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Stirrup O, Krutikov M, Azmi B, Monakhov I, Hayward A, Copas A, Shallcross L. COVID-19-related mortality and hospital admissions in the VIVALDI study cohort: October 2020 to March 2023. J Hosp Infect 2024; 143:105-112. [PMID: 37949372 PMCID: PMC10927615 DOI: 10.1016/j.jhin.2023.10.021] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND Long-term-care facilities (LTCFs) were heavily affected by COVID-19 early in the pandemic, but the impact of the virus has reduced over time with vaccination campaigns and build-up of immunity from prior infection. OBJECTIVES To evaluate the mortality and hospital admissions associated with SARS-CoV-2 in LTCFs in England over the course of the VIVALDI study, from October 2020 to March 2023. METHODS We included residents aged ≥65 years from participating LTCFs who had available follow-up time within the analysis period. We calculated incidence rates (IRs) of COVID-19-linked mortality and hospital admissions per calendar quarter, along with infection fatality ratios (IFRs, within 28 days) and infection hospitalization ratios (IHRs, within 14 days) following positive SARS-CoV-2 test. RESULTS A total of 26,286 residents were included, with at least one positive test for SARS-CoV-2 in 8513 (32.4%). The IR of COVID-19-related mortality peaked in the first quarter (Q1) of 2021 at 0.47 per 1000 person-days (1 kpd) (around a third of all deaths), in comparison with 0.10 per 1 kpd for Q1 2023 which had a similar IR of SARS-CoV-2 infections. There was a fall in observed IFR for SARS-CoV-2 infections from 24.9% to 6.7% between these periods, with a fall in IHR from 12.1% to 8.8%. The population had high overall IRs for mortality for each quarter evaluated, corresponding to annual mortality probability of 28.8-41.3%. CONCLUSIONS Standardized real-time monitoring of hospitalization and mortality following infection in LTCFs could inform policy on the need for non-pharmaceutical interventions to prevent transmission.
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Affiliation(s)
- O Stirrup
- Institute for Global Health, University College London, London, UK.
| | - M Krutikov
- UCL Institute of Health Informatics, London, UK
| | - B Azmi
- UCL Institute of Health Informatics, London, UK
| | | | - A Hayward
- UCL Institute of Epidemiology & Healthcare, London, UK; Health Data Research UK, London, UK
| | - A Copas
- Institute for Global Health, University College London, London, UK
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Evans MJ, Corripio-Miyar Y, Hayward A, Kenyon F, McNeilly TN, Nussey DH. Antagonism between co-infecting gastrointestinal nematodes: A meta-analysis of experimental infections in Sheep. Vet Parasitol 2023; 323:110053. [PMID: 37879240 DOI: 10.1016/j.vetpar.2023.110053] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/08/2023] [Accepted: 10/11/2023] [Indexed: 10/27/2023]
Abstract
Gastrointestinal nematodes (GIN) have enormous global impacts in humans, wildlife and grazing livestock. Within grazing livestock, sheep are of particular global importance and the economics and sustainability of sheep production are greatly constrained by GIN infections. Natural infections are composed of co-infections with multiple species, and while some past work suggests species can interact negatively with one another within the same host, there is wide variation in reported patterns. Here, we undertook a systematic literature search and meta-analysis of experimental GIN co-infections of sheep to determine whether these experimental studies support the hypothesis of antagonistic interactions between different co-infecting GIN, and test whether aspects of parasite biology or experimental design influence the observed effects. A systematic search of the literature yielded 4848 studies, within which, we identified 19 experimental sheep studies comparing post-mortem worm counts across two co-infecting GIN species. Meta-analysis of 67 effects obtained from these studies provides strong evidence for interactions between GIN species. There was wide variation in the strength and direction of these interactions, but the global effect was significantly antagonistic. On average, there was a decrease in the number of worms of one species when a co-infecting species was also present, relative to a mono-infection with that species alone. This effect was dependent on the infectious dose and was rapidly lost after anthelmintic treatment, suggesting that live worms are required for the effect to occur. Individual parasite species varied in the extent to which they both exerted, and were subject to, these interspecies interactions, and these differences are more complex than simply co-localisation within the gastrointestinal tract. Antagonistic interactions between co-infecting GIN may feedback into their epidemiology as well as potentially affecting the clinical impacts of infection. Furthermore, the consequences of these interactions may be heightened when clinical interventions affect only one species within the co-infecting network. Whilst it was not possible to identify the causes of variation between GIN species in the impact of co-infection, these findings point to new avenues for epidemiological, clinical and mechanistic research on GIN co-infections.
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Affiliation(s)
- M J Evans
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, UK; Department for Disease Control, Moredun Research Institute, Penicuik, UK; Institute for Ecology and Evolution, University of Edinburgh, Edinburgh, UK.
| | - Y Corripio-Miyar
- Department for Disease Control, Moredun Research Institute, Penicuik, UK
| | - A Hayward
- Department for Disease Control, Moredun Research Institute, Penicuik, UK
| | - F Kenyon
- Department for Disease Control, Moredun Research Institute, Penicuik, UK
| | - T N McNeilly
- Department for Disease Control, Moredun Research Institute, Penicuik, UK
| | - D H Nussey
- Institute for Ecology and Evolution, University of Edinburgh, Edinburgh, UK
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Inda-Webb ME, Jimenez M, Liu Q, Phan NV, Ahn J, Steiger C, Wentworth A, Riaz A, Zirtiloglu T, Wong K, Ishida K, Fabian N, Jenkins J, Kuosmanen J, Madani W, McNally R, Lai Y, Hayward A, Mimee M, Nadeau P, Chandrakasan AP, Traverso G, Yazicigil RT, Lu TK. Sub-1.4 cm 3 capsule for detecting labile inflammatory biomarkers in situ. Nature 2023; 620:386-392. [PMID: 37495692 DOI: 10.1038/s41586-023-06369-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/26/2023] [Indexed: 07/28/2023]
Abstract
Transient molecules in the gastrointestinal tract such as nitric oxide and hydrogen sulfide are key signals and mediators of inflammation. Owing to their highly reactive nature and extremely short lifetime in the body, these molecules are difficult to detect. Here we develop a miniaturized device that integrates genetically engineered probiotic biosensors with a custom-designed photodetector and readout chip to track these molecules in the gastrointestinal tract. Leveraging the molecular specificity of living sensors1, we genetically encoded bacteria to respond to inflammation-associated molecules by producing luminescence. Low-power electronic readout circuits2 integrated into the device convert the light emitted by the encapsulated bacteria to a wireless signal. We demonstrate in vivo biosensor monitoring in the gastrointestinal tract of small and large animal models and the integration of all components into a sub-1.4 cm3 form factor that is compatible with ingestion and capable of supporting wireless communication. With this device, diseases such as inflammatory bowel disease could be diagnosed earlier than is currently possible, and disease progression could be more accurately tracked. The wireless detection of short-lived, disease-associated molecules with our device could also support timely communication between patients and caregivers, as well as remote personalized care.
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Affiliation(s)
- M E Inda-Webb
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Research Laboratory of Electronics, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - M Jimenez
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Gastroenterology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Q Liu
- Electrical and Computer Engineering Department, Boston University, Boston, MA, USA
| | - N V Phan
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - J Ahn
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - C Steiger
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Gastroenterology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - A Wentworth
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Gastroenterology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - A Riaz
- Electrical and Computer Engineering Department, Boston University, Boston, MA, USA
| | - T Zirtiloglu
- Electrical and Computer Engineering Department, Boston University, Boston, MA, USA
| | - K Wong
- Division of Gastroenterology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - K Ishida
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Gastroenterology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - N Fabian
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Comparative Medicine, MIT, Cambridge, MA, USA
| | - J Jenkins
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - J Kuosmanen
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - W Madani
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Gastroenterology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - R McNally
- Division of Gastroenterology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Y Lai
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Research Laboratory of Electronics, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - A Hayward
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Division of Gastroenterology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Comparative Medicine, MIT, Cambridge, MA, USA
| | - M Mimee
- Department of Microbiology, Biological Sciences Division and Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL, USA
| | | | - A P Chandrakasan
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA
| | - G Traverso
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Division of Gastroenterology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - R T Yazicigil
- Electrical and Computer Engineering Department, Boston University, Boston, MA, USA.
| | - T K Lu
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Research Laboratory of Electronics, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Senti Biosciences, South San Francisco, CA, USA.
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Wang H, Liu J, Huang J, Xiao Q, Hayward A, Li F, Gong Y, Liu Q, Ma M, Fu D, Xiao M. Mapping and Identifying Candidate Genes Enabling Cadmium Accumulation in Brassica napus Revealed by Combined BSA-Seq and RNA-Seq Analysis. Int J Mol Sci 2023; 24:10163. [PMID: 37373312 DOI: 10.3390/ijms241210163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/09/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
Rapeseed has the ability to absorb cadmium in the roots and transfer it to aboveground organs, making it a potential species for remediating soil cadmium (Cd) pollution. However, the genetic and molecular mechanisms underlying this phenomenon in rapeseed are still unclear. In this study, a 'cadmium-enriched' parent, 'P1', with high cadmium transport and accumulation in the shoot (cadmium root: shoot transfer ratio of 153.75%), and a low-cadmium-accumulation parent, 'P2', (with a cadmium transfer ratio of 48.72%) were assessed for Cd concentration using inductively coupled plasma mass spectrometry (ICP-MS). An F2 genetic population was constructed by crossing 'P1' with 'P2' to map QTL intervals and underlying genes associated with cadmium enrichment. Fifty extremely cadmium-enriched F2 individuals and fifty extremely low-accumulation F2 individuals were selected based on cadmium content and cadmium transfer ratio and used for bulk segregant analysis (BSA) in combination with whole genome resequencing. This generated a total of 3,660,999 SNPs and 787,034 InDels between these two segregated phenotypic groups. Based on the delta SNP index (the difference in SNP frequency between the two bulked pools), nine candidate Quantitative trait loci (QTLs) from five chromosomes were identified, and four intervals were validated. RNA sequencing of 'P1' and 'P2' in response to cadmium was also performed and identified 3502 differentially expressed genes (DEGs) between 'P1' and 'P2' under Cd treatment. Finally, 32 candidate DEGs were identified within 9 significant mapping intervals, including genes encoding a glutathione S-transferase (GST), a molecular chaperone (DnaJ), and a phosphoglycerate kinase (PGK), among others. These genes are strong candidates for playing an active role in helping rapeseed cope with cadmium stress. Therefore, this study not only sheds new light on the molecular mechanisms of Cd accumulation in rapeseed but could also be useful for rapeseed breeding programs targeting this trait.
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Affiliation(s)
- Huadong Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jiajia Liu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Juan Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qing Xiao
- Graduate School of Jiangxi Normal University, Jiangxi Normal University, Nanchang 330045, China
| | - Alice Hayward
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane 4072, Australia
| | - Fuyan Li
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yingying Gong
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qian Liu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Miao Ma
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Meili Xiao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China
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5
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Ahsan MU, Barbier F, Hayward A, Powell R, Hofman H, Parfitt SC, Wilkie J, Beveridge CA, Mitter N. Molecular Cues for Phenological Events in the Flowering Cycle in Avocado. Plants (Basel) 2023; 12:2304. [PMID: 37375929 DOI: 10.3390/plants12122304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/09/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023]
Abstract
Reproductively mature horticultural trees undergo an annual flowering cycle that repeats each year of their reproductive life. This annual flowering cycle is critical for horticultural tree productivity. However, the molecular events underlying the regulation of flowering in tropical tree crops such as avocado are not fully understood or documented. In this study, we investigated the potential molecular cues regulating the yearly flowering cycle in avocado for two consecutive crop cycles. Homologues of flowering-related genes were identified and assessed for their expression profiles in various tissues throughout the year. Avocado homologues of known floral genes FT, AP1, LFY, FUL, SPL9, CO and SEP2/AGL4 were upregulated at the typical time of floral induction for avocado trees growing in Queensland, Australia. We suggest these are potential candidate markers for floral initiation in these crops. In addition, DAM and DRM1, which are associated with endodormancy, were downregulated at the time of floral bud break. In this study, a positive correlation between CO activation and FT in avocado leaves to regulate flowering was not seen. Furthermore, the SOC1-SPL4 model described in annual plants appears to be conserved in avocado. Lastly, no correlation of juvenility-related miRNAs miR156, miR172 with any phenological event was observed.
