Monday 28 April 2014

Diabetes Special Edition: Wednesday 30th April




Institute Research Student Seminars

Speakers:  Scott Anderson, PhD student (Diabetes), Sophie Cassidy, PhD student (Diabetes) Fahad Ahmed, PhD student

(Vascular Diabetes)


Venue: Lecture theatre F, ground floor, Dental School

Date and time:  Wednesday 30 April 2014 at 1.00pm


Scott Anderson will present:


“Targeting islet inflammation ex vivo and following transplantation”


Type 1 diabetics, who have lost sensitivity to exogenous insulin, are prone to life threatening bouts of hypoglycaemia. Islet transplantation offers a possible therapy to rectify these life threatening episodes. Current islet transplant outcomes are poor, with less than 10% insulin independence at year 5. Poor results are due to pre transplant stress on donor islets leading to islet death as a result of pro-inflammatory signalling. This research aims to characterise the pro-inflammatory signature in stressed human islets and a rat β cell line. Mesenchymal stem cells, in co-culture and/or co-transplant, and islet filtration will then be used to try and reduce inflammatory signalling. This research could increase the number of viable islets transplanted into recipients, increasing transplant longevity and improving glycaemic control.


Sophie Cassidy will discuss:


“The effects of high intensity intermittent training (HIIT) on cardiac function

in people with Type 2 diabetes”.


The rationale for using exercise as a therapeutic strategy for diabetic cardiomyopathy will be explored as well as an overview of the methods and results so far from my study.


Key words:  Exercise, Type 2 Diabetes, Cardiac


Fahad Ahmed will speak on:

"Metformin improves endothelial progenitor cells number in Type 1 diabetes"

Cardiovascular disease (CVD) remains the main cause of morbidity and mortality in diabetic patients. Metformin has been shown to have cardiovascular benefits in type 2 diabetes. However, this effect has not been studied in type 1 diabetes (T1DM). Our work, whilst controlling for glucose changes, explores, if metformin has cardiovascular benefits in T1DM by studying cardiovascular surrogate outcomes - circulating endothelial progenitor cells (EPC). EPCs are involved in vascular regeneration and/or predict development of atherosclerotic CVD.

Keywords: Type 1 diabetes mellitus, metformin, endothelial progenitor cells and endothelial dysfunction


Chair:  Dr Katrin Jaedicke, Research Associate









SEMINAR TOMORROW 29 April at 2 pm BGI Omics Projects Share for the past 15 years - Dr. Jian TU


Dr. Jian TU – Project Director of BGI Europe—Tuesday 29 April @ 2 pm, Dental Lecture Theatre E



"BGI Omics Projects Share for the past 15 years"

Dr. Jian TU will provide an overview of the most important projects and share demo cases for human, animal/plant and microbial genomics research, from DNA, RNA and epigenetics to the protein level, from 1999-2014.


The BGI (previously known as the Beijing Genomics Institute) is the world’s largest genomics research institute, producing >25% of the world’s genomic data. The BGI was originally set up in 1999 by the Chinese government as their official research institute in their share of the Human Genome Project. Today the BGI is credited with key achievements such as the first de novo sequencing of mammalian and human genomes from short-read data (next-gen sequencing), produced proof-of-principle for the sequencing of the microbiome of the human digestive tract (~150 times larger than the human genome), the sequencing of the SARS virus genome, and so far those of 57,000 different people. Some of BGI’s current research projects include the 1000 human genomes project, the Diabetes-associated Genes and Variations Study, the Cancer Genome Project, and the 10,000 microbial genomes project. In 2014, BGI was reported to be producing 500 genetically-modified cloned pigs a year to test new medicines with genomics readout technology.

Faculty contact:  Diego Miranda-Saavedra (, ext. 8590

Sponsored by: BGI

Friday 25 April 2014

Enzymes, Inflammation and Liver Fibrosis

Just to remind that next week’s INE seminar is to be given by Prof. David Adams, Dean of Medicine and the Director of the NIHR BRU in Liver Disease and the Centre for Liver Research at Birmingham University, on Thursday, 1st May at 5pm in room 2.21 in the Research Beehive, Newcastle University. (Refreshments available from 4.30pm).


David's seminar is entitled “Enzymes, inflammation and liver fibrosis”,


and he is being hosted by John Kirby, so please email him if you would like to speak/go to dinner with David whislt he is here in Newcastle.


