Portfolio Louisa Cockbill, PhD

Contents Most recent freelance work ............................................................................................................... 2

Massive Science ............................................................................................................................. 2

Nature Careers Q&A ...................................................................................................................... 6

Dusk Magazine .............................................................................................................................. 9

Blog contributions ............................................................................................................................12

Nature Career blog .......................................................................................................................12

Real Life Science ...........................................................................................................................12

Science FYI ....................................................................................................................................12

Freelance work for Research Media..................................................................................................13

The significance of haem biosynthesis, International Innovation issue 168, December 2014 .........13

A mine of genetic information, International Innovation issue 170, January 2015 .........................16

Sugars at the cell frontier, International Innovation Online, November 23rd 2015 .........................19

Contributing author for Synapse science magazine ...........................................................................22

The Great Ideas of Biology according to Sir Paul Nurse, February 2012 1st edition ........................22

What the Eph? December 2014, Issue 9 ........................................................................................25

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Most recent freelance work

Massive Science

This tiny fly is teaching the Air Force new aerial tactics

June 9, 2017

The robber fly's novel hunting tactics and visual processing capabilities could be applied to drones and airplanes

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PhD student Sam Fabian is spending another hot summer's day standing in a field in York,

Pennsylvania, surrounded by high-speed camera equipment. Insects buzz around and crawl over Fabian, but he only has eyes for one of them: the tiny robber fly, which is roughly the size of a grain of rice.

Eyes are what brought Fabian out to the scorching field in the first place. Most of the time when it comes to insect eyes, bigger is better. Larger eyes mean more visual sensors, which means better eyesight and better hunting ability. But Holcocephala fusca, the tiny robber fly,

is an exception. Despite being just six millimeters in length, it's a highly successful predator

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in the sky, capable of launching stunning aerial attacks at distances that rival insects ten times its size.

The tiny robber fly is roughly the size of a grain of rice.

PHOTO BY SAM FABIAN

Fabian's adviser at the University of Cambridge in the UK, Paloma T Gonzalez-Bellido, was the one who noticed the particularly striking eyes of the robber fly and wanted to know how this influenced the fly's hunting abilities. Her lab published their study on the robber fly in the journal Current Biology in March.

The team's work suggests that the fly's novel eye design and flight tactics might be used to human advantage. Gonzalez-Bellido's not the only one interested in the answer to that question. Her lab's work is partly funded by the U.S. Air Force, which hopes to learn new tactics and flight mechanics from the fly that it can apply to fighter jets and drones.

Back in the field, Fabian waits patiently with his equipment primed and ready, aiming to capture the rapid aerial attack of the tiny predator. Fabian spots a tiny creature on the edge of

a blade of grass. A second later, the fly is gone and Fabian hopes the camera has captured the movement that he missed in the blink of an eye.

Binocular vision

Gonzalez-Bellido's team started by dissecting robber flies and examining their visual

systems. What they found was an extreme tradeoff: the flies have extremely poor vision in the majority of the eye, but make up for it with a few core souped-up visual sensors. Using these super-sensors, robber flies can see nearly as well as insects that are ten times as large.

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“Robber flies see as well as dragonflies, but only over a very narrow field of view, a bit like using binoculars with a high power but restricted field of view,” said Gonzalez-Bellido during an interview, holding her hands up to her eyes in demonstration.

Lots of insects enlarge certain visual sensors, but the robber fly's adaptation is a particularly

extreme example. Gonzalez-Bellido wanted to find out how this adaptation related to the fly's hunting abilities, which is why she flew Fabian out to America to study robber flies in their natural environment.

Gone fishing

At first glance, Fabian's field setup seems snazzy. To capture the fly's aerial acrobatics, he used a high-resolution camera capable of capturing 1000 images per second pointed at a white-screen backdrop. Then there was the “fly-teaser,” a mechanized fishing rod that jerked a dummy prey the size of a marble around at random to attract the attention of a robber fly.

Fabian's fishing rod and backdrop setup for luring and documenting flies.

STILL IMAGE BY UNIVERSITY OF CAMBRIDGE VIA YOUTUBE

But according to Fabian, the setup wasn't exactly like being on a Hollywood film set. “An occasional storm would blow through and knock all the equipment off its perches or you

would have days where the flies weren’t anywhere to be found. And robber flies weren’t the only insects about, wasps would chase the robber flies off while we were trying to film them,” he explained.

With the help of local knowledge supplied by park rangers, Fabian was able to find the best spots for his filming and the robber flies soon indulged him. Each fly attack took an average of 800 milliseconds, just enough time to blink twice. But on a camera capturing 1000 images per second, that provided 800 high-resolution freeze frames per run, which could be turned

into incredible slow-motion video.

Aerial relay

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Despite the ‘on-set’ challenges, filming the flies in action was perhaps the easiest part of the study. The team had to pull in Doekele G. Stavenga from the computational physics department of the University of Groningen, Netherlands to help calculate flight trajectories using algorithms that assessed speed and angle of interception. From these calculations,

Fabian, Gonzalez-Bellido and lead co-author Trevor Wardill slowly assembled a picture of robber fly flight tactics.

Launching from its perch, the robber fly tracks its prey similarly to how we might track a ball moving through the sky. There's actually a geometrical model that describes this type of interception. It's known as the constant bearing angle model, and describes how creatures use angles to calculate, or in some cases avoid, a collision course.

A 1,000 frame-per-second slow-motion video of a robber fly on its attack run.

ANIMATED GIF BY UNIVERSITY OF CAMBRIDGE VIA YOUTUBE.

But in the latter part of its attack run, the robber fly suddenly deviates from this model. As it closes in on its prey it, it appears to switch tactics, reducing its speed to match that of its prey rather than continuing on its full speed collision course. Study co-author, Dr. Trevor Wardill, explained that this is a bit like the baton pass in a relay race, where runners change from running as fast as possible to a slower pace that maximizes the chances of a successful transfer. The robber fly appears to use the same slowing tactic to increase its chances of a

successful aerial capture.

