Professional Documents
Culture Documents
ISSN 2517-7028
ISSUE 101
ISSN 2517-7028
ISSUE 101
Editor
www.researchoutreach.org 3
CONTENTS
06 A NEEDLE IN A HAYSTACK –
THE FUTURE OF BIG DATA
Dr Yang Feng
Using network modelling to
detect communities using
available nodal information.
10 LYSENIN CHANNELS AS
SINGLE-MOLECULE SENSORS,
CONTROLLED NANO-VALVES,
AND MEMORY ELEMENTS
46
Professor Daniel Fologea
How cells interact with their
environment by selective
transportation.
22 42
Dr Hugo Christenson SLIDES DEGRADE INTO
Why crystals first form in USELESSNESS
topographical defects like Professor Carl Johansson
cracks and crevices. Documenting the amazing
diversity of tardigrades – the
18 FROM EARS TO mysterious ‘water bears’.
ENGINEERING 30 THE REEMS PROGRAMME: Professor Michele Jacob 50 EVADING THE RISE OF 62 ESEB: HELPING
Professor James Windmill DISCOVERING UNTAPPED Provides predoctoral students RANSOMWARE EVOLUTIONARY BIOLOGY 78 PEATLANDS’ PAST SUGGESTS
Learning from insect hearing to TALENT with individualised, in-depth, Professor Elisa Bertino EVOLVE IN EUROPE FAST-CHANGING FUTURE
develop new microphones and Mr Bartlett Sheinberg multidisciplinary research Designing tools to prevent Professor Laurent Keller Professor Sara Hotchkiss
transducers. Contextualising materials training. ransomware infections from ever Uniting and supporting Investigating the effects of
science for community college taking hold. evolutionary biology climate change on kettle hole
22 BUILDING ARTIFICIAL students. 42 EXPANDING CAPACITY OF researchers. ecosystems of the northern US.
INTELLIGENCE FOR SOCIAL NON-COMMUNICABLE 54 BIASES FROM BIG DATA: THE
GOOD 34 SUPPORTING TOMORROW’S DISEASE RESEARCH AND PREJUDICED COMPUTER 66 DEVELOPMENT OF 82 CROSSING KINGDOMS
Dr Long Tran-Thanh ROLE MODELS: HOW THE TRAINING IN THAILAND Professor Olfa Nasraoui IMMUNITY IN BASAL BETWEEN PLANTS, FUNGI
Harnessing AI to solve the most LEADERSHIP ALLIANCE IS Dr Kathleen Potempa Developing tools to lift the lid METAZOANS AND BACTERIA
important societal challenges of ENCOURAGING STUDENTS Helping improve the capability on ‘black box’ algorithms and Dr Mauricio Rodriguez-Lanetty Professor Teresa Pawlowska
our age. FROM UNDERREPRESENTED of the Thai healthcare system in create truly fair alternatives. Investigating immunological Investigating the complex
GROUPS managing chronic diseases. priming in corals and anemones. interrelationship between
26 PUSHING THE BOUNDARIES Dr Medeva Ghee 58 FOSSILISING FOSSIL FUELS endobacteria and their host
– INTERROGATING Developing a workforce 46 TAKING INSPIRATION WITH GREEN ALTERNATIVES 70 SYNTHETIC CELLS plants.
MAGNETISM AT MATERIAL reflective of the diverse fabric of FROM NATURE FOR A NEW Dr Liz Jenkinson HAVE SENSES TOO
INTERFACES
Dr Mikel Holcomb
our society. GENERATION OF QUIET
AEROFOILS
Developing an alternative to
fossil fuels based on three key
Professor Allen Liu
Constructing prototypes of
86
COMMUNICATION
The media’s manipulation
Understanding the behaviour of 38 THE SYNAPSE Professor Phil Joseph components – bacteria, genetic synthetic cells displaying the of scientific perception.
ions at the boundaries between NEUROBIOLOGY TRAINING Reducing noise pollution engineering and sugar. minimal characteristics of life.
two materials. PROGRAM, TRAINING THE through the development of
NEXT GENERATION OF new aerofoil design.
NEUROSCIENTISTS
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Physical Sciences ︱ Dr Yang Feng
A needle in a haystack –
Figure 1: Community detection results when considering school, ethnicity, and gender as the ground
truth. Predicted communities are separated by the middle dash line.
School
6 www.researchoutreach.org www.researchoutreach.org 7
Behind the Bench
Dr Yang Feng
E: yang.feng@columbia.edu T: +1 (212) 851 2139 W: http://www.stat.columbia.edu/~yangfeng/
X A
A c Q&A
Research Objectives What would you say was the with their personal information,
8 www.researchoutreach.org www.researchoutreach.org 9
Physical Sciences ︱ Professor Daniel Fologea
Lysenin channels as
The experimental setup for single
molecule analysis consists of
single lysenin channels inserted
into planar lipid membranes
single-molecule sensors,
produced in a thin Teflon film.
When the analyte molecule is
electrophoretically driven through
the channel it impedes the ionic
flow and yields a drop in the
controlled nano-valves,
current (IB) for the time (T) the
analyte resides within the channel’s
lumen. The electronic signature
recorded during the passage
depends on the size and charge
A
Professor Daniel Fologea, ny cell in your body, whether it WHAT IS LYSENIN? (the fluid within the cell). Once lysenin toxin that deviates considerably from terms, lysenin channels are molecules
an associate professor at Boise is in your brain, blood, muscles, Lysenin is the name of a pore-forming is inserted into the membrane, it forms its previously assumed killer role. with memory, capable of “remembering”
State University, studies the or heart, interacts with its toxin that can be found in fluids from stable nano-sized channels, or pores, Unlike any other pore-forming toxins, the last state they were in. This work
way cells interact with their environment and allows for the selective the main body of an earthworm called through the hydrophobic, or water- lysenin channels are highly regulated demonstrated beyond any doubt that
environment by selective passage of ions and molecules through its redworm or Eisenia fetida. The worm, repelling, cell wall. Prof Fologea and his by transmembrane voltage, multivalent memory in biological systems is not
transportation of ions and membrane. To decipher the functionality typically found in Europe, lives on colleagues use these channels to their metal ions, and temperature. His research necessarily a function of evolved organs
molecules through the cell of cells in health and disease, the decaying organic material and can be advantage, by recreating the way the group proposed using these channels as like the brain, but may be achieved
membrane. His research group intimate mechanisms by which ions and used for composting household and protein forms the pores in the cell wall. cheap and reliable sensors for detecting at single molecule levels.
examines these interactions molecules make their way into and out industrial waste – like sheep manure, toxic metals in water by monitoring the
in order to understand how of cells through their membranes must coffee pulp, and even wood chips. LYSENIN: CHANNEL, SENSOR, changes in the electric currents through Prof Fologea and his team discovered
diseases occur, and how to be better understood. Despite its origins, this protein inside OR MEMORY ELEMENT? channels in the presence of tiny amounts that lysenin, similar to other pore-
use them for biosensing, early the earthworm might be the key to In earlier works published in 2010 and of metal cations (positively charged ions). forming toxins, is a great way to create
diagnosis, and to cure diseases
Under the umbrella of membrane the better diagnosis and treatment 2011, Prof Fologea and his team focused a ‘bio-sensing device’ to study the way
like cancer.
transportation, there are several different of deadly diseases, according to Prof on understanding the biophysical When Prof Fologea’s team investigated molecules move through membranes.
topics of research that Prof Daniel Fologea’s research. properties of lysenin channels by the response of lysenin channels to If they pass an electric current through
Fologea’s membrane biophysics group at reconstituting them in artificial membrane variable external voltages they recorded the lysenin channel, that current is
Boise State University is looking into. One Lysenin destroys cells through cytolysis, systems and investigating their response a striking feature: lysenin channels affected by any tiny changes caused by
of these uses a special protein found in an a process by which a cell bursts due to physical and chemical stimuli. Their responded to the applied voltages in molecules passing through the channel.
unusual organism – a red earthworm. to excess water flowing into the cytosol findings have shown a pore-forming a history-dependent manner. In simple The team can monitor the current, and
watch for these tiny changes, enabling
the detection of even a single molecule
as it passes through the channel in the
membrane. In one of the latest studies
Prof Fologea and his team published
in 2017, they found that lysenin channels
can act as nanosensors, by allowing the
hormone angiotensin II to pass through
channels when an electric field is applied.
Angiotensin II is a peptide that causes
vasoconstriction, the tightening of blood
vessels, and a consequent increase
in blood pressure. In contrast to other
pore-forming proteins that may be
used for similar studies, lysenin has the
advantage of a large pore, therefore
allowing analysis of bigger molecules.
This work is expected to advance our
ability to characterise and even sequence
Lysenin channels are temporarily blocked during the passage of angiotensin II (Ang ii). a) The insertion
of a single channel in the bilayer membrane at -60 mV is observed as a sudden change in the ionic important biomolecules such as DNA
current through the supporting bilayer lipid membrane. No transient changes in the ionic current and proteins. In addition, by endowing
established through two open lysenin channels were observed at -80 mV in the absence of Ang II (b) the channel with biorecognition
and when Ang II was added to the negatively biased reservoir. d) Addition of Ang II to the positively
biased reservoir yielded multiple transient changes in the ionic current, indicative of translocation of elements capable of recognising and
electrophoretically driven peptides. binding disease-specific biomarkers in
10 www.researchoutreach.org www.researchoutreach.org 11
Behind the Bench
Lysenin channels can be used to temporary
permeabilise cell membranes. Left panel:
Lysenin addition to the solution bathing
ATDC5 cells provides access to the cytosol
for otherwise non-permeant fluorescent
Dr Daniel Fologea
molecules (red color). Right panel: Subsequent
addition of chitosan, an irreversible lysenin
channel blocker, preserves cell viability as
demonstrated by the green fluorescence of the
live-cell indicator. In the absence of chitosan,
the lysenin-permeabilised cells die within the E: danielfologea@boisestate.edu T: +1 (208) 426 2664 W: http://physics.boisestate.edu/fologea/
same time frame.
Research Objectives • Dr David Pink, St. Francis Xavier University His research is focused on membrane
Prof Fologea’s work aims to discover • Dr Robert Woodburn, Provena St. Mary biophysics with a special emphasis on using
more detail on the functionality of lysenin Hospital transmembrane transporters as single
channels. • Dr Charles Hanna, Dr Denise Wingett, Dr molecule sensors, bioelectronics elements,
Juliette Tinker, and Dr Julie Oxford, Boise and for controlled transport across artificial
Funding State University and natural membranes.
complex biological fluids, this technique • National Science Foundation
enables early diagnosis of cancer and Lysenin, a protein found inside • National Aeronautics and Space Bio Contact
Administration Dr Daniel Fologea is an associate professor Daniel Fologea, PhD
earthworms, might be the key to early
other diseases.
