Selecting the landing site for 2018 ExoMars Rover

This post was contributed by Birkbeck student, Anja Lanin. Anja attended Dr Peter Grindrod’s lecture, ‘Selecting the landing site for 2018 ExoMars Rover’ during Birkbeck Science Week 2016.

Mars and a rover

Over the last two years, specialist teams in Europe have been working on helping ESA select the landing site for the first European rover on Mars. This is not just a project for PhD-holders, even individual research findings from undergraduate students contribute to the realisation of this mission. Birkbeck students and staff, including the presenter of this talk, Dr Peter Grindrod, have been closely involved. In his talk ‘Selecting the landing site for the ESA 2018 ExoMars rover’, Dr. Grindrod not only brought to light the difficulties in finding an appropriate site in unexplored regions of Mars but also emphasised the problem of balancing safety, and scientific output.

Birkbeck on Mars!

Birkbeck scientists have been directly involved in developing the PanCam stereo-camera system, which is part of the ExoMars instrument payload, led by UCL’s Mullard Space Science Laboratory. This camera will be crucial for understanding the context of rocks and samples investigated by ExoMars.

Risky goals

The ‘search for signs of past and present life on Mars’ is the main goal of this mission, according to Dr Grindrod. The one billion Euro investment will initially rest on the Russian Proton rocket, with an 89% success rate, on the scheduled May 2018 launch date. The precious 300kg solar-powered rover payload is to land on Mars about 7 months later, via parachute and retro-rockets.

Dr Peter Grindrod

Dr Peter Grindrod

Looking for life, but where?

We learn from Dr Grindrod that the rover needs to land on some of the oldest Martian rocks (>3.6 billion years). Why? Geochemical analysis using orbital-based technology indicates that rocks in some of these oldest regions are sedimentary and characterised by hydrated (clay) minerals.

We know that on Earth clay minerals form from the interaction of rocks with water that is neutral in pH and suits terrestrial life. Some of the geologically younger rocks on Mars contain sulfate minerals formed under water-poor conditions and around life-unsuitable acidic water. So we need a site, as Dr Grindrod says, that at one point had some life-friendly water flowing through it depositing soft sedimentary rocks that the rover can get to and drill into.

Access forbidden – the contamination problem

According to Dr Grindrod, the rover is prohibited from landing in what are called ‘Mars Special Regions,’ areas where any terrestrial organisms unintentionally carried by the rover may survive. Thus areas potentially containing terrestrial life-supporting liquid water at present are a no-go. So scientists have been looking for a rover touch-down location in areas where there may have been life in the past but probably not at present.

Zooming in on a landing target

Mars isn’t small, but temperature constraints rule out areas near the cold poles and the seasonally warm southern hemisphere. Equally very hilly areas are also rover unsuitable due to the steep slopes. Keeping these constraints in mind, the most promising geological outcrops scientists were left with covered just 2% of Mars’ surface area. Finally, they had to consider that the rover could land anywhere within a still considerably large ca. 104 x 19 km elliptical area, rather than a particular spot.

Watch Dr Grindrod’s lecture

The chosen few

Two of the eight landing site proposals submitted throughout Europe came from the UK and both made it into the final four.

In the end a site called Oxia Planum was chosen as the destination for the 2018 launch. The location appears to be near the end of an ancient delta-like river drainage network and there may even be different layers present containing different types of clay minerals, possibly suggesting groundwater interaction. However, one problem with this landing site is that some of the surface is covered in small wind ripples – could the small 20 cm ExoMars rover wheels get stuck here??

For the back-up launch date in 2020 two back-up sites have been selected, Mawrth Vallis and Aram Dorsum. The latter location would place the rover near deposits of one of the oldest river systems (now inverted) on Mars and any landing spot would be conveniently located no more than 100 m from a relevant deposit.

Mars, the red planetWhat’s next?

If Oxia Planum for some reason is proved to be not to be safe enough more work is needed to decide which of the back-up sites is best for the alternative 2020 launch. In the end this decision will be up to ESA and the Russian Space Agency.

