Flying in the face of Neurodegeneration

RubenCauchi
Fruit flies are not human. Yet they are close enough to have been used for over 100 years by scientists to find out more about humans. Dr Ruben J. Cauchi writes about his relationship with the fly. He uses it to find out how to stop Alzheimer’s disease, Parkinson’s disease, and Motor Neuron Disease that affect tens of millions

It was a cold and grey February afternoon. Snowflakes were pelting the dreaming spires of Oxford. This gloomy weather did nothing to impede the warmth and buzz exuding from the laboratories crammed in the iconic Sherrington building. Less than a century earlier, this labyrinthine edifice was the habitat of Sir Charles Sherrington whose experiments shaped our understanding of the ‘synapse’ or the minute gaps between one brain cell (neuron) and another. The Sherrington building (part of the Department of Physiology, Anatomy, and Genetics at Oxford University) has undergone several expansions over the years. In its newest wing, nowadays it houses the research group of Dr Ji-Long Liu, a rising star in the field of genetics and cell biology.

For me, this was no ordinary afternoon. Together with Liu’s lab teammates, I was perched on a stereomicroscope whilst holding a delicate brush in my hands. On one side was a tray jammed with vials populated with fruit flies and the usual good strong cuppa. Fruit flies are no house flies: each adult fly is only a few millimetres long, their beautiful bodies are pale with black zebra-like stripes and their eyes a bright apple-red colour. I grabbed a vial, fired a puff of carbon dioxide gas through its fluffy plug and then firmly rapped the upended vial to shake its sleepy occupants onto an illuminated pad. I took a deep breath before peering at them through the eyepieces.

At the time, I was more than mid-way through my doctoral studies, and the results of my experiments were far from extraordinary. I was researching the most common genetic killer of human infants, a neuromuscular degenerative disease known as spinal muscular atrophy or SMA in short. I was exploiting the tiny fruit fly to gain new insight into this catastrophic disease.

I decided to up my efforts by generating a series of mutants or faults in Gemin3, the gene that I was investigating. I was targeting these mutants to different organs such as brain, muscle, or gut. The results of this screen were due today. With a few flicks, I deftly flipped and sorted the minuscule fly bodies into neat piles taking note of differences that are invisible to the untrained eye. The mutants did not produce any dramatic effect. Damn! Another experiment down the drain! Frustrated by the result, I mistakenly knocked over a vial, dislodging its plug. Usually, released flies would happily escape by flying. Strangely, my flies were jumping as if attempting flight but just couldn’t make it into the air — an unexpected but interesting trait or phenotype. I checked the tag on the vial. In these flies the mutant was targeted to that part of the body that powers movement, the so-called ‘motor unit’. Following that afternoon, which will remain forever etched in my memory, the results just flowed in and a few months down the line I would find myself donning my subfusc (Oxford-speak for academic dress) to defend my doctorate.

Fly Superstar

The rise to biological stardom for the fruit fly, scientifically known as Drosophila melanogaster, began in 1907 when my great-great-grandfather (by academic lineage) Thomas Hunt Morgan adopted this organism to understand heredity or genetics. Morgan was the first to harness the major advantages of working with this organism: they have an insatiable sexual appetite and a speedy development (only 10 days) from embryo to adult. This means that large-scale experiments are doable in record time. Morgan’s infamous ‘Fly Room’ at Columbia University in New York set the stage for a new ‘religion’ practiced and preached across the globe.

Morgan spent years searching unsuccessfully for flies with clear, heritable  differences so that he could investigate how they are inherited. A breakthrough happened in April 1910 when he discovered his first mutant, a white-eyed male fly amongst many red-eyed flies. Morgan took great care of this special fly: he kept it in a bottle and after a day’s lab work he used to take it home! At the same time his wife Lilian, who also became a famous geneticist, gave birth to a child. And such was the excitement surrounding Morgan’s discovery that on his first visit to the hospital, Morgan’s wife said: ‘How’s the fly?’ To which, Morgan replied: ‘How’s the baby?’.

When the white-eyed fly was bred or crossed with a virgin red-eyed female, their offspring were all red-eyed. When sisters and brothers were crossed, half of the male progeny gained back their white-eye colour. This hereditary pattern is typical for a sex-linked (recessive) variation, since the gene for eye colour in Drosophila, named by Morgan as the white gene, is on the X chromosome which determines sex. Similar to us, male flies are XY whereas females are XX. This key experiment and numerous others that followed expanded on the knowledge gained through the ingenious cross-breeding experiments of pea plants by the Austrian monk Gregor Mendel half a century earlier. Importantly, this fly-based work found that characteristics like eye colour are inherited from parents through chromosomes — large structures which package DNA in our cells. Furthermore, Morgan and his gifted students uncovered that the thousands of genes in our genome are arranged along chromosomes in a precise order, like beads in a necklace. Each gene can be identified by its specific location on a chromosome.