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Affiliation(s)
- Muhammad Umair Ahsan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Francois Barbier
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alice Hayward
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Rosanna Powell
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Helen Hofman
- Department of Agriculture and Fisheries, Queensland Government, Bundaberg, QLD 4670, Australia
| | - Siegrid Carola Parfitt
- Department of Agriculture and Fisheries, Queensland Government, Bundaberg, QLD 4670, Australia
| | - John Wilkie
- Department of Agriculture and Fisheries, Queensland Government, Bundaberg, QLD 4670, Australia
| | | | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
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Hayward A, Robertson A, Thiruchelvam T, Broadhead M, Tsang VT, Sebire NJ, Issitt RW. Oxygen delivery in pediatric cardiac surgery and its association with acute kidney injury using machine learning. J Thorac Cardiovasc Surg 2023; 165:1505-1516. [PMID: 35840430 DOI: 10.1016/j.jtcvs.2022.05.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 05/05/2022] [Accepted: 05/30/2022] [Indexed: 10/18/2022]
Abstract
OBJECTIVE Acute kidney injury (AKI) after pediatric cardiac surgery with cardiopulmonary bypass (CPB) is a frequently reported complication. In this study we aimed to determine the oxygen delivery indexed to body surface area (Do2i) threshold associated with postoperative AKI in pediatric patients during CPB, and whether it remains clinically important in the context of other known independent risk factors. METHODS A single-institution, retrospective study, encompassing 396 pediatric patients, who underwent heart surgery between April 2019 and April 2021 was undertaken. Time spent below Do2i thresholds were compared to determine the critical value for all stages of AKI occurring within 48 hours of surgery. Do2i threshold was then included in a classification analysis with known risk factors including nephrotoxic drug usage, surgical complexity, intraoperative data, comorbidities and ventricular function data, and vasoactive inotrope requirement to determine Do2i predictive importance. RESULTS Logistic regression models showed cumulative time spent below a Do2i value of 350 mL/min/m2 was associated with AKI. Random forest models, incorporating established risk factors, showed Do2i threshold still maintained predictive importance. Patients who developed post-CPB AKI were younger, had longer CPB and ischemic times, and required higher inotrope support postsurgery. CONCLUSIONS The present data support previous findings that Do2i during CPB is an independent risk factor for AKI development in pediatric patients. Furthermore, the data support previous suggestions of a higher threshold value in children compared with that in adults and indicate that adjustments in Do2i management might reduce incidence of postoperative AKI in the pediatric cardiac surgery population.
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Affiliation(s)
- Alice Hayward
- Department of Perfusion, Great Ormond Street Hospital, London, United Kingdom
| | - Alex Robertson
- Department of Perfusion, Great Ormond Street Hospital, London, United Kingdom
| | - Timothy Thiruchelvam
- Department of Intensive Care, Great Ormond Street Hospital, London, United Kingdom; Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Michael Broadhead
- Department of Anesthetics, Great Ormond Street Hospital, London, United Kingdom
| | - Victor T Tsang
- Institute of Cardiovascular Science, University College London, London, United Kingdom; Department of Cardiothoracic Surgery, Great Ormond Street Hospital, London, United Kingdom
| | - Neil J Sebire
- Digital Research, Informatics and Virtual Environment, NIHR Great Ormond Street Hospital BRC, London, United Kingdom
| | - Richard W Issitt
- Department of Perfusion, Great Ormond Street Hospital, London, United Kingdom; Institute of Cardiovascular Science, University College London, London, United Kingdom; Digital Research, Informatics and Virtual Environment, NIHR Great Ormond Street Hospital BRC, London, United Kingdom.
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Li X, O’brien C, Sommerville K, Mitter N, Hayward A. Innovative cryopreservation technology for Australian macadamia. Cryobiology 2022. [DOI: 10.1016/j.cryobiol.2022.11.198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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O'Donohue B, Hiti-Bandaralage J, Gleeson M, O'Brien C, Harvey MA, van der Ent A, Pinto Irish K, Mitter N, Hayward A. Tissue culture tools for selenium hyperaccumulator Neptunia amplexicaulis for development in phytoextraction. Nat Prod Bioprospect 2022; 12:28. [PMID: 35927534 PMCID: PMC9352830 DOI: 10.1007/s13659-022-00351-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Neptunia amplexicaulis is an herbaceous legume endemic to the Richmond area in central Queensland, Australia and is one of the strongest known Selenium hyperaccumulators on earth, showing significant potential to be utilised in Se phytoextraction applications. Here a protocol was established for in vitro micropropagation of Se hyperaccumulator N. amplexicaulis using nodal segments from in vitro-germinated seedlings. Shoot multiplication was achieved on Murashige and Skoog (MS) basal media supplemented with various concentrations of 6-Benzylaminopurine (BA) (1.0, 2.0, 3.0 mg L-1) alone or in combination with low levels of Naphthaleneacetic acid (NAA) (0.1, 0.2, 0.3 mg L-1), with 2.0 mg L-1 BA + 0.2 mg L-1 NAA found to be most effective. Elongated shoots were rooted in vitro using NAA, with highest root induction rate of 30% observed at 0.2 mg L-1 NAA. About 95% of the in vitro rooted shoots survived acclimatization. Clonally propagated plantlets were dosed with selenate/selenite solution and assessed for Se tissue concentrations using Inductively Coupled Plasma Atomic Emission Spectroscopy (ICP-AES) and found to retain their ability to hyperaccumulate. The protocol developed for this study has potential to be optimised for generating clonal plants of N. amplexicaulis for use in research and phytoextraction industry applications.
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Affiliation(s)
- Billy O'Donohue
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia.
| | - Jayeni Hiti-Bandaralage
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Madeleine Gleeson
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Chris O'Brien
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Maggie-Anne Harvey
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Antony van der Ent
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Katherine Pinto Irish
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Neena Mitter
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Alice Hayward
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
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9
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Crosby L, Lewer D, Appleby Y, Anderson C, Hayward A, Story A. Outcomes of a residential respite service for homeless people with tuberculosis in London, UK: a cross-sectional study. Perspect Public Health 2022; 143:89-96. [PMID: 35506684 PMCID: PMC10068400 DOI: 10.1177/17579139221093544] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND Many countries are seeking to eliminate tuberculosis (TB), but incidence remains high in socially excluded groups such as people experiencing homelessness. There is limited research into the effectiveness of residential respite services (RRS), which provide accomodation and social and clinical support for homeless people with active TB. METHODS We used a register of all cases of TB diagnosed in London between 1 January 2010 and 3 October 2019 to compare characteristics and outcomes of patients treated in an RRS with patients receiving standard care. The primary outcome was successful treatment completion. We used logistic regression to compare likelihood of completing treatment, and simulation to estimate the absolute change in treatment completion resulting from this service. RESULTS A total of 78 homeless patients finished an episode of TB treatment at the RRS. Patients treated in the RRS were more likely than patients treated in standard care to have clinical and social risk factors including drug resistance, history of homelessness, drug or alcohol use, and need for directly observed therapy. After adjusting for these factors, patients treated in the RRS had 2.97 times the odds of completing treatment (95% CI = 1.44-6.96). Treatment ended in failure for 8/78 patients treated in the RRS (10%, 95% CI = 5%-20%). We estimated that in the absence of the RRS, treatment would have ended in failure for 17/78 patients (95% CI = 11-25). CONCLUSION The residential respite service for homeless TB patients with complex social needs was associated with better treatment outcomes.
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Affiliation(s)
- L Crosby
- Collaborative Centre for Inclusion Health, UCL, London, UK.,Research Department of Primary Care and Population Health, UCL, London, UK
| | - D Lewer
- Collaborative Centre for Inclusion Health, University College London, London, UK.,National Infections Service, Public Health England, London, UK
| | - Y Appleby
- Find & Treat, University College London Hospitals, London, UK
| | - C Anderson
- National Infections Service, Public Health England, London, UK
| | - A Hayward
- Collaborative Centre for Inclusion Health, UCL, London, UK
| | - A Story
- Collaborative Centre for Inclusion Health, UCL, London, UK.,Find & Treat, University College London Hospitals, London, UK
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Nath O, Fletcher SJ, Hayward A, Shaw LM, Masouleh AK, Furtado A, Henry RJ, Mitter N. A haplotype resolved chromosomal level avocado genome allows analysis of novel avocado genes. Hortic Res 2022; 9:uhac157. [PMID: 36204209 PMCID: PMC9531333 DOI: 10.1093/hr/uhac157] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 08/01/2022] [Accepted: 07/04/2022] [Indexed: 06/16/2023]
Abstract
Avocado (Persea americana) is a member of the magnoliids, an early branching lineage of angiosperms that has high value globally with the fruit being highly nutritious. Here, we report a chromosome-level genome assembly for the commercial avocado cultivar Hass, which represents 80% of the world's avocado consumption. The DNA contigs produced from Pacific Biosciences HiFi reads were further assembled using a previously published version of the genome supported by a genetic map. The total assembly was 913 Mb with a contig N50 of 84 Mb. Contigs assigned to the 12 chromosomes represented 874 Mb and covered 98.8% of benchmarked single-copy genes from embryophytes. Annotation of protein coding sequences identified 48 915 avocado genes of which 39 207 could be ascribed functions. The genome contained 62.6% repeat elements. Specific biosynthetic pathways of interest in the genome were investigated. The analysis suggested that the predominant pathway of heptose biosynthesis in avocado may be through sedoheptulose 1,7 bisphosphate rather than via alternative routes. Endoglucanase genes were high in number, consistent with avocado using cellulase for fruit ripening. The avocado genome appeared to have a limited number of translocations between homeologous chromosomes, despite having undergone multiple genome duplication events. Proteome clustering with related species permitted identification of genes unique to avocado and other members of the Lauraceae family, as well as genes unique to species diverged near or prior to the divergence of monocots and eudicots. This genome provides a tool to support future advances in the development of elite avocado varieties with higher yields and fruit quality.
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Affiliation(s)
- Onkar Nath
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane 4072 Australia
| | - Stephen J Fletcher
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane 4072 Australia
| | - Alice Hayward
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane 4072 Australia
| | - Lindsay M Shaw
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane 4072 Australia
| | - Ardashir Kharabian Masouleh
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane 4072 Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane 4072 Australia
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11
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Jonsson N, MacLeod M, Hayward A, McNeilly T, Ferguson K, Skuce P. Liver fluke in beef cattle – Impact on production efficiency and associated greenhouse gas emissions estimated using causal inference methods. Prev Vet Med 2022; 200:105579. [DOI: 10.1016/j.prevetmed.2022.105579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 12/07/2021] [Accepted: 01/05/2022] [Indexed: 11/29/2022]
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12
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Chen S, Hayward A, Dey SS, Choudhary M, Witt Hmon KP, Inturrisi FC, Dolatabadian A, Neik TX, Yang H, Siddique KHM, Batley J, Cowling WA. Quantitative Trait Loci for Heat Stress Tolerance in Brassica rapa L. Are Distributed across the Genome and Occur in Diverse Genetic Groups, Flowering Phenologies and Morphotypes. Genes (Basel) 2022; 13:genes13020296. [PMID: 35205341 PMCID: PMC8871826 DOI: 10.3390/genes13020296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/08/2022] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 12/02/2022] Open
Abstract
Heat stress events during flowering in Brassica crops reduce grain yield and are expected to increase in frequency due to global climate change. We evaluated heat stress tolerance and molecular genetic diversity in a global collection of Brassica rapa accessions, including leafy, rooty and oilseed morphotypes with spring, winter and semi-winter flowering phenology. Tolerance to transient daily heat stress during the early reproductive stage was assessed on 142 lines in a controlled environment. Well-watered plants of each genotype were exposed to the control (25/15 °C day/night temperatures) or heat stress (35/25 °C) treatments for 7 d from the first open flower on the main stem. Bud and leaf temperature depression, leaf conductance and chlorophyll content index were recorded during the temperature treatments. A large genetic variation for heat tolerance and sensitivity was found for above-ground biomass, whole plant seed yield and harvest index and seed yield of five pods on the main stem at maturity. Genetic diversity was assessed on 212 lines with 1602 polymorphic SNP markers with a known location in the B. rapa physical map. Phylogenetic analyses confirmed two major genetic populations: one from East and South Asia and one from Europe. Heat stress-tolerant lines were distributed across diverse geographic origins, morphotypes (leafy, rooty and oilseed) and flowering phenologies (spring, winter and semi-winter types). A genome-wide association analysis of heat stress-related yield traits revealed 57 SNPs distributed across all 10 B. rapa chromosomes, some of which were associated with potential candidate genes for heat stress tolerance.