Let’s remember though, as pointed out by Dr Grindrod, once the rover touches down the scientific results are for us, for every scientist involved, for everyone whose money has contributed to the mission, not just the investors but also the public.

 

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Lost planetary worlds: Evidence of the unquiet early Solar System

This post was contributed by Birkbeck student, Anja Lanin. Anja attended Professor Hilary Downes’ lecture, ‘Lost Planetary Worlds’ during Birkbeck Science Week 2016.

Solar System

Professor Hilary Downes has been a research scientist in the Department of Earth and Planetary Sciences at Birkbeck for 30 years. Insights from her own and other workers’ research have left her with a strong interest in the evolution of the Solar System. As it turns out, the orderly Solar System we observe today in fact started out as everything but quiet and orderly. In its early days it was a place of violent collisions between planetary bodies. Many of these have been almost completely lost. Almost! We have evidence of their existence, ranging from the macroscopic to the elemental, and this was the subject of Professor Downes’ enthusiastic talk ‘Lost Worlds of the Solar System.’

Theory: Computer models

Starting her talk by showing a real image of a planet-forming region around stars, as observed by telescope, as well as computer models which together may suggest the organised formation of planets within an accretionary disk, Professor Downes moved on to theoretical considerations of a very different-looking chaotic early Solar System.

Computer simulations of Jupiter’s growth, for example, indicate that many planetary embryos were sent onto wildly eccentric orbits. Other models show planets such as Jupiter and Saturn moving repeatedly closer and then away from the sun causing gravitational chaos in the inner Solar System before the system became more settled.

Evidence from our Solar System planets – shaken and stirred!

The audience were then presented with some very odd and interesting facts about our planets. For one thing, they do not orbit the sun in the original plane (the location of the previous accretionary disk) of the Solar System. Some seem to defy the laws of physics by floating above and some below. Furthermore, some of the planets’ axial tilts have gone ‘wonky.’

While Jupiter and Mercury spin textbook-style perpendicular to the plane, all other planets have been knocked around to the extreme that Uranus has been completely knocked over and is now spinning parallel to the plane. Venus is even more special – it is rotating in the opposite direction to all other planets! These characteristics, according to Professor Downes, strongly suggest violent collisions of the planets with other planetary material.

‘Tangible’ evidence: meteorites within meteorites

So what happened to the impactors? We can actually study collisional space debris which comes to us in the form of meteorites. For many of these meteorites the parent body, for example a planet or an asteroid, is known, but, as Professor Downes emphasises, there are many parentless ungrouped meteorites. Perhaps the most interesting of these are brecciated meteorites which contain fragments of other meteorites. What do we learn from these fragments?

 

Real science reveals real mysteries….

As indicated in the talk, planetary science students at Birkbeck are actively accessing technology (e.g. electron microprobe) that allows them to study the mineralogy and basic chemical make-up of meteorites. This is one way that allows them to determine whether or not meteoritic material comes from a classified or unclassified parent body.

Something that cannot be analysed at Birkbeck yet!, but also yields very important clues, are oxygen isotope ratios. Each known planetary body has a unique oxygen fingerprint, so that previously unregistered ratios hint at lost parent bodies. Professor Downes, relating to her own group’s research, points out a particularly interesting brecciated meteorite fragment, which, surprisingly, turned out to be granitic, i.e. it is mineralogically and texturally similar to granites found on Earth (some of us recognise the rock from kitchen counter tops!).

However! – its oxygen chemistry indicates that it comes neither from Earth nor is it related to the other meteoritic material in which it was included as a fragment. It is therefore not related to the asteroid from which the rest of the meteorite is derived. In addition, a strange associated glass is high in sulfur (S) and chlorine (Cl), and no planet in the Solar System except Mars contains sulfur and chlorine. But the oxygen chemistry again suggests it is not from Mars. Thus, this glass may represent another lost planetary body or planet possibly disintegrated during the early collisional chaos!

There are many examples of odd, unexplained finds in meteorites. Even opal, which we recognise as a semi-precious stone, has been found by Profesor Downes and her colleagues, although its extraterrestrial origin is still unclear. Perhaps a water or ice-rich meteorite crashed into an asteroid and all that is left of this ice or water world is this little piece of opal?