“Flies could be used as models of human disease”

In 1933, Morgan won the Nobel Prize for these great discoveries. The first of six awards was to recognise seminal insights into our biology through this tiny fly. Hence, in 1946 one of Morgan’s protégés, Hermann Muller, was recognised for his fly research demonstrating that X-rays can damage chromosomes. Then in 1995, Ed Lewis, Christiane Nüsslein-Volhard, and Eric Wieschaus shared the Nobel Prize for their herculean efforts in discovering the genes that controlled early development in Drosophila. In the embryo, waves of master genes are triggered that lead to eyes, brains, and the body’s patterning. Similar genes were later found in humans doing the same function. In 2011 Jules Hoffman received the Nobel Prize for finding how the body’s inbuilt immunity works through the use of the fly model organism. I suspect that there is still room for more trophies in the fly triumph cabinet.

At the dawn of this century, the genomics revolution led to the complete DNA sequencing of an organism including fly and human. These monumental projects revealed that an astonishing number (more than two-thirds) of human genes involved in disease have counterparts in the fly. This development meant that flies could be used as models of human disease. It sparked off a renaissance of Drosophila research. The fly was good at modelling neuro-degenerative conditions because their nervous system has stunning similarities to ours. Neuro-degenerative diseases including Alzheimer’s, Parkinson’s, Huntington’s, and Motor Neuron Disease occur when neurons in the brain and spinal cord begin to die slowly. Patients may lose their ability to function independently or think clearly. Symptoms progressively worsen and ultimately, many die. Most neuro-degenerative diseases strike later in life, so we should expect their frequency to soar as our population ages — Alzheimer’s disease may triple in the US alone by 2050.

 

Malta: the right time to fly?

Together with my students in my lab at the University of Malta I am working with flies to learn more about neuro-degenerative disease. We continue to focus on SMA, a genetic disorder arising from the deterioration of motor neurons which are nerves that communicate with and control voluntary muscles. As the motor neurons die, the muscles weaken with drastic effect on the walking, crawling, breathing, swallowing, and head and neck control of unfortunate children afflicted by this condition. The child’s intellectual capacity is unaffected but vulnerability to pneumonia and respiratory failure means that many patients die a few years after diagnosis.

The underlying cause of SMA is usually a gene flaw that results in low levels of a protein called SMN for survival of motor neurons. Inside cells, SMN is bound to other proteins called Gemins. The SMN-Gemins alliance is involved in building the spliceosome, which is the chief editor of messenger RNA molecules. Messenger RNA carry the DNA code that instruct cells how to fabricate proteins. If SMN is absent spliceosomes do not form, correctly-edited messenger RNA are not produced and protein synthesis is heavily disrupted — the cell should shut down. Spliceosomes are required in each of the 120 trillion cells forming our body. Yet, in the disease SMA only motor neurons die. The reason has baffled researchers for decades and remains unsolved.

Is it possible that SMN has another function in motor neurons? And does it act alone? Our flies were crucial in providing some answers to these questions. Our work showed how the SMN-Gemins family is tightly-knit. In this regard, we recently demonstrated that both SMN and Gemins can be detected in prominent spherical specks in different cellular compartments. Within the cytoplasm, these organelles are known as U bodies because they probably are the factories of spliceosome components, which themselves are rich in the chemical Uridine. In the nucleus, the structures containing the SMN-Gemins family hug the mysterious Cajal bodies — discovered over a century ago by Spanish Nobel laureate Santiago Ramón y Cajal.

“We are feeding these flies the Mediterranean diet derivatives to see whether Alzheimer’s can be stopped in flies, which will bring us one step closer to treating it in humans”

And what about the flightless flies? Think about it. Considering that SMA is a neuromuscular disease, it makes perfect sense that on loss of SMN, muscles become so weak that flies are unable to flap their tiny wings fast enough to fly. Our latest work reveals that flightlessness is seen in flies without enough Gemin proteins. This means that SMN does not function alone but hand in hand with the Gemins. Our next step was to find out the pathway connecting the SMN-Gemins family to the motor defects. We linked the Gemin mutant which did not work properly to a tag called green fluorescent protein or GFP. GFP glows under the right light in cells. We managed to create genetically-modified flies with this modified gene — a first for Malta and a powerful tool to solve the mysteries of this disease.

Fluorescent proteins let researchers figure out a protein’s location. And by knowing the location of proteins we gain of lot of information about what they do. Consider this analogy with a VIP. If we tagged the Prime Minister of Malta we would find that he is most probably found in Valletta most time of the year. If we were aliens from another planet, this knowledge would allow us to refine our understanding of the Prime Minister’s function. Therefore, we can eliminate a function in the entertainment industry (weak signal  from Paceville) but we cannot exclude a function in government (strong signal from Valletta). Likewise, we found that our GFP-Gemin mutant is mostly found in the cell’s nucleus. The nucleus houses life’s instruction manual: DNA. Our work now needs to zero in on the other proteins the SMN-Gemins family works with in the nucleus. Doing so will open new therapies to halt neuro-degeneration in children. Back to our analogy, we need to zoom in on Valletta until Auberge de Castille, the Prime Minister’s office, is clearly in focus.

