Scientific Facilities - Newcastle University

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Publication: Serial Block Face Scanning EM. • Publication: Flow Cytometry and Cell Sorting. • Facilities Management
Faculty of Medical Sciences

Scientific Facilities

www.ncl.ac.uk/medicalsciences/research/facilities/

@NCLSciFaci

Scientific Facilities Newsletter: January 2018 Welcome to the Newsletter for the Faculty of Medical Sciences Scientific Facilities In this issue: News: • Bio-Imaging: New Systems are Arriving! • New Hyperion Mass Cytometry System • Publication: Serial Block Face Scanning EM • Publication: Flow Cytometry and Cell Sorting • Facilities Management Software Update • FCCF’s International Speaker • Vacancies in the Core Facilities Events: • Annual Imaging Workshop (7-9 February 2018) • Practicalities of ‘Omics (20 March 2018) • NUSCU Research Day (23 April 2018)

Bio-Imaging: New Systems are Arriving! Two dimensional (2D) images of fixed specimens can yield a lot of information and indeed have been the mainstay of many imaging applications for decades.  However, gone are the days where this imaging approach can lead to cutting edge science, in many cases there is a need to put these 2D observations into the context of the 3D live-cell environment be it the tissue or animal or wider cellular population.  To do this you need the ability to view cellular events as they happen, when they happen and in many cases, under changing conditions. The Bio-Imaging Unit, with the support of the Faculty of Medical Sciences and awards from the University’s Research Infrastructure Fund (RIF) and the Wellcome Trust (Wellcome Centre for Mitochondrial Research), has agreed to the purchase of four advanced imaging systems (see below), adding an extra dimension and capacity to the Faculty’s cellular imaging capabilities.  These systems will allow us to perform: in vivo microscopic imaging of small animals / tissues, live-cell ‘super resolution’, and high-throughput automated image-based cellular screening. It is expected that all systems will be installed and commissioned by the end of February 2018. Imaging Technologies: in vivo multi-photon small animal / tissue imaging, Zeiss LSM880-NLO-Airyscan: this system will be located in the University’s Comparative Biology Centre (CBC) and will primarily be used to image small animals and tissues. Live-cell super resolution imaging, Zeiss LSM880-Airyscan-Fast: this system will be located at the Institute of Genetic Medicine. Live-cell super resolution imaging, Zeiss LSM800-Airyscan: this system will be located in the main Bio-Imaging Facility in the Medical School. Automated live and fixed -cell high-content high-throughput imaging, Zeiss Celldiscoverer 7: this system will be coupled to an automated incubator and plate loading robot, it will be located in the main Bio-Imaging Facility in the Medical School.  To allow us to support these new instruments we’d like to welcome our newest facility member Dr David Bulmer.  David brings with him a background in imaging and microbiology and will be a valuable asset to the Bio-Imaging team. www.ncl.ac.uk/medicalsciences/research/facilities/

New Hyperion Mass Cytometry System Just before Christmas the Newcastle Flow Cytometry Core Facility (FCCF) took delivery of the Hyperion Imaging Mass Cytometry module from Fluidigm that, in concert with the existing and established Helios Mass Cytometry system, enables the measurement of over 35 simultaneous and unique antibodydirected measurements on either FFPE or frozen tissue sections. This is one of only 5 units in the UK and the only one outside London or Cambridge. It will enable researchers to ask questions about cells within tissues to an unprecedented level of phenotypic detail while still preserving the spatial context. Please contact Dr Andrew Filby, head of the FCCF, for further information.

Publication: Serial Block Face Scanning EM One of the most popular techniques in EM Research Services is serial block face scanning electron microscopy (SBF-SEM), which allows 3D reconstruction of cells and their organelles at the ultrastructural level. The user obtains large data sets comprised of hundreds of images that need to be analysed, which can be a daunting task to someone new to the technique. Luckily, one of our PhD students, Erin Cocks, has just published a guide to analysis and reconstruction of SBF-SEM data, which can be found in the Journal of Microscopy. The computer programs used in this type of analysis are sometimes not intuitive so the stepby-step guide also includes videos. Researchers at Newcastle can also take advantage of workshops run by our EM technician, Ross Laws, who teaches basic and advanced use of one of the more popular programs – Microscopy Image Browser (MIB).

Mitochondria segmented using MIB software (A) and 3D reconstructions of the mitochondria using AMIRA (B)

www.ncl.ac.uk/medicalsciences/research/facilities/

Publication: Flow Cytometry and Cell Sorting “Guidelines for the use of flow cytometry and cell sorting in immunological studies” The Newcastle Flow Cytometry Core Facility has been involved in a significant undertaking to author and publish a set of practical guidelines for the Immunology community on all aspects of flow cytometry.  This has now been published in the European Journal of Immunology and has already attracted a lot of attention in the worldwide scientific community.