• Idaho State Board of Education of Biophysics with the Department of Physics Department
Physics and the Biomolecular Sciences Boise State University
LYSENIN AS A CONTROLLED NANO-
VALVE FOR DRUG DELIVERY
diagnosis and treatment of deadly Collaborators Graduate Program at Boise State University. 1910 University Drive
• Dr Greg Salamo and Dr Ralph Henry, He graduated with a PhD in Biophysics from Boise, ID 83725-1570
‘The remarkable biophysical diseases such as cancer University of Arkansas the University of Bucharest in Romania. USA
properties of lysenin channels present
a tremendous potential for multiple
Q&A
scientific, technological, and biomedical transport foreign molecules into and out radiation. Such achievement would
Their future plans are important as well. With regards to graduates, they are
applications,’ says Prof Fologea. The of the cells. Not only drugs, but genes enable concomitant highly localised radio Students interested in biomedical studies required to demonstrate excellent
large pore size may accommodate the could also be introduced into cells to and chemotherapy while significantly are more prone to focus on developing knowledge of Biology, Chemistry,
passage of large molecules, and the manipulate their functionality or correct reducing the remote effects associated You studied physics and biophysics, novel approaches for diagnosis or drug Physics, and Math as a condition for
ability to open and close the pores other deficient genes. Prof Fologea’s with systemic chemotherapy. why did you choose to go into delivery, students from Math and Physics admission into our graduate program.
at will is a feature uncommon among group demonstrated that whether or research about cell membranes? are more interested in developing
pore-forming toxins. To exploit these not a molecule can pass through the LYSENIN RESEARCH PROVIDES The cell membrane plays a fundamental quantitative models of biological To what extent do you have to
role in the functionality of any cell, functionality, while students from Biology develop new experimental tools
capabilities, one of the group’s goals channels can be controlled by external OPPORTUNITIES FOR
beyond the obvious function as a are more inclined towards physiological and equipment to go alongside your
is to transport drugs to diseased sites electric fields, multivalent cations, pH, MULTIDISCIPLINARY MENTORING physical barrier between the interior of insights from a multidisciplinary research?
through lipid-made nano-sized carriers temperature, and even adenosine AND LEARNING the cells and their external environment. perspective. Sometimes we are unable to purchase
mimicking a spherical membrane, triphosphate (ATP), which transports While Prof Fologea and his colleagues are The cell membrane participates in what is required for our investigations
and release them by controlling the chemical energy within cells. Currently, making great strides towards developing crucial physiological functions such as What kind of interdisciplinary because what is available does not
opening and closing of the lysenin the team is focused on using X-rays to cures for diseases like cancer, he also nutrition, controlled transport of ions backgrounds do your students, whether satisfy our needs. Many of our small
and molecules, creating and maintaining they are undergraduates, PhD students tools and devices are homemade, and
channels inserted into it. Similarly, the trigger the release of anti-cancer drugs recognises the importance of mentoring
electrical and chemical gradients, or post-docs, have? Is experience in both the students bring great contributions
channels can be reconstituted directly only at the diseased site, which can future generations of scientists. With this
communication, information storage, physics and biology a must? to such developments. I can say that
into live cell membranes and used to be easily targeted with focused ionising in mind, Prof Fologea dedicates a great and many others. Any attempt to Biophysics is interdisciplinary by definition, many devices, tools, and software
amount of his time to mentoring students produce an artificial cell must start by therefore advanced knowledge from packages developed by our students
in the Biomolecular Sciences Graduate creating the membrane and replicating Physics and Biology is a must for advancing are outperforming their commercially
Program at Boise State University. ’My its functions. The cell membrane is one the field. However, this is not a requirement available counterparts with respect to
Lysenin channels behave of those organelles for which a complete for undergraduate students interested fulfilling our needs.
like memory elements and affiliation with the Biomolecular Sciences
understanding of functionality requires a in starting their research career in my
present a strong hysteresis Graduate Program at Boise State
in conductance (measured in truly multidisciplinary approach. lab. Nonetheless, all the undergraduate What is the ultimate goal for your
University provides unique opportunities students who have worked in my lab ended research, in your own personal
nS) when exposed to variable
external voltages. Lysenin for fruitful collaborations with faculty Your research has a broad remit. How up taking relevant classes outside their opinion?
channels closed by ascending from Biology, Chemistry, Physics, and do you decide what each of your home department, which demonstrates If the results of my research will improve
voltages (red line) re-open
Engineering,’ he says. ‘The program students studies and what you will a strong motivation for gaining someone else’s life, I shall consider my
at lower voltages when the
transmembrane voltage provides a constant flow of graduate focus on next? multidisciplinary knowledge and skills. research goal achieved.
decreases (blue line). students for which multidisciplinary That is always the student’s decision.
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Physical Sciences ︱ Dr Hugo Christenson
Figure 1. Typical images of mica surfaces
showing nucleation density of (a) neo-C5OH
CRYSTAL CLEAR:
crystals on unscratched mica and on (b) mica
scratched with 10 nm diamond powder.
H
Dr Hugo Christenson is a ave you ever sat on a park bench of crystallisation and the environmental START THE TRANSFORMATION substances [neo-pentanol (neo-C5OH)
Reader in the Molecular and on a frosty cold morning? Did conditions that promote crystal growth When a substance transforms from one and carbon tetrabromide (CBr4)] was
Nanoscale Physics Group at you notice that the ice crystals are therefore of great interest. form of matter to another, like water studied on flat surfaces of glass and mica
the University of Leeds. His seem to form first on the chipped parts (a liquid) changing to ice (a solid), it goes using optical microscopy. They were also
present research interests lie of the surface? Did you wonder why? It has long been known that crystal through a phase change. Nucleation studied on identical surfaces that had
in crystallisation – an important The answer to this observation has been nucleation (the first process in the is the initial process of the phase change been scratched with diamond powders.1
process across multiple areas the topic of extensive scientific research. formation of a crystal) almost always that progresses to crystallisation. The particle size of these diamond
of science. Specifically, Dr Ice is the crystallised form of water and occurs on a surface. For example, ice powders can be carefully chosen, giving
Christenson’s work provides crystallisation is an important process crystals in cirrus clouds in the upper When molecules self-assemble in experimental control over the size of
in-depth insight into why crystals in nature and industry. It is an intricate atmosphere will form on a small aerosol an ordered structure they become the grooves on the surface and allowing
first form in topographical part of subjects as wide-ranging as particle rather than in the air itself. what we generally refer to as crystals. the team to look at the effect a change
defects, like cracks and crevices. geology, meteorology, materials science However, the physical and chemical Crystal nucleation can happen in size has. The scratched surfaces were
and medicine and many technological properties of surfaces that are conducive from solution, from vapour, or from then imaged via scanning electron
advances apply crystallisation processes. to crystal nucleation are still not clearly liquid. Dr Christenson’s research has microscopy (SEM).
Understanding this naturally occurring understood. Dr Christenson’s recent concentrated on heterogeneous Dr Christenson and his team studied
phenomenon allows better control of work seeks a clearer “picture” of the nucleation, which occurs when a The results from this experiment clearly nucleation of four different crystals
the process and more efficient uses underlying topographical properties that particular surface assists the process. demonstrated that nucleation increased (carbon tetrabromide, camphor,
of its end product. The fundamentals promote nucleation. on the scratched surfaces (see Figure norbornane, and hexachloroethane)
Dr Christenson has extensively studied 1). Induction time, which is measured from vapour on mica. Instead of
various aspects of phase change from first exposure to the vapour to the manufacturing surface features,
dynamics, investigating what variables first appearance of a crystal visible in naturally present defects on the mica
affect crystal nucleation. Drawing on the microscope, was also studied. The surface were studied.2 These natural
the Classical Nucleation Theory (CNT), induction times on unscratched glass defects are much easier to characterise
than most manufactured features.
Understanding crystallisation allows Repeat experiments were performed
to identify the best nucleation sites
better control of the process and more on each surface. SEM could then be
which describes how physical attributes, and mica were similar. However, the All four compounds were allowed
such as defects or crevices on a surface, induction time significantly decreases to nucleate repeatedly on a number
foster nucleation, Dr Christenson devised when the surface is scratched and, of mica substrates. All four were seen
several experiments to study precisely the larger the particle diameter (and to nucleate preferentially on the same
the effect of these physical features. His therefore the larger the defect), the types of sites which were typically
research associate Dr James Campbell quicker the crystallisation occurs. characterised by an acute wedge
has contributed significantly to the The effects were more pronounced geometry. Figure 2 shows crystals
design of the experiments and carried on mica, probably because the of carbon tetrabromide growing in
out most of the experimental work. scratching gives rise to a greater naturally occurring defects on mica.
number of very small and sharply acute
CONTROLLING THE SURFACE topographical features, whereas on DEEP POCKETS
DEFECTS glass the grooves tended to be less In a third experiment, the formation
Dr Christenson designed a test deep and more rounded in form. of ice and organic crystals were
to investigate the idea that defects observed in mica.3 Well-defined
on a surface could help control crystal NATURALLY PRESENT DEFECTS topographical features with sharp
nucleation. For this experiment, the In an alternative experiment to acute wedges, referred to as “pockets,”
nucleation from vapour of two organic investigate the same problem, which naturally occur when Muscovite
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Behind the Bench
Dr Hugo Christenson
E: h.k.christenson@leeds.ac.uk T: +44 (0) 113 343 3879 W: http://www1.mnp.leeds.ac.uk/hchristenson/
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Physical Sciences ︱ Professor James Windmill
NAVIGATING BY SOUND
While larger animals can detect the
direction of a sound source by the
difference in timing and amplitude
as sound waves are received at each
of their two ears, for smaller animals
such as insects, the distance between
their two hearing organs is likely too
M
fly which lays its eggs on crickets.
