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Galdi P, Cabez MB, Farrugia C, Vaher K, Williams LZJ, Sullivan G, Stoye DQ, Quigley AJ, Makropoulos A, Thrippleton MJ, Bastin ME, Richardson H, Whalley H, Edwards AD, Bajada CJ, Robinson EC, Boardman JP. Feature similarity gradients detect alterations in the neonatal cortex associated with preterm birth. Hum Brain Mapp 2024; 45:e26660. [PMID: 38488444 PMCID: PMC10941526 DOI: 10.1002/hbm.26660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 01/18/2024] [Accepted: 02/29/2024] [Indexed: 03/18/2024] Open
Abstract
The early life environment programmes cortical architecture and cognition across the life course. A measure of cortical organisation that integrates information from multimodal MRI and is unbound by arbitrary parcellations has proven elusive, which hampers efforts to uncover the perinatal origins of cortical health. Here, we use the Vogt-Bailey index to provide a fine-grained description of regional homogeneities and sharp variations in cortical microstructure based on feature gradients, and we investigate the impact of being born preterm on cortical development at term-equivalent age. Compared with term-born controls, preterm infants have a homogeneous microstructure in temporal and occipital lobes, and the medial parietal, cingulate, and frontal cortices, compared with term infants. These observations replicated across two independent datasets and were robust to differences that remain in the data after matching samples and alignment of processing and quality control strategies. We conclude that cortical microstructural architecture is altered in preterm infants in a spatially distributed rather than localised fashion.
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Affiliation(s)
- Paola Galdi
- MRC Centre for Reproductive HealthUniversity of EdinburghEdinburghUK
- School of InformaticsUniversity of EdinburghEdinburghUK
| | | | - Christine Farrugia
- Faculty of EngineeringUniversity of MaltaVallettaMalta
- University of Malta Magnetic Resonance Imaging Platform (UMRI)VallettaMalta
| | - Kadi Vaher
- MRC Centre for Reproductive HealthUniversity of EdinburghEdinburghUK
| | - Logan Z. J. Williams
- Centre for the Developing BrainKing's College LondonLondonUK
- School of Biomedical Engineering and Imaging ScienceKing's College LondonLondonUK
| | - Gemma Sullivan
- MRC Centre for Reproductive HealthUniversity of EdinburghEdinburghUK
- Centre for Clinical Brain SciencesUniversity of EdinburghEdinburghUK
| | - David Q. Stoye
- MRC Centre for Reproductive HealthUniversity of EdinburghEdinburghUK
| | | | | | | | - Mark E. Bastin
- Centre for Clinical Brain SciencesUniversity of EdinburghEdinburghUK
| | - Hilary Richardson
- School of Philosophy, Psychology and Language SciencesUniversity of EdinburghEdinburghUK
| | - Heather Whalley
- Centre for Clinical Brain SciencesUniversity of EdinburghEdinburghUK
- Centre for Genomic and Experimental MedicineUniversity of EdinburghEdinburghUK
| | - A. David Edwards
- Centre for the Developing BrainKing's College LondonLondonUK
- MRC Centre for Neurodevelopmental DisordersKing's College LondonLondonUK
| | - Claude J. Bajada
- University of Malta Magnetic Resonance Imaging Platform (UMRI)VallettaMalta
- Department of Physiology and Biochemistry, Faculty of Medicine and SurgeryUniversity of MaltaVallettaMalta
| | - Emma C. Robinson
- Centre for the Developing BrainKing's College LondonLondonUK
- School of Biomedical Engineering and Imaging ScienceKing's College LondonLondonUK
| | - James P. Boardman
- MRC Centre for Reproductive HealthUniversity of EdinburghEdinburghUK
- Centre for Clinical Brain SciencesUniversity of EdinburghEdinburghUK
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Begum RA, Messenger DJ, Fry SC. Making and breaking of boron bridges in the pectic domain rhamnogalacturonan-II at apoplastic pH in vivo and in vitro. Plant J 2023; 113:1310-1329. [PMID: 36658763 PMCID: PMC10952590 DOI: 10.1111/tpj.16112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 06/17/2023]
Abstract
