Seymour Knowles-Barley PhD

Seymour Knowles-Barley


Publications:
2014
  Analysis of the expression patterns, subcellular localisations and interaction partners of Drosophila proteins using a pigP protein trap library
Lowe, N, Rees, JS, Roote, J, Ryder, E, Armean, IM, Johnson, G, Drummond, E, Spriggs, H, Drummond, J, Magbanua, JP, Naylor, H, Sanson, B, Bastock, R, Huelsmann, S, Trovisco, V, Landgraf, M, Knowles-Barley, S, Armstrong, JD, White-Cooper, H, Hansen, C, Phillips, RG, The UK Drosophila Protein Trap Screening Consortium, Lilley, KS, Russell, S & St Johnston, D 2014, 'Analysis of the expression patterns, subcellular localisations and interaction partners of Drosophila proteins using a pigP protein trap library' Development, vol 141, no. 20, pp. 3994-4005. DOI: 10.1242/dev.111054
Although we now have a wealth of information on the transcription patterns of all the genes in the Drosophila genome, much less is known about the properties of the encoded proteins. To provide information on the expression patterns and subcellular localisations of many proteins in parallel, we have performed a large-scale protein trap screen using a hybrid piggyBac vector carrying an artificial exon encoding yellow fluorescent protein (YFP) and protein affinity tags. From screening 41 million embryos, we recovered 616 verified independent YFP-positive lines representing protein traps in 374 genes, two-thirds of which had not been tagged in previous P element protein trap screens. Over 20 different research groups then characterized the expression patterns of the tagged proteins in a variety of tissues and at several developmental stages. In parallel, we purified many of the tagged proteins from embryos using the affinity tags and identified co-purifying proteins by mass spectrometry. The fly stocks are publicly available through the Kyoto Drosophila Genetics Resource Center. All our data are available via an open access database (Flannotator), which provides comprehensive information on the expression patterns, subcellular localisations and in vivo interaction partners of the trapped proteins. Our resource substantially increases the number of available protein traps in Drosophila and identifies new markers for cellular organelles and structures.
General Information
Organisations: Institute for Adaptive and Neural Computation .
Authors: Lowe, Nick, Rees, Johanna S., Roote, John, Ryder, Ed, Armean, Irina M., Johnson, Glynnis, Drummond, Emma, Spriggs, Helen, Drummond, Jenny, Magbanua, Jose P., Naylor, Huw, Sanson, Bénédicte, Bastock, Rebecca, Huelsmann, Sven, Trovisco, Vitor, Landgraf, Matthias, Knowles-Barley, Seymour, Armstrong, J. Douglas, White-Cooper, Helen, Hansen, Celia, Phillips, Roger G., , , Lilley, Kathryn S., Russell, Steven & St Johnston, Daniel.
Number of pages: 12
Pages: 3994-4005
Publication Date: 2014
Publication Information
Category: Article
Journal: Development
Volume: 141
Issue number: 20
ISSN: 1011-6370
Original Language: English
DOIs: 10.1242/dev.111054
2011
  Biologically inspired EM image alignment and neural reconstruction
Knowles-Barley, S, Butcher, NJ, Meinertzhagen, IA & Armstrong, JD 2011, 'Biologically inspired EM image alignment and neural reconstruction' Bioinformatics, vol 27, no. 16, pp. 2216-2223. DOI: 10.1093/bioinformatics/btr378
Motivation: Three-dimensional reconstruction of consecutive serial-section transmission electron microscopy (ssTEM) images of neural tissue currently requires many hours of manual tracing and annotation. Several computational techniques have already been applied to ssTEM images to facilitate 3D reconstruction and ease this burden.Results: Here, we present an alternative computational approach for ssTEM image analysis. We have used biologically inspired receptive fields as a basis for a ridge detection algorithm to identify cell membranes, synaptic contacts and mitochondria. Detected line segments are used to improve alignment between consecutive images and we have joined small segments of membrane into cell surfaces using a dynamic programming algorithm similar to the Needleman?Wunsch and Smith?Waterman DNA sequence alignment procedures. A shortest path-based approach has been used to close edges and achieve image segmentation. Partial reconstructions were automatically generated and used as a basis for semi-automatic reconstruction of neural tissue. The accuracy of partial reconstructions was evaluated and 96% of membrane could be identified at the cost of 13% false positive detections.Availability: An open-source reference implementation is available in the Supplementary information.Contact: seymour.kb@ed.ac.uk; douglas.armstrong@ed.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online.