Fly infographicSeveral neuro-degenerative diseases occur because of sticky protein clumps that wreak havoc inside, and outside, neurons. This is typical in Alzheimer’s disease, Parkinson’s disease and Motor Neuron Disease. With Dr Neville Vassallo’s research group, and local industry (Institute of Cellular Pharmacology), we are testing chemical derivatives of the Mediterranean diet and flora on fruit flies to see whether they can curb the protein clumps’ toxicity. They definitely do in a test tube. Flies mutated to be remarkably similar to human Alzheimer’s lose their ability to climb up the sides of their vial habitats and die prematurely because of neuro-degeneration. We are feeding these flies the Mediterranean diet derivatives to see whether Alzheimer’s can be stopped in flies, which will bring us one step closer to treating it in humans.

Through flies we have understood human biology. Apart from choosing Mr and Mrs Right, a good geneticist must learn to focus and listen to what flies are really saying. This is easier said than done but achievable. Flies have spurred me to pursue unexpected but interesting paths. In the years to come I, together with my students, will continue to flip, sort, screen and tag, looking for fly mutants who will continue to teach us about ourselves. And yes, we will be all ears!

 

The author is indebted to colleagues at the UoM and worldwide for their constant support and inspiration. The research of Dr Ruben Cauchi (Department of Physiology & Biochemistry, UoM) is funded by the Faculty of Medicine and Surgery, the University of Malta Research Fund and the Malta Council for Science & Technology (MCST) through the National R&I Programme 2012 (Project R&I-2012-066). For more about Dr Cauchi’s research click here.

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Dreamland

Book Review

David K. Randall woke up on his back, his leg bent at an awkward angle, in excruciating pain. To figure out why, he wrote a book about the science of sleep. Clever. Clever doubles as a nice summary of the book.

Another book summary: sleep rules your life. Get a good night’s sleep or else everything suffers: your creativity, memory, attitude, ability to think straight, control your emotions, react to emergencies, sex life, and work. Lack of sleep has cost lives; to sleep is to live.

An extreme statement but Randall holds a very good argument. Zlatko Glusica, an Air India pilot, woke up just before landing and tried to bring a plane down safely with a sluggish brain whose higher brain functions were down. In this state we might talk to lamps, Glusica instead killed himself and 157 others. Lack of sleep and truck drivers are another bad idea, while battles have been lost because of sleep. Sleep prevents disasters.

“Randall covers an immense range of research and topics. This is where the book’s problems start. He did a lot of research and wants us to know that.”

The book is well researched. Randall fires factoid after research study at the reader in a pleasant easy to read style. You’ll learn about the dangers of the first sleeping pill that is now a 30 billion dollar industry, how one in five sleepwalk, and how one in four middle aged men have sleep apnea.

Sleep apnea happens when the airway collapses in either obese people or those with a narrowed throat. A minute can pass before the sufferer briefly wakes up and desperately gulps down some oxygen. Most apnea patients are unaware of their condition. It leads to disrupted sleep and less productivity, memory loss, and heart attacks. Sufferers can use a simple device that gently pushes air into the lungs as an instant cure.

The book is filled with great advice like the above. It’s simple, without hocus pocus, and doesn’t need overly expensive equipment. Relax. Don’t try to sleep too hard. Your brain must disassociate itself from the rest of your body. Don’t drink alcohol or coffee. Expose yourself to light, but not late at night, at night dim lights, avoid screens. Don’t sleep too hot or too cold, the body is meant to cool after 10 pm — let it. Exercise. Simple.

Randall covers an immense range of research and topics. This is where the book’s problems start. He did a lot of research and wants us to know that. At other times, he rambles. A stricter editor would have helped the book.

The author only glosses over hardcore scientific studies. He mentions some science behind daily rhythms in Chapter 9. The book only has 13 chapters. He hardly even mentions the genes or molecular biology related to sleep. The scientist inside me died a little death. There are some amazing stories he missed out on by focusing on the lighter human studies.

Don’t take the above too harshly. Dreamland is a great book to learn more about sleep, just avoid late night tablet reading. You have been warned.

 

Protecting the World’s largest experiment

GianlucaValentino
The particle beams circulating in the CERN Large Hadron Collider (LHC) have enough energy to melt 500kg of copper. How can we protect the machine from itself?

My phone rang, waking me up in the middle of the night. It is 2 a.m., and I (Dr Gianluca Valentino) am driving from the sleepy French village where I live at the foot of the snow-capped Jura mountains to the CERN Control Centre. As groggy as I feel, I am trembling with excitement at finally putting months of my work to the test.

The operators on night shift greet me as I come in through the sliding door. These are the men and women who keep the €8 billion Large Hadron Collider (LHC) running smoothly. The LHC produces 600 million particle collisions per second to allow physicists to examine the fundamentals of the universe. Their most recent discovery is the Higgs boson, a fundamental particle. In 2012, this finding appears to have confirmed the Higgs field theory, which describes how other particles have mass. It helps explain the universe around us.

The empty bottles of champagne on the shelves of the CERN Control Centre are a testimony to the work of thousands of physicists, engineers, and computer scientists. The LHC has now busted record after record rising to stratospheric fame.