This is the first time that this “lock-on” phase has ever been described. But even more interesting than the tactic itself is what it might indicate. Because the fly slows down only when it closes in on its prey, Gonzalez-Bellido and her team describe it as a proactive strategy. But does this mean that the fly is actively making tactical decisions in mid-flight?

Decisions, decisions

It's not yet clear whether the robber fly's ability to change tactics is instinctive or requires a higher level of neural processing. If flies are indeed making decisions, it opens up a host of other questions, like: Do they have the ability to plan ahead? Just how clever is a fly? This is

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a controversial topic for the field, and scientists will need to provide much stronger evidence to change the conventional view that flies simply react to their surroundings.

The Cambridge scientists are now trying to unravel what clues the flies respond to when they change tactics. The most obvious one, given the way the fly slows down, seems to be

distance to prey. The researchers are looking again at robber flies’ amazing eyes to explore how they perceive depth.

Lessons from nature

The team also wants to understand more about how the speedsters' tiny brains manage such

impressive neural processing. The next questions they want to ask include: How has the robbery fly neural network adapted to efficiently focus their binocular-like visual sensors? How do they launch such swift, precise and successful predation while expending so little energy?

Answers to these questions have the potential to yield useful new technologies. For instance, drones drain batteries swiftly because of the high energy requirements of their visual

processing systems. If researchers can learn from the low-energy image processing of the robber fly, power requirements could be minimized and drones' battery life extended.

In a video about the project, Gonzalez-Bellidio explained that “the idea at the moment is that it will be useful for drones to take down illegal drones. Say for example in a concert or in an airport.”

Catching rogue drones? Not bad for a study that started by fishing for robber flies in a field.

Featured article

Wardill TJ, Fabian ST, Pettigrew AC, Stavenga DG, Nordström K, Gonzalez-Bellido PT. A Novel Interception Strategy in a Miniature Robber Fly with Extreme Visual Acuity. Current Biology. 2017;27(6):854–859. https://doi.org/10.1016/j.cub.2017.01.050.

Nature Careers Q&A Turning point: An eye to success

Publication on 11th May 2017 in Nature 545, 255 (2017) doi:10.1038/nj7653-255a

A marine biologist forges a career in business with a diagnostic tool for use by

optometrists.

As a postdoc studying marine biology at the University of Bristol, UK, Shelby Temple invented a device that assesses the health of human eyes. He describes his move out of research to commercialize the device.

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How did you create this tool?

I was characterizing the ability of animals to see polarized light, and was curious about the human perception of polarization. So, using LCD screens, some customized components and the contents of my recycling bin, I invented a device to examine it. When I used the device to measure the threshold of human perception of polarized light, those measurements

corresponded with the density of macular pigment in the eye. A low level correlates with poor vision and is a risk factor for age-related macular degeneration.

What did you do next?

With the support of the business incubator at the University of Bristol and programmes including Innovation to Commercialisation of University Research, I conducted market research and developed the device. I believed that my invention had potential for commercialization, so I left the incubator to launch a start-up company. The university owns the intellectual property and they gave me an exclusive global licence in exchange for equity and royalties.

How did you transition out of your postdoc?

I was able to ease away from lab commitments with funding that allowed me to take a four-month break while doing market research. I passed on a lot of my projects to colleagues, and although I am trying to finish off a few papers, it's really more of a hobby now.

Are you pleased with your present career path?

Yes. I felt like I was stagnating and was frustrated by the lack of opportunities in my home nation of Canada. Commercializing the device seemed like a great opportunity and could allow me to return to Canada in the future.

How does your company run with no revenue?

I won a Biotechnology and Biological Sciences Research Council Enterprise Fellowship, which has paid my salary for the past year. We have a start-up grant from Innovate UK and just completed our first round of investments.

What did your market research find?

Most people, including optometrists, don't know what macular pigments are, so we'll need to educate them. I also learnt how the device would fit into optometrists' business models.

Has it been difficult to move from research?

The learning curve was sharp: I took numerous courses to learn about business planning and modelling, accounting, sales and marketing. It has taken me a long time to shift my thinking to making money — there is a lot of pressure to get the device to the point of sale as soon as possible. It's a fantastic amount of work, but I have also been having a great deal of fun.

What are you doing now?

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We are conducting a more focused, large-scale study to compare our tool's results with results from the existing method for measuring macular-pigment density, so there is a big push to get the next prototype ready for trial. As technical officer, I am working on the manufacturing process and am currently operating out of my house. We hope that by late 2017, a more

developed version of the device will be ready before we invest in large-scale manufacturing. My dream is for the device to be used in every optometrist's office, and maybe in the future by primary-care doctors. I envision it as a standard part of eye-health checks, a bit like a blood-pressure monitor.

What is the best aspect of starting a business?

Building a great team with key skills to complement my own. For instance, the chief operating officer has taken over some of the business planning, which allows me to focus on the science. And it's my company, so I run it with my own ethos. Why not have board meetings that start off with nipping to Devon to surf?

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Dusk Magazine

Tweaking Fast Pyrolysis Technology to Produce Liquid Fuel from Beetle Epidemic Devastated Forest

Posted on June 15, 2017 by Louisa Cockbill in Uncategorized, Technology, Environment // 0

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Swathes of forest stand dead, useless and dangerous they are victims of the mountain pine beetle epidemic. But where some see disaster, others see opportunity. Researchers at the University of Washington (UW)

have developed a practical solution to recycle the dead giants.

Publishing their research in the Journal of Fuel in April, the UW researchers from the School of Environmental and Forest Science outline a new fast pyrolysis method that they believe will enable wide-

spread utilization of the beetle-riddled trees as an energy resource.