Cross-linking of the cell-wall pectin domain rhamnogalacturonan-II (RG-II) via boron bridges between apiose residues is essential for normal plant growth and development, but little is known about its mechanism or reversibility. We characterized the making and breaking of boron bridges in vivo and in vitro at 'apoplastic' pH. RG-II (13-26 μm) was incubated in living Rosa cell cultures and cell-free media with and without 1.2 mm H3 BO3 and cationic chaperones (Ca2+ , Pb2+ , polyhistidine, or arabinogalactan-protein oligopeptides). The cross-linking status of RG-II was monitored electrophoretically. Dimeric RG-II was stable at pH 2.0-7.0 in vivo and in vitro. In-vitro dimerization required a 'catalytic' cation at all pHs tested (1.75-7.0); thus, merely neutralizing the negative charge of RG-II (at pH 1.75) does not enable boron bridging. Pb2+ (20-2500 μm) was highly effective at pH 1.75-4.0, but not 4.75-7.0. Cationic peptides were effective at approximately 1-30 μm; higher concentrations caused less dimerization, probably because two RG-IIs then rarely bonded to the same peptide molecule. Peptides were ineffective at pH 1.75, their pH optimum being 2.5-4.75. d-Apiose (>40 mm) blocked RG-II dimerization in vitro, but did not cleave existing boron bridges. Rosa cells did not take up d-[U-14 C]apiose; therefore, exogenous apiose would block only apoplastic RG-II dimerization in vivo. In conclusion, apoplastic pH neither broke boron bridges nor prevented their formation. Thus boron-starved cells cannot salvage boron from RG-II, and 'acid growth' is not achieved by pH-dependent monomerization of RG-II. Divalent metals and cationic peptides catalyse RG-II dimerization via co-ordinate and ionic bonding respectively (possible and impossible, respectively, at pH 1.75). Exogenous apiose may be useful to distinguish intra- and extra-protoplasmic dimerization.
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Affiliation(s)
- Rifat Ara Begum
- The Edinburgh Cell Wall GroupInstitute of Molecular Plant Sciences, The University of EdinburghDaniel Rutherford Building, The King's Buildings, Max Born CrescentEdinburghEH9 3BFUK
- Present address:
Department of Biochemistry and Molecular Biology, Faculty of Biological SciencesUniversity of DhakaCurzon HallDhaka1000Bangladesh
| | - David J. Messenger
- The Edinburgh Cell Wall GroupInstitute of Molecular Plant Sciences, The University of EdinburghDaniel Rutherford Building, The King's Buildings, Max Born CrescentEdinburghEH9 3BFUK
- Present address:
Unilever U.K. Central Resources LimitedColworth Science ParkSharnbrookMK44 1LQUK
| | - Stephen C. Fry
- The Edinburgh Cell Wall GroupInstitute of Molecular Plant Sciences, The University of EdinburghDaniel Rutherford Building, The King's Buildings, Max Born CrescentEdinburghEH9 3BFUK
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Olorunleke SO, Kirchner M, Duggett N, AbuOun M, Okorie-Kanu OJ, Stevens K, Card RM, Chah KF, Nwanta JA, Brunton LA, Anjum MF. Molecular characterization of extended spectrum cephalosporin resistant Escherichia coli isolated from livestock and in-contact humans in Southeast Nigeria. Front Microbiol 2022; 13:937968. [PMID: 35935201 PMCID: PMC9354541 DOI: 10.3389/fmicb.2022.937968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/05/2022] [Indexed: 11/20/2022] Open
Abstract
The rise in antimicrobial resistance (AMR) in bacteria is reducing therapeutic options for livestock and human health, with a paucity of information globally. To fill this gap, a One-Health approach was taken by sampling livestock on farms (n = 52), abattoir (n = 8), and animal markets (n = 10), and in-contact humans in Southeast Nigeria. Extended spectrum cephalosporin (ESC)-resistant (ESC-R) Escherichia coli was selectively cultured from 975 healthy livestock faecal swabs, and hand swabs from in-contact humans. Antimicrobial susceptibility testing (AST) was performed on all ESC-R E. coli. For isolates showing a multi-drug resistance (MDR) phenotype (n = 196), quantitative real-time PCR (qPCR) was performed for confirmation of extended-spectrum β-lactamase (ESBL) and carbapenemase genes. Whole-genome sequencing (WGS) was performed on a subset (n = 157) for detailed molecular characterisation. The results showed ESC-R E. coli was present in 41.2% of samples, with AST results indicating 48.8% of isolates were phenotypically MDR. qPCR confirmed presence of ESBL genes, with blaCTX-M present in all but others in a subset [blaTEM (62.8%) and blaSHV (0.5%)] of isolates; none harboured transferable carbapenemase genes. Multi-locus sequence typing identified 34 Sequence Types (ST) distributed among different sampling levels; ST196 carrying blaCTX-M-55 was predominant in chickens. Large numbers of single nucleotide polymorphisms (SNPs) in the core genome of isolates, even within the same clade by phylogenetic