Sometimes the solutions to odern microphones, such as to science, insects are an extremely of how the organism’s hearing works It therefore needs to locate its cricket
engineering questions have those used in hearing aids, and varied group of organisms, and have hosts in the dark, which it does by the
already been answered – by transducers such as ultrasound evolved a diverse array of different ‘Supersonus,’ from the South American computer model of the ear’s structure, sound of the male cricket’s mating call.
animals! Rather than ‘reinvent scanners, are remarkably sensitive. hearing organs. Previous research into rainforest; and the loudest (relative to its which can then be used to simulate how Since the mid-nineties, it has been
the wheel,’ therefore, Professor However, they still struggle to deal with insect hearing has largely focused on size) animal on earth – a water boatman it responds to sound. Comparing their known that the Ormia’s two tympanic
James Windmill and his lab issues such as background noise, which the noisiest groups: the grasshoppers, that generates a mating call by rubbing experimental data with the computer membranes (ear drums) which are located
team at the University of may need to be removed by downstream crickets, locusts, and cicadas; however, its penis against its abdomen. models gives the researchers a thorough around the base of their front legs, are
Strathclyde choose to learn from digital processing, or identifying the Prof Windmill’s research covers a wide understanding of how the organism’s directly coupled to each other by a strut.
some of the remarkable feats of direction from which a sound originates. range of other insects including flies To elucidate the mechanisms of hearing hearing works – both in terms of its In effect, the structure forms a tiny, highly
engineering found in the natural Electronics engineer Prof Windmill’s and moths. In the course of their work, in an insect, Prof Windmill’s lab use mechanics, and downstream signal sensitive see-saw which rocks if the
world. In particular, his research highly multi-disciplinary team provide Prof Windmill and colleagues have an array of techniques, including processing at the neural level. sound waves reaching the two tympanic
focuses on using ideas from solutions to these problems, taking discovered some remarkable insects, behavioural observation, microscopy membranes are in any way different in
insect hearing to develop new their inspiration from the natural world, including a moth, the greater wax moth, and X-ray microtomography, 3D laser Then, the baton is passed to the intensity or timing. This ingenious system
microphones and transducers for in particular the insects. with the ability to hear sounds up to 300 vibrometry, and electrical examination engineers, physicists, mathematicians amplifies minute differences in sound
use in fields as wide-ranging as kilohertz, higher than any other animal; of the signals passing through the and material scientists of the team who reaching the two membranes, enabling
medicine and materials science.
INSPIRING INSECTS the insect with the highest frequency auditory nerve. The results are develop new microphones (instruments the insect to detect the direction a sound
With about a million species known call – a genus of katydid dubbed translated into a three-dimensional for sensing acoustic and ultrasonic is coming from.
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MEMS directional microphone in a 3D-printed
housing (UK five-pence coin for scale)
Behind the Bench
Professor James Windmill
E: james.windmill@strath.ac.uk T: +44 (0)141 548 2694 W: http://www.cue.ac.uk
W: http://www.strath.ac.uk/staff/windmilljamesdr/ W: http://www.sasatin.eu
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Physical Sciences ︱ Dr Long Tran-Thanh
A
s artificial intelligence becomes numerous other teams tried to unleash AI minimising the “bother cost” at the same
more and more ubiquitous, we
need to learn how to live and
interact with it. And of course, this goes
Dealing with traffic management
both ways: AI systems also need to learn
how to interact with humans, and take
in a big city like Singapore or London
their preferences or choices into account. is crucial – make one mistake and you
cause instant mayhem
Dr Long Tran-Thanh calls this making AI
more “human-aware” – something that
so far has not been fully exploited. Often,
AI researchers will design a beautifully on the gathered data to find the most time. And it worked. Overall, it has
efficient and rational digital system, efficient ways of reducing energy costs managed to reduce the participating
only for it to fail when faced with the in homes. But it quickly transpired that households’ energy consumption by 35%.
unpredictability of its human users. algorithms which had been super-efficient In the not-so-distant future, Dr Tran-
Dr Tran-Thanh wants to change this and in simulations, proved nearly useless in Thanh’s AI will be implemented in
develop AI platforms that can be used the real world. The reason was simple – Schoonschip, an experimental floating
to tackle some of society’s biggest people rejected their recommendations neighbourhood in Amsterdam.
problems. He wants AI to take into as incompatible with their daily routines.
account that human users are not If you have been doing your laundry on There were a few other projects where
perfectly efficient nor perfectly rational, Saturday afternoon all your life, it will take Dr Tran-Thanh’s team sought to apply
that we are creatures of habit and are more than a machine’s recommendation their human-aware AI idea. One of them
often stubbornly stuck in our ways. to reschedule for 3am on Tuesday. was built to cost-efficiently assign tasks
to workers, each with his or her own
SMOOTHING OUT THE Dr Tran-Thanh and his team then thought hourly rate and skill level, hired through
ENERGY PEAKS about a system that would simply ask expert crowdsourcing platforms. Another
One of the first attempts he made at users about their preferences – for dealt with applying AI to fight drug
making this vision a reality was a home example, “Would you mind turning your trafficking and other situations where
energy management system. The main kettle on an hour later on Wednesdays?” networks needed to defend themselves
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Behind the Bench
Dr Long Tran-Thanh
E: ltt08r@ecs.soton.ac.uk T: +1 442380593715 W: https://www.ecs.soton.ac.uk/people/ltt1m09
Research Objectives • Dr Henry Ngoc Cuong Truong Alex Rogers. He has been conducting
Professor Tran-Thanh develops AI (SenseEye) and Dr Tim Baarslag (CWI active research in a number of key
algorithms aimed at tackling societal Amsterdam) areas of Artificial Intelligence. His
problems and his work focuses on • Dr Bo An (Nanyang Assistant results have been published at top
increasing security for AI. Professor at NTU Singapore) AI conferences and journals and
• Dr Vinh Thong Ta (University of he has received a number of
Funding Central Lancashire) prestigious awards.
EPSRC (EP/N02026X/1) • Dr Matteo Venanzi, Dr Valentin Robu,
Dr The Anh Han, Dr Avi Rosenfeld, Contact
Collaborators Dr Trung Dong Huynh, Dr Michael Dr Long Tran-Thanh
• Professor Nicholas R. Jennings (vice- Kaisers, Dr Marcin Waniek, University of Southampton
provost of Imperial College London) Haifeng Xu University Road
• Professor Alex Rogers (Oxford Southampton
University) Bio SO17 1BJ
• Professor Milind Tambe (University Long Tran-Thanh is a Lecturer United Kingdom
of Southern California Center for (Assistant Professor equivalent) at the
Artificial Intelligence in Society) University of Southampton, UK. He
• Dr Sebastian Stein and Dr Sarvapali obtained his PhD in Computer Science
D. Ramchurn (University of in 2012 at the same university, under
Southampton) the supervision of Nick Jennings and
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Physical Sciences ︱ Dr Mikel Holcomb
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Surface
Behind the Bench
Dr Mikel “Micky” Holcomb
E: mikel.holcomb@mail.wvu.edu T: +1 304 293 5196 W: http://holcombphysics.wixsite.com/home
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Education & Training︱ Mr Bartlett Sheinberg
M
To many, materials science aterials science is a topic at bridging the gap between community
represents a fairly inaccessible, involved in every facet of life. college and university for talented students
complicated topic of science From the car you drive to work, at HCC who will be transferring primarily
requiring a highly academic to the clay on the white cliffs of Dover, into engineering, the physical and biological
approach. Mr Bartlett materials are everywhere and have a sciences, and computational analysis.
Sheinberg’s Research significant impact on life as we know it.
Experiences and Exploration Understanding the extent of this impact As Mr Sheinberg describes it himself:
in Materials Science (REEMS) is critical and should be accessible to “The REEMS programme gives students “Many students come into my office and not realise their own potential talent and IMPACT OF MATERIALS ON SOCIETY
Programme aims to overcome whomever is interested, regardless of an opportunity to see first-hand the say, ‘I really want to do such-and-such’, abilities – REEMS provides that opportunity. During the spring term, the IMOS seminar
this – contextualising materials academic background or financial status. broad scope of materials science. These and one of the things I’ve always tried to Because of this, Mr Sheinberg offers an provides a significant emphasis on
science for community college experiences combine academic experience do is identify those students who possess individual approach to interviewing each contextualising and teaching students about
students. The programme’s Delivering materials science to serious- with recognition of the roles which that intangible gleam in their eye. One of REEMS applicant to ensure that there will the impacts of materials on society. This
approach also aims to instil minded students is vital not only for materials can play in solving important the objectives of the REEMS programme be a demonstrated mutual benefit for the includes “broadening students’ horizons” in
confidence in these students developing the next generation of materials societal issues and lay the foundation is to quantify what that gleam in the eye student and opportunities provided by the terms of how materials have shaped cultures,
and provide them with skills scientists and engineers, but for generating for the identification of interesting and means in terms of their future academic programme. He said: “Applicants might geo-politics and technology advances over
to help them progress in their
a technically prepared workforce. The study meaningful career opportunities. Academic pursuits and their ability to appreciate the have a great academic background and our the past three to four thousand years.
academic careers.
of materials provides an academic umbrella and career exploration really is the key opportunities which the REEMS programme selection of students is based upon why
under which community college students objective of the REEMS programme. We provides as they consider their futures.” they want to become involved in the REEMS Topics in this seminar series discuss the
can appreciate concepts in the physical provide the means for students to take programme and what their expectations are intersection of materials, technology,
and biological sciences, engineering and the first steps towards exploring academic THE IMPORTANCE OF DIVERSITY from it. I like to make sure that there is an anthropology, economics and politics.
computational science. An introduction pathways and potential careers.” HCC is an open admission institution which overlap between what the programme can Mr Sheinberg notes that IMOS plays an
to materials provides an important context provides students with a cost-effective offer, and what the student hopes to take important role in helping students to realise
The REEMS for appreciating their coursework and FINDING THAT SPECIAL SOMETHING education during their time at Houston out of it. their career path.
programme
generates an invaluable self-confidence Following the programme’s success since Community College and supplies a
as they move forward to complete their its inception in 2015, Mr Sheinberg’s role second chance for those students to prove “At HCC, you have a population of roughly He said: “As an example, IMOS begins by
scope of materials REEMS Programme, prevail. are selected for the following year’s
summer research experience. During the
highly diverse population of individuals
from different nationalities, backgrounds
originate from diverse cultures, are highly
motivated and have demonstrated a strong
as we explore both technology, cultural
developments and impacts.
science. Academic OPENING DOORS autumn semester an additional cohort and situations. Many of these students do work ethic. REEMS plays a role in identifying “One of the results of this seminar is that
and career
This programme – entitled Research of students is recruited to apply for these talented students.” students start to ask themselves: if I want
The programme
Experiences and Exploration in Materials entry into the seminar series “Impact of to have a career in science, engineering or
exploration is the Science (REEMS) – is funded by the Division Materials on Society” (IMOS). Over the For Dr Megan Robertson at the University even materials research, what impact can I
key objective
of Materials Research at the National
Science Foundation (NSF) and is aimed
autumn semester, REEMS staff provide
a series of seminars on university transfer
forced me to of Houston, one of REEMS’ partner
institutions, having this diversity is a real
have on society as an engineer or a scientist?