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Molecules that Walk

This post was contributed by Dr Clare Sansom, senior associate lecturer in the Department of Biological Sciences. Dr Sansom attended Dr Anthony Roberts’s lecture during Birkbeck Science Week 2016.

Molecules

The Department of Biological Science’s contribution to Science week 2016 kicked off on 11 April with a lecture by Dr Anthony Roberts, a young Principal Investigator who arrived at Birkbeck in 2014. Anthony received his B.Sc. from Imperial College in London and his Ph.D. from the University of Leeds, and spent four years as a postdoc at Harvard in the USA before moving here to start his own research group as a Sir Henry Dale Fellow of the Wellcome Trust and Royal Society.

Walking molecules and their importance for human health

Anthony began his lecture by explaining that he was going to talk about molecules that have the capacity to produce directed movement – or to ‘walk’ – and their importance for human health. These molecules are all proteins, and the context in which they move is the interior of living cells. Both the proteins he studies, kinesin and dynein, ‘walk’ on a network of highways conceptually not unlike the transport system that we use to move around London. These cellular highways are filaments called microtubules, which, unlike our roads and railway tracks, are able to self-assemble and also to self-destruct.

The ability to move is one of the fundamental properties of life, and scientists and philosophers have been studying it for millennia. Muscles were identified as the organs of movement in antiquity, but it was not until the mid-twentieth century that the molecules involved in muscle contraction could be identified. The Hungarian physiologist Albert Szent-Györgyi discovered the muscle proteins now named actin and myosin using very simple equipment during the Second World War.

These proteins have similarities with kinesin and dynein, although historically they have been easier to study due to their abundance in muscle; actin forms fibrils and the enzyme myosin binds to and ‘walks’ along these filaments. This process, like all movement, requires energy, and this is obtained from the cell’s power source, the small molecule adenosine triphosphate (ATP). The part of the myosin molecule that binds to actin, which is called its head, breaks a phosphate bond in this molecule to liberate energy and power the walking motion; many of these ‘power strokes’ together cause the muscle fibre to contract.

Snapshots

Dr Anthony RobertsIdeally, we would want to watch this, or any other form of molecular motion, in real time, but this is impossible because molecules are far too small: smaller than the wavelength of light, so they cannot be viewed in a light microscope. Studies of molecular structure require techniques like X-ray crystallography and electron microscopy, both of which have been used to study motor molecules.

However, neither of these techniques can do more than generate still images. Movement can only be inferred by taking lots of snapshots of the molecules at different points during the movement cycle, rather like the earliest movies. We have now built up a complete picture of actin and myosin that is detailed enough for the positions of individual atoms to be seen clearly.

Not all movement in nature, however, uses muscles. Single-celled organisms – the ‘animalcules’ observed by pioneer microscopist Antonie van Leeuwenhoek in the 1670s – have directed movement, as do bacteria, and these have neither muscles nor nervous systems. And directed movement also occurs inside cells. A good example of this is the division of replicated DNA between daughter cells during cell division.

The interior of all cells is a viscous mixture, crowded with molecules; it is possible for small molecules to move from one part of a cell to another through diffusion, but this process would be impossibly slow for larger ones. Motor proteins, on the other hand, can carry ‘cargo’ molecules across cells remarkably quickly and efficiently. Motor proteins can traverse a distance of 0.1 mm – the length of a large animal cell – in two minutes, which in terms of lengths per second is approximately three times faster than a car.

Both the motor proteins studied in Anthony’s lab, kinesin and dynein, ‘walk’ along microtubules inside cells. These filaments typically form with one end towards the centre of the cell, and its nucleus, and the other towards the cell periphery, and the motor proteins move in opposite directions: dynein towards the nucleus, and kinesin towards the cell edge.

Any kind of directed movement by molecules is challenging for several reasons. Motor molecules have no equivalent of our nervous systems for controlling movement, and they are far too small to be held on their tracks by gravity; instead, they grip the microtubules using chemical forces. They experience negligible inertia, and are constantly buffeted by other molecules in the cell. It would therefore be catastrophic for the whole of a walking molecule to leave its path at once.