analysis, indicated high genetic diversity. AMR genotyping indicated the predominant blaCTX-M variant was blaCTX-M-15 (87.9%), although blaCTX-M-55, blaCTX-M-64, and blaCTX-M-65 were present; it was notable that blaCTX-M-1, common in livestock, was absent. Other predominant AMR genes included: sul2, qnrS1, strB, blaTEM-1b, tetA-v2, and dfrA14, with prevalence varying according to host livestock species. A blaCTX-M-15 harbouring plasmid from livestock isolates in Ebonyi showed high sequence identity to one from river/sewage water in India, indicating this ESBL plasmid to be globally disseminated, being present beyond the river environment. In conclusion, ESC-R E. coli was widespread in livestock and in-contact humans from Southeast Nigeria. WGS data indicated the isolates were genetically highly diverse, probably representing true diversity of wild type E. coli; they were likely to be MDR with several harbouring blaCTX-M-15. Surprisingly, human isolates had highest numbers of AMR genes and pigs the least.
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Affiliation(s)
- Solomon O. Olorunleke
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
- Department of Veterinary Public Health and Preventive Medicine, University of Nigeria, Nsukka, Enugu, Nigeria
- Department of Animal Science, Ebonyi State University, Abakaliki, Nigeria
| | - Miranda Kirchner
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Nicholas Duggett
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
- School of Health and Life Science, Teesside University, Middlesbrough, United Kingdom
| | - Manal AbuOun
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Onyinye J. Okorie-Kanu
- Department of Veterinary Public Health and Preventive Medicine, University of Nigeria, Nsukka, Enugu, Nigeria
| | - Kim Stevens
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Roderick M. Card
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Kennedy Foinkfu Chah
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Enugu, Nigeria
| | - John A. Nwanta
- Department of Veterinary Public Health and Preventive Medicine, University of Nigeria, Nsukka, Enugu, Nigeria
| | - Lucy A. Brunton
- Veterinary Epidemiology, Economics and Public Health Group, Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Muna F. Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
- *Correspondence: Muna F. Anjum
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Borna RS, Murchie EH, Pyke KA, Roberts JA, Gonzalez‐Carranza ZH. The rice EP3 and OsFBK1 E3 ligases alter plant architecture and flower development, and affect transcript accumulation of microRNA pathway genes and their targets. Plant Biotechnol J 2022; 20:297-309. [PMID: 34543503 PMCID: PMC8753360 DOI: 10.1111/pbi.13710] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/13/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
ERECTA PANICLE 3 (EP3) and ORYZA SATIVA F-BOX KELCH 1 (OsFBK1) proteins share 57% and 54% sequence identity with the Arabidopsis F-box protein HAWAIIAN SKIRT (HWS). Previously we showed that EP3 is a functional orthologue of HWS. Here we demonstrate that OsFBK1 is another functional orthologue of HWS and show the complexity of interaction between EP3 and OsFBK1 genes at different developmental stages of the plant. qRT-PCR expression analyses and studies of EP3-GFP and OsFBK1-RFP promoter reporter lines demonstrate that although EP3 and OsFBK1 expression can be detected in the same tissues some cells exclusively express EP3 or OsFBK1 whilst others co-express both genes. Loss, reduction or gain-of-function lines for EP3 and OsFBK1, show that EP3 and OsFBK1 affect plant architecture, organ size, floral organ number and size, floral morphology, pollen viability, grain size and weight. We have identified the putative orthologue genes of the rice microRNA pathway for ORYZA SATIVA DAWDLE (OsDDL) and ORYZA SATIVA SERRATE (OsSE), and demonstrated that EP3 and OsFBK1 affect their transcript levels as well as those of CROWN ROOT DEFECT 1/ORYZA SATIVA Exportin-5 HASTY (CRD1/OsHST), ORYZA SATIVA DICER-LIKE 1 (OsDCL) and ORYZA SATIVA WEAVY LEAF1 (OsWAF1). We show that EP3 affects OsPri-MIR164, OsNAM1 and OsNAC1 transcript levels. OsNAC1 transcripts are modified by OsFBK1, suggesting two independent regulatory pathways, one via EP3 and OsMIR164 and the other via OsFBK1. Our data propose that EP3 and OsFBK1 conjointly play similar roles in rice to how HWS does in Arabidopsis.
