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Mons B, Neylon C, Velterop J, Dumontier M, da Silva Santos LOB, Wilkinson MD. Cloudy, increasingly FAIR; revisiting the FAIR Data guiding principles for the European Open Science Cloud. ACTA ACUST UNITED AC 2017. [DOI: 10.3233/isu-170824] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Neylon C. Communities need journals. NOTES AND RECORDS: THE ROYAL SOCIETY JOURNAL OF THE HISTORY OF SCIENCE 2016; 70:383-5. [PMID: 30124267 PMCID: PMC5095358 DOI: 10.1098/rsnr.2016.0032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Neylon C, Chan L. Exploring the opportunities and challenges of implementing open research strategies within development institutions. RESEARCH IDEAS AND OUTCOMES 2016. [DOI: 10.3897/rio.2.e8880] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Byrnes J, Baskerville E, Caron B, Neylon C, Tenopir C, Schildhauer M, Budden A, Aarssen L, Lortie C. The four pillars of scholarly publishing: The future and a foundation. IDEAS IN ECOLOGY AND EVOLUTION 2014. [DOI: 10.4033/iee.2014.7.7.f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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Neylon C. Architecting the future of research communication: building the models and analytics for an open access future. PLoS Biol 2013; 11:e1001691. [PMID: 24167448 PMCID: PMC3805469 DOI: 10.1371/journal.pbio.1001691] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
As part of our Tenth Anniversary PLOS Biology Collection, PLOS' director of advocacy, Cameron Neylon, expounds on the need to improve and focus on our sharing infrastructure to maximize the reach of research communication.
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Abstract
It is unlikely that there is any single objective measure of merit, so research assessment therefore requires new multivariate metrics that reflect the context of research, regardless of discipline.
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Milsted AJ, Hale JR, Frey JG, Neylon C. LabTrove: a lightweight, web based, laboratory "blog" as a route towards a marked up record of work in a bioscience research laboratory. PLoS One 2013; 8:e67460. [PMID: 23935832 PMCID: PMC3720848 DOI: 10.1371/journal.pone.0067460] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 05/17/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The electronic laboratory notebook (ELN) has the potential to replace the paper notebook with a marked-up digital record that can be searched and shared. However, it is a challenge to achieve these benefits without losing the usability and flexibility of traditional paper notebooks. We investigate a blog-based platform that addresses the issues associated with the development of a flexible system for recording scientific research. METHODOLOGY/PRINCIPAL FINDINGS We chose a blog-based approach with the journal characteristics of traditional notebooks in mind, recognizing the potential for linking together procedures, materials, samples, observations, data, and analysis reports. We implemented the LabTrove blog system as a server process written in PHP, using a MySQL database to persist posts and other research objects. We incorporated a metadata framework that is both extensible and flexible while promoting consistency and structure where appropriate. Our experience thus far is that LabTrove is capable of providing a successful electronic laboratory recording system. CONCLUSIONS/SIGNIFICANCE LabTrove implements a one-item one-post system, which enables us to uniquely identify each element of the research record, such as data, samples, and protocols. This unique association between a post and a research element affords advantages for monitoring the use of materials and samples and for inspecting research processes. The combination of the one-item one-post system, consistent metadata, and full-text search provides us with a much more effective record than a paper notebook. The LabTrove approach provides a route towards reconciling the tensions and challenges that lie ahead in working towards the long-term goals for ELNs. LabTrove, an electronic laboratory notebook (ELN) system from the Smart Research Framework, based on a blog-type framework with full access control, facilitates the scientific experimental recording requirements for reproducibility, reuse, repurposing, and redeployment.