A single leg with two feet

The structure and function of conventional kinesin are now fairly well understood. It consists of two identical protein chains, and each chain has two major domains separated by a short linker. The larger domain of each chain coils together to form a single long stalk; the smaller domain is globular and attaches to the microtubule, so the molecule looks rather like a single leg with two feet. Each of the feet is an enzyme that generates the energy for the motion by breaking down ATP to form ADP and release a phosphate group, and it cycles between ATP-bound, ADP-bound and empty states.

The step between ADP-bound and empty is a bottleneck that can be relieved when the foot attaches to the microtubule in a particular position, ensuring that the whole molecule moves in the correct direction. The trailing foot is released from the microtubule and the cycle begins again once ATP has bound to the front foot, triggering a conformational change in the whole molecule.

The core of kinesin is similar in structure to myosin, suggesting that these two proteins have a common ancestor. The other microtubule-bound motor protein, dynein, has a different origin. Although we still know comparatively little about it, it was actually the first of the microtubule-bound motor proteins to be discovered: this was in the 1960s, when it was found as the protein that generates the force that allows protozoa and sperm cells to swim. Anthony’s group, however, has been studying how it functions inside cells to move ‘cargo’ – often nucleic acids or other proteins – from the edges of the cell towards its interior. It also helps to pull the duplicated genetic material between the two halves of the cell during cell division.

The structure of Dynein

Dynein

Dynein

Dynein is a much larger and more complex molecule than the other motor proteins. Its structure, like those other proteins, has several components: in this case, a stalk, a ring and a tail, with a linker between the stalk and the ring. Much of what we know about this large structure has come from electron microscopy, and more recently X-ray crystallography.

Anthony’s group and others have developed a model in which the main mechanical element is the linker, which bends and straightens to displace the cargo-bound end of the structure along the microtubule in the direction of travel. The image shown here is a still from an animated model of how dynein generates movement, which remains speculative in places and is helping to stimulate new experiments in these areas. It is also incomplete, as it only shows one half of the molecule: we do know that dynein, like kinesin, is a biped, but exactly how its ‘feet’ are coordinated remains at the frontier of our knowledge.

Anthony ended his talk by discussing some actual and potential medical applications of studies of walking molecules. Some commonly used anti-cancer drugs, including taxol, work by stabilising microtubules to prevent motion and therefore stop cancer cells from dividing. Molecules that interact with motor proteins are also being studied as potential treatments for neurodegenerative diseases and for some types of heart disease. One such compound is a myosin activator, omecamtiv mecarbil, which is showing promise as a treatment for heart failure. And we are likely to discover further applications as we learn more about these fascinating walking molecules.

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Computational Modelling in Structural Biology

This post was contributed by Dr Clare Sansom, senior associate lecturer in the Department of Biological Sciences. Dr Sansom attended Dr Maya Topf’s lecture on Computational Modelling during Birkbeck Science Week 2016.

Brain computer (copyright Marcos Fernandez via Flickr. Image cropped)

Brain computer (copyright Marcos Fernandez via Flickr. Image cropped)

The Wednesday of Birkbeck Science Week – 13 April – was set aside to celebrate women in science, and it included a talk by Maya Topf of the Department of Biological Sciences. Maya, who was educated in Israel and Oxford, came to Birkbeck on an MRC fellowship after a post-doc at UCSF and has rapidly worked up the academic ladder to the position of reader in computational biology. She will be appointed as a full Professor in October this year.

Maya began by explaining that her research involves making models: specifically, three-dimensional models of biological molecules. Models have enabled scientists to make sense of biological processes since Watson and Crick’s double helical model of DNA showed how this molecule could both replicate itself and act as a template for the synthesis of proteins. This model, celebrated in the film Life Story that was shown earlier in Science Week, would not have been possible without the X-ray photographs of DNA fibres obtained by Rosalind Franklin, then working at King’s College.