The outbreak of mountain pine beetles in western North America has destroyed areas of forest the size of Washington State. Cracked and stained, the pine slopes are no good for mainstream lumber and pose a land management problem for the forestry services as the dead trees provide perfect kindling for forest fires and

are liable to fall, endangering the public.

“If you can extract the wood and process it using fast pyrolysis, not only will you free up space and safety hazards in the forest, but you also have the organic liquid that could potentially be used for products,” explained Fernando Resende, senior author and UW Assistant Professor of Bioresource Science and

Engineering, in a UW press release.

Fast pyrolysis is the quick heating of bio-matter to produce a vapor that is condensed into bio-oil, a liquid fuel. The advantage to the new fast pyrolysis reactor invented by the UW researchers is its capability of processing larger chunks of wood, which could defray wood grinding and lumber transportation costs that

have previously acted as a barrier to use of the technique.

“Not only do we want to reduce the costs, but we are hoping to increase the value of what we produce so

we have a better chance of making it commercial,” said Resende.

Bio-oil produced by fast pyrolysis is already being used to fuel some European hospitals, and teams of researchers across the globe are experimenting with the technique to produce other forms of fuel, such as

gasoline and diesel.

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Fast pyrolysis techniques have been in development for 30 years, using different reactor methods to heat bio-matter up to 400-600°C, at 500°C/s, while in the absence of oxygen. The UW researchers were able to decompose larger chunks of wood into bio-oil at equal conversion efficiency to other methods, by using an ablative reactor that rotates the bio-matter while crushing with a heated metal surface.

These new reactors can be converted into mobile units for transportation to sites of forest harvesting and subsequent on-site manufacture of bio-oil. As a mobile unit, the ablative reactor eliminates not only the wood grinding steps that account for 7-9% of current cost but also the lumber transportation step, further

increasing the cost efficiency.

The 42 million acres of dead beetle-riddled trees are perfect fodder for fast pyrolysis, already dried out by the feeding of beetle larvae and fungus that the beetles carry. And although the necessity for surface area exposure limits the scalability of the ablative reactor, this is not a concern for the necessarily smaller mobile units to fit onto the back of flatbed trucks.

This article was written by Louisa Cockbill, a writer for dusk magazine. To learn more about mountain pine beetles and how the forestry services are responding to the epidemic see the supporting post on

Louisa’s blog: Science FYI.

Where them slugs at?

Published online 10th April 2017

Big juicy looking ones, bright yellow oozing ones, and those with a funky pattern. As a hiker you see all kinds of slugs on the trails around Washington or just in your garden. But over winter there is no trace of them, not even a slime trail. Where do all the slugs go? How do slugs survive the winter frosts? Because the slimy suckers are certainly present again now that it’s spring. The first tactic that slugs use to survive the winter is to hide. It’s estimated that only 5% of the slug population is seen above ground at any one time, but in winter, the slime-balls head deeper underground to take refuge from the frost forming at the surface. Once settled, the slugs shutdown and go into hibernation. Hence, the absence of slugs on Washington trails in the winter. The colder the temperature above ground, the further frost penetrates below. So, the deeper the slugs dig, the safer they are. However, if caught out in shallow soils that drop below freezing, ice forms inside the hidden slugs. Professor Kenneth Storey, an expert on animal freezing at the University of Carleton in Ottawa, explains that “Survival depends on the species. Some slugs freeze to death and others are adapted to be freeze-tolerant.” Imported species from more temperate conditions, like the banana slug, don’t have these freeze-tolerant abilities. These slug species are able to persist and thrive in our northern climate because their eggs endure the winter to hatch in the spring, even if the adults never reemerge. And, thus, the new generation arrives just in time to attack your fresh dahlia blooms.

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On the other hand, hardy northern breeds have adapted over thousands of years to survive harsh winters by undergoing drastic changes in their basic bodily processes. One crucial change is an increase in tissue glucose, which makes slugs sugary - like popsicles! “Try freezing a popsicle at the same time as water- the popsicle takes longer to freeze and then is quicker to melt because it is full of sugar!” Storey goes on to explain this phenomenon: “Glucose binds to water molecules, protecting them from freezing. The free, unbound water molecules in a slug still freeze, turning the slug solid, but less ice is present in a sugary animal giving it a better chance of surviving.” And glucose isn’t just slugs’ own brand of anti-freeze; lots of animals use the same tactic to survive the cold, for example, wood frogs. So, there we have it. Slugs lurk hidden, frozen underground in winter. For some species this can be self-burial, but for some slick survivors, now that it’s spring, they just need a moment to defrost. NB For slugs to freeze and survive, the process has to be gradual. If you stick a slug in your freezer (which some forum contributors have gone and done) the slug dies, leaving you with an unsavory ice cube.

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Blog contributions

Nature Career blog Q&As with scientists including: Being a foreign scientist in Trump’s America, 17th April 2017

Tracking down the holy grail of academia, 21st Dec 2016

Real Life Science A range of posts, including:

An opinion piece on- The hairy issue of animal testing: a scientist’s perspective , 30th Nov

2016

Food of the Gods is poison to dogs, 14th Feb 2017

Science FYI Louisa regularly writes content for her own popular-science blog, Science FYI.

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Freelance work for Research Media

Research Media Ltd is based in Bristol, UK and produced the online magazine International

Innovation for the communication and dissemination of research (publication closed end of 2016).

Louisa freelanced for the company 2014-2016, writing researcher profiles.

http://www.researchmedia.co.uk

The significance of haem biosynthesis, International Innovation issue 168,

December 2014

///Standfirst: Researchers at the University of Georgia are revealing new complexities of the

enzymes in the haem biosynthesis pathway. These discoveries have important implications for

haematological disorders and are even revealing potential new antimicrobials///

///Bodycopy///

Haem is an iron-containing tetrapyrrole that is a key component in many proteins, most notably

haemoglobin – the metalloprotein responsible for transporting oxygen in the red blood cells of most

vertebrates. This function, along with many others, make the synthesis of haem an essential process

for life.