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Sanders MR, Clifton LA, Neylon C, Frazier RA, Green RJ. Selected wheat seed defense proteins exhibit competitive binding to model microbial lipid interfaces. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:6890-6900. [PMID: 23767912 DOI: 10.1021/jf401336a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Puroindolines (Pins) and purothionins (Pths) are basic, amphiphilic, cysteine-rich wheat proteins that play a role in plant defense against microbial pathogens. This study examined the co-adsorption and sequential addition of Pins (Pin-a, Pin-b, and a mutant form of Pin-b with Trp-44 to Arg-44 substitution) and β-purothionin (β-Pth) model anionic lipid layers using a combination of surface pressure measurements, external reflection FTIR spectroscopy, and neutron reflectometry. Results highlighted differences in the protein binding mechanisms and in the competitive binding and penetration of lipid layers between respective Pins and β-Pth. Pin-a formed a blanket-like layer of protein below the lipid surface that resulted in the reduction or inhibition of β-Pth penetration of the lipid layer. Wild-type Pin-b participated in co-operative binding with β-Pth, whereas the mutant Pin-b did not bind to the lipid layer in the presence of β-Pth. The results provide further insight into the role of hydrophobic and cationic amino acid residues in antimicrobial activity.
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Clifton LA, Sanders M, Kinane C, Arnold T, Edler KJ, Neylon C, Green RJ, Frazier RA. The role of protein hydrophobicity in thionin-phospholipid interactions: a comparison of α1 and α2-purothionin adsorbed anionic phospholipid monolayers. Phys Chem Chem Phys 2013; 14:13569-79. [PMID: 22955734 DOI: 10.1039/c2cp42029e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The plant defence proteins α1- and α2-purothionin (Pth) are type 1 thionins from common wheat (Triticum aestivum). These highly homologous proteins possess characteristics common amongst antimicrobial peptides and proteins, that is, cationic charge, amphiphilicity and hydrophobicity. Both α1- and α2-Pth possess the same net charge, but differ in relative hydrophobicity as determined by C18 reversed phase HPLC. Brewster angle microscopy, X-ray and neutron reflectometry, external reflection FTIR and associated surface pressure measurements demonstrated that α1 and α2-Pth interact strongly with condensed phase 1,2-dipalmitoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (DPPG) monolayers at the air/liquid interface. Both thionins disrupted the in-plane structure of the anionic phospholipid monolayers, removing lipid during this process and both penetrated the lipid monolayer in addition to adsorbing as a single protein layer to the lipid head-group. However, analysis of the interfacial structures revealed that the α2-Pth showed faster disruption of the lipid film and removed more phospholipid (12%) from the interface than α1-Pth. Correlating the protein properties and lipid binding activity suggests that hydrophobicity plays a key role in the membrane lipid removal activity of thionins.
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Neylon C, Aerts J, Brown CT, Coles SJ, Hatton L, Lemire D, Millman KJ, Murray-Rust P, Perez F, Saunders N, Shah N, Smith A, Varoquaux G, Willighagen E. Changing computational research. The challenges ahead. SOURCE CODE FOR BIOLOGY AND MEDICINE 2012; 7:2. [PMID: 22640749 PMCID: PMC3441321 DOI: 10.1186/1751-0473-7-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 05/28/2012] [Indexed: 11/10/2022]
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Neylon C. Three stories about the conduct of science: Past, future, and present. J Cheminform 2011; 3:35. [PMID: 21999290 PMCID: PMC3198952 DOI: 10.1186/1758-2946-3-35] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 10/14/2011] [Indexed: 11/12/2022] Open
Abstract
In this piece I would like to tell a few stories; three stories to be precise. Firstly I want to explain where I am, where I've come from and what has led me to the views that I hold today. I find myself at an interesting point in my life and career at the same point as the research community is undergoing massive change. The second story is one of what the world might look like at some point in the future. What might we achieve? What might it look like? And what will be possible? Finally I want to ask the question of how we get there from here. What is the unifying idea or movement that actually has the potential to carry us forward in a positive way? At the end of this I'm going to ask you, the reader, to commit to something as part of the process of making that happen.