The LHC is an engineering marvel. A huge circular tunnel 100 m underground and 27 km in circumference. It straddles the Franco-Swiss border and is testimony to the benefit of 50 years of non-military research at CERN, the European Organization for Nuclear Research. CERN is also the birthplace of the World Wide Web.

The LHC works by colliding particles together. In this way physicists can peer into the inner workings of atoms. Two counter-rotating hadron (proton or heavy-ion) beams are accelerated to approach the speed of light using a combination of magnetic and electric fields. A hadron is a particle smaller than atoms, and is made up of several types of quarks, which are fundamental particles (there is nothing smaller than them — for now). The beams circulate at an energy of 7 TeV, which is similar to a French TGV train travelling at 150 km per hour.

For the magnets to work at maximum strength, they need to operate in super-conducting mode. This mode needs the collider to be cooled to -271°C using liquid helium, making it the coldest place in the universe. It is also the hottest place in the universe. Collisions between lead ions have reached temperatures of over 5 trillion °C. Not even supernovae pack this punch.

The two separate beams are brought together and collided at four points where the physics detectors are located. A detector works by gathering all the information generated by the collisions which generate new sub-atomic particles. The detectors track their speed and measure the energy and charge. ‘Gluon fusion’ — when two gluons combine (a type of boson or particle that carries a force) — is the most likely mechanism for Higgs boson production at the LHC.

tunnel2

My role in this huge experiment is to calibrate the LHC’s brakes. Consider a simple analogy. A bike’s brakes need to be positioned at
the right distance from the circulating wheel, and are designed to halt a bike in its tracks from a speed of around 70 km/hr. Too far apart, and when the brakes are applied, the bike won’t stop. Too close together, and the bike won’t even move. In the LHC, the particles travel at nearly 300,000 km/s.

Equipment called collimators act as the LHC’s brakes. The LHC is equipped with 86 of them, 43 per beam. They passively intercept particles travelling at the speed of light, which over time drift from the centre outwards. The machine is unprotected if the collimators are placed too far away from the beam. The beam’s energy, equivalent of 80 kg of TNT, would eventually drill a hole needing months or years to repair. If the collimators are too close to the beam they sweep up too many particles, reducing the beam’s particle population and its lifetime.

Dr Ing. Nicholas Sammut
Dr Ing. Nicholas Sammut

The LHC has four different types of collimators, which clean the particles over multiple stages in the space of a few hundred metres. These collimators also protect the expensive physics detectors from damage if a beam were to hit them directly. If the detectors were hit the LHC would grind to a halt.

What does it take to calibrate these brakes? Each brake or collimator is made up of two metre-long blocks of carbon composite or tungsten, known as ‘jaws’. The jaws should be positioned symmetrically on either side of the beam, and opened to gaps as small as 3 mm to let the beam through. They can be moved in 5 µm increments— that is 20 times less than the width of a typical human hair. The precision is necessary but makes the procedure very tedious.

The beam’s position and size at each collimator are initially unknown. They are determined through a process called beam-based alignment. During alignment, each jaw is moved in steps towards the beam, until it just scrapes the edge. Equipment near the collimator registers the amount of particles they are mopping up. Then, the beam position is calculated as the average of the aligned jaw positions on either side, while the beam size is determined from the jaw gap.

The problem is that there are 86 collimators. Each one needs to be calibrated making the process painfully slow. To calibrate the jaws manually takes several days, totaling 30 hours of beam time. To top it all, the alignment has to be repeated at various stages of the machine cycle, as the beams shrink with increasing energy, and imperfections in the magnetic fields can lead to changes in the beam’s path. This wasted time costs millions and makes the LHC run slower.

Previously, one had to click using a software application for each jaw movement towards the beam. With a step size of 5 µm and a total potential distance of 10 mm, that is 2000 clicks per collimator jaw! Extreme precision is required when moving the collimator jaws. If the jaw moves too much into the beam, the particle loss rate will exceed a certain threshold, and the beam is automatically extracted from the LHC. A few hours are wasted until the operators get the machine back and the alignment procedure is restarted.

Dr Ralph Assman

Over the course of my Ph.D., I automated the alignment, speeding it up by developing several algorithms — computer programs that carry out a specific task. The LHC now runs on a feedback loop that automatically moves the jaws into the correct place without scraping away too much beam. The feedback loop enables many collimators to be moved simultaneously, instead of one at a time. A pattern recognition algorithm determines whether the characteristic signal observed when a jaw touches the beam is present or not. This automates what was previously a manual, visual check performed by the operator.

The sun’s rays begin to filter through the CERN Control Centre, and the Jura mountains are resplendent in their morning glory. The procedure is complete: all collimators are aligned in just under 4 hours, the fastest time ever achieved.

In early 2013, the LHC was shut down for a couple of years for important upgrades. Before then my algorithms helped save hundreds of hours; since the LHC costs €150,000 per hour to run, millions of euros were also saved. This software was part of the puzzle to provide more time for the LHC’s physics programme and is now here to stay.

The morning shift crew comes in. The change of guard is performed to keep the machine running 24 hours a day, 7 days a week, while I head home to catch up on lost sleep.