With this significance in mind, Professor Harry Dailey, Director of the Biomedical and Health Sciences

Institute at the University of Georgia, is dedicated to the investigation of haem biosynthesis. A

particular focus of his group is elucidating how the enzymes involved in the terminal stages of

synthesis function, and how they are regulated. To this end, the lab has cloned and biochemically

characterised a number of the haem synthesis enzymes, and one characterisation of particular note

is that of the final enzyme in the pathway, ferrochelatase. Dailey first identi fied ferrochelatase as a

graduate student, and has since discovered that the enzyme undergoes molecular motion to

efficiently interact with several protein partners during its catalytic cycle. It was through

considerable structural based modelling that this group was able to propose that a multi-enzyme

complex exists among the terminal haem synthesis enzymes.

Haem synthesis malfunction

Haem biosynthesis occurs in the liver and bone marrow, and if there are any defects in the pathway

it can lead to a range of diseases that are collectively known as porphyrias, a general name given to

diseases resulting from the accumulation of a haem biosynthesis pathway intermediate. The type of

porphyria is determined by which enzyme in the pathway malfunctions and the hae m intermediate

that accumulates. One of the Georgia group’s particular interests is the array of mechanisms that

result in enzyme functions being disrupted in the haem synthesis pathway.

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There are eight known types of porphyria and the majority of these are genetically inherited, in most

cases in an autosomal dominant fashion. Fortunately, not every carrier develops symptoms and so

porphyrias are a relatively rare group of diseases. Apart from a couple of porphyrias, which are seen

in childhood, the majority of sufferers of porphyria only develop symptoms in or after puberty;

triggers of disease onset aren’t entirely clear, but some proposed candidates include hormonal

alterations, dietary changes and drug use.

Porphyrias have varying symptoms and severity between types as well as within a type: “Depending

upon the specific mutation, clinical manifestations of porphyrias may be mainly acute neurological

attacks or chronic dermatological issues/photosensitivity,” outlines Dailey. The acute neurological

attacks are thought to be caused by the accumulating haem intermediate attacking peripheral

nerves. Symptoms of these acute attacks include abdominal pain and nausea, along with a high pulse

rate and pain in the arms and legs. In some porphyrias patients can display skin sensitivity that

ranges from mild blistering to severe scarring and high susceptibility to infections.

Diagnosis of porphyria

Diagnosis of these rare diseases can be tricky because the symptoms are nonspecific. If an individual

without a family history has suspected porphyria, then blood and urine samples can be tested for

the activity of terminal stage haem enzymes. In fact, it was a test involving the exposure of urine to

sunlight that gave porphyria its name, derived from the ancient Greek word for purple, as this is the

colour urine containing certain haem intermediates turns. However, this method can give false

results so it has to be combined with liver tissue enzyme activity or DNA tests.

Dailey’s group played a major role in the identification of the R59W mutation in the haem synthesis

enzyme protoporphyrinogen oxidase as one of the mutations responsible for causing variegate

porphyria – a condition that includes both acute attacks and chronic skin sensitivity. The R59W

mutation abolishes an AvaI binding site in the enzyme and therefore disrupts its function. This

mutation is very common in variegate porphyria patients in South Africa, and its identification has

contributed to the understanding of how the disease evolved in the region.

Haem synthesis and antibiotic resistance

Another translational focus of the Dailey lab has come about through examination of bacterial haem

synthesis enzymes. The requirement for haem in so many organisms suggests a common evolution

of haem biosynthesis and the conservation of many enzymes across species, from bacteria to

humans. However, in the last decade as bacterial genomes have become available it has become

clear that some bacterial genomes are ‘missing’ essential haem synthesis enzymes. Through a

combination of bioinformatics and biochemical expertise Dailey’s group, along with Dr Svetlana

Gerdes at Argonne National Labs, has been exploring which enzymes are ‘missing’. “To date we have

identified and characterised three ‘missing’ bacterial enzymes,” Dailey expands. “But most

importantly we have determined that gram-positive bacteria utilise a different means from gram-

negative bacteria and higher organisms when carrying out the final few steps of haem synthesis.”

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In an age of rising antibiotic resistance, the need for novel antimicrobial targets is more pressing

than ever before, and it appears that this is exactly what this team has uncovered. “The uniqueness

of the protein and the reaction that it catalyses make this an excellent target for the devel opment of

new antimicrobial compounds,” Dailey enthuses. This is an exciting discovery that has the potential

for far-reaching impact in the ongoing struggle against bacterial infections.

Continued importance

The Dailey lab is expanding its research into how proteins in the haem biosynthesis pathway

interact, always striving towards a more detailed understanding of this crucial process. One new

focus involves scrutinising the post-translational modifications that regulate the haem synthesis

enzymes’ activity. Another new interest of the group is to try and understand how the cells share

metabolic intermediates, and how this affects haem synthesis, by examining cellular metabolic flux.

The lab’s particular aim is to tease out the differences between erythroid and nonerythroid cell

haem synthesis.

The significance of haem in many biological systems’ pathways is highlighted by the highly

translatable work that this team has undertaken over the past three decades. The research is

already having an impact on diagnostic options for suspected cases of porphyria, and now Dailey is

collaborating with the University of Utah to identify antimicrobials that target gram-positive

bacteria’s unique haem synthesis enzyme. The new light these investigations continue to shed both

on haematological disorders and across other areas is promising, and suggests a bright future for this

team.