General Information
Organisations: Institute for Adaptive and Neural Computation .
Authors: Knowles-Barley, Seymour, Butcher, Nancy J., Meinertzhagen, Ian A. & Armstrong, J. Douglas.
Keywords: (, , . )
Number of pages: 8
Pages: 2216-2223
Publication Date: 2011
Publication Information
Category: Article
Journal: Bioinformatics
Volume: 27
Issue number: 16
Original Language: English
DOIs: 10.1093/bioinformatics/btr378
2010
  Algorithms for automatic neuron tracing in noisy 3D image stacks
Knowles-Barley, S, Phillipson, G, Teriakidis, A, Sterratt, D, Larkworthy, T, O'Leary, T, Down, MP, Hennig, M, Withers, JPJ & Hull, M 2010, 'Algorithms for automatic neuron tracing in noisy 3D image stacks' Neuroscience Day 2010, Edinubrgh, United Kingdom, 29/03/10 - 29/03/10, .
General Information
Organisations: Institute for Adaptive and Neural Computation .
Authors: Knowles-Barley, Seymour, Phillipson, Graeme, Teriakidis, Adrianna, Sterratt, David, Larkworthy, Thomas, O'Leary, Timothy, Down, Matthew P., Hennig, Matthias, Withers, James P. J. & Hull, Michael.
Publication Date: 2010
Publication Information
Category: Poster
Original Language: English
  GPU Computing for 3D Data Annotation
Knowles-Barley, S, Teriakidis, A, Phillipson, G, Sterratt, D & Willshaw, D 2010, 'GPU Computing for 3D Data Annotation'.
A quick, flexible, accurate and automatic volumetric image processing software package will enable biomedical researchers to analyse orders of magnitude more data. In particular this could have a huge impact on the advancement of the field of neuroscience and our understanding of the brain. For certain operations Graphics Processing Unit (GPU) processing is many times faster than performing the same operations on a standard computer Central Processing Unit (CPU).
General Information
Organisations: Institute for Adaptive and Neural Computation .
Authors: Knowles-Barley, Seymour, Teriakidis, Adrianna, Phillipson, Graeme, Sterratt, David & Willshaw, David.
Publication Date: 2010
Publication Information
Category: Poster
Original Language: English
  GPU Computing for Neural Circuit Reconstruction
Knowles-Barley, S & Armstrong, JD 2010, 'GPU Computing for Neural Circuit Reconstruction' Journal of neurogenetics, vol 24, pp. 42-42.
General Information
Organisations: Institute for Adaptive and Neural Computation .
Authors: Knowles-Barley, Seymour & Armstrong, J. Douglas.
Number of pages: 1
Pages: 42-42
Publication Date: Dec 2010
Publication Information
Category: Meeting abstract
Journal: Journal of neurogenetics
Volume: 24
ISSN: 0167-7063
Original Language: English
  BrainTrap: a database of 3D protein expression patterns in the Drosophila brain
Knowles-Barley, S, Longair, M & Armstrong, JD 2010, 'BrainTrap: a database of 3D protein expression patterns in the Drosophila brain' Database: The Journal of Biological Databases and Curation, vol 2010, baq005, pp. 1-9. DOI: 10.1093/database/baq005
Protein-trap strains of Drosophila melanogaster provide a very useful tool for examining the 3D-expression patterns of proteins and purification of protein complexes. Here we present BrainTrap, available at http://fruitfly.inf.ed.ac.uk/braintrap, an online database of 3D confocal datasets showing reporter gene expression and protein localization in the adult brain of Drosophila. Full size images throughout the volume of the entire brain can be viewed interactively in a web browser. The database includes searchable annotations linked to the FlyBase Drosophila anatomy ontology. Anatomical search criteria can be specified using automatic completion and a hierarchical browser for the ontology. The provenance of all annotation is retained and the location where the annotator made the conclusion can be highlighted.Database URL: http://fruitfly.inf.ed.ac.uk/braintrap
General Information
Organisations: Institute for Adaptive and Neural Computation .
Authors: Knowles-Barley, Seymour, Longair, Mark & Armstrong, J Douglas.
Number of pages: 9
Pages: 1-9
Publication Date: 2010
Publication Information
Category: Article
Journal: Database: The Journal of Biological Databases and Curation
Volume: 2010
Original Language: English
DOIs: 10.1093/database/baq005
  Dietary Modulation of Drosophila Sleep-Wake Behaviour
Catterson, JH, Knowles-Barley, S, James, K, Heck, MMS, Harmar, AJ & Hartley, PS 2010, 'Dietary Modulation of Drosophila Sleep-Wake Behaviour' PLoS One, vol 5, no. 8, e12062. DOI: 10.1371/journal.pone.0012062

