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  • Oxford University Press  (21)
  • eLife Sciences Publications  (7)
  • International Union of Crystallography  (4)
  • International Union of Crystallography (IUCr)  (4)
  • 1
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    Adult chondrogenesis and spontaneous cartilage repair in the skate, Leucoraja erinacea (2020)
    eLife Sciences Publications
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Marconi, A., Hancock-Ronemus, A., & Gillis, J. A. Adult chondrogenesis and spontaneous cartilage repair in the skate, Leucoraja erinacea. Elife, 9, (2020): e53414, doi:10.7554/elife.53414.
    Description: Mammalian articular cartilage is an avascular tissue with poor capacity for spontaneous repair. Here, we show that embryonic development of cartilage in the skate (Leucoraja erinacea) mirrors that of mammals, with developing chondrocytes co-expressing genes encoding the transcription factors Sox5, Sox6 and Sox9. However, in skate, transcriptional features of developing cartilage persist into adulthood, both in peripheral chondrocytes and in cells of the fibrous perichondrium that ensheaths the skeleton. Using pulse-chase label retention experiments and multiplexed in situ hybridization, we identify a population of cycling Sox5/6/9+ perichondral progenitor cells that generate new cartilage during adult growth, and we show that persistence of chondrogenesis in adult skates correlates with ability to spontaneously repair cartilage injuries. Skates therefore offer a unique model for adult chondrogenesis and cartilage repair and may serve as inspiration for novel cell-based therapies for skeletal pathologies, such as osteoarthritis.
    Description: The authors acknowledge Dr. Kate Rawlinson, Prof. Brian Hall, Dr. Kate Criswell, Dr. Victoria Sleight, Christine Hirschberger and Jenaid Rees for a collective many years of helpful discussion around the topic of cartilage development and repair, Janice Simmons, Dan Calzarette, Scott Bennett, David Remsen and the staff of the Marine Biological Laboratory Marine Resources Center for expert assistance with animal maintenance and care, and Helen Skelton (Dept. of Pathology, University of Cambridge) and Debbie Sabin (Dept. of Veterinary Medicine, University of Cambridge) for assistance with adult skate tissue processing. This work was funded by the Wellcome Trust (PhD studentship 102175/Z/13/Z to AM), the Royal Society (University Research Fellowships UF130182 and URF/R/191007 and Research Fellows Enhancement Award RGF\EA\180087 to JAG), the Isaac Newton Trust (award 14.23z to JAG) and by a research grant from the Fisheries Society of the British Isles (to JAG).
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 2
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    Gill developmental program in the teleost mandibular arch (2022)
    eLife Sciences Publications
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    Publication Date: 2022-10-18
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Thiruppathy, M., Fabian, P., Gillis, J. A., & Crump, J. G. Gill developmental program in the teleost mandibular arch. Elife, 11, (2022): e78170, https://doi.org/10.7554/eLife.78170.
    Description: Whereas no known living vertebrate possesses gills derived from the jaw-forming mandibular arch, it has been proposed that the jaw arose through modifications of an ancestral mandibular gill. Here, we show that the zebrafish pseudobranch, which regulates blood pressure in the eye, develops from mandibular arch mesenchyme and first pouch epithelia and shares gene expression, enhancer utilization, and developmental gata3 dependence with the gills. Combined with work in chondrichthyans, our findings in a teleost fish point to the presence of a mandibular pseudobranch with serial homology to gills in the last common ancestor of jawed vertebrates, consistent with a gill origin of vertebrate jaws.