///Pullquote: In an age of rising antibiotic resistance, the need for novel antimicrobial targets is

more pressing than ever before, and it appears that this is exactly what this team has uncovered///

///Boxout: The history of haem///

As a highly prevalent compound across the tree of life, haem has a rich evolutionary history. A

number of studies have explored the early evolution of haem synthesis, and the consensus is that a

core set of enzymes – common to all tetrapyrrole synthesising compounds – evolved together to

produce a tetrapyrrolle intermediate. Current data suggests that cobalamin (B12 precursor) evolved

first, followed by protohaem and then chlorophylls – well known for their involvement in

photosynthesis. The fact that each of these enzymes plays an important but completely different

catalytic role in nature is a testament to the the chemical versatility of tetrapyrroles.

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A mine of genetic information, International Innovation issue 170, January

2015

/// Header: A Mine of genetic information ///

/// Standfirst: Researchers from the University of Western Australia are one of the groups involved

in the Collaborative Cross Consortium with a unique venture to improve the study of genetics

through the development of a ///

/// Bodycopy ///

Characterisation of the genetics that underlie the complex traits presented in disease is traditionally

a lengthy, expensive, case-by-case process for researchers to undertake. Even with recent advances

in genetic technologies such as genome-wide association studies (GWAS); identifying disease-

associated genes still tends to be a challenge. The international Collaborative Cross Consortium is

hoping to change this status quo via an extensive mouse breeding programme that has produced a

series of genetic strains that capture 90 per cent of the species’ genetic diversity. This represents an

invaluable resource in which to study any murine characteristic that has a genetic basis, and allows

the mapping of that characteristic to the specific causal or modifier gene.

The largest collection of collaborative cross strains is found at the University of Western Australia

where Professor Grant Morahan heads up The Gene Mine project. “This resource is a genetic

reference population with highly defined genotypes that can be tested to see how genetics mediates

disease outcomes or traits of interest,” he enthuses.

///Subhead: The breeding programme ///

The Gene Mine project has expanded upon an already well -known genetic concept; examining the

inheritance pattern of recombinant inbred strains to map genes. Instead of the usual two-founder

strains of mice, in Morahan’s project, eight founder mice were selected i n order to maximise the

genetic diversity of the ensuing population, ie. wild strains were used alongside well -known disease

models. The founder strains are referred to as the G0 generation and the G1 offspring from their

crosses were crossbred again to form the G2 which underwent the final cross to produce the G3

animals. At this stage, the inbreeding protocol was initiated: 23 generations of inbreeding were

performed to fix the alleles in each strain so that all cousins were genetically identical. This al lows

tests to be repeated on a number of mice with exactly the same genetic background, allowing

greater scope for studying a phenotype under different environmental stresses, for example.

Taking the hundreds of strains produced from the eight founders and applying Mendelian genetic

principles, the collaborative cross has substantially increased gene mapping power. The statistical

analysis to identify genes that are causal for a trait involves high performance computation, for

which The Gene Mine project has provided functionality in their GeneMiner software. The mice,

their genotypes and the software is now ready to be utilised after a decade spent inbreeding.

///Subhead: Golden potential ///

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Making use of The Gene Mine resource avoids the need for repetiti ve breeding programmes, DNA

sampling and genotyping, and so reduces the cost and length of time involved in mice genetics. “The

Gene Mine takes the genetics out of genetic studies! All researchers need to do is test the strains

and analyse the data using our online programs, and they can discover genes for their traits of

interest,” explains Morahan. Carrying out analyses in this manner enables genes for particular traits

to be mapped and the genetic sequence identified within hours of obtaining the phenoty pic data.

This approach to gene discovery is much faster, less complicated and more accurate than other

methods of gene mapping.

The chemical mutagen ENU (N-ethyl-N-nitrosoureatance), for example, can be used to generate a

mutation in approximately one allele per 700. The mutated gene is then mapped by positional

cloning and associated with any observed phenotypic alteration. Unfortunately, this method is ‘hit or

miss’, with many drawbacks and a much slower time frame. Alternatively, GWAS, can be used to

define many genetic variants associated with disease susceptibility. Although useful in clinical

studies, this approach is expensive, and the very nature of its use in humans presents a range of

difficulties, from cohort size to ethical considerations. In contrast, studying The Gene Mine animals is

cost-effective and allows a more thorough examination of the genetics in any tissue of the mice at

differing developmental age etc. so that more information is gathered before inspection of the

human homologue.

///Subhead: Undermining disease ///

Not only does The Gene Mine project allow rapid identification of genes but, with 90 per cent of

mouse genetic diversity represented by the strains, it also provides expressed phenotypes of

virtually any mouse trait that could be used as new models for diseases. For example, there is great

disparity in weight independent of diet, and spontaneous tumours develop in mice with particular

genotypes. These two specific phenotypes could be useful models for diabetes and cancer

respectively. Models aid in both advancing our understanding of the underlying molecular

mechanism of disease and as platform to test new treatments in vivo.

Mice bred in The Gene Mine project have already been key to the discovery of disease prevention

genes. In a collaboration with Dr Graeme Walker from the University of Queensland, Australia, a

transgenic mouse model of malignant melanoma was crossed with strains from The Gene Mine.

Monitoring of melanoma-type lesion development in the mice post-sunburn (exposure to ultraviolet

radiation) has led to the identification of strains that were resistant to the development of

melanoma and the genes that acted to protect those mice. Finding a gene or genes that could

protect against the effect of both the oncogenes present in the transgenic mouse and the exposure

to the ultraviolet carcinogen presents a tantalising possibility to mimic the effects of this ‘protector

gene’ to guard against the human disease.

///Subhead: New territory ///

The Gene Mine opens up new unchartered territory for gene discovery with a ready-to-test

heterogeneous population of mice that have highly defined genotypes available. “Simply, gene

discovery involves looking for what genetic markers are common to a group of individuals who share

a disease or trait, and not shared by those who are not affected,” Morahan summarises. In its

current state, The Gene Mine is accessible to any innovative researcher to identify a few promising

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mouse strains, test for a particular phenotype and use the established software to yield new genes

of interest in their field. Dr Lars Ittner from the University of Sydney, Australia, is one such

researcher who is utilising The Gene Mine to identify genes that induce tau tangles in the brain that

lead to dementia. The mice strains produced in the collaborative cross represent a substantial

resource which, after a decade of crossing has come to the surface ready to be utilised by

opportunistic researchers.

