Polymer physics modelling predicts interactions in cancer genomes.
An interdisciplinary team of physicists and biologists, including Dr Chris Brackley from the Institute for Condensed Matter and Complex Systems at the University of Edinburgh, and Dr Lisa Russel and Dr Daniel Rico from Newcastle University, used polymer physics based simulations to make predictions of the three-dimensional organisation of chromosomes near to sites of incorrect repair.
Their model predicts which enhancer sites will contact the genes in different cancer cells. The lab-based team can then perform experiments where these sites are targeted, with the aim of reversing the disease state. Not only are the simulations a useful tool for helping direct the experiments, but they also give important insight into the biological and physical processes which lead to the loops forming.
Gene regulation
The chromosomes in our cell nuclei are long fibres made up from DNA and proteins. One mechanism through which genes are regulated is via changes in the three-dimensional organisation of the chromosomes. For example, often, to activate a gene, sites on the chromosome called ‘enhancers’ have to be brought into physical contact with the gene, folding the chromosome into a loop.
Many cancers arise when the chromosomes are broken, and then incorrectly repaired. For example, the broken ends of two different chromosomes can become joined together; genes near to the join can find themselves in contact with enhancers they would not normally encounter. This leads to chemical modification of the chromosome near these genes (chemical ‘marks’ known as H3K4 tri-methylation, or H3K4me3 are deposited). These ‘oncogenes’ then become constantly active, promoting continuous cell division and cancer.
Dr Lisa Russel, Cancer Biologist at Newcastle University said:
Not only do the simulations allow us to understand how the H3K4me3 domains translocate, but they suggest sites on the DNA which can then betargeted in experiments that aim to reverse the disease.
Published work
The work is part of a set of three papers from the same groups of authors which feature of the cover of the July 2022 edition of Genome Research. Together, these works show that H3K4me3 broad domains are associated with regulatory elements of cell identity genes, called super-enhancers, that are ‘hijacked’ to interact with other genes in cancer cells; this is associated with the disappearance of the H3K4me3 domains from cell identity genes, and their appearance over oncogenes. The work showed that the regulation of H3K4me3 broad domains is associated with leukemogenesis and suggests that the presence of these structures might be used for epigenetic prioritisation of cancer-relevant genes.
Science–art collaboration
The teams also worked together with multimedia science artist Dr Dimple Devadas, who produced a series of artworks inspired by the projects. One of the artworks was used on the journal cover, and the others appear in an online exhibition Science as Genome art, showcasing this coming together of cancer biology, polymer physics, and art.
Observations from the James Webb Space Telescope have revealed the most distant galaxy so far.
A team of astronomers led by the University of Edinburgh have discovered what they believe is the most distant galaxy ever observed.
The galaxy has a redshift of 16.7. Redshift is used to measure distances in the cosmos, and describes the way light coming from an object has been stretched by the expansion of the universe to redder wavelengths. The higher the redshift number, the more distant it is and the earlier it is being viewed in cosmic history.
The galaxy discovered is called CEERS-93316, and is 35 billion light-years away. It is taken from a project called the Cosmic Evolution Early Release Science (CEERS) Survey which is taking some of the first observations with the James Webb Space Telescope (JWST).
The colour image of CEERS-93316, recently featured by BBC News, was made by Edinburgh undergraduate physics students Sophie Jewell and Clara Pollock, who are undertaking summer projects in the Institute for Astronomy, funded by summer studentship bursaries from the School of Physics and Astronomy.
The same team have also published an analysis of the first spectroscopic data from the JWST, led by Leverhulme Fellow Adam Carnall. This work confirms the vast potential of JWST spectroscopy for performing detailed studies of the earliest galaxies, such as CEERS-93316. This work was recently reported on by Science News.
James Webb Space Telescope (JWST)
The JWST is the successor to the Hubble Space Telescope, was launched in December 2021 and first collected images from its home at the second Sun-Earth Lagrange point in June 2022. JWST observations will include the first stars, formation of the first galaxies, our own solar system, and will tell us more about the atmospheres of potentially habitable exoplanets.