How am I going to impact society? What
opportunities, networking opportunities
with materials professionals, and one-
become a better, benefit. She said: “My university has
a significant number of students who
problems can I solve? The identification
of societal problems and challenges and a
on-one transfer guidance. The REEMS more vigorous transfer from community colleges, so this realisation of the importance of materials
student and,
programme welcomes students across is an important avenue for us. We have a science in solving those challenges is one of
all academic interests and majors. lot of students who work while they’re at the key objectives of the seminar series.”
and Dr Sheinberg,
their attitude towards their study and of being in such a multicultural city, as it can series and preparation for the summer
a demonstrated interest in discovery offer new perspectives to research – I think research experiences.
30 www.researchoutreach.org www.researchoutreach.org 31
administration of the programme, one of Sheinberg’s fatherly persona, stating that his agreed as well, stating: “The REEMS
Mr Sheinberg is like the critical components of the programme “really friendly personality … [and] helpful programme helps me and my graduate
a father to us – you
are the multi-faceted roles which each of the approach throughout the programme” had students in that it actually forces us to
REEMS research faculty play in the process. made it a “blessing getting to know him”. explain our science in a way that makes
on what he has done the research faculty members. These are the
people who really inspire the students – the
research faculty mentor for two additional
REEMS students at Rice University, agrees
it to people who are completely new to
the topic. It is always helpful for us to learn
for me. No one will linchpins that make this thing work. Students that the programme’s success is down to how to do that more generally and more
32 www.researchoutreach.org www.researchoutreach.org 33
Education & Training︱ Dr Medeva Ghee
Supporting tomorrow’s
role models:
how the Leadership Alliance is encouraging
students from underrepresented groups Victoria Cole, undergraduate student. Justin Holmer, Associate Professor of Mathematics (left), and Mamikon
Gulian, undergraduate (right).
D
If the balance of espite making up almost complex societal needs of its diverse go together’.
underrepresented groups in 40% of the United States population if it is to remain a key player on and prejudices, provide continuous
population (a proportion which the global, political and economic stage. DEGREES OF SUCCESS
social support and to address identity
American academic institutions
and the research workforce is is on the rise), underrepresented So what impact has the Alliance had?
development
to be effectively addressed, ethnic and racial minorities receive a To address this critical need, broader The Leadership Alliance celebrated
it is imperative that young much smaller proportion of university and more reliable pathways must be more than 450 Doctoral Scholar alumni
people have role models. For degrees, especially in the fields of opened for students and researchers from with PhD/MD-PhD degrees in 2017,
over 25 years, The Leadership science, technology, engineering and underrepresented groups to enter and the academic pathway. One Leadership faculty mentors and administrators of whom 60% are women in STEM. Its
Alliance, a consortium of over mathematics (STEM) (around 20% of stay in the research workforce. A positive Alliance alumna, Scharri Walker PhD, together to celebrate the summer success is perhaps most attributable to
30 institutions, has provided undergraduate degrees and less than trend for historically underrepresented now Chair of the Biology Department research of the undergraduates, who its measured and consistent approach
support in the shape of 8% of doctorates). In addition, women groups in academia in the United States at Tougaloo College, which is also her make either oral or poster presentations, to inspiring students to pursue research
encouragement, mentorship and remain hugely underrepresented in STEM is gaining momentum, with the number alma mater, noted that when she was many for the first time. The LANS also careers and then connecting them with
training. This effort has directly subjects across the world. Despite these of degrees overall for this demographic most struggling with her PhD studies, provides activities designed to improve the means to do so. There has been
resulted in the achievement challenges, students and researchers from slowly increasing over the last 20 years. the Alliance provided an internship and postgraduate skills and inform career a steadily increasing demand from
of over 450 PhDs/MD-PhDs diverse ethnic and cultural backgrounds More recently, academics have focused mentors that inspired her to continue: decisions, as well as showcasing work of students to take part in the programmes.
by Alliance alumni. So how are make massively valuable contributions; on what actions institutions can take ‘they were the living, breathing examples emerging scholars and alumni who act In post-programme surveys, up to 75%
they tipping the scales and, in
fresh perspectives and diverse to break down barriers preventing of who I wanted to become’. as role models for the undergraduates. of participants consistently say that the
Executive Director Dr Medeva
experiences are a positive force for students from underrepresented groups The Leadership Alliance’s most recent summer programme has strengthened
Ghee’s words, populating a
research and necessary for tackling from realising their potential. Critically, The Leadership Alliance has developed project is the SYnergistic Network to their ‘commitment to pursue a research
‘workforce reflective of the
challenging problems. Indeed, the United it is necessary to overturn stereotypes a number of programmes designed to Enhance Research that Grows Innovation career’, suggesting that the activities
diverse fabric of our society’?
States needs a competitive research and prejudices, provide continuous bring together and motivate students. (SYNERGI). This multi-institutional network
workforce that explicitly understands the social support and to address identity The Summer Research Early Identification aims to extend the Alliance’s programme
development. It is through these Program (SR-EIP), established in 1993, throughout the academic year, hosting
David Stout, PhD, AAAS Science processes that organisations like The brings undergraduate students from all regional conferences to advise faculty
and Technology Policy Fellow. Leadership Alliance have been promoting (not just science) subject fields together and teachers, workshops for students
inclusion and diversity in the STEM for intense research experiences at some to prepare for academic and research
disciplines as well as the humanities of the United States’ top institutions; 50% development, and making online and
and social sciences for over 25 years. of these students have never participated in-person mentoring available at all times,
in a summer research event before. with an especial focus on professional
FORWARD TOGETHER Believing that the future of research relies development for graduate students.
The Leadership Alliance is a national upon connecting with young scholars as
consortium of more than 35 institutions early as possible, the Alliance launched Perhaps the most significant part of the
(including prominent Minority Serving the First Year Research Experience (FYRE) whole programme process is the fact that
Institutions (MSIs), PhD granting programme for first year students from alumni become part of the mentorship
institutions and private industry) headed Alliance MSIs. To increase opportunities cycle, consolidating the pathway for new
by Executive Director Dr Medeva Ghee, for students in the humanities and social students. Undergraduates are advised
who maintains that the solution to sciences, the Leadership Alliance started by graduates, graduates are mentored
underrepresentation is not fundamentally the Leadership Alliance Mellon Initiative by doctoral candidates who become
a difficult one: talent should be promoted in 2009. In 1995, the first Leadership role models for the entire student body
for talent’s sake. What is needed is Alliance National Symposium (LANS) and who are supported themselves by
persistence and presence throughout was held, bringing SR-EIP participants, the Alliance’s professional and academic
a young person’s career, with support Doctoral Scholars (SR-EIP alumni who guides. The Leadership Alliance works Student Chloe Edmonds in the library.
provided at critical transition points along have obtained a PhD or MD-PhD degree), by the African proverb, ‘If you want to go
34 www.researchoutreach.org www.researchoutreach.org 35
Behind the Bench
Dr Medeva Ghee
The solution to misrepresentation is E: TheLeadershipAlliance@Brown.edu T: +1 401 863 1474 W: www.theleadershipalliance.org
Q&A
Members of the Leadership Alliance include thirty-five of the nation’s leading research
and teaching academic institutions and one associate member from industry: among faculty and administrators Alliance as a model for diversity on the
from diverse institutional types that global stage.
• Brooklyn College • Princeton University Academia and research institutions inform discussions on institutional
• Brown University • Spelman College have a reputation for being transformation. These collaborative The Leadership Alliance has clearly
• Chaminade University of Honolulu • Stanford University traditional and stuck in their ways. efforts speak to the power of the helped so many individuals, but is
• Claflin University • Tougaloo College With regards to underrepresented partnership. there a particular ‘success story’ you
• Columbia University • Tufts University groups do you think attitudes are would like to briefly mention?
• Cornell University • University of Chicago changing/have changed? The Leadership Alliance has just I recently attended a job talk of
• Dartmouth College • University of Colorado Boulder Attitudes are changing. Over the years, celebrated its 25th birthday; where a Leadership Alliance alumnus,
• Dillard University • University of Maryland, Baltimore County we have developed and sustained would you like to see the organisation who participated in the summer
• Harvard University • University of Miami strategic partnerships between at its 50th birthday? programme in 1999, interviewing
• Heritage University • University of Pennsylvania Minority-Serving Institutions and I would like to see the Leadership Alliance for a faculty position at an Alliance
• Howard University • University of Puerto Rico PhD granting institutions that have reach its goal of achieving equity and institution. As I sat in the lecture, I was
• Hunter College • University of South Florida contributed to this change. This has equality in academia and the broader beaming with pride as I considered
• Johns Hopkins University • University of Virginia resulted in a heightened awareness research workforce, that is to say, the how the Alliance community cultivated
• Montana State University • Vanderbilt University of institutional cultures and values workforce is truly representative of the and nurtured his talent throughout
• Morehouse College • Washington University in St. Louis that have provided opportunities national population of underrepresented the years to produce a scholar who
• Morgan State University • Xavier University of Louisiana for students from underrepresented groups. There is also the capacity for the is transforming the academy by
• New York University • Yale University groups to be exposed to competitive Alliance to expand its partnership and way of his scholarship and cultural
• North Carolina Agricultural • [Associate Member] Novartis Institutes training environments and have provide opportunities for students to background.