/// Pullquote: The Gene Mine is a resource in which to study any mouse characteristic that has a

genetic basis, and to map that characteristic to the specific causal or modifier gene ///

/// Boxout: Geniad: The investors behind The Gene Mine ///

In 2004, inspired by The Gene Mine’s visionary plan, a group of investors founded Geniad Ltd to

support the Collaborative Cross Consortium breeding programme. The group is now seeking

collaborators to utilise The Gene Mine resource. Each new gene or phenotype discovered by

researchers adds to the collective knowledge that is publicly available and makes The Gene Mine

ever more useful for future studies. An initial long term investment from the Geniad Ltd founders –

including their Chief Scientific Officer Professor Grant Morahan – that has been a decade in the

breeding, has resulted in a complete collection of mouse strains that hold almost limitless potential

for research.

Portfolio Louisa Cockbill, PhD

Sugars at the cell frontier, International Innovation Online, November 23 rd

2015

///Standfirst: Researchers at the Albert Einstein College of Medicine are investigating glycosylation

in development and disease///

///Bodycopy///

///Subheading: Attached to sugar/The icing on the cell///

Glycoproteins are formed through the attachment of sugar chains known as glycans or

polysaccharides, in a process called glycosylation. Glycosylation is a post-translational modification

that alters the properties of proteins, effecting localisation, stability and binding. The cell surface is

decorated with glycans to such an extent that these sugar chains have been described as the primary

frontier of the cell. Glycans on cell surface glycoproteins are important for interactions: for growth

factor receptor recognition of ligand, binding, subsequent signalling into the cell and cellular

response.

Dr. Pamela Stanley is Professor of Cell Biology at the Albert Einstein College of Medicine and is

investigating the role of glycan attachment to proteins in development, immunity and disease. This

includes the role of glycans in T and B cell development, the congenital disorders of glycosylation

(CDG), tumour growth and spermatogenesis. Dr Stanley has taken a genetic approach in her studies,

generating Chinese Hamster Ovary (CHO) glycosylation mutants via lectin selection in order to

identify glycosylation enzymes and their individual functions.

///Subheading: Notch in the sugar cane/Growth factors are sweet!///

Of particular focus in the Stanley laboratory, is the glycosylation of the Notch growth factor

receptors. Notch receptors bind to Notch ligands (Delta or Jagged in mammals) on adjacent cells

causing a conformational change, which results in cleavage of the extracellular domain followed by

cleavage of the intracellular domain. The intracellular domain goes to the nucleus and combines

with other transcriptional activators to alter gene expression in a manner that manipulate s cell

growth or fate. Notch has epidermal growth factor (EGF) repeats that have been found to be O-

xylose, O-glucose, O-fucose and O-N-acetylglucosamine (GlcNAc) targets.

Dr. Stanley and her group have found that O-fucose additions modulate the interaction of Notch

with Delta/Jagged, and that a mutation in Notch that blocks fucose addition prevents Notch binding

to its ligands. This finding was shown to be physiologically relevant in immune cell development. The

EGF11/12 region of Notch1 that binds to fucose was mutated in mice and found to reduce thymus

size, number of antibodies and number of T cell subsets. O-GlcNAc additions to Notch receptors

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have also been shown to cause immune cell dysfunction. For instance, mis-expression of the GlcNAc

transferase, lunatic fringe (Lfng), prevents T cell interactions with the thymic stroma, critical for T cell

development.

///Subheading: The sugar patterns in disease///

The Stanley group has shown that there are other physiological effects of altering the glycosylation

of cell surface receptors, for instance mice with a complete loss of Lfng have reduced Notch ligand

binding and subsequent skeletal abnormalities. This is similar to the human CDG, type 3

spondylcostal dysostosis, caused by a mutation in Lfng and characterised by abnormal skeletal

development. Another GLcNAc transferase, EGF domain specific O-GlcNAc transferase (EOGT), was

identified and the Stanley group has found that knockout of EOGT causes wing blisters in flies that

are suppressed by Notch mutations. A loss of EOGT has also been described as one of the genetic

abnormalities that cause Adams-Oliver syndrome, CDG that displays altered digitation and calcium

deposits in the brain.

Enzymes involved in GlcNAc addition have also been studied in relation to other biological

dysfunctions. For instance, the Mgat3 enzyme, responsible for transfe rring the bisecting GlcNAc to

N-glycan complexes, has been studied in breast cancer. Dr. Stanley explains how disruption of Mgat3

has been found to play a role in breast tumourigenesis: “Mice lacking the enzyme had enhanced

tumour growth and metastasis. This is because in the normal mouse, the addition of the bisecting

GlcNAc reduces signalling through growth factor receptors and retards tumour growth.”

///Subheading: Sugar in spermatogenesis///

Investigation of the Mgat enzymes led to the discovery of the physiological inhibitor of Mgat1,

GlcNAc transferase I inhibitor protein long form (GnT1IP-L). This inhibitor is mainly expressed in the

testes. This finding has led to a branching of Dr. Stanley’s research into the role of glycosylation in

spermatogenesis. Using the Cre recombinase system, Mgat1 was knocked out in spermatogonia

causing spermatids to display enhanced binding to sertoli cells, leading to fusion and formation of

giant syncytia that blocked spermatogenesis. The Stanley lab is continuing to investigate the

mechanism underlying this phenotype, with recent data showing that GnT1IP-L interacts with Mgat1

in the Golgi. The levels of Mgat1 and GnT1IP-L are also being investigated in biopsies of testes

containing abnormal sperm.