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Affiliation(s)
- Sheng Chen
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia; (S.S.D.); (M.C.); (K.P.W.H.); (K.H.M.S.); (J.B.); (W.A.C.)
- School of Agriculture and Environment, The University of Western Australia, Perth, WA 6001, Australia
- Correspondence:
| | - Alice Hayward
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia;
| | - Shyam S. Dey
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia; (S.S.D.); (M.C.); (K.P.W.H.); (K.H.M.S.); (J.B.); (W.A.C.)
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Mukesh Choudhary
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia; (S.S.D.); (M.C.); (K.P.W.H.); (K.H.M.S.); (J.B.); (W.A.C.)
- School of Agriculture and Environment, The University of Western Australia, Perth, WA 6001, Australia
| | - Khaing P. Witt Hmon
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia; (S.S.D.); (M.C.); (K.P.W.H.); (K.H.M.S.); (J.B.); (W.A.C.)
| | - Fabian C. Inturrisi
- School of Biological Sciences, The University of Western Australia, Perth, WA 6001, Australia; (F.C.I.); (A.D.); (T.X.N.); (H.Y.)
| | - Aria Dolatabadian
- School of Biological Sciences, The University of Western Australia, Perth, WA 6001, Australia; (F.C.I.); (A.D.); (T.X.N.); (H.Y.)
| | - Ting Xiang Neik
- School of Biological Sciences, The University of Western Australia, Perth, WA 6001, Australia; (F.C.I.); (A.D.); (T.X.N.); (H.Y.)
| | - Hua Yang
- School of Biological Sciences, The University of Western Australia, Perth, WA 6001, Australia; (F.C.I.); (A.D.); (T.X.N.); (H.Y.)
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia; (S.S.D.); (M.C.); (K.P.W.H.); (K.H.M.S.); (J.B.); (W.A.C.)
- School of Agriculture and Environment, The University of Western Australia, Perth, WA 6001, Australia
| | - Jacqueline Batley
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia; (S.S.D.); (M.C.); (K.P.W.H.); (K.H.M.S.); (J.B.); (W.A.C.)
- School of Biological Sciences, The University of Western Australia, Perth, WA 6001, Australia; (F.C.I.); (A.D.); (T.X.N.); (H.Y.)
| | - Wallace A. Cowling
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia; (S.S.D.); (M.C.); (K.P.W.H.); (K.H.M.S.); (J.B.); (W.A.C.)
- School of Agriculture and Environment, The University of Western Australia, Perth, WA 6001, Australia
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13
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Nath O, Fletcher SJ, Hayward A, Shaw LM, Agarwal R, Furtado A, Henry RJ, Mitter N. A Comprehensive High-Quality DNA and RNA Extraction Protocol for a Range of Cultivars and Tissue Types of the Woody Crop Avocado. Plants 2022; 11:plants11030242. [PMID: 35161230 PMCID: PMC8838124 DOI: 10.3390/plants11030242] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 01/11/2023]
Abstract
High-quality DNA and RNA forms the basis of genomic and genetic investigations. The extraction of DNA and RNA from woody trees, like avocado (Persea americana Mill.), is challenging due to compounds which interact with nucleic acids and influence separation. Previously reported methods of DNA and RNA extraction from avocado have issues of low yield, quality and applicability across different cultivars and tissue types. In the current study, methods have been optimised for high-quality DNA extraction from 40 avocado cultivars and RNA extraction from multiple tissue types, including roots, stem, leaves, flowers and fruits. The method is based on the modification of the cetyltrimethylammonium bromide buffer, centred around the specific optimisation of chemicals, such as sodium dodecyl sulphate, polyvinylpyrrolidone, sodium sulphite, polyethylene glycol and β-mercaptoethanol. The DNA extraction method yielded high-molecular weight DNA from the leaf tissue of 40 avocado cultivars belonging to Mexican, Guatemalan and West Indian avocado horticultural groups. The method was further optimised for RNA extraction from different avocado plant parts, enabling extraction using amounts as low as ~10 mg of starting material. The DNA and RNA extracted was successfully used for long- and short-read sequencing and gene expression analysis. The methods developed may also be applicable to other recalcitrant plant species.
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O’Brien C, Hiti-Bandaralage J, Folgado R, Hayward A, Lahmeyer S, Folsom J, Mitter N. Cryopreservation of Woody Crops: The Avocado Case. Plants (Basel) 2021; 10:934. [PMID: 34067138 PMCID: PMC8151510 DOI: 10.3390/plants10050934] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 04/29/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
Recent development and implementation of crop cryopreservation protocols has increased the capacity to maintain recalcitrant seeded germplasm collections via cryopreserved in vitro material. To preserve the greatest possible plant genetic resources globally for future food security and breeding programs, it is essential to integrate in situ and ex situ conservation methods into a cohesive conservation plan. In vitro storage using tissue culture and cryopreservation techniques offers promising complementary tools that can be used to promote this approach. These techniques can be employed for crops difficult or impossible to maintain in seed banks for long-term conservation. This includes woody perennial plants, recalcitrant seed crops or crops with no seeds at all and vegetatively or clonally propagated crops where seeds are not true-to-type. Many of the world's most important crops for food, nutrition and livelihoods, are vegetatively propagated or have recalcitrant seeds. This review will look at ex situ conservation, namely field repositories and in vitro storage for some of these economically important crops, focusing on conservation strategies for avocado. To date, cultivar-specific multiplication protocols have been established for maintaining multiple avocado cultivars in tissue culture. Cryopreservation of avocado somatic embryos and somatic embryogenesis have been successful. In addition, a shoot-tip cryopreservation protocol has been developed for cryo-storage and regeneration of true-to-type clonal avocado plants.
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Affiliation(s)
- Chris O’Brien
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia; (J.H.-B.); (A.H.); (N.M.)
| | - Jayeni Hiti-Bandaralage
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia; (J.H.-B.); (A.H.); (N.M.)
| | - Raquel Folgado
- The Huntington Library, Art Museum, and Botanical Gardens, 1151 Oxford Road, San Marino, CA 91108, USA; (R.F.); (S.L.); (J.F.)
| | - Alice Hayward
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia; (J.H.-B.); (A.H.); (N.M.)
| | - Sean Lahmeyer
- The Huntington Library, Art Museum, and Botanical Gardens, 1151 Oxford Road, San Marino, CA 91108, USA; (R.F.); (S.L.); (J.F.)
| | - Jim Folsom
- The Huntington Library, Art Museum, and Botanical Gardens, 1151 Oxford Road, San Marino, CA 91108, USA; (R.F.); (S.L.); (J.F.)
| | - Neena Mitter
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia; (J.H.-B.); (A.H.); (N.M.)
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15
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Dutey-Magni PF, Gill MJ, McNulty D, Sohal G, Hayward A, Shallcross L, Anderson N, Crayton E, Forbes G, Jhass A, Richardson E, Richardson M, Rockenschaub P, Smith C, Sutton E, Traina R, Atkins L, Conolly A, Denaxas S, Fragaszy E, Horne R, Kostkova P, Lorencatto F, Michie S, Mindell J, Robson J, Royston C, Tarrant C, Thomas J, West J, Williams H, Elsay N, Fuller C. Feasibility study of hospital antimicrobial stewardship analytics using electronic health records. JAC Antimicrob Resist 2021; 3:dlab018. [PMID: 34223095 PMCID: PMC8210026 DOI: 10.1093/jacamr/dlab018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 10/06/2020] [Accepted: 01/27/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Hospital antimicrobial stewardship (AMS) programmes are multidisciplinary initiatives to optimize antimicrobial use. Most hospitals depend on time-consuming manual audits to monitor clinicians' prescribing. But much of the information needed could be sourced from electronic health records (EHRs). OBJECTIVES To develop an informatics methodology to analyse characteristics of hospital AMS practice using routine electronic prescribing and laboratory records. METHODS Feasibility study using electronic prescribing, laboratory and clinical coding records from adult patients admitted to six specialities at Queen Elizabeth Hospital, Birmingham, UK (September 2017-August 2018). The study involved: (i) a review of AMS standards of care; (ii) their translation into concepts measurable from commonly available EHRs; and (iii) a pilot application in an EHR cohort study (n = 61679 admissions). RESULTS We developed data modelling methods to characterize antimicrobial use (antimicrobial therapy episode linkage methods, therapy table, therapy changes). Prescriptions were linked into antimicrobial therapy episodes (mean 2.4 prescriptions/episode; mean length of therapy 5.8 days), enabling several actionable findings. For example, 22% of therapy episodes for low-severity community-acquired pneumonia were congruent with prescribing guidelines, with a tendency to use broader-spectrum antibiotics. Analysis of therapy changes revealed IV to oral therapy switching was delayed by an average 3.6 days (95% CI: 3.4-3.7). Microbial cultures were performed prior to treatment initiation in just 22% of antibacterial prescriptions. The proposed methods enabled fine-grained monitoring of AMS practice down to specialities, wards and individual clinical teams by case mix, enabling more meaningful peer comparison. CONCLUSIONS It is feasible to use hospital EHRs to construct rapid, meaningful measures of prescribing quality with potential to support quality improvement interventions (audit/feedback to prescribers), engagement with front-line clinicians on optimizing prescribing, and AMS impact evaluation studies.
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Affiliation(s)
- P F Dutey-Magni
- Institute of Health Informatics, University College London, London, UK
| | - M J Gill
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - D McNulty
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - G Sohal
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - A Hayward
- Institute of Epidemiology & Health Care, University College London, London, UK
| | - L Shallcross
- Institute of Health Informatics, University College London, London, UK
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16
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Melville LA, Hayward A, Morgan ER, Shaw DJ, McBean D, Andrews L, Morrison A, Kenyon F. Precision worm control in grazing lambs by targeting group treatment based on performance of sentinels. Animal 2021; 15:100176. [PMID: 33637437 DOI: 10.1016/j.animal.2021.100176] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 12/21/2020] [Accepted: 01/04/2021] [Indexed: 10/22/2022] Open
Abstract
Given the economic impact of gastrointestinal nematode infection on livestock farming worldwide, and increasing anthelmintic resistance, it is imperative to develop practical, efficient and sustainable control strategies. Targeted selective treatment (TST), whereby anthelmintic treatments are administered to animals individually, based on selection criteria such as weight gain, has been shown to successfully maintain animal productivity whilst reducing the selection pressure for anthelmintic resistance and the economic cost of treatment in experimental and commercial settings. Despite the benefits of the TST approach, the equipment and time required to monitor animals individually make this strategy unsuitable for some farming enterprises. The sentinel group approach aims to maintain the benefits observed using TST whilst reducing these requirements. The study involved two experiments, each following a group of 80 lambs through their first grazing season. Anthelmintic treatment of the whole group was determined by monitoring the weight gain of identified sentinel lambs within it every 2 weeks: when 40% of the sentinel lambs failed to reach their weight gain targets, the whole group was treated. The sentinel lambs consisted of 45% of the group (n = 36) in experiment one and 20% (n = 16) in experiment two. A control group of 20 lambs was co-grazed with the main group during both experiments; in experiment one, the sentinel approach was compared with a TST approach, in which control lambs were treated on an individual basis in response to weight gain. In experiment two, the sentinel approach was compared with conventional prophylaxis, where all lambs in the control group were treated at strategic time points throughout the season (= strategic prophylactic treatment). The sentinel lambs were found to be representative of overall group performance regardless of the proportion of sentinels within the group: they recorded similar growth rates and reached weight gain targets simultaneously at each time point and overall. Live-weight gain was also similar between sentinel and control animals in both experiments. The findings of the current study suggest that monitoring sentinel lambs comprising 20% of a group of grazing lambs is sufficient to determine the need for anthelmintic treatment within the whole group, and that this approach maintains production in line with conventional or TST treatment regimes.