Kevin Trinh, undergraduate at Bowdoin College, and Technical State University for BioMedical Research
Earth Sciences lab. resulted in the sharing of best practices conduct research internationally. I see the
36 www.researchoutreach.org www.researchoutreach.org 37
Education & Training︱ Professor Michele Jacob
R
bioinformatics, electrophysiology and
esearch into synaptic functions Dye filled neurons after electrophysiological recording of their activity in the hypothalamus in acute animal behaviour methods, provided via
Research into the functions of synapses is crucial to understanding the mouse brain slices. Generated by Dominique Ameroso, in the lab of Maribel Rios.
mechanisms of highly prevalent brain disorders such as epilepsy, autism and is key to understanding many state-of-the-art core facilities and PhD-
Alzheimer’s disease. Professor Michele Jacob is the director of the Synapse neurological diseases including Founded by Professor Kathleen Dunlap, level managers in the NINDS-funded
Neurobiology Training Program (SNTP), located at Tufts Sackler School Alzheimer’s, Parkinson’s, ALS, autism- Mechanisms that alter synaptic activity SNTP is now in its nineth year of training Center for Neuroscience Research at
of Graduate Biomedical Sciences in Boston. SNTP provides predoctoral spectrum disorders, depression, anxiety, affect our behaviours, learning and students. The program is now under the Tufts. SNTP training emphasises critical
students with individualised, in-depth, multidisciplinary research training epilepsy and insomnias. Synapses are memory formation. Many disorders of directorship of Professor Michele Jacob, thinking and multidisciplinary approaches
to investigate critical areas of synaptic function associated with disease specialised contact sites between single the nervous system involve fundamental an expert in synapse neurobiology. for effective and influential research.
and behaviour. Alumni of SNTP have gone on to receive recognition for nerve cells and their target cells that alterations in synaptic function, and Her research has focused on defining
both their research discoveries and their impressive contribution to various function in rapid information processing. hundreds of mutations in synaptic molecular mechanisms that direct the STUDENT RESEARCH AREAS
public engagement initiatives. They form the basis of our central proteins have been implicated in proper maturation and function of Since 2009, the SNTP has helped
nervous system’s functions. human diseases augment the
such as epilepsy,
autism and cognitive
Students graduate with the neuroscience
community by
impairments. multi-faceted research skills necessary generating a cohort
38 www.researchoutreach.org www.researchoutreach.org 39
director Dr Michele Jacob. The research
involved identifying novel molecular
Behind the Bench
changes that lead to autistic behaviours,
learning disabilities and chronic seizures,
and resulted in publications in Nature’s
Professor Michele Jacob
Molecular Psychiatry, a chapter in E: Michele.Jacob@tufts.edu T: +1 617 636 2429 W: http://sackler.tufts.edu/Faculty-and-Research/
Faculty-Profiles/Michele-Jacob-Profile W: http://sackler.tufts.edu/Academics/Neuroscience-Welcome
Springer’s Encyclopaedia of Signalling
Molecules 2nd Edition, and Elsevier’s Measuring the levels of D-serine in the hippocampus in vivo by microdialysis and HPLC, the levels
Neurobiology of Disease Journal. correlate with wakefulness and activity of the mouse. Generated by Michaela Tolman, in the lab of Phil
Haydon.
Sackler School of Graduate Biomedical University School of Medicine and the identifying the synaptic alterations that
Elizabeth Hanson, PhD worked on Sciences University of California, San Diego. She impair brain function and behaviour.
a study of glial cell modulation of Dept. of Neuroscience headed a research lab at the Worcester
excitatory synaptic activity in the Tufts University Foundation for Biomedical Research, Research Objectives
normal developing cortex, compared 136 Harrison Avenue and, in 1997, joined Tufts University The goals of the SNTP are to produce
to a cortex associated with epilepsy Boston, MA 02111 USA Sackler Biomedical Graduate School, graduates who are exceptional
caused by a traumatic brain injury. where she is currently Professor of research scientists addressing critical
Bio Neuroscience. neurological problems of consequence
Guided by Dr Chris Dulla, Hanson’s
The director of the Synapse to human health.
work has been published in Wiley’s
Neurobiology Training Program (SNTP), Collaborators
Glia Journal, Elsevier’s Neurobiology of
Professor Michele Jacob, received The twenty SNTP faculty mentors Funding
Disease and the high impact Journal of
her PhD degree from Yale University are experts in multifaceted research • National Institutes of Health (NIH)
Neuroscience. Inhibitory interneurons fail to mature properly in the absence of proper activation and brain function is
permanently disrupted. Generated by Elizabeth Hanson, in the lab of Chris Dulla.
School of Medicine, and completed approaches for investigating synaptic • National Institute of Neurological
postdoctoral training at Columbia function in the healthy brain and in Diseases and Strokes (NINDS)
Michaela Tolman, currently working with
Dr Phil Haydon, is identifying how non-
Q&A
neuronal glial cells modulate synaptic or industry and maintain successful, attest to SNTP trainees’ intellectual
activity to regulate wakefulness, and SNTP students have undertaken an independent research programs. Dual curiosity, interactive attitude, sense
40 www.researchoutreach.org www.researchoutreach.org 41
C
Education & Training︱ Dr Kathleen Potempa
ases of non-communicable to the global population. In Thailand, non- collaboration for this current project
Expanding capacity
diseases (i.e., illnesses such as communicable diseases have become the with Thai collaborator Dr Benjaporn
diabetes or cancer – NCDs) are leading cause of morbidity and mortality. Rajataramya. The project aims to provide
growing worldwide, and are responsible Yet most NCDs are preventable or a five-year training program to enhance
for an increasing number of mortalities treatable, which strongly indicates a need the NCD research capabilities of Thai
of non-communicable
each year. This growth coincides with for improved healthcare and improved scientists including nurses and other
rapid globalisation and urbanisation in NCD training and research for healthcare health professionals. Additionally, the
developing countries, which have brought professionals, such as nurses. programme supports translation of NCD
about changes in lifestyles and eating Dr Kathleen Potempa’s research research into practice, enabling better
training in Thailand
Growth of NCDs is occurring globally, countries, HIV/AIDS is a significant
cause of mortality. However, the Thai
causing an increasing number of government was one of the first to
significantly advance their control of
mortalities every year this disease. In 2003, a collaboration
between Thai and American academic
institutions was formed to manage
Dr Kathleen Potempa is the expansion of HIV/AIDS into more
Professor at the School of populations as well as to provide the
Nursing in the University of opportunity to treat HIV more widely
Michigan, where she served because of a new government policy
as Dean from 2006 to 2016. A instituting a universal health plan. This
globally renowned leader in effort aimed to empower nurses within
nursing, education and science, the country’s health infrastructure,
she has a long academic career ultimately expanding the capacity of
focusing on cardiovascular the public health service to manage
fitness in physically impaired the rising number of cases of HIV/AIDS.
populations, nursing, leadership, This collaboration was successful – by
and community-based 2009 it had expanded the capability of
approaches to improving health. Thailand’s healthcare system to cope
She is currently collaborating with the challenges created by infectious
with Dr Benjaporn Rajataramya diseases, particularly HIV and AIDS. The
to improve the capability of
infrastructure created an opportunity
the Thai healthcare system in
to consider other projects that would
managing chronic diseases.
leverage this expanded capacity such as
the rising occurrence of NCDs.
RISING NCDs
In 2011, Thailand’s public health
landscape was shifting towards a
growing incidence of NCDs, with a
concomitant increase in mortality.
As with other developing countries,
this rise in NCDs was associated with
urbanisation and globalisation, which
promote a shift from traditional, high
activity/low calorie lifestyles towards
more western lifestyles, which are
associated with lower physical activity
and higher calorie intake. Along with this
shift comes increasing risk of developing
chronic diseases, such as heart disease,
cancer and diabetes, which are some of
the illnesses categorised as NCDs. Prior
to 2012, training for treating NCDs had
not been emphasised because of the
42 www.researchoutreach.org www.researchoutreach.org 43
primary focus on infectious diseases,
injuries and other more prevalent
causes of illness at that time. A study Behind the Bench
Dr Kathleen Potempa
by Dr Potempa and Thai collaborators,
however, found that nurses and other
health professionals were not confident
in their ability to care for those with E: potempa@med.umich.edu T: +1 734 615 0085 W: https://postdoctoratencd.wordpress.com/
cancer and heart disease, and less
than half of the nurses surveyed were
confident in their ability to treat more
University of Michigan School of Funding Bio
common NCDs like hypertension and Nursing National Institutes for Health, Fogarty Dr Kathleen Potempa, Professor
diabetes. The need for more information 426 North Ingalls International Center at the University of Michigan, is an
about how to prevent and treat NCDs in Ann Arbor internationally recognised leader in
Thailand was apparent. MI 48109-5482 Collaborators nursing, education, and science, as
USA • Dr Benjaporn Rajataramya, well as the integration of education,
For nurses and other health Praboromarajchanok Institute for practice, and research in clinical
Research Objectives Health Workforce Development, settings. Former positions include
professionals, the need to refocus their
Dr Kathleen Potempa’s research Thailand progressive leadership in health
research on NCDs was of increasing program has focused on fatigue, • Dr Philip Furspan, University of systems and in higher education. She is
importance to provide evidence-based exercise, and cardiovascular fitness Michigan School of Nursing a member of the National Academy of
guidance to clinicians and public health in physically impaired populations. • Dr Debra Barton, University of Medicine and the American Academy
policy makers in the new era of NCD She directs the Training Program for Michigan School of Nursing of Nursing.
prevalence. Because nurses and other Strengthening Non-Communicable • Dr Naruemol Singha-Dong,
health professionals with PhDs were Disease Research and Training Suranaree University of Technology,
Capacity in Thailand. Thailand
an important part of the research
workforce in Thailand, Dr Potempa and
Q&A
Dr Rajataramya embarked on this current to find mutually beneficial solutions developing countries continue their
programme to advance research training to prevention and treatment of NCDs development?
for expanded NCD research. through research. Our work will not only NCDs are clearly on the rise globally
What are the main challenges that benefit Thailand and the US, but the with parallel increases in urbanisation
NCD RESEARCH AND TRAINING you expect to face in your current growing number of countries who also and ageing populations. The global
To ameliorate the threat of NCDs, Dr work? are facing this global challenge. community will benefit from countries
Potempa and Dr Rajataramya’s work We are finishing year three of this working together to share knowledge
aims to improve the research training of five-year project and find that the To what extent do you feel that and effective practices as they are
nurses and other scientists by proposing enthusiasm for this work is strong. A urbanisation is a cause of increasing developed through research and
a five-year post-doctoral training big challenge has involved choosing cases of NCDs in developing innovation.
programme. The programme aims to our trainees from among the many countries?
provide two years of post-doctoral NCD highly capable applicants. Going While the changing patterns of work Do you think that projects similar to the
research training for ten PhDs, offer short forward we want to support those and lifestyle that urbanisation often one you are currently conducting could
term NCD training for 20 investigators, who complete the training to continue brings undoubtedly contribute to the be applied to healthcare systems in
and provide forums for researchers their research in Thailand. Finding rising prevalence of NCDs, the ageing other countries?
and administrators to discuss and financial support for research is always of populations also contributes. As The Fogarty International Center
identify ways to further NCD research a challenge. However, we prepare infectious disease prevalence and other of the National Institutes of Health
in Thailand, thus strengthening the our fellows to be highly competitive sources of acute disease decline people provides support to many countries
existing foundation for NCD research. in obtaining research grants both are living longer. A longer life leads to by addressing research and research
This project will increase the capacity of in Thailand and from international more exposure to conditions that give training capacity. We are grateful
the Thai health infrastructure to manage research support institutions. rise to NCDs – unhealthy diet, smoking, for their funding and support of this
the increasing burden of NCDs and lack of exercise, stress, etc., all acting on project. The US itself benefits from
promote efforts to reduce and prevent What prompted your interest in this genetic predispositions. Our research these activities as we learn a great
their growth, ultimately improving the
prevention and treatment of these
The global community will benefit from project?