What is a collimator?

How does a particle accelerator work?

 

 

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Shipping’s Black Cloud

Over summer Dr Edward Duca visited the beautiful Island of Gozo, meeting Prof. Ray Ellul and his team based in Xewkija and the Giordan Lighthouse. Gozo is a tourist hotspot because of its beautiful landscapes, churches, and natural beauty. These same reasons attracted Ellul to obtain baseline readings of air pollutants; human effects should be minimal. Their equipment told them a different story.

They’re very big, anything from 10,000 tonnes to 100,000 tonnes,’ atmospheric physicist Prof. Ray Ellul is telling me about the 30,000 large ships his team observed passing between Malta and Sicily over a year. This shipping superhighway sees one third of the world’s traffic pass by carrying goods from Asia to Europe and back.

M/T "XANTHIA" - Yard no. 108 by: AKER AUKRA AS - AKER YARDS

The problem could be massive. ‘A typical 50,000 tonner will have an engine equivalent to 85 MW,’ Malta’s two electricity plants churn out nearly 600 MW. You only need a few of these to rival the Islands’ power stations.

Ellul continues, ‘this is far far worse. We are right in the middle of it and with winds from the northwest we get the benefit of everything.’ Northwest winds blow 70% of the time over Malta and Gozo, which means that around two thirds of the time the pollutants streaming out of these ships are travelling over Malta. Even in Gozo, where traffic is less intense, air quality is being affected.

“Ships currently use heavy fuel oil with 3.5% sulfur; this needs to go down to at least 0.5%. The problem is that it doubles cost”

Malta is dependent on shipping. Malta’s Flag has the largest registered tonnage of ships in Europe; shipping brings in millions for Malta. We cannot afford to divert 30,000 ships to another sea. Yet Malta is part of the EU and our politicians could ‘go to Brussels with the data and say we need to ensure that shipping switches to cleaner fuels when passing through the Mediterranean.’ Politicians would also need to go to the Arab League to strike a deal with North Africa. Ships currently use heavy fuel oil with 3.5% sulfur; this needs to go down to at least 0.5%. The problem is that it doubles the costs. Malta’s battle at home and abroad won’t be easy, but the Baltic Sea has already taken these measures.

German Dreams

The research station in Gozo is a full-fledged Global Atmospheric Watch station with a team of five behind it. Now it can monitor a whole swathe of pollutants but its beginning was much more humble, built on the efforts of Ellul, who was drawn into studying the atmosphere in the 80s when he shifted his career from chemistry to physics.

In the early 90s the late rector, Rev. Prof. Peter Serracino Inglott, wanted the University to start building some form of research projects. ‘At that time, we knew absolutely nothing about what was wrong with Maltese air and Mediterranean pollution,’ explained Ellul. Building a fully fledged monitoring station seemed to be the key, so Ellul sent ‘handwritten letters with postage stamps’ to the Max Planck Institute in Mainz. Nobel prize winner Paul J. Crutzen wrote back inviting him to spend a year’s sabbatical in Germany, but their help didn’t stop there. ‘He helped us set-up the first measuring station, [to analyse the pollutants] ozone, then sulphur dioxide, then carbon monoxide. That’s the system we had in 1996 — […] 2 or 3 instruments.’

They lived off German generosity until 2008 when Malta started tapping into EU money. After some ERDF money and an Italy-Malta project on Etna called VAMOS SEGURO (see Etna, THINK issue 06, pg. 40), Ellul now manages a team of five. In homage to his early German supporters he has structured the research team around a Max Planck model — ‘one of the best systems in the World for science’.

Paradise Lost?

lloyds-register-logo

Getting data about ships is not easy. ‘It is very sensitive information and there is a lot of secrecy behind it,’ explains Ing. Francelle Azzopardi, a Ph.D. student in Ellul’s team. It is also very expensive. Lloyd’s is the World’s ship registry that tracks all ships, knowing their size, location, engine type, fuel used — basically a researcher’s dream. However, they charge tens of thousands. Ellul took the decision that they gather all the data themselves.

After 2004, all international ships above 300 gross tons need to have a tracking device. Automatically, these ships are traced around the world and anyone can have a peek on www.marinetraffic.com (just check the traffic around Malta). Every half hour the team’s administrator Miriam Azzopardi saves the data then integrates it into the Gozitan database. This answers the questions: where was this ship? which ship was it? how big is it? Easy.

“Ship emission expert James Corbett calculates that worldwide around around 60,000 people die every year due to ship emissions”

co2-emission

If only! The problem is that the researchers also need to know fuel type, engine size, pollution reduction measures, and so on. Then they would know which ship is where, how many pollutants are being emitted, and how many are reaching Malta and Gozo. To get over this hurdle, they contacted Transport Malta (more than once) to ask for the information they needed. ‘About 50% of the ships passing there [by us or Suez are] Malta registered,’ explained Ellul. With this information in hand they could put two and two together. They could create a model for ship emissions close to the Islands and use the model to get the bigger picture.