///Subheading: The future of glycosylation research///

Dr. Stanley’s research has highlighted how glycosylation is critical in developmental cell biology; in

particular that of the immune and reproductive systems. The Stanley lab is continuing to investigate

immune system development through elucidating the individual roles of Fringe enzymes. Other work

of the lab includes development of mouse models defective in O-GlcNAc addition in order to

Portfolio Louisa Cockbill, PhD

understand the role of this type of Notch receptor glycosylation. Dr Stanley’s research has clear

implications in human disease, particularly in elucidating the mechanisms that cause CDG and

possibly also in immune and reproductive dysfunctions. The genetic studies of the Stanley lab

continue to reveal complexity displayed on the sugary frontier of the cell.

///Pullquote: The cell surface is decorated with glycans to such an extent that these sugar chains

have been described as the primary frontier of the cell. ////

///Alternative Pullquote: investigating the role of glycan attachment to proteins in development,

immunity and disease///

///Alternative Pullquote: O-fucose additions modulate the interaction of Notch with Delta/Jagged ///

///Boxout: Glycoprotein therapeutics: The glycosylation of proteins (and lipids) has been revealed to

be essential for their function, making glycosylation an important consideration for therapeutic

targeting and effectiveness. Cue the birth of glycoprotein therapeutics. Chinese hamster ovary (CHO)

cells are hemizygous and have a high number of segregation like events, which makes the cells

ideally suited to select stable mutants from. These properties coupled with the high similarity of CHO

and human glycan allowed the Stanley lab to produce the CHO glycosylation mutants, which now

provide the biotechnology industry with the ideal tools for manipulating the glycosylation profiles of

therapeutics.///

///Alternative Boxout: Glycans in trafficking: Glycosylation of proteins is important in the trafficking

of proteins through intracellular compartments as well as in receptor function at the cell surface. Dr.

Stanley’s group has discovered that the loss of only one N-glycan transferase causes alterations in

the shape and size of the Golgi. In the endoplasmic reticulum (ER), glycans are involved in

chaperoning protein folding and in degradation of misfolded proteins.///

Portfolio Louisa Cockbill, PhD

'The Great Ideas of Biology'

1. The cell as the basic unit of life

3. Evolution by natural selection 2. The gene as the basis of

hereditary traits

5. Biology as an organised system

4. Life as chemistry- the mechanistic basis of life

Contributing author for Synapse science magazine

Synapse science magazine is the popular science publication produced by the University of Bristol’s

student run society, Synapse. Louisa was a member of Synapse since it began in 2011 until

completing her studies in 2016. Contributions have included editorial and committee responsibilities

as well as authorship of several articles in the magazine and on the blog:

www.synapsebristol.blogspot.com

The Great Ideas of Biology according to Sir Paul Nurse, February 2012 1st

edition

Sir Paul Nurse

On the 21st of November 2011 the annual Sir Anthony Epstein lecture was taken by Sir Paul Nurse.

Our knight for the evening was a geneticist and cell biologist by trade who holds the position of Chief

Executive and Director of the Francis Crick Institute (the UK centre for medical research and

innovation). He is also the President of the Royal Society whi le still finding time to run his own

research lab. Along with his colleagues Hartwell and Hunt, Paul Nurse was awarded the 2001 Nobel

Prize in Physiology and Medicine for the discovery of the proteins that control cell division. This

breakthrough affects many areas of cell biology not least cancer research where disruption of these

very proteins is essential for aberrant tumour proliferation.

Keep it simple

In the diagram below are the four great ideas of biology according to Paul, and his proposal of a fifth

that he made to the packed audience in the great hall of Wills Memorial Building. The talk started

with a focus on the work of Hooke and then Grew who both observed plants under high

magnification which led to the discovery of ‘the cell as the basic unit of life’; as the first proposed

great idea of the evening. These simple observations were made possible by the advances in

microscopy and helped Paul begin to illustrate that experimentation with simplistic systems has

aided the better understanding of complex systems over history. This emerged as a theme for the

talk, with Paul himself as a prime example, utilising relatively simplistic yeast in his Nobel Prize

winning discovery. According to Paul the work of Gregor Mendel, who he affectionately referred to

as the ‘great gardening monk’, was another master of simplicity. Paul clearly had great respect for

the systematic approach that Mendel took to understand the particulate theory of hereditary

through studying the simple characteristics of pea plants to expound an abstract theory which he

went on to prove in a quantitative manner. Mendel is also known as the founder of genetics and

helped to form Paul’s second great idea of biology, as ‘the gene as the basis of hereditary traits’.

Portfolio Louisa Cockbill, PhD

Learning from physics and chemistry

Talking of Mendel led Paul onto another theme; that biologists should learn from physicists. Not the

most popular idea, but our prominent speaker argued that instead of obsessing over infinitesimal

details that biologists should look at the bigger picture, and not be afraid in daring to suggest

outrageous theories. For instance, Darwin published ‘On the Origin of Species’ a book which

proposed ‘evolution by natural selection’. This was proposed as the third great idea of the evening

which again came from simple observations, this time of finches on the Galapagos.

In the fourth great idea of biology, ‘Life as chemistry’, Paul argued the importance of the chemical

reactions within cells for the mechanistic basis of life. Again this discovery was rooted in simple

observation, this time by the chemist Antoine Lavoisier observing the similarities between guinea

pigs breathing and coal burning which led him to draw a connection between respiration and carbon

dioxide intake. Louis Pasteur then worked with yeast, leading to the birth of biochemistry- the

chemical reactions and processes within the biological system.

In the slightly more controversial fifth great idea of biology Paul explained how he felt that ‘biology

as an organised system’ is an important principal to grasp. The speaker compared biology to circuit

boards where there are many interconnecting networks which may seem mind boggling but all the

connections fit together to make the electrical item function. It is our job as biologists to not only

pick apart a single strand of the circuit, an incredibly complex job as any researcher well knows, but

to also bear in mind how this one process contributes to the network. The audience were warned

that in discovering biological networks it is important not to force the easiest or most logical

conclusion on our work but to adopt abstract reasoning like a Physicist in order to uncover the true

mind blowing possibilities that Biology seems endlessly capable of.