PhD student Callum Donnan who is based in the Institute for Astronomy and involved in the project commented: “We’re using a telescope that was designed to do precisely this kind of thing, and it’s amazing.”
Next steps
Observations from the JWST have yet to undergo full spectroscopic examination. This process will reveal the spectra of galaxies and will explain how the light (originally visible wavelengths) has been stretched into the infrared. The spectroscopy will also reveal the chemical composition of objects.
Callum Donnan explains: “We can look at the colours in our galaxy in a broad sense, and it’s quite blue, which suggests a younger stellar population. But it’s not blue enough that this galaxy is made up of metal-free stars”.
The discovery by the Edinburgh team will be short lived however – astronomers expect to find ever more distant objects via the images from the JWST over the coming weeks, months and years.
Image gallery
The world’s largest and most sensitive dark matter experiment has come to life and is delivering results, moving a step closer to offering clues about one of the biggest mysteries of the Universe.
The LUX-ZEPLIN Dark Matter Experiment (LZ), based at the Sanford Underground Research Facility in South Dakota, US, has gathered its first result – showing the experiment is successfully operating as designed.
What is LUX-ZEPLIN?
LZ is intricately and innovatively designed to find direct evidence of dark matter – a mysterious invisible substance thought to make up most of the mass of the Universe. Dark matter is particularly challenging to detect, as it does not emit or absorb light or any other form of radiation. The LZ detector will try to capture the very rare and very faint interactions between dark matter and its 7-tonne liquid xenon target.
The international project led by the Department of Energy’s (DOE) Lawrence Berkeley National Laboratory (Berkeley Lab) has now announced the detector is running as hoped after years of careful set-up. The tests show that LZ already is the world’s most sensitive dark matter detector, with plans to collect about 20 times more data in the coming years. After the successful start, full-scale observations can begin with the hope of finding the first direct evidence of dark matter.
The legacy of ZEPLIN
LZ involves an international team of 250 scientists and engineers from 35 institutions from the US, UK, Portugal, and South Korea. The UK team, funded by the Science and Technology Facilities Council (STFC), consists of more than 50 people from the universities of Bristol, Edinburgh, Imperial, Liverpool, Oxford, Royal Holloway, Sheffield and UCL and STFC’s Rutherford Appleton Laboratory.
Many of these UK groups came from the ZEPLIN programme, which developed the liquid xenon technology for dark matter searches at STFC’s Boulby Underground Laboratory. The UK ZEPLIN groups then joined the LUX experiment in the USA in 2012 and started designing LZ around that time.
Professor Alex Murphy who leads Edinburgh’s group on the project said:
“It’s great to see all these years of development, from ZEPLIN through LUX and now LZ come together. It’s been a huge team effort”
Hunting the dark matter
LZ is the largest and most sensitive experiment searching for dark matter particles. These theorised elementary particles interact with gravity – which is how we know about the existence of dark matter in the first place – and possibly through a new weak interaction too. These first results place strong constraints on one possibility for what dark matter might be, Weakly Interacting Massive Particles (WIMPs). WIMPs would be expected to collide with ordinary matter – albeit very rarely and very faintly. This is why very quiet and very sensitive particle detectors are needed for WIMP detection.
How does it work?
At the centre of the experiment is a large liquid xenon particle detector maintained at -100oC, surrounded by photo-sensors. If a dark matter particle interacts with a xenon atom, and produces even a tiny amount of light, the sensors will capture it. In order to see these rare interactions, the team have had to carefully remove all natural background radiation from the detector materials first.
By operating around a mile underground, LZ is shielded from the cosmic rays that bombard experiments located at the surface of the earth. The detector and its cryostat sit inside a huge water tank to protect the experiment from particles and radiation coming from the laboratory walls.
Finally, the team made sure that the liquid xenon itself is as pure as possible by carefully removing a key contaminant through a complex years-long process.