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Neylon C. Time for total openness. New Sci 2011. [DOI: 10.1016/s0262-4079(11)62148-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Smith WS, Hale JR, Neylon C. Applying neutral drift to the directed molecular evolution of a β-glucuronidase into a β-galactosidase: Two different evolutionary pathways lead to the same variant. BMC Res Notes 2011; 4:138. [PMID: 21548964 PMCID: PMC3118342 DOI: 10.1186/1756-0500-4-138] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 05/06/2011] [Indexed: 01/31/2023] Open
Abstract
Background Directed protein evolution has been used to modify protein activity and research has been carried out to enhance the production of high quality mutant libraries. Many theoretical approaches suggest that allowing a population to undergo neutral selection may be valuable in directed evolution experiments. Findings Here we report on an investigation into the value of neutral selection in a classical model system for directed evolution, the conversion of the E. coli β-glucuronidase to a β-galactosidase activity. We find that neutral selection, i.e. selection for retaining glucuronidase activity, can efficiently identify the majority of sites of mutation that have been identified as beneficial for galactosidase activity in previous experiments. Each variant demonstrating increased galactosidase activity identified by our neutral drift experiments contained a mutation at one of four sites, T509, S557, N566 or W529. All of these sites have previously been identified using direct selection for beta galactosidase activity. Conclusions Our results are consistent with others that show that a neutral selection approach can be effective in selecting improved variants. However, we interpret our results to show that neutral selection is, in this case, not a more efficient approach than conventional directed evolution approaches. However, the neutral approach is likely to be beneficial when the resulting library can be screened for a range of related activities. More detailed statistical studies to resolve the apparent differences between this system and others are likely to be a fruitful avenue for future research.
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Charlton TR, Coleman RLS, Dalgliesh RM, Kinane CJ, Neylon C, Langridge S, Plomp J, Webb NGJ, Webster JRP. Advances in Neutron Reflectometry at ISIS. ACTA ACUST UNITED AC 2011. [DOI: 10.1080/10448632.2011.569278] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Clifton LA, Sanders MR, Castelletto V, Rogers SE, Heenan RK, Neylon C, Frazier RA, Green RJ. Puroindoline-a, a lipid binding protein from common wheat, spontaneously forms prolate protein micelles in solution. Phys Chem Chem Phys 2011; 13:8881-8. [PMID: 21451840 DOI: 10.1039/c0cp02247k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The self-assembly in solution of puroindoline-a (Pin-a), an amphiphilic lipid binding protein from common wheat, was investigated by small angle neutron scattering, dynamic light scattering and size exclusion chromatography. Pin-a was found to form monodisperse prolate ellipsoidal micelles with a major axial radius of 112 ± 4.5 Å and minor axial radius of 40.4 ± 0.18 Å. These protein micelles were formed by the spontaneous self-assembly of 38 Pin-a molecules in solution and were stable over a wide pH range (3.5-11) and at elevated temperatures (20-65 °C). Pin-a micelles could be disrupted upon addition of the non-ionic surfactant dodecyl-β-maltoside, suggesting that the protein self-assembly is driven by hydrophobic forces, consisting of intermolecular interactions between Trp residues located within a well-defined Trp-rich domain of Pin-a.
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Broder GR, Ranasinghe RT, Neylon C, Morgan H, Roach PL. Kinetics and Thermodynamics of Biotinylated Oligonucleotide Probe Binding to Particle-Immobilized Avidin and Implications for Multiplexing Applications. Anal Chem 2011; 83:2005-11. [DOI: 10.1021/ac102762q] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Clifton LA, Sanders MR, Hughes AV, Neylon C, Frazier RA, Green RJ. Lipid binding interactions of antimicrobial plant seed defence proteins: puroindoline-a and β-purothionin. Phys Chem Chem Phys 2011; 13:17153-62. [DOI: 10.1039/c1cp21799b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Brewer A, Siligardi G, Neylon C, Stulz E. Introducing structural flexibility into porphyrin-DNA zipper arrays. Org Biomol Chem 2010; 9:777-82. [PMID: 21103551 DOI: 10.1039/c0ob00535e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A more flexible nucleotide building block for the synthesis of new DNA based porphyrin-zipper arrays is described. Changing the rigid acetylene linker between the porphyrin substituent and the 2'-deoxyuridine to a more flexible propargyl amide containing linkage leads in part to an increased duplex stability. The CD spectra reveal different electronic interactions between the porphyrins depending on the type of linker used. Molecular modelling suggests large variation of the relative orientation of the porphyrins within the major groove of the DNA. The porphyrins can be metallated post-synthetically with different metals as shown with zinc, cobalt and copper. The spectroscopic features do not alter drastically upon metallation apart from the CD spectra, and the stability of the metal complex is highly dependent on the nature of the metal. As shown by CD spectroscopy, the zinc porphyrin is rapidly demetallated at high temperatures. Globular structure determination using SAXS indicates that a molecular assembly comprised of a two to four helical bundle dominates in solution at higher concentrations (≥50 μM) which is not observed by spectroscopy at lower concentrations (≤1 μM).