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Affiliation(s)
- L A Melville
- Department of disease control, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Scotland EH26 0PZ, UK.
| | - A Hayward
- Department of disease control, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Scotland EH26 0PZ, UK
| | - E R Morgan
- Queens University Belfast, School of Biological Sciences, 19, Chlorine Gardens, Belfast BT9 5DL, UK
| | - D J Shaw
- Royal (Dick) School of Veterinary Studies & Roslin Institute, The University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
| | - D McBean
- Department of disease control, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Scotland EH26 0PZ, UK
| | - L Andrews
- Department of disease control, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Scotland EH26 0PZ, UK
| | - A Morrison
- Department of disease control, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Scotland EH26 0PZ, UK
| | - F Kenyon
- Department of disease control, Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Scotland EH26 0PZ, UK
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Aisyah D, Shallcross L, Kozlakidis Z, Vlachou M, Hayward A. Assessing HCV distribution among ‘Hard to Reach’ populations in London using whole genome sequencing: Report from the TB reach study. Int J Infect Dis 2020. [DOI: 10.1016/j.ijid.2020.09.1309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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18
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Nguyen V, Aldridge R, Blackburn R, Hayward A, Greaves F, Flowers J. Does the NHS Diabetes Prevention Programme prevent diabetes? A population-based matched cohort study. Eur J Public Health 2020. [DOI: 10.1093/eurpub/ckaa165.1184] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
To reduce the incidence of type 2 diabetes (T2DM) in England, the National Health Service piloted the Diabetes Prevention Programme (DPP). The DPP aims to prevent T2DM by providing high-risk adults with access to 13 face-to-face sessions over nine months that focus on diet and weight management. The DPP has been shown to improve intermediate outcomes for T2DM prevention (weight loss and glycated haemoglobin (HbA1c) reduction). However, there is a lack of evidence examining incident T2DM as the outcome.
Methods
We conducted a retrospective observational cohort study using linked electronic health records from primary (Clinical Practice Research Datalink) and secondary (Hospital Episode Statistics) care for June 2016 to January 2019. We compared rates of new T2DM diagnoses among eligible adults who were referred to the DPP with rates for propensity score-matched (ratio of 1:4) controls who were eligible for the DPP but were not invited. DPP eligibility was defined as having HbA1c levels of 42-47 mmol/mol or fasting plasma glucose (FPG) levels of 5.5-6.9 mmol/L. Adults with pre-existing T2DM were excluded. Time to the first record of T2DM was modelled using Cox regression with age, alcohol intake, body mass index, ethnicity, sex, HbA1c, index of multiple deprivation and smoking status included as covariates.
Results
We identified 2205 individuals who participated in the DPP and 8820 matched controls with a similar breakdown in age, sex, HbA1c and FPG. During the 2.5-year study period, 4.13% of DPP individuals developed T2DM vs 6.42% of controls. Our results indicate that DPP referrals were associated with a 59% reduction T2DM incidence rates [adjusted hazard ratio=0.41;95%CI=0.38-0.44].
Conclusions
This is the first study to investigate the impact of the DPP on T2DM, relative to usual care. Our results provide support for the effectiveness of DPP in preventing T2DM onset and are compatible with findings for similar interventions in other settings.
Key messages
The evidence suggests that providing consistent face-to-face sessions which concentrate on diet and weight management can reduce short-term T2DM incidences in high-risk adults. With a 59% reduction in T2DM rates in DPP referees relative to eligible adults who were not referred, the DPP is effective in reducing short-term T2DM incidences in high-risk adults.
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Affiliation(s)
- V Nguyen
- Institute of Health Informatics, University College London, London, UK
| | - R Aldridge
- Institute of Health Informatics, University College London, London, UK
| | - R Blackburn
- Institute of Health Informatics, University College London, London, UK
| | - A Hayward
- Institute of Epidemiology and Health Care, University College London, London, UK
| | - F Greaves
- Public Health Data Science, Public Health England, London, UK
| | - J Flowers
- Public Health Data Science, Public Health England, London, UK
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Pathak N, Patel P, Mathur R, Burns R, Gonzalez-Izquierdo A, Denaxas S, Sonnenberg P, Hayward A, Aldridge R. Validity of UK electronic health records to study migrant health: a population-based cohort study. Eur J Public Health 2020. [DOI: 10.1093/eurpub/ckaa166.768] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
An estimated 14.3% (9.4 million people) of people living in the UK in 2019 were international migrants. Despite this, little is known about how migrants access and use healthcare services. To use electronic healthcare records (EHRs) to study migration health, a valid migration phenotype is necessary: a transparent reproducible algorithm using clinical terminology codes to determine migration status. We have previously described the validity of a migration phenotype in CALIBER data using the Clinical Practice Research Datalink (CPRD), the largest UK primary care EHR. This study further evaluates the phenotype by examining certainty of migration status.
Methods
This is a population-based cohort study of individuals in CPRD Gold (1997-2018) with a Read term indicating migration to the UK. We describe completeness of recording of migration over time: percentage of individuals recorded as migrants. We also describe cohort size based on certainty of migration status: “definite” (country of birth or visa status terms), “probable” (non-English first/main language terms), and “possible” (non-UK origin terms).
Results
Overall, 2.5% (403,768/16,071,111) of CPRD had ≥1 of 434 terms indicating migration to the UK. The percentage of recorded migrants per year increased from 0.2% (4,417/2,210,551) in 1997 to 3.64% (100,626/2,761,397) in 2018, following a similar trend to national migration data. 44.27% (178,749/403,768) were “definite” migrants and 53.68% (216,731/403,768) were “probable” migrants. Only 2.05%(8,288/16,071,111) were “possible” migrants.
Conclusions
We have created a large cohort of international migrants in the UK and certainty of migration status is high. This cohort can be used to study migration health in UK primary care EHR. The large contribution of language terms make this phenotype particularly suitable for understanding healthcare access and use by non-English speaking migrants who may face additional barriers to care.
Key messages
We have developed a way to study migration health in UK primary care electronic health records. Our method is particularly useful to study healthcare for non-English speaking migrants who may face additional barriers to care.
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Affiliation(s)
- N Pathak
- Institute of Health Informatics, University College London, London, UK
| | - P Patel
- Institute of Health Informatics, University College London, London, UK
| | - R Mathur
- Department of Non-communicable Disease Epidemiology, LSHTM, London, UK
| | - R Burns
- Institute of Health Informatics, University College London, London, UK
| | | | - S Denaxas
- Institute of Health Informatics, University College London, London, UK
| | - P Sonnenberg
- Institute for Global Health, University College London, London, UK
| | - A Hayward
- Institute for Epidemiology and Healthcare, University College London, London, UK
| | - R Aldridge
- Institute of Health Informatics, University College London, London, UK
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20
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O'Brien C, Bandaralage JH, Folgado R, Lahmeyer S, Hayward A, Mitter N. The Use Of Sucrose Pre-Culture For Cryopreservation Of Avocado (Persea Americana Mill.) Cultivar ‘Velvick’. Cryobiology 2019. [DOI: 10.1016/j.cryobiol.2019.10.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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21
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Ahsan MU, Hayward A, Alam M, Bandaralage JH, Topp B, Beveridge CA, Mitter N. Scion control of miRNA abundance and tree maturity in grafted avocado. BMC Plant Biol 2019; 19:382. [PMID: 31481026 PMCID: PMC6724330 DOI: 10.1186/s12870-019-1994-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 05/29/2019] [Accepted: 08/27/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Grafting is the common propagation method for avocado and primarily benefits orchard production by reducing the time to tree productivity. It also allows use of scions and rootstocks specifically selected for improved productivity and commercial acceptance. Rootstocks in avocado may be propagated from mature tree cuttings ('mature'), or from seed ('juvenile'). While the use of mature scion material hastens early bearing/maturity and economic return, the molecular factors involved in the role of the scion and/or rootstock in early bearing/reduced juvenility of the grafted tree are still unknown. RESULTS Here, we utilized juvenility and flowering associated miRNAs; miR156 and miR172 and their putative target genes to screen pre-graft and post-graft material in different combinations from avocado. The abundance of mature miR156, miR172 and the miR156 target gene SPL4, showed a strong correlation to the maturity of the scion and rootstock material in avocado. Graft transmissibility of miR156 and miR172 has been explored in annual plants. Here, we show that the scion may be responsible for grafted tree maturity involving these factors, while the rootstock maturity does not significantly influence miRNA abundance in the scion. We also demonstrate that the presence of leaves on cutting rootstocks supports graft success and contributes towards intergraft signalling involving the carbohydrate-marker TPS1. CONCLUSION Here, we suggest that the scion largely controls the molecular 'maturity' of grafted avocado trees, however, leaves on the rootstock not only promote graft success, but can influence miRNA and mRNA abundance in the scion. This constitutes the first study on scion and rootstock contribution towards grafted tree maturity using the miR156-SPL4-miR172 regulatory module as a marker for juvenility and reproductive competence.
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Affiliation(s)
- Muhammad Umair Ahsan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland 4072 Australia
| | - Alice Hayward
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland 4072 Australia
| | - Mobashwer Alam
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland 4072 Australia
| | - Jayeni Hiti Bandaralage
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland 4072 Australia
| | - Bruce Topp
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland 4072 Australia
| | - Christine Anne Beveridge
- School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, Queensland 4072 Australia
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland 4072 Australia
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22
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Ahsan MU, Hayward A, Alam M, Bandaralage JH, Topp B, Beveridge CA, Mitter N. Scion control of miRNA abundance and tree maturity in grafted avocado. BMC Plant Biol 2019; 19:382. [PMID: 31481026 DOI: 10.1186/s12870-019-1994-1995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/27/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Grafting is the common propagation method for avocado and primarily benefits orchard production by reducing the time to tree productivity. It also allows use of scions and rootstocks specifically selected for improved productivity and commercial acceptance. Rootstocks in avocado may be propagated from mature tree cuttings ('mature'), or from seed ('juvenile'). While the use of mature scion material hastens early bearing/maturity and economic return, the molecular factors involved in the role of the scion and/or rootstock in early bearing/reduced juvenility of the grafted tree are still unknown. RESULTS Here, we utilized juvenility and flowering associated miRNAs; miR156 and miR172 and their putative target genes to screen pre-graft and post-graft material in different combinations from avocado. The abundance of mature miR156, miR172 and the miR156 target gene SPL4, showed a strong correlation to the maturity of the scion and rootstock material in avocado. Graft transmissibility of miR156 and miR172 has been explored in annual plants. Here, we show that the scion may be responsible for grafted tree maturity involving these factors, while the rootstock maturity does not significantly influence miRNA abundance in the scion. We also demonstrate that the presence of leaves on cutting rootstocks supports graft success and contributes towards intergraft signalling involving the carbohydrate-marker TPS1. CONCLUSION Here, we suggest that the scion largely controls the molecular 'maturity' of grafted avocado trees, however, leaves on the rootstock not only promote graft success, but can influence miRNA and mRNA abundance in the scion. This constitutes the first study on scion and rootstock contribution towards grafted tree maturity using the miR156-SPL4-miR172 regulatory module as a marker for juvenility and reproductive competence.
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Affiliation(s)
- Muhammad Umair Ahsan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia
| | - Alice Hayward
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia
| | - Mobashwer Alam
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia
| | - Jayeni Hiti Bandaralage
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia
| | - Bruce Topp
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia
| | - Christine Anne Beveridge
- School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland, 4072, Australia.
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23
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Gupta RK, Lipman M, Story A, Hayward A, de Vries G, van Hest R, Erkens C, Rangaka MX, Abubakar I. Active case finding and treatment adherence in risk groups in the tuberculosis pre-elimination era. Int J Tuberc Lung Dis 2019; 22:479-487. [PMID: 29663951 DOI: 10.5588/ijtld.17.0767] [Citation(s) in RCA: 13] [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] [Indexed: 11/10/2022] Open
Abstract
Vulnerable populations, including homeless persons, high-risk drug and alcohol users, prison inmates and other marginalised populations, contribute a disproportionate burden of tuberculosis (TB) cases in low-incidence settings. Drivers of this disease burden include an increased risk of both TB transmission in congregate settings, and progression from infection to active disease. Late diagnosis and poor treatment completion further propagate the epidemic and fuel the acquisition of drug resistance. These groups are therefore a major priority for TB control programmes in low-incidence settings. Targeted strategies include active case finding (ACF) initiatives and interventions to improve treatment completion, both of which should be tailored to local populations. ACF usually deploys mobile X-ray unit screening, which allows sensitive, high-throughput screening with immediate availability of results. Such initiatives have been found to be effective and cost-effective, and associated with reductions in proxy measures of transmission in hard-to-reach groups. The addition of point-of-care molecular diagnostics and automated X-ray readers may further streamline the screening pathway. There is little evidence to support interventions to improve adherence among these risk groups. Such approaches include enhanced case management and directly observed treatment, while video-observed therapy (currently under evaluation) appears to be a promising tool for the future. Integrating outreach services to include both case detection and case-management interventions that share a resource infrastructure may allow cost-effectiveness to be maximised. Integrating screening and treatment for other diseases that are prevalent among targeted risk groups into TB outreach interventions may further improve cost-effectiveness. This article reviews the existing literature, and highlights priorities for further research.