The great history of biology

Throughout the talk passion and humour were used to

persuade the audience of the ‘great ideas’. For instance, to

emphasise the importance of the cell, a picture of sperm trying

to fertilise the egg was displayed and Sir Paul challenged

everyone present to remember that at one time they all looked

like this. This drew quite a laugh from the hall and Paul went

further to stimulate and challenge people’s perspective through

bringing to our attention the fact that it was in fact Darwin’s

grandfather, Erasmus who first began to argue evolution.

Indeed it appeared that the scientific knight found the exploits

of the grandfather in many aspects rather more interesting

than that of the grandson, as he owns several of Erasmus

Darwin’s scientific poetry books! Sir Paul brought a historical

account alive through his deep interest in the tales of the great

scientists, in whose footsteps he seems set to follow. For

instance by becoming the President of the Royal Society, an

organisation established in the 17th century that encourages scientific discussion and debate which

so many of the founders of science were also members of.

Microscopic Image of sperm trying to

penetrate an egg Sir Paul calls the audience in the great hall

of Will’s Memorial to remember that one day we all looked like this.

Taken from the lillypad chronicles

http://brcrandall.blogspot.com/2008_01_01_archive.html

Portfolio Louisa Cockbill, PhD

Throughout the humorous historic tale Paul clearly aimed to show the audience the bigger picture of

biology through giving ‘the great ideas’ the emphasis they deserve. His goal seemed to be

highlighting what has worked in the past in order to stimulate scientific discovery for the future.

At the end of his seminar, when asked what area of biology the highly intelligent speaker would

advise their child to study, Paul answered that it must be an area they are passionate in, a quality

that he clearly contains in vast quantities. He also expounded that on going into research that the

interrogator’s child should pick an area that is ‘amenable’. It is no surprise that through Paul’s own

personal experience and his evident great interest in the history of biology that he would

recommend research in a simplistic system as holding the best potential for discovery of other, great

ideas of biology.

Portfolio Louisa Cockbill, PhD

What the Eph? December 2014, Issue 9

Ephs are receptors on the outer rim of cells, like the lock in the front door of a house which only

recognises the correct key. In the case of the Eph receptors, they recognise the correct ephrin key

expressed on the outer of a neighbouring cell. Ephs are what is known as promiscuous receptors,

which means that a number of ephrin keys will fit into the Eph ‘lock’.

There are number of different Ephs and ephrins and the response of the cell after the key has fitted

into the lock depends on the specific key and lock combo. Broadly, the A category of Ephs recognise

the A ephrins and the B category of Ephs recognise the B ephrins. When EphAs from one cell

recognise an ephrin A from another cell they sense they are getting in the way and are repelled from

one another. However, in the case of the B type Eph-ephrin interaction the opposite effect occurs;

the EphB expressing cell recognises the ephrin B on the other cell and takes it as a sign to get

friendly and so shimmies on closer to its neighbour.

Why are the Ephs important?

Ephs are important for function in many tissues of the body. For instance, during development of the

foetal brain, cells move to different areas to establish sections important for particular functions.

Ephs act as a guidance system for the cells in this instance, with the repelling A type ephrins lining

the path edge to keep cells from meandering and a gradient of B type ephrins beckoning the cel ls

onwards into position.

Ephs and ephrins are also shown to kick start various signals that activate a stream of knock-on

events which can alter cell behaviour such as growth, cellular death etc. As the Eph system sits in a

position to control various cellular behaviours it often means that the Eph-ephrin status is

manipulated in cancer for the cancer cell’s survival.

Research from the Nobes lab, here at the University of Bristol, investigates the Eph role in prostate

cancer. EphA2 along with EphB3 and 4 are found to be expressed at higher levels in prostate cancer

than compared to benign tumours (1-3). The combo of highly expressing Ephs are thought to enable

cancer cells to be both repelled away from other tumour cells via EphA2 interactions and to move

towards and past healthy neighbouring cells through attractive EphB3 and 4 interactions. These Eph

interactions in prostate cancer are linked to migratory behaviour of cells which is prevented when

the Eph interactions are blocked (3, 4). The Eph interactions involvement in cancer cell movement

raises the possibility that Ephs are important for cancer cell migration away from the original tumour

to form metastatic tumours in other organs of the body.

If you want to know more about Ephs and ephrins and their role in the movement of prostate cancer

cells, check out this link to the Nobes lab in Bristol’s School of Biochemistry.

http://www.bristol.ac.uk/biochemistry/research/kn.html

1. Walker-Daniels J, Coffman K, Azimi M, Rhim JS, Bostwick DG, Snyder P, et al . Overexpression

of the EphA2 tyrosine kinase in prostate cancer. Prostate. 1999;41(4):275-80.

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2. Lin K-T, Gong J, Li C-F, Jang T-H, Chen W-L, Chen H-J, et al. Vav3-Rac1 Signaling Regulates

Prostate Cancer Metastasis with Elevated Vav3 Expression Correlating with Prostate Cancer

Progression and Posttreatment Recurrence. 2012.

3. Astin JW, Batson J, Kadir S, Charlet J, Persad RA, Gillatt D, et al. Competition amongst Eph

receptors regulates contact inhibition of locomotion and invasiveness in prostate cancer cells.

Nature Cell Biology. 2010;12(12):1194-204.

4. Batson J, Maccarthy-Morrogh L, Archer A, Tanton H, Nobes CD. EphA receptors regulate

prostate cancer cell dissemination through Vav2-RhoA mediated cell-cell repulsion. Biol Open.

2014;3(6):453-62.