Facilities Management Software Update Newcastle University recently signed a contract with Stratocore to implement facility management software across all nine Core Facilities in the Faculty of Medical Sciences. The software, known as Platform Pilot Management System (PPMS), will allow all services, reservations, orders, assistance, training, maintenance, technical incidents, and projects to be managed from a convenient web-portal connected to an auditable, data management system. Gillian Brown is working on the implementation of the software: For those who do not know me, I’m a Project Manager within NUIT-FMS and am currently rolling out the Achiever Medical software (human tissue sample tracking) across the 11 Biobanks. I do have a history with the University having worked here from 1998-2013, firstly within the IT department and then within the School of Medical Sciences Education Development. I returned to the University in April as, for the last 3 years, I’ve been working for the Higher Education Academy advising clinical, teaching, and technical staff about Fellowships and accredited programmes. I have been tasked to manage the implementation of PPMS across the Core Facilities and have already met with most Facility Managers to discuss their specific requirements for implementation. Once I’ve met with all managers, I’ll put a timeline together so that the rollout of PPMS will be staged in three groups with three facilities in each group. I am in discussions with Stratocore about staff training and creation of a development system for you to ‘play with’ before going LIVE. I’m in touch with the Facility Managers and will keep you updated on the PPMS rollout within the newsletter, but if anyone has questions, please don’t hesitate to drop me a line: 

[email protected] www.ncl.ac.uk/medicalsciences/research/facilities/

FCCF’s International Speaker As part of his scholarship with the International Society for the Advancement of Cytometry (ISAC), Dr Andrew Filby (head of Newcastle’s Flow Cytometry Core Facility) has been invited as a guest lecturer to speak at the national University of La Plata in Argentina in March this year. The meeting will be open to attendees from all over South America and will focus on how cytometry and cytometry technologies are driving discovery and understanding in all areas of cell biology. Dr Filby will speak about several aspects of cytometry including fluorescence and mass-based as well as imaging cytometry.

Vacancies in the Core Facilities Scientific Officer (Bioinformatics)

Closing date 9 Feb 2018

Newcastle University has recently made a substantial investment in genomics, and is among the first UK Universities to acquire an Illumina NovaSeq 6000. The Bioinformatics Support Unit (BSU) will be building the software infrastructure to support primary processing of the data produced by this platform. The BSU are therefore looking to recruit two bioinformaticians, who will support the establishing and running of a bioinformatics service for a highly scalable high-throughput sequencer, and who will be based alongside the Genomics Core Facility. Find out more

Technician (Flow Cytometry)

Closing date 6 Feb 2018

There is an exiciting opporunity for a research technician to join the Flow Cytometry Core Facility (FCCF) in collaboration with the Newcastle University Single Cell Unit (NUSCU). The post will directly involve developing and applying a wide range of cytometrybased techniques focused around single-cell analysis with access to truly cutting edge cytometry technology including the Hyperion Imaging Mass Cytometry system and the BD Symphony Flow Cytometer. Find out more www.ncl.ac.uk/medicalsciences/research/facilities/

Annual Imaging Workshop 7 - 9 February 2018 Clore Suite, Hancock Museum

The Bio-Imaging Unit are again running their popular imaging workshop (sponsored by Zeiss) which aims to provide a grounding in microscopy and fluorescence imaging techniques. The event will cover the following key topics and assumes little prior microscopy knowledge: • The microscope - anatomy, basic setup, alignment and contrast techniques. • Fluorescence microscopy – concepts, dyes, filters techniques etc. • Imaging basics - bit depth & dynamic range, image processing (ImageJ). • Image detection - Scientific cameras, PMTs and their applications. • Imaging systems - wide field microscopy vs confocal microscopy. • Imaging techniques - spectral profiling, FRAP, FRET, TIRF, super resolution time lapse etc. The course fee includes lunch and refreshments on days 1 and 2. Event format & cost: • Day 1 – Microscope and imaging fundamentals including basic fluorescence (£50) • Day 2 – Confocal microscopy and advanced imaging technologies and applications (£50) (Days 1 and 2: £75) • Day 3 – Image analysis workshop (Image J and Imaris: £10 each) • Facility Tour (date tbc, 30 mins, free) The event would be ideal for research students and postdocs that use or plan to use microscopy for their research. The event is always oversubscribed so please urge those that are interested to register early.  If you are unable to secure a place, please contact the Bio-Imaging Unit as we regularly run training events throughout the year. Register for the Workshop Contact the Facility for further details www.ncl.ac.uk/medicalsciences/research/facilities/



Scientific Facilities Conference 2018: Practicalities of ‘Omics Tuesday 20 March 2018 David Shaw Lecture Theatre, Newcastle University

https://conferences.ncl.ac.uk/practicalities2018 The Practicalities of... Conferences are organised by the Scientific Facility Managers, and this year’s event will be based around four Core Facilities: 

• Proteomics  • Genomics • Bioinformatics • High Throughput Screening

The draft programme is now online, featuring speakers from LifeArc, the Royal Marsden Hospital, and Newcastle University. 

Register to attend or visit the conference website for full details.

Sponsored by:

NUSCU Research Day 2018 Save the date! 23 April 2018, The Boiler House This year’s Newcastle University Single Cell Unit (NUSCU) Research Day will be held in the new Boiler House event space. Further details to follow. To register your interest please contact Helen Snowdon.  www.ncl.ac.uk/medicalsciences/research/facilities/