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Affiliation(s)
- Rita S. Borna
- Plant and Crop Sciences DivisionSchool of BiosciencesUniversity of NottinghamNottinghamUK
- Present address:
Department of BotanyUniversity of DhakaDhaka1000Bangladesh
| | - Erik H. Murchie
- Plant and Crop Sciences DivisionSchool of BiosciencesUniversity of NottinghamNottinghamUK
| | - Kevin A. Pyke
- Plant and Crop Sciences DivisionSchool of BiosciencesUniversity of NottinghamNottinghamUK
| | - Jeremy A. Roberts
- Plant and Crop Sciences DivisionSchool of BiosciencesUniversity of NottinghamNottinghamUK
- Present address:
Faculty of Science and EngineeringSchool of Biological & Marine SciencesUniversity of PlymouthDevonUK
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Ng CK, Putra SL, Kennerley J, Habgood R, Roy RA, Raymond JL, Thompson IP, Huang WE. Genetic engineering biofilms in situ using ultrasound-mediated DNA delivery. Microb Biotechnol 2021; 14:1580-1593. [PMID: 33993638 PMCID: PMC8313276 DOI: 10.1111/1751-7915.13823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/15/2021] [Accepted: 04/17/2021] [Indexed: 11/27/2022] Open
Abstract
The ability to directly modify native and established biofilms has enormous potential in understanding microbial ecology and application of biofilm in 'real-world' systems. However, efficient genetic transformation of established biofilms at any scale remains challenging. In this study, we applied an ultrasound-mediated DNA delivery (UDD) technique to introduce plasmid to established non-competent biofilms in situ. Two different plasmids containing genes coding for superfolder green fluorescent protein (sfGFP) and the flavin synthesis pathway were introduced into established bacterial biofilms in microfluidic flow (transformation efficiency of 3.9 ± 0.3 × 10-7 cells in biofilm) and microbial fuel cells (MFCs), respectively, both employing UDD. Gene expression and functional effects of genetically modified bacterial biofilms were observed, where some cells in UDD-treated Pseudomonas putida UWC1 biofilms expressed sfGFP in flow cells and UDD-treated Shewanella oneidensis MR-1 biofilms generated significantly (P < 0.05) greater (61%) bioelectricity production (21.9 ± 1.2 µA cm-2 ) in MFC than a wild-type control group (~ 13.6 ± 1.6 µA cm-2 ). The effects of UDD were amplified in subsequent growth under selection pressure due to antibiotic resistance and metabolism enhancement. UDD-induced gene transfer on biofilms grown in both microbial flow cells and MFC systems was successfully demonstrated, with working volumes of 0.16 cm3 and 300 cm3 , respectively, demonstrating a significant scale-up in operating volume. This is the first study to report on a potentially scalable direct genetic engineering method for established non-competent biofilms, which can be exploited in enhancing their capability towards environmental, industrial and medical applications.
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Affiliation(s)
- Chun Kiat Ng
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
- Oxford Suzhou Centre for Advanced Research388 Ruoshui Road, Suzhou Industrial ParkJiangsu215123P.R. China
| | - Samuel L. Putra
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
| | - Joseph Kennerley
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
| | - Robert Habgood
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
| | - Ronald A. Roy
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
- Oxford Suzhou Centre for Advanced Research388 Ruoshui Road, Suzhou Industrial ParkJiangsu215123P.R. China
| | - Jason L. Raymond
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
- Oxford Suzhou Centre for Advanced Research388 Ruoshui Road, Suzhou Industrial ParkJiangsu215123P.R. China
| | - Ian P. Thompson
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
- Oxford Suzhou Centre for Advanced Research388 Ruoshui Road, Suzhou Industrial ParkJiangsu215123P.R. China
| | - Wei E. Huang
- Department of Engineering ScienceUniversity of OxfordParks RoadOxfordOX1 3PJUK
- Oxford Suzhou Centre for Advanced Research388 Ruoshui Road, Suzhou Industrial ParkJiangsu215123P.R. China
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