Prof Murphy commented: “With LZ running so well, we should be able to really test the WIMP model for dark matter. There are many other possibilities for what dark matter might be too, several of which are a real focus for the Edinburgh team. It’s a really exciting time for the field.”
IMAGE INFORMATION
Title: LZ Surface Lab
Credit: Matthew Kapust, Sanford Underground Research Facility
Computer simulation shows the seeding of super-massive black holes is a natural by-product of the formation of the cosmic web.
Super-massive black holes which are billion of times more massive than the sun have been detected at the centres of galaxies across the Universe. Most famously our own Milky-Way hosts a super-massive black hole a few million times the mass of the sun at its centre. Despite all this evidence for their existence, the origin of super-massive black holes is an unsolved open question in astrophysics.
A team of international researchers including Professor Sadegh Khochfar from the School’s Institute for Astronomy used 2 million processor hours on super-computers in the UK to show for the first time that that the seeding of super-massive black holes is a natural by-product of the formation of the cosmic web in a Universe dominated by dark energy and cold dark matter. The results provide an answer to the long-standing question on the seeds of super-massive black holes and why they are so ubiquitous in galaxies.
The collaboration setup cosmological simulations that followed the evolution of dark matter and gas in the Universe as it collapses along the network of cosmic filaments. As gas moves along the filaments it reaches the most massive dark matter haloes present in the Universe, which sit at the crossing of filaments. In the present study, four filaments converge onto the dark matter halo under investigation and provide cold and dense gas streams that collide at the centre of the halo and form turbulent gaseous clouds. The ability of this gas to further collapse and form stars is severely suppressed by the presence of turbulence and only picks up once the mass of the clouds has increased to allow catastrophic collapse forming super-massive stars several ten thousand times the mass of the sun. The lifetime of super-massive stars is around a million years, after which they will collapse to form a black hole of similar mass, the seed of super-massive black holes that we see today.
Professor Khochfar commented:
This simulation is pointing the way to finally settle the 20-year-old question on the birth of super-massive black holes in the Universe. The beauty of the proposed black hole seeding channel is that it does not require any fine tuning and is a natural consequence of structure formation along the cosmic web in a Universe that consists of dark energy and dark matter.
The School welcomes applications from both external and internal scientists interested in applying for personal fellowships. We have an internal deadline on 18 July 2022 for STFC Ernest Rutherford, Royal Society University Research and EPSRC Postdoctoral and Open Fellowships.
We are keen to attract outstanding researchers from Edinburgh and across the world to join us as Postdoctoral Fellows. We offer a high quality research environment and support for you in your fellowship application process.
Fellowship opportunities
The School operates an internal review process for the following fellowship opportunities which have a deadline of noon, Monday 18 July 2022:
- STFC Ernest Rutherford Fellowships
- Royal Society University Research Fellowships
- EPSRC Postdoctoral and Open Fellowships
We also welcome applicants for other fellowships, the full list of which can be found on the weblink below.
Application information
Candidates are expected to have a PhD in Physics, Astronomy or a related discipline, and in most cases a few years research experience, as well as the ability to present clear evidence of their potential to undertake leading research.
The School of Physics and Astronomy is committed to advancing equality and diversity, welcoming applications from everyone irrespective of gender, ethnic group or nationality.
How to apply
Candidates must submit a research statement, CV and list of publications. Full application information can be found on the weblink below.
Congratulations to Dr William Barter who has been awarded a UK Research and Innovation (UKRI) Future Leaders Fellowship, and will be joining the School of Physics and Astronomy’s Particle Physics Experiment Group.
Fellowship scheme
The UKRI Future Leaders Fellowships have been instigated to ensure the strong supply of talented individuals needed for a vibrant environment for research and innovation in the UK.
In this round, 84 pioneering researchers, tech entrepreneurs, business leaders and innovators across different sectors and disciplines in Scotland will benefit from a £98 million cash boost to convert their innovative ideas to transformational products and services.