The purpose of computational modelling

And the main purpose of modelling molecules is the same now as it was in the 1950s: to discover how they function, and specifically how they function in the environment of the cell. We still have no means of observing what protein molecules – the tiny ‘machines’ that drive all cellular processes – look like when they are at work; all we have is models that may be more or less precise. The very first protein structures to be determined were of the oxygen-carrying proteins myoglobin and haemoglobin, and the first of these, published in 1960, were very imprecise: it was possible to see the shape of the chain but no individual atom positions. These, and all early protein structures, were obtained by X-ray crystallography; ten years later the same group used the same technique to determine a structure in which all atoms except hydrogens could be seen.

DNAThese two proteins have now also been studied using two other structural biology techniques, nuclear magnetic resonance and, most recently, electron microscopy. This last technique is best suited for studying large proteins and complexes of many protein chains, and therefore not suitable for studying most forms of haemoglobin, a small, simple protein. Haemoglobin in earthworms, however, functions as a complex of many individual molecules. Electron microscopy gave a low-resolution picture of the overall shape of these molecules, much like those first haemoglobin structures, and a more precise picture was built up by ‘docking’ atomic-resolution X-ray structures of a single haemoglobin molecule into the shape of the fold.

During the last half-century these three techniques have generated structures for a wide range of proteins, leading to insights in many areas of biochemistry: how the body’s catalysts, the enzymes, work; how drugs bind to their receptors; and how a ‘large’ molecular complex, the ribosome, can synthesise all the proteins that a cell needs from RNA templates. The first atomic structures of this ‘molecular machine’ were obtained in the early 2000s and have transformed our view of protein translation since then (see these videos from the Howard Hughes Medical Institute in the US: basic and more advanced versions).

But, as real proteins are too small to be visible with even the best light microscopes, we need to realise that even these experimental structures are models. Each of the three techniques has its own advantages and limitations. X-ray crystallography needs protein crystals, which can be difficult or even impossible to obtain for particular proteins; electron microscopy cannot be used to study small proteins, but NMR works best with these. All three techniques are complex, time-consuming and expensive, and therefore proteins with known structures are greatly outnumbered by those without structures. There are probably about 43,000 known structures of ‘distinctly different’ proteins known compared to over half a million well-characterised protein sequences.

Bridging the sequence-structure gap

Maya explained that much of her group’s work concerns trying to bridge this ‘sequence-structure gap’ by using computers to model unknown protein structures. There are several ways of doing this; if the computers are powerful enough and the molecule is small enough (and the smallest proteins can be) it is possible to generate a model structure ‘from first principles’ using physics. These techniques assume that the molecules are likely to occupy conformations in which their energy is low. The best results simulate protein folding to produce model structures that can be very close to the experimentally-determined ones, but these require an enormous amount of computational power. Less expensive computer modelling methods tend to rely more on experimental data; Maya collaborates with Helen Saibil in Biological Sciences to fit atomic structures of individual proteins to lower-resolution maps of protein complexes that were generated by electron microscopy. Proteins studied in this way include GroEL, a ‘molecular chaperone’ that forms a chamber that isolates unstructured proteins so that they can fold.

Dr Maya Topf

Dr Maya Topf

Another method of modelling protein structures uses evolution, and relies on the fact that there are remarkably few different basic protein structures – each of the 43,000 known protein structures takes up one of only about 1,000 different folds. Just as all birds have the same basic pattern, with two legs and two wings, all proteins with a particular function will usually have a similar fold. It is therefore possible to model the structure of a protein based on one or more of its evolutionary relatives, in a technique called ‘homology modelling’. In some cases, it is possible to produce a usable model from the structure of a related protein from a very different type of organism. It was more than a decade after the publication of the first bacterial ribosome structures before similar structures could be obtained from mammalian ribosomes, but many useful results were obtained during that time by modelling mammalian ribosome sequences using the bacterial structures and low-resolution electron microscopy data.

Maya ended her talk by stressing that structural biology is a science of model-building. It requires experimental data complemented by physics and by evolution, and, almost above all, it requires powerful computers. Generally, the more sources of information can be combined into a model, the nearer the ‘correct’ structure that model will be: and to quote the statistician George Box, ‘all models are wrong, but some are useful’.

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