Liaskou E, Jeffery LE, Trivedi PJ, Reynolds GM, Suresh S, Bruns T, Adams DH, Sansom DM, Hirschfield GM.

Gastroenterology. 2014 Apr 8. pii: S0016-5085(14)00452-1. 

Activated macrophages promote hepatitis C virus entry in a tumor necrosis factor-dependent manner.

Fletcher NF, Sutaria R, Jo J, Barnes A, Blahova M, Meredith LW, Cosset FL, Curbishley SM, Adams DH, Bertoletti A, McKeating JA.

Hepatology. 2014 Apr;59(4):1320-30. 


Antitumor CD8(+) T cells in hepatocellular carcinoma: Present but exhausted.

Li KK, Adams DH.

Hepatology. 2014 Apr;59(4):1232-4. 


Evaluation of serum lysyl oxidase as a blood test for colorectal cancer.

Ward ST, Weston CJ, Hepburn E, Damery S, Hejmadi RK, Morton DG, Middleton G, Ismail T, Adams DH.

Eur J Surg Oncol. 2013 Nov 6. pii: S0748-7983(13)00871-8. 


Mucosal immunity in liver autoimmunity: a comprehensive review.

Trivedi PJ, Adams DH.

J Autoimmun. 2013 Oct;46:97-111. 


Primary sclerosing cholangitis.

Hirschfield GM, Karlsen TH, Lindor KD, Adams DH.

Lancet. 2013 Nov 9;382(9904):1587-99. 


The regulation of T-cell recruitment to the human liver during acute liver failure.

Tuncer C, Oo YH, Murphy N, Adams DH, Lalor PF.

Liver Int. 2013 Jul;33(6):852-63. 


Cellular localization and trafficking of vascular adhesion protein-1 as revealed by an N-terminal GFP fusion protein.

Weston CJ, Shepherd EL, Adams DH.

J Neural Transm. 2013 Jun;120(6):951-61. 


An in vitro model of human acute ethanol exposure that incorporates CXCR3- and CXCR4-dependent recruitment of immune cells.

Karim S, Liaskou E, Hadley S, Youster J, Faint J, Adams DH, Lalor PF.

Toxicol Sci. 2013 Mar;132(1):131-41. d

Wednesday 23 April 2014

ICM Seminars: Liver Regeneration, RA Cytokines and Bioinformatics

Institute Research Seminar “Can we improve liver regeneration for clinical benefit?”  Wednesday 7th May 2014 at 4pm Lecture Theatre E, Ground Floor, Dental School.  Guest Speaker: Professor Stuart J Forbes, Professor of Transplantation and Regenerative Medicine at Edinburgh University.


Institute Research Day ’How is cytokine production regulated in the RA synovium?’’ Monday 2 June 9.30am RB Green Lecture Theatre Room, Dental School.  Guest speaker: Prof Iain McInnes, Director of Institute of Infection, Immunity and Inflammation, Glasgow University.


Faculty Bioinformatics and Systems Biology Seminar Series  

Bart Deplancke – Swiss Federal Institute of Technology, Lausanne-Thursday 24 April at 3.30 pm, Dental Lecture Theatre D

Sarah Teichmann, EBI/Sanger – Thursday 8th May at 2pm, David Shaw Lecture Theatre.


Congratulations to Professor Sophie Hambleton and Professor David Young

Congratulations to Sophie Hambleton and David Young on their promotion to Chair with effect from 1 August 2014




Bart Deplancke – Swiss Federal Institute of Technology, Lausanne--Thursday 24 April @ 3.30 pm, Dental Lecture Theatre D


This seminar is very relevant for anyone working on transcriptional control. Bart’s lab has developed an impressive microfluidics platform to measure transcription factor binding affinities, and by combining this with other experimental and computational tools he has successfully identified novel central regulators of fundamental processes.