    Description: National Institute of Dental and Craniofacial Research (5R35DE027550) - J. Gage Crump National Institute of Dental and Craniofacial Research (5K99DE029858) - Peter Fabian National Institute of Dental and Craniofacial Research (1F31DE030706) - Mathi Thiruppathy Royal Society (UF130182) & Royal Society (URF\R\191007) - J. Andrew Gillis
    Repository Name: Woods Hole Open Access Server
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  • 3
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    Resegmentation is an ancestral feature of the gnathostome vertebral skeleton (2020)
    eLife Sciences Publications
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Criswell, K. E., & Gillis, J. A. Resegmentation is an ancestral feature of the gnathostome vertebral skeleton. Elife, 9, (2020): e51696, doi:10.7554/elife.51696.
    Description: The vertebral skeleton is a defining feature of vertebrate animals. However, the mode of vertebral segmentation varies considerably between major lineages. In tetrapods, adjacent somite halves recombine to form a single vertebra through the process of ‘resegmentation’. In teleost fishes, there is considerable mixing between cells of the anterior and posterior somite halves, without clear resegmentation. To determine whether resegmentation is a tetrapod novelty, or an ancestral feature of jawed vertebrates, we tested the relationship between somites and vertebrae in a cartilaginous fish, the skate (Leucoraja erinacea). Using cell lineage tracing, we show that skate trunk vertebrae arise through tetrapod-like resegmentation, with anterior and posterior halves of each vertebra deriving from adjacent somites. We further show that tail vertebrae also arise through resegmentation, though with a duplication of the number of vertebrae per body segment. These findings resolve axial resegmentation as an ancestral feature of the jawed vertebrate body plan.
    Description: Royal Society (NF160762) Katharine E Criswell Royal Society (UF130182) J. Andrew Gillis Marine Biological Laboratory Katharine E. Criswell
    Repository Name: Woods Hole Open Access Server
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  • 4
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    Embryonic origin and serial homology of gill arches and paired fins in the skate, Leucoraja erinacea (2021)
    eLife Sciences Publications
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sleight, V. A., & Gillis, J. A. Embryonic origin and serial homology of gill arches and paired fins in the skate, Leucoraja erinacea. Elife, 9, (2020): e60635, doi:10.7554/eLife.60635.
    Description: Paired fins are a defining feature of the jawed vertebrate body plan, but their evolutionary origin remains unresolved. Gegenbaur proposed that paired fins evolved as gill arch serial homologues, but this hypothesis is now widely discounted, owing largely to the presumed distinct embryonic origins of these structures from mesoderm and neural crest, respectively. Here, we use cell lineage tracing to test the embryonic origin of the pharyngeal and paired fin skeleton in the skate (Leucoraja erinacea). We find that while the jaw and hyoid arch skeleton derive from neural crest, and the pectoral fin skeleton from mesoderm, the gill arches are of dual origin, receiving contributions from both germ layers. We propose that gill arches and paired fins are serially homologous as derivatives of a continuous, dual-origin mesenchyme with common skeletogenic competence, and that this serial homology accounts for their parallel anatomical organization and shared responses to axial patterning signals.
    Description: This project benefited from technical advice from Dr. Matt Wayland and use of the Imaging Facility, Department of Zoology, supported by a Sir Isaac Newton Trust Research Grant (18.07ii(c)). This research was supported by a Royal Society University Research Fellowship (UF130182) and grants from the Leverhulme Trust (RPG-2016–373) and the University of Cambridge Sir Isaac Newton Trust (14.23z) to JAG, and by a Junior Research Fellowship from Wolfson College, Cambridge and Whitman Early Career Fellowship from the Marine Biology Laboratory to VAS.
