132 research outputs found
Image data of pyrenoids in Chlamydomonas and proto-pyrenoid condensates in higher plant chloroplasts
No full textA collection of image data from the manuscript 'Condensation of Rubisco into a proto-pyrenoid in higher plant chloroplasts' by Nicky Atkinson, Yuwei Mao, Kher Xing Chan and Alistair J. McCormick. The .zip file contains raw data for Figure 1 (confocal and TEM images in Arabidopsis and Chlamydomonas), Figure 3e (Immunogold TEM images of proto-pyrenoid condensates in Arabidopsis) and Supplementary Figure 2c (TEM Images of pyrenoids in wild-type Chlamydomonas cells).
## Technical note ##
Files in the "Rubisco antibody" folder with the '.dm3' filename extension can be viewed using ImageJ/Fiji see https://imagej.nih.gov/ij/
Image data of pyrenoids in Chlamydomonas and proto-pyrenoid condensates in higher plant chloroplasts
No full textA collection of image data from the manuscript 'Condensation of Rubisco into a proto-pyrenoid in higher plant chloroplasts' by Nicky Atkinson, Yuwei Mao, Kher Xing Chan and Alistair J. McCormick. The .zip file contains raw data for Figure 1 (confocal and TEM images in Arabidopsis and Chlamydomonas), Figure 3e (Immunogold TEM images of proto-pyrenoid condensates in Arabidopsis) and Supplementary Figure 2c (TEM Images of pyrenoids in wild-type Chlamydomonas cells). ## Technical note ## Files in the "Rubisco antibody" folder with the '.dm3' filename extension can be viewed using ImageJ/Fiji see https://imagej.nih.gov/ij/ .McCormick, Alistair; Atkinson, Nicky; Kher Xing, Chan. (2020). Image data of pyrenoids in Chlamydomonas and proto-pyrenoid condensates in higher plant chloroplasts, [image]. University of Edinburgh. School of Biological Sciences. Institute of Molecular Plant Sciences. https://doi.org/10.7488/ds/2945
Author Correction: Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction
No full textIn the original version of this Article, Martin C. J. Bootsma, Perry J. van Genderen, Abraham Goorhuis, Martin Grobusch, Nicky Molhoek, Astrid M. L. Oude Lashof, Ellen E. Stobberingh & Henri A. Verbrugh were incorrectly listed as the COMBAT consortium. This error has now been corrected in the HTML and PDF versions of the Article, and in the accompanying supplementary material.</p
Author Correction: Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction (Scientific Reports, (2017), 7, 1, (15364), 10.1038/s41598-017-15539-7)
No full textIn the original version of this Article, Martin C. J. Bootsma, Perry J. van Genderen, Abraham Goorhuis, Martin Grobusch, Nicky Molhoek, Astrid M. L. Oude Lashof, Ellen E. Stobberingh & Henri A. Verbrugh were incorrectly listed as the COMBAT consortium. This error has now been corrected in the HTML and PDF versions of the Article, and in the accompanying supplementary material
Author Correction: Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction (vol 7, 15364, 2017): Global phylogenetic analysis of Escherichia coli and plasmids carrying the mcr-1 gene indicates bacterial diversity but plasmid restriction (Scientific Reports, (2017), 7, 1, (15364), 10.1038/s41598-017-15539-7)
No full textIn the original version of this Article, Martin C. J. Bootsma, Perry J. van Genderen, Abraham Goorhuis, Martin Grobusch, Nicky Molhoek, Astrid M. L. Oude Lashof, Ellen E. Stobberingh & Henri A. Verbrugh were incorrectly listed as the COMBAT consortium. This error has now been corrected in the HTML and PDF versions of the Article, and in the accompanying supplementary material
Asking more of qualitative synthesis: a response to Sally Thorne
No full textThis is the author accepted manuscript. The final version is available from SAGE Publications via the DOI in this record.We continue the conversation initiated by Sally Thorne’s observations about ‘metasynthetic madness’. We note that the variety of labels used to describe qualitative syntheses often reflect authors’ disciplines and geographical locations. The purpose of systematic literature searching is to redress authors’ lack of citation of relevant earlier work and to reassure policy makers that qualitative syntheses are systematic and transparent. There is clearly a need to develop other methods of searching to supplement electronic searches. If searches produce large numbers of articles, sampling strategies may be needed to choose which articles to synthesize. The quality of any synthesis is dependent on the quality of the primary articles; both primary research and qualitative synthesis need to move beyond description and towards theory and explanation. Synthesizers need to pay attention to those articles which do not seem to fit their emerging analysis if they are to avoid stifling new ideas.Nicky Britten, Ruth Garside and Julia Frost were partially supported by the National Institute for Health Research (NIHR) Collaboration for Leadership in Applied Health Research and Care South West Peninsula (PenCLAHRC). Catherine Pope is a member of NIHR Collaboration for Leadership in Applied Health Research and Care Wessex (CLAHRC Wessex). Chris Cooper is funded by an NIHR Health Technology Assessment Programme Grant
