ISMB staff retreat 2019 at London Zoo

On a sunny day in June, just before the summer solstice, staff from the ISMB at UCL and Birkbeck had their (now) annual retreat this year at the London Zoo. In our busy lives as academics, these away-days provide us with the rare opportunity to catch up with our colleagues from across Torrington Place in a relaxed atmosphere and to make new friends!

We met at the Terrace Restaurant in the ‘Outback’, where we kick-started the day with tea and coffee, surrounded by emus and wallabies. Tabitha had expertly prepared maps that indicated our exploratory trail through the Zoo, incorporating show-and-tell and feeding times for maximum knowledge gathering and entertainment. Watching dragons, flightless birds, pigs and monkeys with moustaches and coatis – which is not pronounced like the garment (I learned that day), but rather co-ah-ti, gave people plenty to discuss over a very nice BBQ-style lunch back at the restaurant.  We then had time to continue our short trip round the zoo to catch up with some more amazing animals before listening to the two science presentations by Drs Alexa Varah and Nathalie Petorelli from the Institute of Zoology about ‘The costs of herbicide resistance in UK agriculture’ and ‘Satellite remote sensing – a conservation revolution’. Despite the fact that our research at the ISMB is somewhat remote from these topics, there was great interest from the audience and lively discussions ensued. It was a brilliant day out, and I’m looking much forward to the retreat in 2020.

Tine Arnvig, UCL-ISMB

Flightless birds

Monkey with moustache

Men in blue

See-through butterfly

Posted by ublmcr01 in Events, News, Uncategorised

Professor Bart Hoogenboom’s group publish paper in ACS Nano

Professor Bart Hoogenboom’s research group published a paper titled ‘Quantification of Biomolecular Dynamics inside Real and Synthetic Nuclear Pore Complexes using Time-Resolved Atomic Force Microscopy’ in ACS Nano in June 2019.

The full paper is available here.

Posted by ublmcr01 in News, Publications, Uncategorised

Studying protein conformation using a new cyclic ion mobility mass spectrometry (cIMMS) device

Dr Konstantinos Thalassinos

We are the first group to publish a paper on how a new cyclic ion-mobility mass-spectrometry (cIMMS) device, manufactured by Waters, can be used to probe protein structure and dynamics. In particular, the tandem ion mobility capabilities of the instrument allow us to probe in very fine detail protein unfolding pathways and for the first time to do so for co-existing and interconverting conformers. We are now using this technology to study proteins involved in protein misfolding diseases such as human amyloid islet polypeptide.

The paper is:
Eldrid, C.; Ujma, J.; Kalfas, S.; Tomczyk, N.; Giles, K.; Morris, M.; Thalassinos, K. Gas Phase Stability of Protein Ions in a Cyclic Ion Mobility Spectrometry Traveling Wave Device. Anal. Chem. 2019, 91 (12), 7554–7561 https://doi.org/10.1021/acs.analchem.8b05641

A video where I and other people in the field describe the cIMMS technology:

The link to the Waters site:


Posted by ublmcr01 in Lab news, News, Publications, Uncategorised

Gorjan Stojanovski and Hugo Villanueva win prizes at ISMB Graduate Symposium

Congratulations to Gorjan Stojanovski and Hugo Villanueva, who were awarded prizes for their research presentations at this year’s ISMB Graduate Symposium. The Symposium was held in the Clore Management Centre at Birkbeck on Thursday 25th and Friday 26th April.


Gorjan, from Professor John Ward’s group, presented on ‘Applying bacterial competition to evolve novel antibiotics.’


Hugo, from Professor Elena Orlova’s group, presented on ‘Refactoring phages as repurposed nanomachines.’