On the discovery of new particles
William is a particle physicist, leading research and research teams at the Large Hadron Collider, with over a decade of experience studying the weak force (which is responsible for radioactivity) and differences between matter and anti-matter. With the award of the Future Leaders Fellowship, William seeks the discovery of new fundamental particles. In our best theory of particle interactions at a quantum level, electrons are expected to behave in the same way as their heavier counterparts, the muon and the tau-lepton. However, recent measurements suggest that muons and electrons behave differently. Attempts to explain these results invoke new, currently unknown, fundamental particles, and also suggest that clear signs of this 'new physics' will be visible in analogous measurements of tau-leptons. William will develop novel techniques to detect these tau-leptons, and will use these techniques to search for definitive evidence of new particles. Such a discovery would herald a paradigm shift in our understanding of the universe.
Congratulations to Professor Wilson Poon whose contributions to the field of rheology have been recognised by the Eugene C. Bingham Medal.
Eugene C. Bingham Medal
The Eugene C.Bingham Medal is the highest award of the Society of Rheology and is given annually to an individual who has made outstanding contributions to the field of rheology.
The citation of Professor Poon’s award reads: “By combining rheological and microstructural measurements on carefully characterized model systems, Wilson Poon has transformed our understanding of the flow of colloidal gels, attractive and repulsive colloidal glasses, and non-Brownian suspensions of frictional particles. He has thereby elucidated universal principles underpinning the formulation of many industrial products.”
The Award will be presented at the 93rd Society of Rheology Annual Meeting to be held in Chicago, Illinois in October 2022, and will be accompanied by a plenary lecture by Professor Poon.
Soft Matter and Rheology
Based in the School’s Institute for Condensed Matter and Complex Systems, Professor Poon has spent many years working on 'model' colloids to study phenomena that are ubiquitous across condensed matter and statistical physics, particularly the structure and dynamics of arrested states such as glasses and gels. Understanding such states and how they flow – the science of ‘rheology’, is one of the grand challenges facing 21st century physics; precisely because of their interesting flow properties, such states occur widely in a very large range of industrial processes and products.
To exploit the latter connections, Professor Poon set up the Edinburgh Complex Fluids Partnership (ECFP) in 2012 to coordinate knowledge exchange with industry. ECFP clients now span many sectors, from food and confectionaries through personal care to specialty and agri-chemicals. He stresses that this is a genuine process of bidirectional knowledge exchange, and not a unidirectional ‘knowledge transfer’ from academia to industry as is often portrayed in discussions of such partnerships. Thus, some of his most impactful recent contributions, such as the work on the rheology of non-Brownian suspension mentioned in the Bingham citation, has arisen from real-life industrial problems and partly performed with industrial partners such as Mars Chocolate and Johnson Matthey.
Professor Poon’s other research interest includes suspensions of ‘active particles’ in the form of swimming bacteria. He has recently started investigating the ‘physics of death’ – how the phenomenon we call ‘life’ relies ineluctably on highly-organised processes of ‘self disassembly’ that feed back into equally highly-organised processes of ‘self assembly’. He also teaches and researches theology, the latter word being, amusingly, often a typo for the word ‘rheology’. Professor Poon is therefore looking forward to the almost inevitable announcement some day that he has been awarded the Bingham Medal for Theology!
A new European Space Agency science mission, proposed by the UK, to 3D-map a comet for the first time has reached a major milestone, moving from the design phase to implementation.
Comet Interceptor mission
The Comet Interceptor mission, which will further our understanding of the evolution of comets and will help solve some of the mysteries of the Universe, has been formally adopted by the European Space Agency (ESA).
Due for launch in 2029, the mission will see one main spacecraft and two robotic probes travel to an as-yet unidentified comet and map it in three dimensions.
The mission was first proposed by an international team led by University College London’s Mullard Space Science Laboratory (MSSL) in Surrey and the University of Edinburgh.