Enter their final problem: how do you model it? Enter the Finns. Ing. Francelle Azzopardi travelled to the Finnish Meterological Institute. They had already modeled the Baltic Sea, now they wanted access to the Maltese data, in return the Maltese team wanted access to their model called STEAM.

STEAM is a very advanced model. It gathers all the ships’ properties like engine power, fuel type, and ship size. This is combined with its operating environment including speed, friction, wave action, and so on. STEAM then spits out where the team should be seeing the highest pollution indicators. Malta was surrounded.

Apart from the model, the team have seen a clear link between ships and pollution. At the Giordan lighthouse they can measure a whole host of pollutants sulphur dioxide, various nitrogen oxides, particulate matter, black and brown carbon levels, ozone, radioactivity levels, heavy metals, Persistent Organic Pollutants (POPs) and more. When the wind blows from the Northwest, they regularly show peaks of sulfur dioxide, nitrogen oxides, carbon dioxide, carbon monoxide, hydrocarbons which are all indicative of fossil fuel burning either from ships or Sicilian industry. They also picked up relatively high levels of heavy metals especially Vanadium, a heavy metal pollutant. Such metals are more common in heavy fuel oil used by ships.

shipping4

Alexander Smyth is the team’s research officer who spends three months in Paris every year analysing filters that capture pollutants from the atmosphere. Two different filter types are placed in the Giordan Lighthouse. One filter for particles smaller than 2.5 micrometers and another filter for particles around 2 to 10 microns. ‘With the 2.5 filter we can see anthropogenic emissions or ship emissions because they tend to be the smaller particles. The filters are exposed for three to four days, and then they need to be stored in the fridge. Afterwards, I take them to Paris and conduct an array of analyses,’ continued Alexander. The most worrying pollutant he saw was Vanadium.

Vanadium is a toxic metal. When inhaled, ‘it can penetrate to the alveoli of the lungs and cause cancer, a worst case scenario,’ outlined Alexander. It can also cause respiratory and developmental problems — none are good news. The only good news is that ‘they are in very small amounts’. Quantity is very important for toxicity, and they are seeing nanograms per cubic metre, a couple of orders of magnitude more are needed to cause serious problems. No huge alarm bells need to be raised, although Vanadium does stick around in bones and these effects still need more studies.

Vanadium seems to be coming from both Malta and shipping traffic. ‘The highest peaks of vanadium are from the south [of Malta, but the largest number of times I detected came] from the northwest, [from ships],’ said Smyth. ‘There is a larger influence from ships compared to local pollution at the Giordan lighthouse.’

s13

Vanadium is not the only pollutant that could be affecting the health of Maltese citizens. Smyth also saw lots of different Persistent Organic Pollutants (POPs). At low concentrations these compounds can affect immunity leading to more disease, at higher concentrations they can lead to cancer. The local researchers still need to figure out their effect on Malta’s health. Francelle Azzopardi also saw peaks of sulfur dioxide and nitrogen oxides. No surprise here as shipping is thought to cause up to a third of the World’s nitrogen oxides and a tenth of the sulfur dioxide pollution.

Inhaling high levels of sulfur dioxide leads to many problems. It is associated with respiratory disease, preterm births, and at very high levels, death. It can affect plants and other animals. Nitrogen oxides also cause respiratory disease, but can also cause headaches, reduce appetite, and worsen heart disease leading to death. These are pollutants that we want to keep as low as possible.

Ship emission expert James Corbett (University of Delaware) calculates that worldwide around 60,000 people die every year due to ship emissions. Most deaths come from the coastlines of Europe, East Asia, and South Asia. Shipping causes around 4% of climate change emissions. This is set to double by 2050. In major ports, shipping can be the main cause of air pollution on land.

Another unexpected pollutant was ozone, normally formed when oxygen reacts with light. Yet the Giordan lighthouse was not the first to start measuring this gas. It all started with the Jesuits, scholarly catholic monks.

Monks at work

A lot of time is needed to see changes in our atmosphere. Researchers need to gather data over years. To speed up the process, Ellul was hunting around Malta and Gozo for ancient meteorological data about the Islands’ past atmosphere.

He was tipped off that there were still some records at a seminary in Gozo. ‘We expected to find just meteorological data and instead we also found ozone data as well. It was a complete surprise and a stroke of very good luck. We were able to find out what happened to ozone levels in the Mediterranean over the last hundred years.’

Jesuit monks meticulously measured ozone levels from 1884 to 1900. They analysed them seeing that the concentration of ozone was a mere 8 to 12 parts per billion by volume, ppbv. Ellul compared these to a 10-year study he conducted from 1997 to 2006. ‘We measure around 50ppb on average throughout the year,’ which is nearly 5 times more over a mere 100 years.

The situation is quite bad for Malta. In the past, the minimum was in summer and the maximum in winter and spring. Now, this has reversed with spring and summer having the highest ozone levels because of the reactions between hydrocarbons and nitrogen oxides. These come from cars, industry, and ships.