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw (2021)
    Oxford University Press
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hirschberger, C., Sleight, V. A., Criswell, K. E., Clark, S. J., & Gillis, J. A. Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw. Molecular Biology and Evolution, (2021): msab123, https://doi.org/10.1093/molbev/msab123
    Description: The origin of the jaw is a long-standing problem in vertebrate evolutionary biology. Classical hypotheses of serial homology propose that the upper and lower jaw evolved through modifications of dorsal and ventral gill arch skeletal elements, respectively. If the jaw and gill arches are derived members of a primitive branchial series, we predict that they would share common developmental patterning mechanisms. Using candidate and RNAseq/differential gene expression analyses, we find broad conservation of dorsoventral patterning mechanisms within the developing mandibular, hyoid and gill arches of a cartilaginous fish, the skate (Leucoraja erinacea). Shared features include expression of genes encoding members of the ventralising BMP and endothelin signalling pathways and their effectors, the joint markers nkx3.2 and gdf5 and pro-chondrogenic transcription factor barx1, and the dorsal territory marker pou3f3. Additionally, we find that mesenchymal expression of eya1/six1 is an ancestral feature of the mandibular arch of jawed vertebrates, while differences in notch signalling distinguish the mandibular and gill arches in skate. Comparative transcriptomic analyses of mandibular and gill arch tissues reveal additional genes differentially expressed along the dorsoventral axis of the pharyngeal arches, including scamp5 as a novel marker of the dorsal mandibular arch, as well as distinct transcriptional features of mandibular and gill arch muscle progenitors and developing gill buds. Taken together, our findings reveal conserved patterning mechanisms in the pharyngeal arches of jawed vertebrates, consistent with serial homology of their skeletal derivatives, as well as unique transcriptional features that may underpin distinct jaw and gill arch morphologies.
    Description: This work was supported by a Biotechnology and Biological Sciences Research Council Doctoral Training Partnership studentship to CH, by a Wolfson College Junior Research Fellowship and MBL Whitman Early Career Fellowship to VAS, and by a Royal Society University Research Fellowship (UF130182 and URF\R\191007), Royal Society Research Grant (RG140377) and University of Cambridge Sir Isaac Newton Trust Grant (14.23z) to JAG.
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  • 6
    Electronic Resource
    Electronic Resource
    Note on the statistical approach to the phase problem (1956)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 9 (1956), S. 616-616 
    Details
    ISSN: 0001-5520
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0365110X56001662
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  • 7
    Electronic Resource
    Electronic Resource
    An application of electronic computing to X-ray crystallography (1958)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 11 (1958), S. 833-834 
    Details
    ISSN: 0001-5520
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0365110X5800236X
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  • 8
    Electronic Resource
    Electronic Resource
    Structure-factor relations and phase determination (1948)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 1 (1948), S. 76-80 
    Details
    ISSN: 0001-5520
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0365110X48000211
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  • 9
    Electronic Resource
    Electronic Resource
    The application of the Harker–Kasper method of phase determination (1948)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 1 (1948), S. 174-179 
    Details
    ISSN: 0001-5520
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0365110X48000508
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  • 10
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    Positive and negative forms of replicability in gene network analysis (2016)
    Oxford University Press
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    Publication Date: 2016-03-26
    Description: Motivation: Gene networks have become a central tool in the analysis of genomic data but are widely regarded as hard to interpret. This has motivated a great deal of comparative evaluation and research into best practices. We explore the possibility that this may lead to overfitting in the field as a whole. Results: We construct a model of ‘research communities’ sampling from real gene network data and machine learning methods to characterize performance trends. Our analysis reveals an important principle limiting the value of replication, namely that targeting it directly causes ‘easy’ or uninformative replication to dominate analyses. We find that when sampling across network data and algorithms with similar variability, the relationship between replicability and accuracy is positive (Spearman’s correlation, r s ~0.33) but where no such constraint is imposed, the relationship becomes negative for a given gene function ( r s ~ –0.13). We predict factors driving replicability in some prior analyses of gene networks and show that they are unconnected with the correctness of the original result, instead reflecting replicable biases. Without these biases, the original results also vanish replicably. We show these effects can occur quite far upstream in network data and that there is a strong tendency within protein–protein interaction data for highly replicable interactions to be associated with poor quality control. Availability and implementation: Algorithms, network data and a guide to the code available at: https://github.com/wimverleyen/AggregateGeneFunctionPrediction . Contact: jgillis@cshl.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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