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Affiliation(s)
- R K Gupta
- Institute for Global Health, University College London (UCL), London, UK
| | - M Lipman
- UCL-TB and UCL Respiratory, UCL, London, Royal Free London National Health Service Foundation Trust, London, UK
| | - A Story
- Find & Treat, UCL Hospitals, London, UK
| | - A Hayward
- Institute of Epidemiology and Health Care, UCL, London, UK
| | - G de Vries
- KNCV Tuberculosis Foundation, The Hague, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - R van Hest
- Department of Tuberculosis Control, Regional Public Health Service Groningen, Groningen, The Netherlands; Department of Pulmonary Diseases and Tuberculosis, University Medical Centre Groningen, Groningen, The Netherlands
| | - C Erkens
- KNCV Tuberculosis Foundation, The Hague, The Netherlands
| | - M X Rangaka
- Institute for Global Health, University College London (UCL), London, UK
| | - I Abubakar
- Institute for Global Health, University College London (UCL), London, UK
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24
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Ahsan MU, Hayward A, Irihimovitch V, Fletcher S, Tanurdzic M, Pocock A, Beveridge CA, Mitter N. Juvenility and Vegetative Phase Transition in Tropical/Subtropical Tree Crops. Front Plant Sci 2019; 10:729. [PMID: 31214234 PMCID: PMC6558100 DOI: 10.3389/fpls.2019.00729] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/16/2019] [Indexed: 05/16/2023]
Abstract
In plants, juvenile to adult phase transition is regulated by the sequential activity of two microRNAs: miR156 and miR172. A decline in miR156 and increase in miR172 abundance is associated with phase transition. There is very limited information on phase transition in economically important horticultural tree crops, which have a significantly long vegetative phase affecting fruit bearing. Here, we profiled various molecular cues known to be involved in phase transition and flowering, including the microRNAs miR156 and miR172, in three horticultural tree crops: avocado (Persea americana), mango (Mangifera indica), and macadamia (Macadamia integrifolia). We observed that miR156 expression decreases as these trees age and can potentially be used as a juvenility marker. Consistent with findings in annual plants, we also observed conserved regulation of the miR156-SPL3/4/5 regulatory module in these genetically distant tree crops, suggesting that this pathway may play a highly conserved role in vegetative identity. Meanwhile, the abundance of miR172 and its target AP2-like genes as well as the accumulation level of SPL9 transcripts were not related with plant age in these crops except in avocado where miR172 expression increased steadily. Finally, we demonstrate that various floral genes, including AP1 and SOC1 were upregulated in the reproductive phase and can be used as potential markers for the reproductive phase transition. Overall, this study provides an insight into the molecular associations of juvenility and phase transition in horticultural trees where crop breeding and improvement are encumbered by long juvenile phases.
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Affiliation(s)
- Muhammad Umair Ahsan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Alice Hayward
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Vered Irihimovitch
- The Volcani Center, Agricultural Research Organization, Institute of Plant Sciences, Rishon LeZion, Israel
| | - Stephen Fletcher
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Milos Tanurdzic
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Alexander Pocock
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | | | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
- *Correspondence: Neena Mitter,
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25
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Aisyah DN, Shallcross L, Hayward A, Aldridge RW, Hemming S, Yates S, Ferenando G, Possas L, Garber E, Watson JM, Geretti AM, McHugh TD, Lipman M, Story A. Hepatitis C among vulnerable populations: A seroprevalence study of homeless, people who inject drugs and prisoners in London. J Viral Hepat 2018; 25:1260-1269. [PMID: 29851232 DOI: 10.1111/jvh.12936] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 05/17/2018] [Indexed: 01/17/2023]
Abstract
Injecting drugs substantially increases the risk of hepatitis C virus (HCV) infection and is common in the homeless and prisoners. Capturing accurate data on disease prevalence within these groups is challenging but is essential to inform strategies to reduce HCV transmission. The aim of this study was to estimate the prevalence of HCV in these populations. We conducted a cross-sectional study between May 2011 and June 2013 in London and, using convenience sampling, recruited participants from hostels for the homeless, drug treatment services and a prison. A questionnaire was administered and blood samples were tested for hepatitis C. We recruited 491 individuals who were homeless (40.7%), 205 drug users (17%) and 511 prisoners (42.3%). Eight per cent of patients (98/1207, 95% CI: 6.7%-9.8%) had active HCV infection and 3% (38/1207, 95% CI: 2.3%-4.3%) past HCV infection. Overall, one quarter (51/205) of people recruited in drug treatment services, 13% (65/491) of people from homeless residential sites and 4% (20/511) prisoners in this study were anti-HCV positive. Seventy-seven of the 136 (56.6%, 95% CI: 47.9%-65%) of HCV infected participants identified had a history of all three risk factors (homelessness, imprisonment and drug use), 27.3% (95% CI: 20.1%-35.6%) had 2 overlapping risk factors, and 15.4% (95% CI: 10.6%-23.7%) one risk factor. Drug treatment services, prisons and homelessness services provide good opportunities for identifying hepatitis C-infected individuals. Effective models need to be developed to ensure case identification in these settings that can lead to an effective treatment and an efficient HCV prevention.
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Affiliation(s)
- D N Aisyah
- UCL Infectious Disease Informatics, Farr Institute of Health Informatics, London, UK.,Faculty of Public Health Universitas Indonesia, Depok, Indonesia
| | - L Shallcross
- UCL Infectious Disease Informatics, Farr Institute of Health Informatics, London, UK
| | - A Hayward
- UCL Infectious Disease Informatics, Farr Institute of Health Informatics, London, UK.,Institute of Epidemiology and Health Care, University College London, London, UK
| | - R W Aldridge
- UCL Infectious Disease Informatics, Farr Institute of Health Informatics, London, UK.,Centre for Public Health Data Science, Institute of Health Informatics, University College London, London, UK
| | - S Hemming
- UCL Infectious Disease Informatics, Farr Institute of Health Informatics, London, UK.,Centre for Public Health Data Science, Institute of Health Informatics, University College London, London, UK.,Royal Free London NHS Foundation Trust, London, UK
| | - S Yates
- UCL Infectious Disease Informatics, Farr Institute of Health Informatics, London, UK.,Centre for Public Health Data Science, Institute of Health Informatics, University College London, London, UK.,Royal Free London NHS Foundation Trust, London, UK
| | - G Ferenando
- UCL Infectious Disease Informatics, Farr Institute of Health Informatics, London, UK.,Centre for Public Health Data Science, Institute of Health Informatics, University College London, London, UK.,Royal Free London NHS Foundation Trust, London, UK
| | - L Possas
- UCL Infectious Disease Informatics, Farr Institute of Health Informatics, London, UK.,Centre for Public Health Data Science, Institute of Health Informatics, University College London, London, UK.,Royal Free London NHS Foundation Trust, London, UK
| | - E Garber
- UCL Infectious Disease Informatics, Farr Institute of Health Informatics, London, UK.,Centre for Public Health Data Science, Institute of Health Informatics, University College London, London, UK.,Royal Free London NHS Foundation Trust, London, UK
| | - J M Watson
- Centre for Public Health Data Science, Institute of Health Informatics, University College London, London, UK
| | - A M Geretti
- Institute of Infection & Global Health, University of Liverpool, Liverpool, UK
| | - T D McHugh
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London, UK
| | - M Lipman
- Royal Free London NHS Foundation Trust, London, UK.,UCL Respiratory, Division of Medicine, University College London, London, UK
| | - A Story
- University College London Hospitals, London, UK
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26
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Aisyah DN, Shallcross L, Hully AJ, O'Brien A, Hayward A. Assessing hepatitis C spontaneous clearance and understanding associated factors-A systematic review and meta-analysis. J Viral Hepat 2018; 25:680-698. [PMID: 29345844 DOI: 10.1111/jvh.12866] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/14/2017] [Indexed: 12/11/2022]
Abstract
New advances in the treatment of hepatitis C provide high levels of sustained viral response but their expense limits availability in publicly funded health systems. The aim of this review was to estimate the proportion of patients who will spontaneously clear HCV, to identify factors that are associated with clearance and to support better targeting of directly acting antivirals. We searched Ovid EMBASE, Ovid MEDLINE and PubMed from 1 January 1994 to 30 June 2015 for studies reporting hepatitis C spontaneous clearance and/or demographic, clinical and behavioural factors associated with clearance. We undertook meta-analyses to estimate the odds of clearance for each predictor. Forty-three studies met the inclusion criteria, representing 20 110 individuals, and 6 of these studies included sufficient data to estimate spontaneous clearance. The proportion achieving clearance within 3, 6, 12 and 24 months following infection were, respectively, 19.8% (95% CI: 2.6%-47.5%), 27.9% (95% CI: 17.2%-41.8%), 36.1% (95% CI: 23.5%-50.9%) and 37.1% (95% CI: 23.7%-52.8%). Individuals who had not spontaneously cleared by 12 months were unlikely to do so. The likelihood of spontaneous clearance was lower in males and individuals with HIV co-infection, the absence of HBV co-infection, asymptomatic infection, black or nonindigenous race, nongenotype 1 infection, older age and alcohol or drug problems. This study suggests that patients continue to spontaneously clear HCV for at least 12 months following initial infection. However, injecting drug users are comparatively less likely to achieve clearance; thus, they should be considered a priority for early treatment given the continuing risks that these individuals pose for onwards transmission.
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Affiliation(s)
- D N Aisyah
- UCL Infectious Disease Informatics, Farr Institute of Health Informatics, London, UK.,Faculty of Public Health, Universitas Indonesia, Depok, Indonesia
| | - L Shallcross
- UCL Infectious Disease Informatics, Farr Institute of Health Informatics, London, UK
| | - A J Hully
- Kings College London School of Medicine, London, UK
| | - A O'Brien
- UCL Division of Medicine, London, UK
| | - A Hayward
- UCL Infectious Disease Informatics, Farr Institute of Health Informatics, London, UK.,Institute of Epidemiology and Health Care, University College London, London, UK
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27
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Douglass K, Jacquet G, Hayward A, Dreifuss B, Tupesis J. Development of a Global Health Milestones Tool for Emergency Medicine
Trainees: A Pilot Project. Ann Glob Health 2017. [DOI: 10.1016/j.aogh.2017.03.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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28
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Hayward A, Tsuboi M, Owusu C, Kotrschal A, Buechel SD, Zidar J, Cornwallis CK, Løvlie H, Kolm N. Evolutionary associations between host traits and parasite load: insights from Lake Tanganyika cichlids. J Evol Biol 2017; 30:1056-1067. [DOI: 10.1111/jeb.13053] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/27/2017] [Accepted: 02/07/2017] [Indexed: 01/05/2023]
Affiliation(s)
- A. Hayward
- Centre for Ecology and Conservation; University of Exeter; Penryn UK
| | - M. Tsuboi
- Department of Animal Ecology; Uppsala University; Uppsala Sweden
| | - C. Owusu
- Department of Animal Ecology; Uppsala University; Uppsala Sweden
| | - A. Kotrschal
- Department of Zoology; Stockholm University; Stockholm Sweden
| | - S. D. Buechel
- Department of Zoology; Stockholm University; Stockholm Sweden
| | - J. Zidar
- IFM Biology; Linköping University; Linköping Sweden
| | | | - H. Løvlie
- IFM Biology; Linköping University; Linköping Sweden
| | - N. Kolm
- Department of Zoology; Stockholm University; Stockholm Sweden
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29
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Xu H, Song J, Luo H, Zhang Y, Li Q, Zhu Y, Xu J, Li Y, Song C, Wang B, Sun W, Shen G, Zhang X, Qian J, Ji A, Xu Z, Luo X, He L, Li C, Sun C, Yan H, Cui G, Li X, Li X, Wei J, Liu J, Wang Y, Hayward A, Nelson D, Ning Z, Peters RJ, Qi X, Chen S. Analysis of the Genome Sequence of the Medicinal Plant Salvia miltiorrhiza. Mol Plant 2016; 9:949-52. [PMID: 27018390 PMCID: PMC5517341 DOI: 10.1016/j.molp.2016.03.010] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 02/21/2016] [Accepted: 03/09/2016] [Indexed: 05/18/2023]
Affiliation(s)
- Haibin Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Jingyuan Song
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Hongmei Luo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Yujun Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qiushi Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Yingjie Zhu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Ying Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Chi Song
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Bo Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Guoan Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xin Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Jun Qian
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Aijia Ji
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Zhichao Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Xiang Luo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Liu He
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Chuyuan Li
- Guangzhou Pharmaceutical Holding Limited, Guangzhou 510140, China
| | - Chao Sun
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Haixia Yan
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Guanghong Cui
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Xian'en Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Jianhe Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Juyan Liu
- Guangzhou Pharmaceutical Holding Limited, Guangzhou 510140, China
| | - Yitao Wang
- Institute of Chinese Medical Sciences, University of Macau, Macau 999078, China
| | - Alice Hayward
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane 4072, Australia
| | - David Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Zemin Ning
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011 USA
| | - Xiaoquan Qi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China.