Posted by ublmcr01 in Achievements, News, Student news, Uncategorised

Arrival of the new Multiwavelength Beckman Optima analytical ultracentrifuge at the UCL Molecular Interactions Facility

We are very grateful to the UCL Capital Equipment Fund for the purchase of the new Beckman AUC Optima for the UCL Molecular Interactions Facility that arrived on 25th March 2019. This was installed after Easter and is starting to become operational. This is the first machine of its type to be installed permanently at an UK university. The pictures show (1) the arrival of the instrument on wheels, (2) what we found when the boxes were opened, and (3) the big smiles of our user community. The major development with this new AUC machine is the capability to measure macromolecular sedimentation across a full absorbance wavelength range, and not with a single wavelength as with the old Beckman AUC Proteome. Other advantages are the capacity to measure samples that are more dilute than with the old AUC. The instrument is highly complementary in scope to macromolecular data collected by NMR, crystallography, mass spectrometry, calorimetry and X-ray and neutron scattering. This should make a big difference to biophysical studies where measuring monodispersity or dissociation constants Kd values are important. For example, the binding of ligands with different chromophores can be monitored simultaneously but independently of the protein that they bind to. In the study of heterogeneous interactions, protein complexes in which one is labelled and the other is not can be monitored in detail, or likewise proteins with haem groups that absorb strongly in the visible region. We have already completed with Dr Lindsay McDermott (pictured) an interesting first project where different fatty acids with two distinct fluorescently-tagged chromophores bind to a lipid binding protein called zinc alpha2 glycoprotein. An account of how this method can be used to follow DNA or RNA binding to a protein at three wavelengths for DNA/RNA, protein and their complex is reported in a short review by Borries Demeler on the new multiwavelength AUC published in the current issue of the Biochemist, published by our Biochemical Society: http://www.portlandpresspublishing.com/sites/default/files/biochemist/Biochemist%20Biophysics/BioAPR19_All%28Demeler%29.pdf?dm_i=4WUK,532Y,250YBQ,HPBK,1

Do please email Prof Steve Perkins (s.perkins@ucl.ac.uk) or Mr Jayesh Gor (J.gor@ucl.ac.uk) if you are interested in discussing possibilities, or even applying this new instrument for your research.


Posted by ublmcr01 in Lab news, News, Uncategorised

Dr Salvador Tomas awarded Leverhulme Research Project Grant

Dr Salvador Tomas has been awarded a Leverhulme Research Project Grant to study and develop lipid vesicle-based, stimuli-responsive nanoreactors

Lipid vesicles resemble empty cells, a starting point where to build up programmable cell-like robots by the step-wise addition of molecular machinery. Developing such robots requires that we understand how chemical transformations are influenced by confinement within the boundaries of lipid vesicles. Dr Tomas research group has recently reported evidence that confinement promotes the very chemical reactions that enable the assembly of complex molecular machinery, essential to the function of natural and artificial cells. The aim of the project is to characterise rigorously this confinement effect and to exploit it to build cell-like devices programmed to perform chemical reactions in response to specific external stimuli.

More information about Dr Tomas’s research can be found on his ISMB profile.

Posted by ublmcr01 in Grants awarded, News, Uncategorised

Dr Tine Arnvig awarded MRC Grant

November 2018

The ISMB’s Dr Tine Arnvig has been awarded an MRC grant to investigate ‘Conditional termination of transcription in Mycobacterium tuberculosis’. The aim of the project is to 1. define transcriptional terminator motifs on a global scale in the human pathogen Mycobacterium tuberculosis and 2. to investigate post-transcriptional control of gene expression associated with inherent drug-resistance genes and anti-TB drugs.
Above: Left panel illustrates the principle of regulated or conditional termination, leading to expression of genes under specific growth conditions only. Right panel shows cording M. tuberculosis (photo credit Robin Chamberland).


Moreover, Tine will be hosting a research fellow, Terry Kipkorir, for two years from March 2019.  Terry has been awarded a Newton International Fellowship with Tine as co-applicant, and he will be working at the SMB on post-transcriptional regulation of methionine metabolism in Mycobacterium tuberculosis.

Posted by ubcg49z in Uncategorised