SAGA1 and SAGA2 promote starch formation around proto-pyrenoids in Arabidopsis chloroplasts
No full textThe pyrenoid is a chloroplastic microcompartment in which most algae and some terrestrial plants condense the primary carboxylase, Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) as part of a CO2-concentrating mechanism that improves the efficiency of CO2 capture. Engineering a pyrenoid-based CO2-concentrating mechanism (pCCM) into C3 crop plants is a promising strategy to enhance yield capacities and resilience to the changing climate. Many pyrenoids are characterized by a sheath of starch plates that is proposed to act as a barrier to limit CO2 diffusion. Recently, we have reconstituted a phase-separated “proto-pyrenoid” Rubisco matrix in the model C3 plant Arabidopsis thaliana using proteins from the alga with the most well-studied pyrenoid, Chlamydomonas reinhardtii [N. Atkinson, Y. Mao, K. X. Chan, A. J. McCormick, Nat. Commun.11, 6303 (2020)]. Here, we describe the impact of introducing the Chlamydomonas proteins StArch Granules Abnormal 1 (SAGA1) and SAGA2, which are associated with the regulation of pyrenoid starch biogenesis and morphology. We show that SAGA1 localizes to the proto-pyrenoid in engineered Arabidopsis plants, which results in the formation of atypical spherical starch granules enclosed within the proto-pyrenoid condensate and adjacent plate-like granules that partially cover the condensate, but without modifying the total amount of chloroplastic starch accrued. Additional expression of SAGA2 further increases the proportion of starch synthesized as adjacent plate-like granules that fully encircle the proto-pyrenoid. Our findings pave the way to assembling a diffusion barrier as part of a functional pCCM in vascular plants, while also advancing our understanding of the roles of SAGA1 and SAGA2 in starch sheath formation and broadening the avenues for engineering starch morphology
The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterization of the innate cellular pathways underlying virus attenuation and enhanced replication
No full textMost RNA viruses infecting mammals and other vertebrates show profound suppression of CpG and UpA dinucleotide frequencies. To investigate this functionally, mutants of the picornavirus, echovirus 7 (E7), were constructed with altered CpG and UpA compositions in two 1.1-1.3 Kbase regions. Those with increased frequencies of CpG and UpA showed impaired replication kinetics and higher RNA/infectivity ratios compared with wild-type virus. Remarkably, mutants with CpGs and UpAs removed showed enhanced replication, larger plaques and rapidly outcompeted wild-type virus on co-infections. Luciferase-expressing E7 sub-genomic replicons with CpGs and UpAs removed from the reporter gene showed 100-fold greater luminescence. E7 and mutants were equivalently sensitive to exogenously added interferon-β, showed no evidence for differential recognition by ADAR1 or pattern recognition receptors RIG-I, MDA5 or PKR. However, kinase inhibitors roscovitine and C16 partially or entirely reversed the attenuated phenotype of high CpG and UpA mutants, potentially through inhibition of currently uncharacterized pattern recognition receptors that respond to RNA composition. Generating viruses with enhanced replication kinetics has applications in vaccine production and reporter gene construction. More fundamentally, the findings introduce a new evolutionary paradigm where dinucleotide composition of viral genomes is subjected to selection pressures independently of coding capacity and profoundly influences host-pathogen interactions
A mixed-methods Quick Strike research protocol to learn about children with complex health conditions and their families
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