The Thai people are forward thinking
is aimed at finding ways to prevent the
occurrence of disease or to help people
deal through these research efforts
that can be applied here at home.
diseases in the long-term. countries working together to share and committed to finding solutions to stay healthy even with chronic exposure Countries with similar issues may have
health care challenges through policy, to adverse health conditions. As well, novel solutions that can be shared
CONCLUSION knowledge and effective practices research and practice. As one of the we aim to find culturally appropriate and translated effectively to other
Growth of NCDs is occurring globally, first countries to effectively address interventions for treatment of NCDs cultures and circumstances. We think
causing an increasing number of calorie intake lifestyles. To address this, If you would like to find out more about infectious disease challenges such as which typically require life-long that our approach, building capacity
mortalities every year. This growth is improved training and research into the training programme please visit the HIV, malaria and others, we knew they management. for NCD research and training, with its
influenced by a shift in many developing NCDs needs to occur, which would allow website http://postdoctoratencd.umich. would be wonderful collaborators in associated translation of findings into
countries, associated with urbanisation countries to refocus their health systems edu/ addressing the rapid growth in NCDs. Do you expect that we will continue to health care practice, is essential for all
and westernisation, from high activity- and health policy on the prevention and We are committed to working together see a rise in the prevalence of NCDs as countries with rising NCD.
low calorie intake to low activity-high treatment of such diseases.
44 www.researchoutreach.org www.researchoutreach.org 45
Engineering & Technology ︱ Professor Phil Joseph
of quiet aerofoils
The aerodynamic force is heavily concentrate their prey inside a ‘net’ of turbulent flow. Their experiments proved
influenced by the ‘angle of attack’ – the bubbles which the fish cannot cross. The that a drastic noise reduction can be
angle between achieved by
the aerofoil and
the direction of
Replicating the scalloped design of combining the
two modifications.
flow of the fluid. humpback whale flippers on wind turbine An important
A
blades resulted in reduced drag, quieter
For example, finding of the
Constant exposure to noise is an increasing problem in developed ccording to health studies, loud think of an study is that
countries, with impacts not only on industry but also our health. Key culprits
often accused of creating noise include airports and wind farms. Professor
noise is not only responsible
for hearing loss but also causes
aeroplane moving
along a runway.
functioning, and increased efficiency the serration
can change the
Phil Joseph from University of Southampton is heading up a team of psychological and physical stress, and The angle of hydrodynamical
scientists focused on reducing noise pollution through the development can contribute to reduced workplace the aerofoil (the wings of the aircraft) in scalloped edges of their flippers allow and acoustical fields simultaneously.
of new aerofoil design. The team, from a consortium of four universities productivity. It is also the biggest work- relation to the direction of flow (in this them to make a more acute angle of turn Noise reduction by serration is found to
(Nottingham, Southampton, City (London) and Brunel) with industrial related problem affecting workers in case, the aircraft’s movement means the than would be possible with smooth be a collective effort underpinned by the
support from Airbus and Vestas, have achieved noticeable noise reductions the construction and manufacturing air is flowing parallel to the aircraft but in edges: it allows for an abrupt change of reduction of the turbulent energy of the
of about 10dB – far surpassing previous designs. sectors. Those who live near airports the opposite direction) is very important the position without the so-called stall. flow, as well as the acoustical destructive
and wind turbines frequently complain for lift off. The idea of serrated leading edges is interference across the edges.
of dizziness, headaches and sleep passing now from the test phase into
disturbance. The noise generated by As a side effect of the unsteady the production process: replicating SECRETS OF SHARK SKIN
wind farms or aeroplanes taking off and aerodynamic force acting on the this scalloped design on wind turbine Another promising technology that the
landing is emitted across a wide area aerofoil, noise is also produced. This blades resulted in reduced drag, quieter group is planning to work on involves
and is difficult to eliminate. One group noise increases when the unsteady functioning, and increased efficiency. using ‘riblets’ to reduce noise. Riblets
of scientists directed by Prof Phil Joseph force is acting on the wings or blades are longitudinal raised grooves on the
and including Dr Tze Pei Chong, Professor at large angles of attack. As a result of OWL-INSPIRED TURBINE BLADES surface which successfully reduce drag
Kwing-So Choi, Professor Alfredo Pinelli regions of turbulent air passing over Owls are well-known for their noiseless in pipework systems and wind turbines.
and Dr Mohammad Omidyeganeh, is the aerofoil leading and trailing edges, technique of hunting: they can silently Riblets have been used by America’s
focused on overcoming this problem. acoustic waves are created. Acoustic approach their prey without being Cup yachts and for swim suits to improve
They plan to introduce new designs waves can bend around obstacles and detected thanks to the unique serration speed in competition. Flight tests of
of aerofoils which are more efficient in spread out from small openings. The feature at the edges of their wings. riblets have been carried out using Airbus
reducing noise and can be applied in a creation of noise by rotating aerofoils is Modification of both leading-edge A320 to show reduction of drag by two
wide range of conditions, conserving their more complex than air passing over a and trailing-edge geometries using percent. The pattern used is similar to
performances. stationary aerofoil. The faster the blades serrations, as in the owl’s wings, can that present on shark skin, which is not
cut the air, the higher the frequency not only improve the aerodynamical smooth but covered with tooth-like
CAUSES OF NOISE of the noise generated
The precise mechanisms behind noise there. The trailing eddies Vortical flow around an aerofoil at high loading condition
generation on aerofoils are not wholly generate random noise,
understood, although it is known that the frequency of which
the dominant sound source is located on is higher at the tip of a
the aerofoil surface (the blade of a wind wind turbine for example,
turbine or an aeroplane’s wing). Aerofoils because it is moving
generally have a rounded leading edge faster.
(that hits the air first) and a sharp trailing
edge (from which the air flows off). When HUMPBACK WHALE
the leading edge of the aerofoil interacts AND WIND TURBINES
with a turbulent fluid flow (this can be a Nature has always been
liquid or a gas e.g., the atmosphere), an an inexhaustible source
aerodynamic force is produced. of ideas for technological
innovations. For the
Aerodynamic force is composed of drag team of scientists
and lift, both generated when an aerofoil aiming to reduce noise
(e.g., an aircraft’s wings) interacts with generated by aerofoils,
a fluid (e.g., the atmosphere). We can the observation of the
think about drag as friction between the humpback whale’s flipper
46 www.researchoutreach.org www.researchoutreach.org 47
Behind the Bench
Close-up of wing structure
of a barn owl
Curved
leading-edge
serration
Trailing
edge
fringes
Trailing edge
Professor Phillip Joseph Dr Tze Pei Chong Professor Kwing-So Choi Professor Alfredo Pinelli Dr Mohammad
Professor of Acoustics Senior Lecturer at Professor of Fluid Mechanics Professor of Fluid Simulation Omidyeganeh
at the Institute of Sound the Department of at the Department of at the School of Engineering Lecturer at the School
and Vibration Research, Mechanical, Aerospace Mechanical, Materials and and Mathematical Sciences, of Engineering and
University of Southampton and Civil Engineering, Manufacturing Engineering, City University London Mathematical Sciences,
Brunel University University of Nottingham City University London
Leading edge
Curved aeration E: kwing-so.choi@nottingham.ac.uk T: +44 0115 95 13792
W: www.southampton.ac.uk/engineering/research/centres/isvr.page W: www.nottingham.ac.uk/engineering/
Owl-inspired aerofoil with curved-serrated Simulation of a turbulent detached flow on a wing at high angle of attack. Colours highlight the Research Objectives Collaborators Contact
leading edge presence and strength of vortices in the flow.
The team’s work aims to reduce • Professor Ugo Piomelli (Queen’s Prof Kwing-So Choi
the noise generated by aerofoils University, Canada) Faculty of Engineering
scales called denticles. This skin with its
tiny V-shaped scales, decreases both
The noise generated by wind turbines through three separate technologies. • Dr Oksana Stalnov (Technion, Israel) University Park
The results have applications in the Nottingham
turbulence and drag. As a result, sharks or aeroplanes taking off and landing is aerospace and renewable energy Industrial partners NG7 2RD UK
can swim faster and more quietly.
emitted across a wide area and is difficult
sectors. • Vestas Technologies UK
• Airbus Group Limited
COMPUTER SIMULATIONS
The team’s research project to eliminate Funding
EPSRC
combines these three nature-inspired
technologies using computer terms, it determines whether fluid Currently, the group’s work is supported
Q&A
modelling with promising results. flow is laminar or turbulent. Low Re by an EPSRC grant. The main goal is to Are any of your technologies currently reduces noise (see owls), increases
They are developing and optimising characterises smooth and slow flow; integrate all of their findings in order to in use? the lift force (see hump-back whales)
these technologies to be available for high Re describes chaotic and unstable reduce noise in aircraft engines, aircraft No, not yet. and reduces skin-friction drag (see
a wider range of loading conditions fluid movement. wings, wind turbines and cooling fans. Can you describe how Large eddy sharks). We – humans are learning
and flow speeds. The increasing popularity of unmanned simulation works and why exactly What was the most surprising finding from them for industrial applications.
The crucial requirement for the air vehicles (drones) in a wide range of you are using this method? you made during your research?
The team run a computer simulation reduction of aerofoil noise is that flow fields (military operations, humanitarian In the majority of industrial and Although the history of aircraft and What are the next steps to further
of fluids to recreate turbulent flows along the boundary should remain in aid) also motivates increased research natural turbulent flows the size ratio associated aerofoil development is old, improve the designs that you have
appearing in oceans or the atmosphere. direct contact with the aerodynamic of aerofoils under large angles of attack between the smallest and the largest yet we were able to find a new shape proposed?