Professor Colin Snodgrass, who is based at the University of Edinburgh’s Institute for Astronomy, was deputy lead on the proposal, and leads the target selection team that is working to identify suitable comets, commented:
It is very exciting to be part of a mission that follows a completely new approach: designing and building the spacecraft before the target is even discovered. This opens up opportunities to visit space objects that were completely inaccessible before, such as comets entering the inner solar system for the very first time, or possibly even interstellar objects that formed around a distant star.
The UK Space Agency has so far provided £2.3 million in funding for two instruments on the mission: The Modular InfraRed Molecules and Ices Sensor (MIRMIS) instrument is led by the University of Oxford. MIRMIS will deliver a unique dataset, providing information such as the comet’s shape, size and rotation state. The Fluxgate Magnetometer (FGM) sensor led by Imperial College London and located on the ESA probe will provide high accuracy and high-time resolution measurements of the comet’s magnetic field strength and direction. One of the two robotic probes will be built by the Japanese Space Agency, with the team working to find a contractor for the main spacecraft and the other robotic probe.
Understanding the origins of our Solar System
Comets are what is left over when a planetary system forms and in each ancient object is preserved information about the formation of the Solar System 4.6 billion years ago.
Comet Interceptor would be the first mission to travel to a comet which has never previously encountered the inner Solar System.
To do this, it will need to launch and reach a holding position around 1 million miles away from Earth. There it will lie in wait – possibly for years - until astronomers on the ground spot a suitable comet for it to intercept. The two probes will make closer passes of the comet’s nucleus and beam their data back to the main craft.
This new ambush tactic is the first of its kind. The fly-by of the three spacecraft, including the two probes, which measure less than a meter across, is likely to take just a few hours but could illuminate conditions that prevailed more than 4 billion years ago.
Previous missions have studied comets trapped in short-period orbits around the Sun, meaning they have been significantly altered by our star’s light and heat. Breaking from that mould, Comet Interceptor will target a pristine comet on its first approach to the Sun.
The scientists are likely to target a comet travelling from the Oort Cloud — a band of icy debris that lies about halfway between the Sun and the next nearest star.
This debris was formed during the conception of the Solar System but was rapidly ejected to its outermost edge. Unlike more familiar comets, their surface will not have been vaporised by the Sun’s energy — a process that leads to dust building up on a comet, obscuring its original state.
Once the probes reach a pristine comet, they will study and scrutinise the chemical composition of it, with one aim being to evaluate whether similar objects may have brought water to planet Earth in the past.
Image gallery
The European Space Agency has released a new tranche of processed data from the Gaia space observatory – the result of several years’ work by hundreds of scientists, including a team at the Institute for Astronomy.
220 million spectra
On June 13th 2022 the European Space Agency releases a new tranche of processed data from the Gaia space observatory to the world scientific community. The release incorporates a rich variety of position, distance, spectroscopic and classification information for hundreds of thousands of solar system objects, 1.6 billion stars (including nearly ten million variable types and one million binaries), and millions of candidate galaxies and distant quasars. The spectroscopy alone amounts to some 220 million individual spectra, by far the largest haul of such data ever assembled. The data release is the result of several years’ work by hundreds of European scientists including a team at the Institute for Astronomy, based in the School of Physics and Astronomy.
Collaboration
The European Space Agency's Gaia space observatory has been scanning the entire sky since mid-2014, making position and brightness measurements as objects transit its focal plane.
Many hundreds of individual measurements for each of several billion objects have been amassed over the last seven years, and the satellite is still going strong with a projected life time now estimated at 10 years in total. Raw data from the giga-pixel cameras on-board is transmitted continuously to the ground where a network of data processing centres calibrate and prepare the data for science exploitation by the world astronomical community.
Edinburgh scientists and technical experts in the Institute for Astronomy are involved in this endeavour which is staffed by several hundred scientists, engineers and operations personnel spread around Europe. The UK part of the collaboration involves the universities of Edinburgh, Cambridge, Leicester, Bristol and University College London. Here in Edinburgh responsibilities include instrumental calibrations and core processing software for the imaging systems at the head of the data flow, and also preparing the final science-ready data products and delivery systems at the tails of the pipelines, all in collaboration with colleagues in the pan-European Gaia Data Processing and Analysis Consortium.