Over the Eastern Mediterranean ozone levels have gradually decreased. Over Malta, in the Central Mediterranean, they remained the same. Ellul thinks this could be because of an anticyclone over the central Mediterranean bringing pollutants from Europe over Malta and Gozo. The levels of ozone in Malta and Gozo are the highest in Europe, and it could be mostly Europe’s fault. Our excessive traffic doesn’t help.

Ozone can be quite a mean pollutant. While stratospheric ozone blocks out harmful UV rays, low-level ozone can directly damage our health or react with other pollutants to create toxic smog. It’s been known to start harming humans at levels greater than 50 ppbv. It inflames airways causing difficulty breathing, coughing and great discomfort. Some research has linked it to heart attacks — a pollutant not to be taken lightly.

Over those 10 years Ellul and his team saw 20 episodes in summer where ozone levels exceeded 90 ppbv. Some were during the night, unlikely to be of local origin but due to transport phenomena in the central Mediterranean and shipping. Ellul does nod towards the possibility of air recirculation from Malta. The atmosphere is a complicated creature.

Plants also suffer from ozone. Above 40 ppbv yield from fields decreases. Gozo is definitely being affected; we could be producing more.

The devil is in the details

Ellul and his team have found a potentially big contributor to the Islands’ pollution. This would be over and above our obvious traffic problem. Yet Ellul admits that ‘there is no particular trend, it’s too short a time span. What it tells us is that what we think is a clean atmosphere is not really a clean atmosphere at all. The levels are significant.’ Azzopardi honestly says ‘I can [only] give you an idea of what is happening’.

The team needs to study the problem for longer. It needs some statistics. Clearly they see a link between ships passing by Malta and peaks in pollution levels, but the Islands need to know if shipping pollution levels beat industry, traffic, or Saharan dust. What is ships’ contribution to Malta’s health problems?

When the team knows the extent of pollution, they can see whether they go above European standards. Ozone already does, and likely to be due to pollution from the European continent. If they can extend it to a whole host of other pollutants that skyrocket above European standards due to ship traffic, then ‘our politicians,’ says Ellul, can go to Brussels to enforce new legislation. That could control Mediterranean shipping traffic to clean up our air. At least it would solve one significant problem that Malta cannot solve on its own.

The main problem is economic. A ship can be made greener by reducing its sulfur fuel content. Low sulfur fuels are double the price of the bunker fuel they currently use. New legislation would need enforcement, which is costly. Ships could also be upgraded, again at a price. Passing these laws is not going to be easy.

Ships have been a pollution black hole for a while. The fuels ships burn contains 3,000 times more sulfur than cars are allowed to burn. Quite unfair. Going back to Corbett’s figures estimating European deaths at 27,000, the current rise in shipping pollution could end up killing hundreds of thousands if not millions before new legislation is enforced. Now that would be truly unfair.

shipping5

Cosmetic research?

Carnival revellers (male and female) recently plastered their faces with lipstick, mascara, facepaint, nail polish, and dozens of other cosmetic products. Few of these wondered about the extensive research needed to overcome the packaging challenges behind these beauty-enhancing devices.

Challenges are numerous and diverse: how can a make-up cosmetic case minimize the chances of the customer opening a dry and flaked product? How can a lipstick container be designed in an elegant and smooth way that opens silently? What functions can make a cosmetic case more useful, secure, and light in a handbag? How can a cosmetic case’s button be improved to prevent broken nails?

A company like Toly Ltd (based in Malta) needs these questions answered to provide a world-class product. To remain competitive and innovative, research and development need support. Chairman and CEO, Andy Gatesy strove to meet these challenges head on by working with the University of Malta (UoM). Toly has forged a long-term joint research collaboration with UoM, in particular the Department of Industrial & Manufacturing Engineering (DIME). Through this collaboration, many undergraduate students had the possibility of applying their theoretical background to real world problems, which results in win-win-win scenarios, for Toly, the student, and DIME. Lippenstifte

Toly also partnered with DIME and other University Departments in nationally funded research initiatives such as the MCST R&I Automate project. This concerned industrial automation and two ERDF projects — one of them intended to amplify innovation in the manufacturing industry and another one on improving energy efficiency in manufacturing.

Toly’s belief in the research potential of the UoM is reflected in regularly sponsored projects. It recruits UoM graduates to help it remain innovative and competitive. It also allows an Associate Professor to spend time from his sabbatical period to follow product development. “We cannot predict the future but we can create it”, said Mr Gatesy. Experience has shown that joint research with UoM is essential for Toly to develop its future growth towards a global market. 

How to become a cosmetic engineer?

The left brain is logical, the right side is creative

In the 1960s, psychologists Roger Sperry and Michael Gazzaniga performed experiments on patients who had the connections between the left and right side of the brain cut as an extreme treatment for epilepsy. They stimulated each side of the brain separately and asked patients to draw, arrange blocks, talk about their emotions, and so on. These simple experiments proved insightful but misguided.

From their experiments they concluded that the left hemisphere was logical, rational, and good with numbers (the scientist), the right hemisphere was creative, imaginative, and took in the big picture (the artist). This overly simplistic reasoning is drowning out the real beauty of our brain. The real deal is a lot more complex. Take speech. Classically, the left side of the brain is meant to handle it all. Right-handed people do mostly use the left side, but left-handed people tend to use the right side. Imaging studies of brains show that the brain lights up like a firefly using multiple areas for speech. Most complex actions need multiple brain areas.