The simulations use Navier-Stokes surface. Using a simulation called Large and at reduced size. The team’s research vortices may become huge to an of aerofoil that is more efficient and To further improve the aerofoil
equations governing the motion of eddy numerical simulation, the team shows that for noise reduction, the best extent where it becomes impossible to reduces noise at the same time. designs, our next step is to test our
fluids: these are similar to Newton’s were able to demonstrate that aerofoils strategies involve the modification of computationally resolve all the eddies new aerofoils and blades on aircraft
second law but are applied to fluids with leading-edge undulations had the noise source – the turbine blades. embedded in the flow. To overcome What parts of your work do you find and gas turbines to see if they work
(gas or liquids). The computer calculates boundary layer-flows that remained Integrating three innovative leading- this problem a filter that separates the the most interesting and why? as well as in laboratories.
the solutions to these equations for a attached to the surface under higher edge profiles – double-wavelength, small eddies from the large ones is We find it very interesting that nature
specific set of conditions and allows angles of attack than in previous chopped-peak and slit-root serrations applied to the Navier-Stokes equations has developed the best aerofoil that
the team to predict the velocity and designs. During the past decade, they – simultaneously provides reduction leading to a new set of equations that
pressure of the fluid in a particular area. have demonstrated that leading-edge of noise and enhances the general model the motion of the large eddies
The parameter that determines undulations could increase the lift by aerodynamic performance. Thanks only. These equations incorporate a We were able to find a new shape
the computational cost for finding
a numerical solution of the Navier-
60 percent and reduce drag by the
same amount. They also showed that
to these discoveries, we are closer to
obtaining clean energy from quiet wind
model that mimics the drainage of
energy exerted by the filtered small- of aerofoil that is more efficient and
Stokes equation is Reynold’s number
(Re), describing the ratio of inertial
undulations can dramatically decrease
the produced noise with a reduction of
farms and reducing noise pollution
from airports.
scale motions from the resolved large
scales.
reduces noise at the same time
to viscous forces. In more simple about 10dB.
48 www.researchoutreach.org www.researchoutreach.org 49
Engineering & Technology ︱ Professor Elisa Bertino
R
ransomware encryption to recover
ansomware dominated the daily files is often nearly impossible but
news in May 2017, with the arrival Professor Bertino has another clever
of WannaCry. An unwelcome arrival trick. Rather than trying to break the
on personal and company computers encryption on affected files, she focuses
alike, the software took files hostage on prevention approaches that stop the
and demanded payment for users to be initial encryption process, rendering
able to get their files back. WannaCry the ransomware essentially useless.
is probably one of the most famous Her research group have already
examples of ransomware, malicious demonstrated this approach to be highly
software that makes the victim’s files successful in stopping ransomware
inaccessible through encryption. infections and these tools may be the
Encryption ‘locks’ the data, making it answer to avoiding a repeat of the
unreadable to anyone without a very WannaCry events.
specific ‘key’.
KEEPING SECRETS
What made WannaCry such an The encryption process is at the heart
exceptional attack was the sheer of how malicious software or ‘malware’,
number of infected computers (thought like ransomware, operates. Encryption
to be around 200,000) and also the is a way of hiding information so that
nature of some of the organisations anyone who wants to read the real
affected. Alarmingly, one high-profile information must possess a special kind
victim was the UK’s National Health of key.
Service hospital computer systems.
This affected not just the computers Reversing the encryption processes
relied upon for administrative tasks, but on a file, or ‘decrypting’ it, is not
those responsible for the analysis of test always a trivial or easy task. Encryption
50 www.researchoutreach.org www.researchoutreach.org 51
Behind the Bench
Professor Elisa Bertino
E: bertino@cs.purdue.edu T: +1 765 496 2399 W: www.cs.purdue.edu/people/bertino
Q&A
to undo any damage caused by particularly vulnerable? ransomware, e.g. malicious encryption.
trivial or easy task the malware and restore the files Organisations where timely access to To understand such differences, we
to operation. data is critical are certainly vulnerable. performed a user survey to better
comes in many flavours and strengths. computer’s filesystem. In conjunction Also the vulnerability of organisations assess whether users encrypt their files,
Some keys are kept entirely secret, with this, it looks for any anomalies in THE FUTURE FIGHT depends on their maturity status with and which files they encrypt.
so only the ‘sender’ and ‘receiver’ of the processes that read and write to the Professor Bertino and two of her PhD Do you think having ‘anti- respect to the adoption of security
the information have a copy. Others, filesystem, that are the signals for the students in the Computer Science ransomware’ software will become practices and tools, and the security How do you think ‘better user
counterintuitively, are publicly available encryption process to occur. This early Department at Purdue University, Anand as common as an antivirus? training of their staff. In this respect, behaviour’ can be encouraged to
and rely on the generation of a paired warning detection system allows the Mudgerikar and Shagufta Mehnaz, Today there is awareness that data hospitals are a perfect target for prevent some of the issues with
private, or secret, key for encryption. tool to spot an attack very early and halt are working to further develop this security is a key requirement. Therefore ransomware as critical care for patients malware?
The generation process relies on the encryption. approach. One strategy is to deploy tools for in-depth protection of data relies on timely access to up-to-date Better user behaviour is always critical
an algorithm that can be used to decoy files, that would be of no interest are being developed and deployed by information from patient records. for enhancing security. As with all
generate more simple or complex keys PREVENTION TACTICS to the user but equally likely to be industry in many different application Without real-time access to drug malware, it is important that users
depending on the security requirement. Professor Bertino is not the first to targeted by the ransomware, as another domains. A notable example of histories, surgery directives and other be aware of suspicious messages
attempt the search for warning signs to part of the early warning detection such tools is represented by data information, patient care can get delayed requiring for example the user to click
Breaking encryption could be done by stop ransomware. However, approaches system. Attempts to encrypt those leakage protection tools aimed at or halted, with serious consequences. In on certain websites or to download
interception of the keys or by trying to that either just look for file encryption files would be a strong indication of preventing data from being stolen addition, medical information systems and open an e-mail message
guess the correct key. A brute force events or anomalous process requests a ransomware attack as users would by skilful adversaries. Blocking and and networks are today very complex – attachment. Also installing an antivirus
approach, where a computer tries to tend to flag a large number of false not usually encrypt such files. She recovering ransomware attacks is thus making difficult their comprehensive and backing up files are good practices
guess all the possible combinations positives and are generally ineffective in and her students are also focusing today another relevant frontier for protection, and hospitals often to do that may drastically reduce the number
that could comprise the key, means halting real attacks. They can be fooled on ransomware attacks aimed at data cybersecurity. Good practices not have IT security staff. Therefore, it is of successful ransomware attacks.
that a correct guess on a reasonable by the ransomware encrypting files more different targets, such as IoT (Internet involve frequent backup of files – so not a surprise that many hospitals have
Professor Bertino’s
timescale is highly implausible. slowly or trigger when the user is trying of Things) devices. that files can be recovered in the been targeted by ransomware and have
Where things get even harder is that to encrypt their own files. event of a ransomware attack – and preferred to pay the ransom rather than
some malware can require a unique
decryption key for each infected The joint approach of Professor Bertino
Given the increasing volume of
sensitive data stored on systems and
anomaly detection tools, like the
ones we are developing. At present,
endanger patients’ health.
approach is
computer. has proved highly effective for 15
different types of ransomware attack.
networks that are connected to the
internet, it is likely that ransomware will
state-of-the-art, anti-ransomware
tools are still complex and are still
What is the most technically
challenging aspect of creating your
highly successful
This is why Professor Bertino’s When the early warning system triggers continue to seem a lucrative tactic for in an early research stage. However, prevention tool? in stopping
ransomware
approach is so successful. Her tool in the event of an attack, it can stop cybercriminals. However, with tools like once these tools are engineered for The most challenging aspect has been
essentially lies in wait for the signs of further encryption but, if some files are Professor Bertino’s, malware will need wide-scale deployment, they will be to identify the features that allow our
a malicious attack. This could be the
sudden encryption of a large number
already encrypted before the process
is blocked, the tool can record the
to become even more sophisticated
to be effective.
used by organisations with important
data assets.
tool to distinguish between encryption
performed by a user – and thus legitimate
infections
of files, resulting in a change to the parameters used for the process and,
52 www.researchoutreach.org www.researchoutreach.org 53
Engineering & Technology ︱ Professor Olfa Nasraoui
B
ig data is a generic term for any
54 www.researchoutreach.org www.researchoutreach.org 55
Behind the Bench
Prof Olfa Nasraoui’s
students at the
Knowledge Discovery
and Web Mining lab.
Rrom left to right:
Wenlong Sun, Mahsa
Badami, Gopi Nutakki.
Knowledge Discovery & Web Mining Computer Engineering and Computer Funding
Lab Science from the University of Missouri- • National Science Foundation
Dept. of Computer Engineering & Columbia in 1999. She has more than • Kentucky Science & Engineering
Computer Science 160 refereed publications, including Foundation
Speed School of Engineering over 40 journal papers and book
University of Louisville chapters and eight edited volumes. Collaborators
Louisville, Kentucky 40292 USA Students: Wenlong Sun
Research Objectives Former students: Behnoush Abdollahi ,
Bio Professor Nasraoui’s work focuses on Mahsa Badami, Gopi Nutakki
Olfa Nasraoui is a Professor of Big Data. She examines how Machine Colleague: Prof Patrick Shafto, Rutgers
Computer Engineering and Learning can lead to unreliable and University, who collaborated with
user and system. For recommendation, as deep learning networks and matrix
Computer Science, Endowed Chair biased models, problems around Professor Nasraoui on her work on filter
it is impossible to train the algorithm on factorisation. This means that the model
of e-commerce, and the founding explainability and whether increased bubbles.
stale benchmark datasets which is why cannot give explanations for why certain
director of the Knowledge Discovery personalisation contributes to
Professor Nasraoui and her students results are achieved. The results obtained and Web Mining Lab at the University polarisation of opinions.