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30
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Aldridge RW, Yates S, Hemming S, Possas L, Garber E, Lipman M, Mchugh T, Story A, Hayward A. Latent TB Infection and Blood Borne Viruses in a London Prison: A Cross Sectional Survey. Int J Epidemiol 2015. [DOI: 10.1093/ije/dyv096.452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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31
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Mason AS, Takahira J, Atri C, Samans B, Hayward A, Cowling WA, Batley J, Nelson MN. Microspore culture reveals complex meiotic behaviour in a trigenomic Brassica hybrid. BMC Plant Biol 2015; 15:173. [PMID: 26152188 PMCID: PMC4493989 DOI: 10.1186/s12870-015-0555-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/16/2015] [Indexed: 05/10/2023]
Abstract
BACKGROUND Development of synthetic allohexaploid Brassica (2n = AABBCC) would be beneficial for agriculture, as allelic contributions from three genomes could increase hybrid vigour and broaden adaptation. Microspore culture of a near-allohexaploid hybrid derived from the cross (B. napus × B. carinata) × B. juncea was undertaken in order to assess the frequency and distribution of homologous and homoeologous crossovers in this trigenomic hybrid. SNP and SSR molecular markers were used to detect inheritance of A, B and C genome alleles in microspore-derived (MD) progeny. SNP allele copy number was also assessed. The MD progeny were also compared to progeny derived by self-pollination and open-pollination for fertility (estimated by self-pollinated seed set and pollen viability) and DNA ploidy (measured by flow cytometry). RESULTS In the trigenomic hybrid, homologous chromosome pairs A(j)-A(n), B(j)-B(c) and C(n)-C(c) had similar meiotic crossover frequencies and segregation to that previously observed in established Brassica species, as demonstrated by marker haplotype analysis of the MD population. Homoeologous pairing between chromosomes A1-C1, A2-C2 and A7-C6 was detected at frequencies of 12-18 %, with other homoeologous chromosome regions associating from 8 % (A3-C3) to 0-1 % (A8-C8, A8-C9) of the time. Copy number analysis revealed eight instances of additional chromosomes and 20 instances of chromosomes present in one copy in somatically doubled MD progeny. Presence of chromosome A6 was positively correlated with self-pollinated seed set and pollen viability in the MD population. Many MD progeny were unable to produce self-pollinated seed (76 %) or viable pollen (53 %), although one MD plant produced 198 self-pollinated seeds. Average fertility was significantly lower in progeny obtained by microspore culture than progeny obtained by self-pollination or open-pollination, after excluding MD progeny which had not undergone chromosome doubling. CONCLUSIONS Based on SNP data analysis of the microspore-derived progeny, crossover frequency per chromosome in the allohexaploid hybrid was found to be similar to that in established Brassica species, suggesting that the higher chromosome number did not significantly disrupt cellular regulation of meiosis. SNP allele copy number analysis revealed the occurrence not only of homoeologous duplication/deletion events but also other cryptic duplications and deletions that may have been the result of mitotic instability. Microspore culture simplified the assessment of chromosome behaviour in the allohexaploid hybrid but yielded progeny with lower fertility and a greater range of ploidy levels compared to progeny obtained by self- or open-pollination.
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Affiliation(s)
- Annaliese S Mason
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, 4072, Australia.
- Centre for Integrative Legume Research, The University of Queensland, Brisbane, 4072, Australia.
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Junko Takahira
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, Perth, Australia.
| | - Chhaya Atri
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, Perth, Australia.
- Plant Breeding & Genetics Department, Punjab Agricultural University, Ferozepur Road, Ludhiana, Punjab, 141004, India.
| | - Birgit Samans
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Alice Hayward
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, 4072, Australia.
- Centre for Integrative Legume Research, The University of Queensland, Brisbane, 4072, Australia.
| | - Wallace A Cowling
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, Perth, Australia.
| | - Jacqueline Batley
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, 4072, Australia.
- Centre for Integrative Legume Research, The University of Queensland, Brisbane, 4072, Australia.
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, Perth, Australia.
| | - Matthew N Nelson
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, Perth, Australia.
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, Perth, Australia.
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Zhu Y, Xu J, Sun C, Zhou S, Xu H, Nelson DR, Qian J, Song J, Luo H, Xiang L, Li Y, Xu Z, Ji A, Wang L, Lu S, Hayward A, Sun W, Li X, Schwartz DC, Wang Y, Chen S. Chromosome-level genome map provides insights into diverse defense mechanisms in the medicinal fungus Ganoderma sinense. Sci Rep 2015; 5:11087. [PMID: 26046933 PMCID: PMC4457147 DOI: 10.1038/srep11087] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 05/14/2015] [Indexed: 11/30/2022] Open
Abstract
Fungi have evolved powerful genomic and chemical defense systems to protect themselves against genetic destabilization and other organisms. However, the precise molecular basis involved in fungal defense remain largely unknown in Basidiomycetes. Here the complete genome sequence, as well as DNA methylation patterns and small RNA transcriptomes, was analyzed to provide a holistic overview of secondary metabolism and defense processes in the model medicinal fungus, Ganoderma sinense. We reported the 48.96 Mb genome sequence of G. sinense, consisting of 12 chromosomes and encoding 15,688 genes. More than thirty gene clusters involved in the biosynthesis of secondary metabolites, as well as a large array of genes responsible for their transport and regulation were highlighted. In addition, components of genome defense mechanisms, namely repeat-induced point mutation (RIP), DNA methylation and small RNA-mediated gene silencing, were revealed in G. sinense. Systematic bioinformatic investigation of the genome and methylome suggested that RIP and DNA methylation combinatorially maintain G. sinense genome stability by inactivating invasive genetic material and transposable elements. The elucidation of the G. sinense genome and epigenome provides an unparalleled opportunity to advance our understanding of secondary metabolism and fungal defense mechanisms.
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Affiliation(s)
- Yingjie Zhu
- 1] Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China [2] Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Jiang Xu
- 1] Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China [2] Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Chao Sun
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Haibin Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Jun Qian
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Jingyuan Song
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Hongmei Luo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Li Xiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Ying Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Zhichao Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Aijia Ji
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Lizhi Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
| | - Alice Hayward
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia, 4072
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - David C Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, UW Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Yitao Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, 999078, China
| | - Shilin Chen
- 1] Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China [2] Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences &Peking Union Medical College, Beijing 100193, China
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Wang B, Sun W, Li Q, Li Y, Luo H, Song J, Sun C, Qian J, Zhu Y, Hayward A, Xu H, Chen S. Genome-wide identification of phenolic acid biosynthetic genes in Salvia miltiorrhiza. Planta 2015; 241:711-25. [PMID: 25471478 DOI: 10.1007/s00425-014-2212-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 11/23/2014] [Indexed: 05/20/2023]
Abstract
MAIN CONCLUSION Twenty-nine genes related to phenolic acid biosynthesis were identified in the Salvia miltiorrhiza genome. Nineteen of these are described for the first time, with ten genes experimentally correlating to phenolic acid biosynthesis. Vast stores of secondary metabolites exist in plants, many of which possess biological activities related to human health. Phenolic acid derivatives are a class of valuable bioactive pharmaceuticals abundant in the widely used Chinese medicinal herb, Salvia miltiorrhiza. The biosynthetic pathway for phenolic acids differs in this species from that of other investigated plants. However, the molecular basis for this is unknown, with systematic analysis of the genes involved not yet performed. As the first step towards unraveling this complex biosynthetic pathway in S. miltiorrhiza, the current genome assembly was searched for putatively involved genes. Twenty-nine genes were revealed, 19 of which are described here for the first time. These include 15 genes predicted in the phenylpropanoid pathway; seven genes in the tyrosine-derived pathway; six genes encoding putative hydroxycinnamoyltransferases, and one CYP98A, namely CYP98A78. The promoter regions, gene structures and expression patterns of these genes were examined. Furthermore, conserved domains and phylogenetic relationships with homologous proteins in other species were revealed. Most of the key enzymes, including 4-coumarate: CoA ligase, 4-hydroxyphenylpyruvate reductase and hydroxycinnamoyltransferase, were found in multiple copies, each exhibiting different characteristics. Ten genes putatively involved in rosmarinic acid biosynthesis are also described. These findings provide a foundation for further analysis of this complex and diverse pathway, with potential to enhance the synthesis of water-soluble medicinal compounds in S. miltiorrhiza.
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Affiliation(s)
- Bo Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China,
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Liu F, Xia Y, Wu L, Fu D, Hayward A, Luo J, Yan X, Xiong X, Fu P, Wu G, Lu C. Enhanced seed oil content by overexpressing genes related to triacylglyceride synthesis. Gene 2015; 557:163-71. [PMID: 25523093 DOI: 10.1016/j.gene.2014.12.029] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/12/2014] [Accepted: 12/13/2014] [Indexed: 11/20/2022]
Abstract
Oilseed rape (Brassica napus) is one of the most important oilseed crops globally. To meet increasing demand for oil-based products, the ability to enhance desirable oil content in the seed is required. This study assessed the capability of five genes in the triacylglyceride (TAG) synthesis pathway to enhance oil content. The genes BnGPDH, BnGPAT, BnDGAT, ScGPDH and ScLPAAT were overexpressed separately in a tobacco (Nicotiana benthamiana) model system, and simultaneously by pyramiding in B. napus, under the control of a seed specific Napin promoter. ScLPAAT transgenic plants showed a significant increase of 6.84% to 8.55% in oil content in tobacco seeds, while a ~4% increase was noted for BnGPDH and BnGPAT transgenic seeds. Seed-specific overexpression of all four genes in B. napus resulted in as high a 12.57% to 14.46% increased in seed oil content when compared to WT, equaling close to the sum of the single-gene overexpression increases in tobacco. Taken together, our study demonstrates that BnGPDH, BnGPAT and ScLPAAT may effectively increase seed oil content, and that simultaneous overexpression of these in transgenic B. napus may further enhance the desirable oil content relative to single-gene overexpressors.
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Affiliation(s)
- Fang Liu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No. 2 Xudong 2nd Road, Wuhan 430062, China.
| | - Yuping Xia
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No. 2 Xudong 2nd Road, Wuhan 430062, China.
| | - Lei Wu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No. 2 Xudong 2nd Road, Wuhan 430062, China.
| | - Donghui Fu
- The Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Alice Hayward
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Queensland 4072, Australia.
| | - Junling Luo
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No. 2 Xudong 2nd Road, Wuhan 430062, China.
| | - Xiaohong Yan
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No. 2 Xudong 2nd Road, Wuhan 430062, China.
| | - Xiaojuan Xiong
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No. 2 Xudong 2nd Road, Wuhan 430062, China.
| | - Ping Fu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No. 2 Xudong 2nd Road, Wuhan 430062, China.
| | - Gang Wu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No. 2 Xudong 2nd Road, Wuhan 430062, China.
| | - Changming Lu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, No. 2 Xudong 2nd Road, Wuhan 430062, China.