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Abstract
The authors discuss the value of article-level metrics in determining an article's scientific impact.
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Neylon C. Head in the clouds: Re-imagining the experimental laboratory record for the web-based networked world. AUTOMATED EXPERIMENTATION 2009; 1:3. [PMID: 20098590 PMCID: PMC2809323 DOI: 10.1186/1759-4499-1-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Accepted: 10/29/2009] [Indexed: 12/04/2022]
Abstract
The means we use to record the process of carrying out research remains tied to the concept of a paginated paper notebook despite the advances over the past decade in web based communication and publication tools. The development of these tools offers an opportunity to re-imagine what the laboratory record would look like if it were re-built in a web-native form. In this paper I describe a distributed approach to the laboratory record based which uses the most appropriate tool available to house and publish each specific object created during the research process, whether they be a physical sample, a digital data object, or the record of how one was created from another. I propose that the web-native laboratory record would act as a feed of relationships between these items. This approach can be seen as complementary to, rather than competitive with, integrative approaches that aim to aggregate relevant objects together to describe knowledge. The potential for the recent announcement of the Google Wave protocol to have a significant impact on realizing this vision is discussed along with the issues of security and provenance that are raised by such an approach.
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Weber G, Haslam N, Essex JW, Neylon C. Thermal equivalence of DNA duplexes for probe design. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:034106. [PMID: 21817251 DOI: 10.1088/0953-8984/21/3/034106] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We present the theory of thermal equivalence in the framework of the Peyrard-Bishop model and some of its anharmonic variants. The thermal equivalence gives rise to a melting index τ which maps closely the experimental DNA melting temperatures for short DNA sequences. We show that the efficient calculation of the melting index can be used to analyse the parameters of the Peyrard-Bishop model and propose an improved set of Morse potential parameters. With this new set we are able to calculate some of the experimental melting temperatures to ± 1.2 °C. We review some of the concepts of sequencing probe design and show how to use the melting index to explore the possibilities of gene coverage by tuning the model parameters.
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Teixeira SCM, Ankner J, Bellissent-Funel MC, Bewley R, Blakeley MP, Coates L, Dahint R, Dalgliesh R, Dencher N, Dhont J, Fischer P, Forsyth VT, Fragneto G, Frick B, Geue T, Gilles R, Gutberlet T, Haertlein M, Hauß T, Häußler W, Heller WT, Herwig K, Holderer O, Juranyi F, Kampmann R, Knott R, Kohlbrecher J, Kreuger S, Langan P, Lechner R, Lynn G, Majkrzak C, May R, Meilleur F, Mo Y, Mortensen K, Myles DAA, Natali F, Neylon C, Niimura N, Ollivier J, Ostermann A, Peters J, Pieper J, Rühm A, Schwahn D, Shibata K, Soper AK, Straessle T, Suzuki UI, Tanaka I, Tehei M, Timmins P, Torikai N, Unruh T, Urban V, Vavrin R, Weiss K, Zaccai G. New sources and instrumentation for neutrons in biology. Chem Phys 2009; 345:133-151. [PMID: 19132140 PMCID: PMC2614686 DOI: 10.1016/j.chemphys.2008.02.030] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Neutron radiation offers significant advantages for the study of biological molecular structure and dynamics. A broad and significant effort towards instrumental and methodological development to facilitate biology experiments at neutron sources worldwide is reviewed.
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Neylon C, Wu S. Open Science: tools, approaches, and implications. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2009:540-544. [PMID: 19209729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Open Science is gathering pace both as a grass roots effort amongst scientists to enable them to share the outputs of their research more effectively, and as a policy initiative for research funders to gain a greater return on their investment. In this workshop, we will discuss the current state of the art in collaborative research tools, the social challenges facing those adopting and advocating more openness, and the development of standards, policies and best practices for Open Science.
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