Precision
The Gaia telescopes and detection systems are highly complex and the data streams require much detailed treatment to extract the best possible measurements. Many repeat cycles of pipeline processing involving iteratively refined software must be undertaken in order to reach the ultimate precision which, in terms of position alone, is equivalent to resolving 3 cm sized features at the distance of the Moon (e.g. the width of a Lunar astronaut's gloved finger seen from Earth!).
Data release 3
Periodic data releases started in September 2016 and occurred at two-yearly intervals thereafter, each presenting increasing amounts of data and increasingly advanced data products. The latest, Data Release 3, occurs on June 13th this year and amounts to some 10 terabytes of products from measurements taken in the first three years of the mission. This latest release is a major milestone in that, for the first time, calibrated spectra for a significant fraction of the entire billion-source catalogue are provided, in addition to detailed astrophysical parameters for nearly half a billion sources enabling categorisation of their stellar types (luminosities, radii, etc). Nearly 34 million stars are provided with line-of-sight velocities from Doppler shift measurements of the lines in their high-resolution spectra, the largest radial velocity survey ever created. In conjunction with the positions, distances and angular movement of those stars this yields a full "six-dimensional" view of their locations and space velocities within the Milky Way. The release includes detailed data for around one million multiple star systems where two or more stars are in close orbits around each other. This supersedes all work on such systems undertaken in astronomy in the centuries since the invention of the telescope. These are just a few examples from the treasury of Gaia Data Release 3 - further details of the release are given in the links below.
Dr. Nick Rowell, Institute for Astronomy, School of Physics and Astronomy said:
The Gaia space telescope scans the sky 24 hours a day, measuring and cataloging every object bright enough to be detected by its sensors. This ranges from asteroids in the Solar System, through nearby stars, all the way to quasars in the distant universe.
Dr. Nigel Hambly, Institute for Astronomy, School of Physics and Astronomy, said:
Gaia is the mission that keeps on giving. Data releases up to now have yielded on average four to five research papers per day in international journals of research in astronomy and astrophysics. This is a figure that even surpasses that for the NASA/ESA Hubble Space Telescope. The mission is literally re-writing astronomy text books, but we're nowhere near the end yet. The latest release of data comprises merely 30% of the measurements in the projected final mission catalogue, yet it is nonetheless a huge leap forward in astronomical survey science.
Polymeric additives enable homogeneous drying of dispersed particles.
Have you ever spilled your coffee? You may have noticed how the coffee dries into an intriguing stain with a bright centre and a dark ring encircling it.
This ‘coffee ring’ forms because the liquid evaporates faster at the edges, inducing a flow from the droplet interior towards the outside. Suspended solid coffee particles thus accumulate at the drop edge, causing the characteristic ring pattern.
Inks and any other liquids containing solid materials behave like coffee – particles accumulate around the edges upon drying. The resulting uneven particle distribution presents a major challenge in ink-jet printed electronic devices, as it can lead to failure and a loss of performance.
In their Nature Communications paper, a team of researchers from the University of Edinburgh and the Friedrich-Alexander-University Erlangen-Nuremberg present a simple, yet versatile strategy to overcome the omnipresent coffee ring effect and achieve homogeneous drying patterns of particle dispersions. The strategy the researchers apply is to modify dispersed particles with polymeric additives. This induces additional steric repulsion, which prevents particle accumulation at the droplet edge and promotes adsorption to the droplet surface, resulting in a homogeneous particle film upon drying.
Importantly, the presented method is independent of particle shape and is applicable to a variety of commercial pigment particles and different dispersion media. The simplicity and versatility of the method paves the way towards reliable coatings and ink-jet printed electronic devices in a wide range of advanced technologies.