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Zeng S, Liu Y, Pan L, Hayward A, Wang Y. Identification and characterization of miRNAs in ripening fruit of Lycium barbarum L. using high-throughput sequencing. Front Plant Sci 2015; 6:778. [PMID: 26442086 PMCID: PMC4585183 DOI: 10.3389/fpls.2015.00778] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 09/10/2015] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNAs) are master regulators of gene activity documented to play central roles in fruit ripening in model plant species, yet little is known of their roles in Lycium barbarum L. fruits. In this study, miRNA levels in L. barbarum fruit samples at four developmental stages, were assayed using Illumina HiSeqTM2000. This revealed the presence of 50 novel miRNAs and 38 known miRNAs in L. barbarum fruits. Of the novel miRNAs, 36 were specific to L. barbarum fruits compared with L. chinense. A number of stage-specific miRNAs were identified and GO terms were assigned to 194 unigenes targeted by miRNAs. The majority of GO terms of unigenes targeted by differentially expressed miRNAs are "intracellular organelle," "binding," "metabolic process," "pigmentation," and "biological regulation." Enriched KEGG analysis indicated that nucleotide excision repair and ubiquitin mediated proteolysis were over-represented during the initial stage of ripening, with ABC transporters and sulfur metabolism pathways active during the middle stages and ABC transporters and spliceosome enriched in the final stages of ripening. Several miRNAs and their targets serving as potential regulators in L. barbarum fruit ripening were identified using quantitative reverse transcription polymerase chain reaction. The miRNA-target interactions were predicted for L. barbarum ripening regulators including miR156/157 with LbCNR and LbWRKY8, and miR171 with LbGRAS. Additionally, regulatory interactions potentially controlling fruit quality and nutritional value via sugar and secondary metabolite accumulation were identified. These include miR156 targeting of fructokinase and 1-deoxy-D-xylulose-5-phosphate synthase and miR164 targeting of beta-fructofuranosidase. In sum, valuable information revealed by small RNA sequencing in this study will provide a solid foundation for uncovering the miRNA-mediated mechanism of fruit ripening and quality in this nutritional food.
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Affiliation(s)
- Shaohua Zeng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- *Correspondence: Shaohua Zeng and Ying Wang, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China ;
| | - Yongliang Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Lizhu Pan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
| | - Alice Hayward
- Queensland Alliance for Agriculture and Food Innovation, The University of QueenslandSt Lucia, QLD, Australia
| | - Ying Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of SciencesGuangzhou, China
- *Correspondence: Shaohua Zeng and Ying Wang, South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Road, Tianhe District, Guangzhou 510650, China ;
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Ferenando G, Hemming S, Yates S, Possas L, Garber E, Gant V, Aldridge R, Geretti A, Harvey J, Hayward A, Lipman M, McHugh T, Story A. S61 High Levels Of Latent Tb Infection, Blood Borne Viruses, Poor Treatment Outcomes And Unmet Need Among Hard To Reach Groups In London: The Tb Reach Study. Thorax 2014. [DOI: 10.1136/thoraxjnl-2014-206260.67] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Aldridge R, Yates S, Hemming S, Possas L, Ferenando G, Garber E, Hayward A, McHugh T, Lipman M, Story A. S80 Impact Of Peer Educators On Uptake Of Mobile X-ray Tuberculosis Screening At Homeless Hostels: A Cluster Randomised Controlled Trial. Thorax 2014. [DOI: 10.1136/thoraxjnl-2014-206260.86] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Liu F, Xiong X, Wu L, Fu D, Hayward A, Zeng X, Cao Y, Wu Y, Li Y, Wu G. BraLTP1, a lipid transfer protein gene involved in epicuticular wax deposition, cell proliferation and flower development in Brassica napus. PLoS One 2014; 9:e110272. [PMID: 25314222 PMCID: PMC4196963 DOI: 10.1371/journal.pone.0110272] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [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: 07/11/2014] [Accepted: 09/10/2014] [Indexed: 11/19/2022] Open
Abstract
Plant non-specific lipid transfer proteins (nsLTPs) constitute large multigene families that possess complex physiological functions, many of which remain unclear. This study isolated and characterized the function of a lipid transfer protein gene, BraLTP1 from Brassica rapa, in the important oilseed crops Brassica napus. BraLTP1 encodes a predicted secretory protein, in the little known VI Class of nsLTP families. Overexpression of BnaLTP1 in B. napus caused abnormal green coloration and reduced wax deposition on leaves and detailed wax analysis revealed 17-80% reduction in various major wax components, which resulted in significant water-loss relative to wild type. BnaLTP1 overexpressing leaves exhibited morphological disfiguration and abaxially curled leaf edges, and leaf cross-sections revealed cell overproliferation that was correlated to increased cytokinin levels (tZ, tZR, iP, and iPR) in leaves and high expression of the cytokinin biosynthsis gene IPT3. BnaLTP1-overexpressing plants also displayed morphological disfiguration of flowers, with early-onset and elongated carpel development and outwardly curled stamen. This was consistent with altered expression of a a number of ABC model genes related to flower development. Together, these results suggest that BraLTP1 is a new nsLTP gene involved in wax production or deposition, with additional direct or indirect effects on cell division and flower development.
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Affiliation(s)
- Fang Liu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaojuan Xiong
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Lei Wu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Donghui Fu
- The Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, China
| | - Alice Hayward
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Queensland, Australia
| | - Xinhua Zeng
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yinglong Cao
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuhua Wu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yunjing Li
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Gang Wu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
- * E-mail:
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Dalton-Morgan J, Hayward A, Alamery S, Tollenaere R, Mason AS, Campbell E, Patel D, Lorenc MT, Yi B, Long Y, Meng J, Raman R, Raman H, Lawley C, Edwards D, Batley J. A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes. Funct Integr Genomics 2014; 14:643-55. [PMID: 25147024 DOI: 10.1007/s10142-014-0391-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 08/02/2014] [Accepted: 08/11/2014] [Indexed: 11/25/2022]
Abstract
Single-nucleotide polymorphisms (SNPs)are molecular markers based on nucleotide variation and can be used for genotyping assays across populations and to track genomic inheritance. SNPs offer a comprehensive genotyping alternative to whole-genome sequencing for both agricultural and research purposes including molecular breeding and diagnostics, genome evolution and genetic diversity analyses, genetic mapping, and trait association studies. Here genomic SNPs were discovered between four cultivars of the important amphidiploid oilseed species Brassica napus and used to develop a B. napus Infinium™ array containing 5,306 SNPs randomly dispersed across the genome. Assay success was high, with >94 % of these producing a reproducible, polymorphic genotype in the 1,070 samples screened. Although the assay was designed to B. napus, successful SNP amplification was achieved in the B. napus progenitor species, Brassica rapa and Brassica oleracea, and to a lesser extent in the related species Brassica nigra. Phylogenetic analysis was consistent with the expected relationships between B. napus individuals. This study presents an efficient custom SNP assay development pipeline in the complex polyploid Brassica genome and demonstrates the utility of the array for high-throughput genotyping in a number of related Brassica species. It also demonstrates the utility of this assay in genotyping resistance genes on chromosome A7, which segregate amongst the 1,070 samples.
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Affiliation(s)
- Jessica Dalton-Morgan
- Centre for Integrative Legume Research and School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia
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Fu D, Xiao M, Hayward A, Jiang G, Zhu L, Zhou Q, Li J, Zhang M. What is crop heterosis: new insights into an old topic. J Appl Genet 2014; 56:1-13. [PMID: 25027629 DOI: 10.1007/s13353-014-0231-z] [Citation(s) in RCA: 26] [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: 05/12/2014] [Revised: 06/28/2014] [Accepted: 07/01/2014] [Indexed: 01/09/2023]
Abstract
Heterosis (or hybrid vigor) refers to a natural phenomenon whereby hybrid offspring of genetically diverse individuals out-perform their parents in multiple traits including yield, adaptability and resistances to biotic and abiotic stressors. Innovations in technology and research continue to clarify the mechanisms underlying crop heterosis, however the intrinsic relationship between the biological basis of heterosis remain unclear. In this review, we aim to provide insight into the molecular genetic basis of heterosis by presenting recent advances in the 'omics' of heterosis and the role of non-coding regions, particularly in relation to energy-use efficiency. We propose that future research should focus on integrating the expanding datasets from different species and hybrid combinations, to mine key heterotic genes and unravel interactive 'omics' networks associated with heterosis. Improved understanding of heterosis and the biological basis for its manipulation in agriculture should help to streamline its use in enhancing crop productivity.
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Affiliation(s)
- Donghui Fu
- The Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China,
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Liu D, Sun W, Yuan Y, Zhang N, Hayward A, Liu Y, Wang Y. Phylogenetic analyses provide the first insights into the evolution of OVATE family proteins in land plants. Ann Bot 2014; 113:1219-33. [PMID: 24812252 PMCID: PMC4030818 DOI: 10.1093/aob/mcu061] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [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: 11/05/2013] [Accepted: 03/07/2014] [Indexed: 05/22/2023]
Abstract
BACKGROUND AND AIMS The OVATE gene encodes a nuclear-localized regulatory protein belonging to a distinct family of plant-specific proteins known as the OVATE family proteins (OFPs). OVATE was first identified as a key regulator of fruit shape in tomato, with nonsense mutants displaying pear-shaped fruits. However, the role of OFPs in plant development has been poorly characterized. METHODS Public databases were searched and a total of 265 putative OVATE protein sequences were identified from 13 sequenced plant genomes that represent the major evolutionary lineages of land plants. A phylogenetic analysis was conducted based on the alignment of the conserved OVATE domain from these 13 selected plant genomes. The expression patterns of tomato SlOFP genes were analysed via quantitative real-time PCR. The pattern of OVATE gene duplication resulting in the expansion of the gene family was determined in arabidopsis, rice and tomato. KEY RESULTS Genes for OFPs were found to be present in all the sampled land plant genomes, including the early-diverged lineages, mosses and lycophytes. Phylogenetic analysis based on the amino acid sequences of the conserved OVATE domain defined 11 sub-groups of OFPs in angiosperms. Different evolutionary mechanisms are proposed for OVATE family evolution, namely conserved evolution and divergent expansion. Characterization of the AtOFP family in arabidopsis, the OsOFP family in rice and the SlOFP family in tomato provided further details regarding the evolutionary framework and revealed a major contribution of tandem and segmental duplications towards expansion of the OVATE gene family. CONCLUSIONS This first genome-wide survey on OFPs provides new insights into the evolution of the OVATE protein family and establishes a solid base for future functional genomics studies on this important but poorly characterized regulatory protein family in plants.
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Affiliation(s)
- Di Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Sun
- Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Science, Beijing 100700, China Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yaowu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Ning Zhang
- Department of Biology, the Huck Institute of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Alice Hayward
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yongliang Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
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Mason AS, Batley J, Bayer PE, Hayward A, Cowling WA, Nelson MN. High-resolution molecular karyotyping uncovers pairing between ancestrally related Brassica chromosomes. New Phytol 2014; 202:964-974. [PMID: 24471809 DOI: 10.1111/nph.12706] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [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: 10/04/2013] [Accepted: 12/20/2013] [Indexed: 05/18/2023]
Abstract
How do chromosomal regions with differing degrees of homology and homeology interact at meiosis? We provide a novel analytical method based on simple genetics principles which can help to answer this important question. This method interrogates high-throughput molecular marker data in order to infer chromosome behavior at meiosis in interspecific hybrids. We validated this method using high-resolution molecular marker karyotyping in two experimental Brassica populations derived from interspecific crosses among B. juncea, B. napus and B. carinata, using a single nucleotide polymorphism chip. This method of analysis successfully identified meiotic interactions between chromosomes sharing different degrees of similarity: full-length homologs; full-length homeologs; large sections of primary homeologs; and small sections of secondary homeologs. This analytical method can be applied to any allopolyploid species or fertile interspecific hybrid in order to detect meiotic associations. This genetic information can then be used to identify which genomic regions share functional homeology (i.e., retain enough similarity to allow pairing and segregation at meiosis). When applied to interspecific hybrids for which reference genome sequences are available, the question of how differing degrees of homology and homeology affect meiotic interactions may finally be resolved.