Are we still growing Tall?

For the last 150 years, the human species has been getting taller. In Western nations, people are around 10 cms taller (nearly 4 inches). Better public health and diets during childhood have fuelled the rise. Women preferring taller men who then have taller offspring could also have pushed the increase.

Unfortunately, this won’t last forever. There are physical limits. People above 188cm (6ft 2in) are more likely to suffer back problems. Above 203cm (6ft 8in), the heart finds it difficult to pump blood and heart problems increase.

Playing with Solid State Benzene

molecular structure

Computational chemistry is a powerful interdisciplinary field where traditional chemistry experiments are replaced by computer simulations. They make use of the underlying physics to calculate chemical or material properties. The field is evolving as fast as the increase in computational power. The great shift towards computational experiments in the field is not surprising since they may reduce research costs by up to 90% — a welcome statistic during this financial crisis.

Keith M. Azzopardi (supervised by Dr Daphne Attard) used two distinct computational techniques to uncover the structure of a carcinogenic chemical called solid state benzene. He also looked into its mechanical properties, especially its auxetic capability, materials that become thicker when stretched. By studying benzene, Azzopardi is testing the approach to see if it can work. Many natural products incorporate the benzene ring, even though they are not toxic.

The crystalline structures of solid state benzene were reproduced using computer modelling. The first technique used the ab initio method, that uses the actual physical equations of each atom involved. This approach is intense for both the computer and the researcher. It showed that four of the seven phases of benzene could be auxetic.

The second less intensive technique is known as molecular mechanics. To simplify matters it assumes that atoms are made of balls and the bonds in between sticks. It makes the process much faster but may be unreliable on its own due to some major assumptions. For modelling benzene, molecular mechanics was insufficient.

Taken together, the results show that molecular mechanics could be a useful, quick starting point, which needs further improvement through the ab intio method.

 

This research was performed as part of a Masters of Science in Metamaterials at the Faculty of Science. It is partially funded by the Strategic Educational Pathways Scholarship (Malta). This Scholarship is part-financed by the European Union – European Social Fund (ESF) under Operational Programme II –Cohesion Policy 2007-2013, “Empowering People for More Jobs and a Better Quality Of Life”. It was carried out using computational facilities (ALBERT, the University’s supercomputer) procured through the European Regional Development Fund, Project ERDF-080 ‘A Supercomputing Laboratory for the University of Malta’.

Xemxija and Earthquakes

On February 22, 2011, a magnitude 6.3 earthquake struck the city of Christchurch, New Zealand, killing 181 people and causing widespread destruction. Curiously, this damage was not evenly distributed, even for areas right next to each other. This phenomenon is called the site effect and depends on the underlying geology.

Malta, unlike New Zealand, is not typically associated with earthquakes. The islands lack a seismic building code and many structures could be damaged with moderate shaking. Malta’s past records list several earthquakes that have damaged buildings and even caused some to collapse. Apart from not being reinforced, buildings have been built on less stable ground, which increases risk.

 

Setting up the Micromed Tromino, the instrument used to perform recordings of ambient noise measurements
Setting up the Micromed Tromino, the instrument used to perform recordings of ambient noise measurements

Sharon Pace (supervised by Dr Pauline Galea) investigated this effect in one test area — Xemxija, in the north of Malta. She studied how sites in Xemxija would respond to the energy from an earthquake by using a portable seismograph to record ambient noise (caused by sea waves, vehicular traffic, and other anthropogenic sources) at over 100 points across the village (pictured). The ground’s surface can be considered a vibrating platform, which can be shaken both by ambient noise as well as stronger waves from earthquakes. The ground may “resonate” at particular frequencies, or not at all, depending on the kind of rock or soil layers making up the top 30 to 50 metres. Analysis of ambient noise shows if such resonance phenomena exist, how they are related to the local geology, and how this would translate into actual earthquake shaking.

 

Resonant peak frequency distribution patterns around the Xemxija area
Resonant peak frequency distribution patterns around the Xemxija area

At Xemxija, the study confirmed that the presence of clay (whether at the surface or buried) does amplify the grounds motion at certain frequencies.  The results match previous studies in other areas, but this research went further by constructing geological models that can determine the ground’s underlying structure .

Taken together, the survey shows areas in Xemxija that might need extra support to survive future earthquakes and prevent deaths. Xemxija is not the only area with soft clay geology, the urbanised area of Mellieħa and historic citadel Mdina are built on top of similar structures. Considering the importance of these areas means that more studies are needed to better understand the structure of Maltese buildings and how they would respond to earthquakes.

 

This research was performed as part of a Masters of Science in Physics at the Faculty of Science. It was partially funded by the Strategic Educational Pathways Scholarship (Malta). This scholarship is part-financed by the European Union — European Social Fund (ESF) under Operational Programme II — Cohesion Policy 2007 – 2013, “Empowering People for More Jobs and a Better Quality of Life”.