"Systems-based, quantitative analysis of the regulatory network mediating fat cell differentiation"


Adipogenesis is highly relevant both from a medical research perspective and as a prime model of cellular differentiation. In the first part of my talk, I will present my lab’s efforts to examine whether the current adipogenic regulatory model is exhaustive. To this end, we systematically overexpressed individual transcription factors (TFs) in mouse pre-adipocytes and probed their effect on fat cell differentiation. We identified 26 mostly novel pro-adipogenic TFs (out of 734) and established the top candidate ZEB1 as a central regulator of in vitro and in vivo fat cell differentiation, acting by directly targeting the majority of known early and late adipogenic transcriptional regulators. In the second part, I will introduce a novel targeted proteomics method that we developed with the goal of deriving absolute abundance data for TFs-I will show how we used these data together with binding energetics and chromatin state data to formulate a genome-wide DNA binding model for the adipogenic master regulator PPARγ. Interestingly, this model accurately explains the increase in PPARγ binding sites during the final differentiation stage despite a concurrent saturation in PPARγ copy number. In the final part, I will summarize our findings regarding the molecular role of co-repressors during adipogenesis. Specifically, I will show how some of these co-repressors function as gatekeepers within the adipogenic regulatory network as they directly fine-tune the transcription of pro- and anti-adipogenic genes.


Faculty contact:  Diego Miranda-Saavedra (, ext. 8590

Sponsored by: Panasonic



Thursday 10 April 2014

Immunology NE seminar NEXT Monday 14th April 4pm Immune Cell Activation

Monday 14th April, Katja Fink from the Singapore Immunology Network will be visiting and presenting some of her data at 4pm In the Research Beehive (room 2.22), Newcastle University.
"Skin-associated dengue infection and immune cell activation"  

TODAY: Integrated Research into Musculoskeletal Ageing

IAH Seminar - Integrated research into musculoskeletal ageing

Location: Great Gable Seminar Room, CARU, Campus for Ageing and Vitality
Time/Date: 10th April 2014, 12:15 - 13:00

You are invited to the IAH research seminar which will take place on Thursday 10 April 2014 in the Great Gable Seminar Room, CARU, Campus for Ageing and Vitality. The meeting will start at 12.15 and will be followed at approximately 13.00 by a sandwich lunch.

The presentations today will be given by Dr Carole Proctor and the title of her talk will be 'Integrated research into musculoskeletal ageing'.


The MRC/Arthritis Research UK Centre for Integrated research into Musculoskeletal Ageing (CIMA) is a collaboration between the universities of Liverpool, Newcastle and Sheffield. The talk will be divided into two parts.  In the first part, I will give an overview of the research being carried out within CIMA with particular focus on systems biology approaches.  In the second part I will present a more detailed example of a computational integrative model which has been developed to investigate the common molecular mechanisms involved in musculoskeletal ageing.

Wednesday 9 April 2014

Osteoarthritis Latest

Check it Out:

Conclusions Our data for the first time identifies a role for ubiquitination and the proteasome in the induction of OA via regulation of inflammatory mediator-induced MMP13 expression. These data open avenues of research to determine whether the proteasome, or K48-linked ubiquitination, are potential therapeutic targets in OA.

Tuesday 8 April 2014

Cytokine Production in the RA Synovium: June 2nd

Institute Research Day ''How is cytokine production regulated in the RA synovium?'' Monday 2 June 9.30am RB Green Lecture Theatre Room, Dental School.  Guest speaker: Prof Iain McInnes, Director of Institute of Infection, Immunity and Inflammation, Glasgow University.

Monday 7 April 2014

Fluorescent nanosensors - Wednesday 9th April



Institute Research Seminar


Guest speaker: Dr Jon Aylott

[Associate Professor in Analytical Bioscience, School of Pharmacy, University of Nottingham]


Venue:  Lecture theatre E, ground floor, Dental School

Date and time:  Wednesday 9 April 2014 at 4.00pm


Dr Aylott will discuss:


"Fluorescent nanosensors: in situ measurements of biological systems".

Optical nanosensors are the primary focus of this research and utilise the sensitivity of fluorescence to make quantitative real-time measurements of small molecule concentrations within single cells. Nanosensors capable of measuring glucose, oxygen, calcium, zinc and pH and proteases have been demonstrated. This presentation will describe some of the methods that we are currently using to develop new sensors and detail a range of applications for nanosensors. These include the development of self-reporting scaffolds for measuring metabolic health in 3D culture systems; measuring the intestinal pH of C.elegans nematodes; and using reactive oxygen generating nanoprobes for modulating human mesenchymal stem cell behaviour.


Key words:  Fluorescence based nanosensors, real-time measurements, single cell analysis.