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Affiliation(s)
- Annaliese S Mason
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, 4072, Qld, Australia
- Centre for Integrative Legume Research, The University of Queensland, Brisbane, 4072, Qld, Australia
| | - Jacqueline Batley
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, 4072, Qld, Australia
- Centre for Integrative Legume Research, The University of Queensland, Brisbane, 4072, Qld, Australia
| | - Philipp Emanuel Bayer
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, 4072, Qld, Australia
- Australian Centre for Plant Functional Genomics, The University of Queensland, Brisbane, 4072, Qld, Australia
| | - Alice Hayward
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, 4072, Qld, Australia
- Centre for Integrative Legume Research, The University of Queensland, Brisbane, 4072, Qld, Australia
| | - Wallace A Cowling
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia
| | - Matthew N Nelson
- The UWA Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia
- School of Plant Biology, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia
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Zeng S, Wu M, Zou C, Liu X, Shen X, Hayward A, Liu C, Wang Y. Comparative analysis of anthocyanin biosynthesis during fruit development in two Lycium species. Physiol Plant 2014; 150:505-16. [PMID: 24661321 DOI: 10.1111/ppl.12131] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 11/07/2013] [Accepted: 11/09/2013] [Indexed: 05/20/2023]
Abstract
Dietary consumption of functional foods enriched in anthocyanins benefit for human health by protection against far-ranging human diseases. Delphinidin-derived anthocyanins (valuable as blue pigments and antioxidants) are accumulated specifically in the fruits of Lycium ruthenicum but not in the fruits of Lycium barbarum, suggesting the differences of anthocyanin biosynthesis between the two species. In this study, anthocyanin profiling confirmed that anthocyanins were increasingly accumulated during fruit ripening in L. ruthenicum, and sharply increased at full expanded mature fruit, while no anthocyanin were detected at any stage of L. barbarum fruit development. Several genes involved in anthocyanin biosynthesis were characterized in L. ruthenicum and L. barbarum fruits. Expression profiling of these genes during fruit development showed a significant positive correlation between transcript abundance and anthocyanin accumulation in L. ruthenicum fruit. Meanwhile, transcripts in L. barbarum fruit were either undetectable or were downregulated during fruit ripening, before increasing slightly in the final stages of maturation. In addition, the ratio of LrF3'5H/LrF3'H transcription showed a gradual increase before 6 days after breaker (DAB) and a sharp enhancement at 10 DAB. Our results suggest that the expression patterns of both regulatory and structural genes and the transcriptional ratio of branch-node structural genes F3'5'H/F3'H may determine the phenotypic difference in anthocyanin biosynthesis between L. ruthenicum and L. barbarum fruits.
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Affiliation(s)
- Shaohua Zeng
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, P. R. China
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van Hest NA, Aldridge RW, de Vries G, Sandgren A, Hauer B, Hayward A, Arrazola de Oñate W, Haas W, Codecasa LR, Caylà JA, Story A, Antoine D, Gori A, Quabeck L, Jonsson J, Wanlin M, Orcau Å, Rodes A, Dedicoat M, Antoun F, van Deutekom H, Keizer S, Abubakar I. Tuberculosis control in big cities and urban risk groups in the European Union: a consensus statement. ACTA ACUST UNITED AC 2014; 19. [PMID: 24626210 DOI: 10.2807/1560-7917.es2014.19.9.20728] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In low-incidence countries in the European Union (EU), tuberculosis (TB) is concentrated in big cities, especially among certain urban high-risk groups including immigrants from TB high-incidence countries, homeless people, and those with a history of drug and alcohol misuse. Elimination of TB in European big cities requires control measures focused on multiple layers of the urban population. The particular complexities of major EU metropolises, for example high population density and social structure, create specific opportunities for transmission, but also enable targeted TB control interventions, not efficient in the general population, to be effective or cost effective. Lessons can be learnt from across the EU and this consensus statement on TB control in big cities and urban risk groups was prepared by a working group representing various EU big cities, brought together on the initiative of the European Centre for Disease Prevention and Control. The consensus statement describes general and specific social, educational, operational, organisational, legal and monitoring TB control interventions in EU big cities, as well as providing recommendations for big city TB control, based upon a conceptual TB transmission and control model.
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Affiliation(s)
- N A van Hest
- Municipal Public Health Service Rotterdam-Rijnmond, Rotterdam, the Netherlands
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Sun W, Huang W, Li Z, Song C, Liu D, Liu Y, Hayward A, Liu Y, Huang H, Wang Y. Functional and evolutionary analysis of the AP1/SEP/AGL6 superclade of MADS-box genes in the basal eudicot Epimedium sagittatum. Ann Bot 2014; 113:653-68. [PMID: 24532606 PMCID: PMC3936592 DOI: 10.1093/aob/mct301] [Citation(s) in RCA: 7] [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: 05/08/2023]
Abstract
BACKGROUND AND AIMS MADS-box transcriptional regulators play important roles during plant development. Based on phylogenetic reconstruction, the AP1/SEP/AGL6 superclade of floral MADS-box genes underwent one or two duplication events in the common ancestor of the core eudicots. However, the functional evolution of the AP1/SEP/AGL6 superclade in basal eudicots remains uncharacterized. Epimedium sagittatum is a basal eudicot species valued for its medicinal properties and showing unique floral morphology. In this study, structural and functional variation of FUL-like (AP1 subfamily), SEP-like and AGL6-like genes in this species was investigated to further our understanding of flower evolution in angiosperms. Detailed investigations into the microsynteny and evolutionary history of the floral A and E class MADS-box genes in eudicots were undertaken and used to trace their genomic rearrangements. METHODS One AP1-like gene, two SEP-like genes and one AGL6-like gene were cloned from E. sagittatum. Their expression patterns were examined using quantitative RT-PCR in different vegetative and reproductive organs at two developmental stages. Yeast two-hybrid assays were carried out among AP1/SEP/AGL6 superclade, AP3/PI and AGAMOUS subfamily members for elucidation of dimerization patterns. In addition, possible formation of a ternary complex involving B class proteins with the A class protein EsFUL-like, the E class SEP-like protein EsAGL2-1 or the AGL6-class protein EsAGL6 were detected using yeast three-hybrid assays. Transgenic Arabidopsis or tobacco plants expressing EsFUL-like, EsAGL2-1 and EsAGL6-like under the cauliflower mosaic virus (CaMV) 35S promoter were generated and analysed. Genomic studies of AP1 syntenic regions in arabidopsis, columbine, strawberry, papaya, peach, grapevine and tomato were conducted for microsyntenic analyses. KEY RESULTS Sequence and phylogenetic analyses showed that EsFUL-like is a member of the AP1 (A class) subfamily, EsAGL2-1 and EsAGL2-2 belong to the SEP-like (E class) subfamily, and EsAGL6-like belongs to the AGL6 (AGL6 class) subfamily. Quantitative RT-PCR analyses revealed that the transcripts of the four genes are absent, or minimal, in vegetative tissues and are most highly expressed in floral organs. Yeast two-hybrid results revealed that of the eight MADS-box proteins tested, only EsAGL6-like, EsAGL2-1 and EsAGL2 were able to form strong homo- and heterodimers, with EsAGL6-like and EsAGL2-1 showing similar interaction patterns. Yeast three-hybrid analysis revealed that EsFUL1-like, EsAGL6-like and EsAGL2-1 (representing the three major lineages of the Epimedium AGL/SEP/ALG6 superclade) could act as bridging proteins in ternary complexes with both EsAP3-2 (B class) and EsPI (B class), which do not heterodimerize themselves. Syntenic analyses of sequenced basal eudicots, rosids and asterids showed that most AP1-like and SEP-like genes have been tightly associated as neighbours since the origin of basal eudicots. Ectopic expression of EsFUL-like in arabidopsis caused early flowering through endogenous high-level expression of AP1 and formation of secondary flowers between the first and second whorls. Tobacco plants with ectopic expression of EsAGL2-1 showed shortened pistils and styles, as well as axillary and extra petals in the initial flower. CONCLUSIONS This study provides a description of EsFUL-like, EsAGL2-1, EsAGL2-2 and EsAGL6-like function divergence and conservation in comparison with a selection of model core eudicots. The study also highlights how organization in genomic segments containing A and E class genes in sequenced model species has resulted in similar topologies of AP1 and SEP-like gene trees.
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Affiliation(s)
- Wei Sun
- Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Science, Beijing, 100700, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
| | - Wenjun Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Zhineng Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Chi Song
- Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Science, Beijing, 100700, China
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Di Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Yongliang Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
| | - Alice Hayward
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
| | - Yifei Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
| | - Hongwen Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
- For correspondence. E-mail or
| | - Ying Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China
- For correspondence. E-mail or
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Wei L, Xiao M, Hayward A, Fu D. Applications and challenges of next-generation sequencing in Brassica species. Planta 2013; 238:1005-24. [PMID: 24062086 DOI: 10.1007/s00425-013-1961-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [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: 09/07/2013] [Accepted: 09/12/2013] [Indexed: 05/09/2023]
Abstract
Next-generation sequencing (NGS) produces numerous (often millions) short DNA sequence reads, typically varying between 25 and 400 bp in length, at a relatively low cost and in a short time. This revolutionary technology is being increasingly applied in whole-genome, transcriptome, epigenome and small RNA sequencing, molecular marker and gene discovery, comparative and evolutionary genomics, and association studies. The Brassica genus comprises some of the most agro-economically important crops, providing abundant vegetables, condiments, fodder, oil and medicinal products. Many Brassica species have undergone the process of polyploidization, which makes their genomes exceptionally complex and can create difficulties in genomics research. NGS injects new vigor into Brassica research, yet also faces specific challenges in the analysis of complex crop genomes and traits. In this article, we review the advantages and limitations of different NGS technologies and their applications and challenges, using Brassica as an advanced model system for agronomically important, polyploid crops. Specifically, we focus on the use of NGS for genome resequencing, transcriptome sequencing, development of single-nucleotide polymorphism markers, and identification of novel microRNAs and their targets. We present trends and advances in NGS technology in relation to Brassica crop improvement, with wide application for sophisticated genomics research into agronomically important polyploid crops.
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Affiliation(s)
- Lijuan Wei
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Meili Xiao
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Alice Hayward
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, 4072, Australia
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China.
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Zander M, Patel DA, Van de Wouw A, Lai K, Lorenc MT, Campbell E, Hayward A, Edwards D, Raman H, Batley J. Identifying genetic diversity of avirulence genes in Leptosphaeria maculans using whole genome sequencing. Funct Integr Genomics 2013; 13:295-308. [PMID: 23793572 DOI: 10.1007/s10142-013-0324-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 05/07/2013] [Accepted: 05/12/2013] [Indexed: 12/18/2022]
Abstract
Next generation sequencing technology allows rapid re-sequencing of individuals, as well as the discovery of single nucleotide polymorphisms (SNPs), for genomic diversity and evolutionary analyses. By sequencing two isolates of the fungal plant pathogen Leptosphaeria maculans, the causal agent of blackleg disease in Brassica crops, we have generated a resource of over 76 million sequence reads aligned to the reference genome. We identified over 21,000 SNPs with an overall SNP frequency of one SNP every 2,065 bp. Sequence validation of a selection of these SNPs in additional isolates collected throughout Australia indicates a high degree of polymorphism in the Australian population. In preliminary phylogenetic analysis, isolates from Western Australia clustered together and those collected from Brassica juncea stubble were identical. These SNPs provide a novel marker resource to study the genetic diversity of this pathogen. We demonstrate that re-sequencing provides a method of validating previously characterised SNPs and analysing differences in important genes, such as the disease related avirulence genes of L. maculans. Understanding the genetic characteristics of this devastating pathogen is vital in developing long-term solutions to managing blackleg disease in Brassica crops.
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Affiliation(s)
- Manuel Zander
- School of Agriculture and Food Sciences and Centre for Integrative Legume Research, University of Queensland, Brisbane, Queensland 4072, Australia
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Hocking C, Taylor A, Hayward A. Early discharge and ambulatory care of low-risk patients with neutropenic fever in Australia. Intern Med J 2013; 43:591-5. [DOI: 10.1111/imj.12117] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 10/10/2012] [Indexed: 12/01/2022]
Affiliation(s)
- C. Hocking
- Department of Medical Oncology; Royal Adelaide Hospital; Adelaide South Australia Australia
| | - A. Taylor
- Department of Medical Oncology; Royal Adelaide Hospital; Adelaide South Australia Australia
| | - A. Hayward
- Department of Medical Oncology; Royal Adelaide Hospital; Adelaide South Australia Australia
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Yates S, Hemming S, Possas L, Fernando G, Gant V, Garber E, Geretti AM, Harvey J, Hayward A, Lipman M, McHugh T, Watson J, Story A. S1 High Levels of Latent TB Infection, Blood Borne Viruses and Unmet Need Among Hard to Reach Groups in London: The TB Reach Study. Thorax 2012. [DOI: 10.1136/thoraxjnl-2012-202678.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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