote with a completed genome sequence.
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Affiliation(s)
- Ryan S Austin
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, ON, Canada
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Austin RS, Rodriguez JM, Dunne S, Moazzez R, Bartlett DW. The effect of increasing sodium fluoride concentrations on erosion and attrition of enamel and dentine in vitro. J Dent 2010; 38:782-7. [PMID: 20600557 DOI: 10.1016/j.jdent.2010.06.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 06/22/2010] [Accepted: 06/22/2010] [Indexed: 10/19/2022] Open
Abstract
OBJECTIVES To investigate the effect of an aqueous sodium fluoride solution of increasing concentration on erosion and attrition of enamel and dentine in vitro. METHODS Enamel and dentine sections from caries-free human third molars were polished flat and taped (exposing a 3 mm x 3 mm area) before being randomly allocated to 1 of 5 groups per substrate (n=10/gp): G1 (distilled water control); G2 (225 ppm NaF); G3 (1450 ppm NaF); G4 (5000 ppm NaF); G5 (19,000 ppm NaF). All specimens were subjected to 5, 10 and 15 cycles of experimental wear [1 cycle=artificial saliva (2h, pH 7.0)+erosion (0.3% citric acid, pH 3.2, 5 min)+fluoride/control (5 min)+attrition (60 linear strokes in artificial saliva from enamel antagonists loaded to 300 g)]. Following tape removal, step height (SH) in mum was measured using optical profilometry. RESULTS When the number of cycles increased the amount of tooth surface loss increased significantly in enamel and dentine after attrition and erosion and for dentine after attrition. Attrition and erosion resulted in greater surface loss than attrition alone after 15 cycles of experimental wear of enamel. 5000 ppm and 19,000 ppm sodium fluoride solutions had a protective effect on erosive and attritional enamel tooth wear in vitro, however no other groups showed significant differences. CONCLUSIONS The more intensive the fluoride regime the more protection was afforded to enamel from attrition and erosion. However, in this study no such protective effect was demonstrated for dentine.
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Affiliation(s)
- R S Austin
- Department of Primary Dental Care, King's College London Dental Institute, Caldecot Road, Denmark Hill, London SE5 9RW, United Kingdom.
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Abstract
Because intraoperative sonography displays segmental anatomy, allows discovery of more lesions than previously suspected from preoperative imaging, surgical inspection, or palpation, and permits more certain diagnosis of problematic masses, it facilitates surgical decision-making when liver resection or cryoablation is anticipated. Intraoperative sonography provides a guidance modality to accurately place cryosurgery probes in liver masses. More precise treatment of metastatic and primary tumors of the liver is possible with cryoablation because intraoperative sonography provides a means of monitoring the growth of the enlarging freeze zone to insure adequate surgical margins. Postoperative detection of acute complications after cryosurgery is best done with computed tomography. Normally cryosurgery defects shrink with time and lose the peripheral contrast opacification seen after surgery. Gas collections, seen as a result of tissue necrosis, must be discriminated from infection. Tumor recurrence can be detected well with computed tomography or magnetic resonance imaging following hepatic cryosurgery.
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Affiliation(s)
- W H Brewer
- Department of Radiology, Virginia Commonwealth University, Richmond 23298-0615, USA
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