Biography:   Jonathan Aylott gained his degree and PhD in Chemistry from the University of East Anglia. He then undertook a Postdoctoral Fellowship in Raoul Kopelman's laboratory at the University of Michigan. In 2000, he returned to the UK to take up a Lectureship in Analytical Science at the Department of Chemistry, University of Hull. In 2004 he was appointed Lecturer in Analytical Bioscience in the School of Pharmacy at Nottingham and promoted to Associate Professor in 2011. Jon's research interests focus on the design, development and implementation of miniaturized analytical devices. Such devices can then be applied to measuring biological samples in-situ and in real-time, generating a better understanding of disease states. Jon takes a multi-disciplinary and collaborative approach to research and has obtained funding from a variety of sources to investigate the use of nanosensors in a variety of biological applications including, embryo development, stem cell biology, biofilms, photodynamic therapy and regenerative medicine.






Jon will be in Newcastle during the afternoon of 9 April – please contact Philip Manning (

if you would like an opportunity to speak with him



Chair:  Dr Philip Manning


+ Refreshments will be available in the Bites café after the meeting +








Thursday 3 April 2014

Powerpoint to High Resolution .tff and .jpg Files for Journal Submission

From ppt slides:

-          Save ppt as pdf

-          To create Fig with multiple graphs: open new ppt file with slide in A4 format

-          Copy paste (with edit-snapshot tool) individual figures to A4 format

-          Save as single multiple figure



To transfer from ppt to photoshop (see also FlowJo instructions) :

-          Go to RAS – open Photoshop

-          From ppt file, copy figure (ctrl A (copy all), ctrl C (copy)

-          Click on Photoshop

-          File – new – opends dialog box

-          Select “clipboard” & add file name (leave grayscale for B&W or CMYK/RGB for colour) – click ok – opens sheet

-          Click on sheet – ctrl V (pastes all)



From photoshop menu:

-          Image – image size

-          change resolution to 300 or 600 dpi – ok (fig hugely enlarges)

-          from menu select “Layer”

-          go dwon drop-down menu to “Flatten image”

-          go to File – save as

-          select tiff/jpeg & give file name

-          save to your PC



April 2014

Desa Lilic


Wednesday 2 April 2014

MRG Lab Meeting: Osteoarthritis and Osteosarcoma

Friday 4th April 2014 at 9.00am in the Baddiley Clark Lecture Theatre.




Rachel Harry - Post Doc (PI - John Isaacs)




Kenny Rankin - Title of Talk "Evaluation of MT1-MMP as a novel biomarker in osteosarcoma"


Adrian Falconer - 1st year PhD Student (PI - Drew Rowan) Title of Talk "The role of non-catalytic domains in the serine proteinase matriptase"


Emma Rogers - MRes/PhD Student (PI - John Loughlin - second supervisors Kenny Rankin and Louise Reynard) Title of Talk "The functional analysis of a novel osteoarthritis susceptibility locus on chromosome 9q33.1"


Tuesday 1 April 2014

10th April Musculoskeletal Ageing

An integrated approach to Musculoskeletal Ageing


Location: Great Gable Seminar Room, CARU, Campus for Ageing and Vitality

Time/Date: 10th April 2014, 12:15 - 13:00

GM-CSF, Dendritic cells, RA and Biofilm growth on fluoridated denture material




Institute Research Student Seminars

Speakers:  Gary Reynolds, PhD student (Musculoskeletal) and

Sufian Al-Sammarraie, PhD student (Oral & Dental Sciences)


Venue: Seminar room L2.5, 2nd floor, Leech Building, Medical School

Date and time:  Wednesday 2 April 2013 at 1.00pm


Gary Reynolds will discuss:


"The role of T cell-derived GM-CSF in inflammatory dendritic cell development

in rheumatoid arthritis".


A monocyte-derived population of cells with characteristics of dendritic cells has been described in inflammatory states in mice. An equivalent population has been identified in humans but the factors governing their development are not clear. GM-CSF is implicated as it is employed in in-vitro models of monocyte-derived dendritic cell development. The role of synovial T cell-derived GM-CSF in this process is discussed.


Key words:   GM-CSF, Dendritic cells, Rheumatoid arthritis



Sufian Al-Sammarraie will speak on:


"Biofilm growth on fluoridated denture material”


In this study, we evaluated the efficacy of a new fluoride-releasing copolymer material for reducing single- and mixed-species biofilm formation on oral appliances. A model system has been developed for this study



Keywords:  Denture plaque, qPCR, Mixed biofilm


Chair:  Darren Johnson, PhD student (Dermatology)