Background: A complex relationship exists between diet and sleep but despite its impact on human health, this relationship remains uncharacterized and poorly understood. Drosophila melanogaster is an important model for the study of metabolism and behaviour, however the effect of diet upon Drosophila sleep remains largely unaddressed.

Methodology/Principal Findings: Using automated behavioural monitoring, a capillary feeding assay and pharmacological treatments, we examined the effect of dietary yeast and sucrose upon Drosophila sleep-wake behaviour for three consecutive days. We found that dietary yeast deconsolidated the sleep-wake behaviour of flies by promoting arousal from sleep in males and shortening periods of locomotor activity in females. We also demonstrate that arousal from nocturnal sleep exhibits a significant ultradian rhythmicity with a periodicity of 85 minutes. Increasing the dietary sucrose concentration from 5% to 35% had no effect on total sucrose ingestion per day nor any affect on arousal, however it did lengthen the time that males and females remained active. Higher dietary sucrose led to reduced total sleep by male but not female flies. Locomotor activity was reduced by feeding flies Metformin, a drug that inhibits oxidative phosphorylation, however Metformin did not affect any aspects of sleep.

Conclusions: We conclude that arousal from sleep is under ultradian control and regulated in a sex-dependent manner by dietary yeast and that dietary sucrose regulates the length of time that flies sustain periods of wakefulness. These findings highlight Drosophila as an important model with which to understand how diet impacts upon sleep and wakefulness in mammals and humans.


General Information
Organisations: Deanery of Biomedical Sciences.
Authors: Catterson, James H., Knowles-Barley, Seymour, James, Katherine, Heck, Margarete M. S., Harmar, Anthony J. & Hartley, Paul S..
Keywords: (, , . )
Number of pages: 11
Publication Date: Aug 2010
Publication Information
Category: Article
Journal: PLoS One
Volume: 5
Issue number: 8
ISSN: 1932-6203
Original Language: English
DOIs: 10.1371/journal.pone.0012062
  Circadian control of mouse heart rate and blood pressure by the suprachiasmatic nuclei
Sheward, WJ, Naylor, E, Knowles-Barley, S, Armstrong, JD, Brooker, GA, Seckl, JR, Turek, FW, Holmes, MC, Zee, PC & Harmar, AJ 2010, 'Circadian control of mouse heart rate and blood pressure by the suprachiasmatic nuclei: behavioral effects are more significant than direct outputs' PLoS One, vol 5, no. 3, e9783. DOI: 10.1371/journal.pone.0009783

Background: Diurnal variations in the incidence of events such as heart attack and stroke suggest a role for circadian rhythms in the etiology of cardiovascular disease. The aim of this study was to assess the influence of the suprachiasmatic nucleus (SCN) circadian clock on cardiovascular function.

Methodology/Principal Findings: Heart rate (HR), blood pressure (BP) and locomotor activity (LA) were measured in circadian mutant (Vipr2(-/-)) mice and wild type littermates, using implanted radio-telemetry devices. Sleep and wakefulness were studied in similar mice implanted with electroencephalograph (EEG) electrodes. There was less diurnal variation in the frequency and duration of bouts of rest/activity and sleep/wake in Vipr2(-/-) mice than in wild type (WT) and short "ultradian" episodes of arousal were more prominent, especially in constant conditions (DD). Activity was an important determinant of circadian variation in BP and HR in animals of both genotypes; altered timing of episodes of activity and rest (as well as sleep and wakefulness) across the day accounted for most of the difference between Vipr2(-/-) mice and WT. However, there was also a modest circadian rhythm of resting HR and BP that was independent of LA.

Conclusions/Significance: If appropriate methods of analysis are used that take into account sleep and locomotor activity level, mice are a good model for understanding the contribution of circadian timing to cardiovascular function. Future studies of the influence of sleep and wakefulness on cardiovascular physiology may help to explain accumulating evidence linking disrupted sleep with cardiovascular disease in man.


General Information
Organisations: Edinburgh Imaging Facilities.
Authors: Sheward, W. J., Naylor, E., Knowles-Barley, Seymour, Armstrong, J. D., Brooker, G. A., Seckl, J. R., Turek, F. W., Holmes, M. C., Zee, P. C. & Harmar, A. J..
Keywords: (Animals, Behavior, Animal, Blood Pressure, Cardiovascular Physiological Phenomena, Circadian Rhythm, Electroencephalography, Heart Rate, Hemodynamics, Male, Mice, Mice, Inbred C57BL, Mice, Transgenic, Movement, Suprachiasmatic Nucleus. )
Number of pages: 9
Publication Date: 22 Mar 2010
Publication Information
Category: Article
Journal: PLoS One
Volume: 5
Issue number: 3
ISSN: 1932-6203
Original Language: English
DOIs: 10.1371/journal.pone.0009783
2009
  BrainTrap: The Fly Brain Protein Trap Database
Knowles-Barley, S, Longair, M & Armstrong, D 2009, 'BrainTrap: The Fly Brain Protein Trap Database' Neurobiology of Drosophila, Cold Spring Harbor , United States, 29/09/09 - 3/10/09, .
Protein-trap strains of Drosophila melanogaster provide a very useful tool for examining the 3D expression patterns of proteins and purification of protein complexes. Here we present BrainTrap, available at: http://fruitfly.inf.ed.ac.uk/braintrap BrainTrap is an online database of 3D confocal datasets showing reporter gene expression and protein localisation in the adult brain of Drosophila; it provides a valuable resource for further Drosophila neurobiology and protein research.
General Information
Organisations: Institute for Adaptive and Neural Computation .
Authors: Knowles-Barley, Seymour, Longair, Mark & Armstrong, Douglas.
Publication Date: 2009
Publication Information
Category: Poster
Original Language: English
  Receptive fields for EM image alignment and neural reconstruction
Knowles-Barley, S 2009, 'Receptive fields for EM image alignment and neural reconstruction' MPG HHMI High-Resolution Circuit Reconstruction, Berlin, Germany, 20/09/09 - 23/09/09, .
General Information
Organisations: Neuroinformatics DTC.
Authors: Knowles-Barley, Seymour.
Publication Date: 2009
Publication Information
Category: Poster
Original Language: English