Wenlong Sun and Mahsa Badami, along may be accurate, but it is not clear how of Louisville. She received her PhD in
with collaborator Prof Patrick Shafto, they were obtained so it is difficult to
have created cognitive models to try and probe their reliability.
benchmark such rating systems and also
what are called counter-polarising systems. Open, or ‘white box’ systems, are typically
Q&A
These break the positive feedback less accurate but the rules and decision Prof Nasraoui (centre) at the Doctoral hooding
loop between the user and system and trees which are utilised in the process ceremony with her former PhD students, Unfair predictions: Suppose that an Are white box algorithms more
Behnoush Abdollahi (left) and Gopi Nutakki
encourage the recommendation of items are interpretable. This offers several (right). algorithm learns a predictive model difficult to create than black box
that will be genuinely new to the user, advantages. It is possible to assess the for some risk scoring using data ones?
freeing them from their algorithmic chains validity of a prediction or, if there are issues with accuracy, but tries to remain Can you discuss an example of about people that includes certain White box models are easier to create.
and feedback loops. errors, understand why these prediction more explainable in its decisions and biased machine learning results demographic attributes. If the data itself However they tend to be less powerful
errors occurred. Professor Nasraoui and results than alternative black box causing poor decisions? hides some systemic societal biases, then than black box models in making
OPENING THE BOX her former doctoral student Behnoush methods. I can think of two cases: the predictive model will simply learn accurate predictions. This is one reason
All of these factors are why Professor Abdollahi have been developing such Filter bubbles: Suppose that an and echo those biases. One example is why black box models are popular.
Nasraoui feels there is a pressing need for a system for recommendations that CAREFUL DECISIONS algorithm learns that you like a certain a model to predict which individuals are
transparency in machine learning models. continues to proactively learn to make Professor Nasraoui’s work as part of the category of news simply because you likely to be indicted for consuming illegal Given the importance of machine
Many models are ‘black boxes’, such explainable predictions, overcoming Knowledge Discovery and Web Mining happened to have clicked on a few drugs when people from certain ethnic learning algorithms, will there be
Lab has far-reaching implications in the popular items at some initial point, and backgrounds tend to be suspected, standards and legislation around
Transparency Fairness
fields of big data and machine learning. then all news starts getting filtered screened, arrested, and prosecuted at a using ‘fair’ algorithms?
The issue of bias in data, either through through this narrow lens built by the higher rate. This has already started: the European
sampling or issues with feedback loops model. If all the news you see happens Union recently passed a law requiring
in the algorithm, means that the results to be visible to you because it passed Do users notice when extensive that algorithmic predictions that have
Data ML Model Prediction
of any machine learning approach should through the algorithmic filter, and you content filtering is occurring with an impact on humans must provide an
be carefully considered and Professor therefore do not click on any alternative feedback loops? explanation for the reasoning behind
Nasraoui has been developing tool and views, the algorithm will perceive your Most users are not aware that advanced the prediction. The city of New York is
algorithms to do that. She is also working limitation in discovery as a narrow algorithms act like gateways between also considering a bill that will assign
on alternative approaches to black box interest and will keep reinforcing them and the information they could a task force to monitor the fairness of
Explainability methods that may help users make fully its filter, hiding even more diverse potentially discover. Often users are predictive algorithms that influence
Module informed decisions about the data they options from your recommended missing out on information that could be decisions concerning people to try to
are using, something that is becoming items. discovered without even realising it. This prevent biased and unfair algorithms
increasing critical with the growing is the biggest danger to discovery. that discriminate.
reliance on the results of these types of
Explainability plays a critical role in transparency. The latter is a pillar of fairness in machine learning models. analysis.
56 www.researchoutreach.org www.researchoutreach.org 57
Engineering & Technology ︱ Dr Liz Jenkinson
Fossilising
in Manchester back in 1912. This
discovered a method that could use
bacterial fermentation (the conversion
of sugar into products) to produce
acetone, n-Butanol, and ethanol from
fossil fuels
carbohydrates such as starch and
glucose. Over a hundred years later,
Green Biologics have taken this concept
many steps further. Their research
with green
follows the same principle of bacterial
fermentation, using a bacterium called
Clostridium as a biocatalyst to create
n-Butanol and acetone but Green
alternatives
Biologics have improved both the
bacterium and the process to produce
cost-effective, higher-quality chemicals
when compared to the fossil-derived
versions. These chemicals can then
be used directly or reacted to make
Green Biologics are a renewable chemicals company who are not only derivatives, before being used in
changing the face of renewable chemicals, but are changing the world products such as paints, fragrances,
while they are at it. Dr Liz Jenkinson is one of the lead researchers at the cosmetics, lubricants and even as
company, and it is her work that is providing the answer to the question: ingredients for food.
is there an alternative to fossil fuels? Her work proves that the answer is
yes, and that it only relies on three key components – bacteria, genetic JUST A SPOONFUL OF SUGAR…
engineering and sugar. The whole process, in effect, revolves
around breaking down sugar, and
W
converting it into n-Butanol and
ith the unprecedented threat This is where Green Biologics and the acetone via bacterial fermentation
of climate change making excellent work of a dedicated team of using Clostridia microbial strains. The
the planet’s temperature molecular microbiologists, analytical simpler and more accessible the sugars,
warmer year on year, there is a growing chemists and fermentation scientists the more efficient this process is. For
need for greener, environmentally-friendly comes in. The Oxford-based institution example Clostridia will quite happily
alternative products. It has been well and its US-based subsidiary have ferment glucose which is a C6 sugar or
documented over the years that fossil recently opened the first renewable ABE xylose which is a C5 sugar. However,
fuels are in limited supply and yet, they manufacturing plant in the USA since the the feedstocks used for a commercial
are the source used to power the world. second World War, to convert the sugar fermentation process are rarely simple
They run our cars, heat our homes, and from corn into the products acetone and and without this, the Clostridia microbial
are even used to produce a variety of n-Butanol along with by-products of corn strain is unable to ferment correctly
products such as medicines, cosmetics, oil and animal feed. These chemicals to produce the required products
plastics and lubricants. If you brushed and their modified derivatives can then quickly enough and at high enough
your teeth this morning, or if you have be used in a wide range of everyday concentrations.
ever played tennis, the toothpaste and products directly replacing the same
balls you used were probably produced chemicals that are currently made from ...HELPS THE CLOSTRIDIA
using fossil fuels. fossil fuels. FERMENT…
The team at Green Biologics have
So, the question is: if we are to reduce FROM MANCHESTER TO OXFORD overcome this issue through a
our dependency on fossil fuels, how are GBL’s research follows on from the combination of advanced engineering
we going to continue our modern way original acetone–butanol–ethanol and strain improvement methods. Using
of living? (ABE) fermentation work carried out methods such as adaptive lab evolution,
they have developed improved
Green Biologics’s research follows on clostridial strains to use in the process
58 www.researchoutreach.org www.researchoutreach.org 59
…IN THE MOST DELIGHTFUL WAY
This plant – known as Central Minnesota
Renewables – currently uses the ABE
fermentation process with Clostridia to
butanol and acetone produced during
ABE fermentation.
CLEAVING CLOSTRIDIA
Behind the Bench
ferment sugars found in corn. However,
it is hoped that future research and
The ability to edit genomes and utilise
synthetic biology within Clostridia The Dr Liz Jenkinson
technological developments will move enables new biological pathways to Biomass E: liz.jenkinson@greenbiologics.com T: +44 (0)1235 435710 W: www.greenbiologics.com @GreenBioLtd
the process towards using sugars be added or removed. This, in turn,
route to the
found in lignocellulosic feedstocks (i.e., generates different products that can
corn stover, bagasse, woody biomass). be utilised across different industries.
consumer
Currently, the C5 and C6 sugars In one example of Dr Jenkinson’s work, Office: 80F Park Drive, Milton Park head of the strain development team at customers with more sustainable,
Abingdon, Oxford Green Biologics, utilising her expertise green alternatives for everyday
contained within these feedstocks are a novel pathway was added to the products such as paints, cosmetics and
OX14 4RY in molecular biology to develop
inaccessible to Clostridia and are unable fermentation process using CLEAVETM UK key tools capable of manipulating food ingredients.
to be broken down directly. Future technology to produce a chemical Clostridia microbial strains. She is
research will therefore look to establish particularly valuable within the food Lab: 45A Western Avenue, Milton Park also in charge of several Innovate Funding
hydrolysis pre-treatments that will allow industry. In another example, CLEAVETM Biomass Abingdon, Oxford UK funded grant projects, primarily Green Biologics has benefitted from
the sugars to be accessed and converted. was used to alter the ratio of butanol OX14 4RU focused on synthetic biology. private and public funding including
UK investors Swire Pacific, Sofinnova,
and acetone produced during the ABE
Research Objectives Capricorn Ventures, Morningside
This is just one of Green Biologics’s fermentation process, depending on Bio Dr Jenkinson’s research focuses on and Oxford Capital partners, and UK,
current research focuses, progressing the quantity required and the value Dr Jenkinson received a Bachelor’s using microbial engineering and European and American agencies
in conjunction with Dr Jenkinson’s of each product. Not only that, but by
C5 and C6 degree in Molecular Genetics in
Biotechnology at Sussex University
synthetic biology techniques to
utilise Clostridia microbial strains
including Innovate UK, Horizon2020,
ERANET, and US Department of
sugars
ground-breaking work using CLEAVE™ optimising and inserting new enzymatic
technology. This technology is a different genes into the Clostridia, the microbes before undertaking a PhD in Biology as biocatalysts. She and her team Energy
way of applying CRISPR gene-editing can be modified to break down more at York University. She is currently the at Green Biologics aim to provide
technology, designed to make highly complex carbohydrates, which supports
Q&A
specific changes in the clostridial DNA and ties into Green Biologic’s other area
(for example deleting a specific region of research – accessing sugars contained Bio-based biofuel is related to cost. Butanol can be the advances made with fermentation
of a gene or making a single base pair within lignocellulosic feedstocks.
n-butanol What made you decide to get
used instead of petrol and the founder of technology development mean we
& acetone
change). It can also be used to integrate Butylfuel, Dave Ramey, has shown this by can be competitive again, especially
specific genes into Clostridia microbial A SWEET FUTURE involved with Green Biologics? driving a Buick across the US powered by in the high-value market sectors.
strains. These genes can be pinpointed, Although the research undertaken by When I joined, the company was 100% n-butanol (http://www.butyldude. Synthetic biology has great potential
edited and developed to incorporate the Dr Jenkinson and her team is yet to be still working in many different areas, com/the-2005-trip.html). At the moment, for engineering organisms to make
including research contracts, before our production costs cannot compete products that we need, but if we can
new functionalities required. published, the emergence of CLEAVETM
focusing on Clostridia and chemical with petrol, primarily due to the cost work with nature to give us a head
technology as a potential, scientifically- Bio-based production. For me the interest was of feedstocks. In an ideal process our start, as we have with Clostridia, then
In other words, CLEAVETM technology proven, alternative method to fossil fuels
esters and in the science – we were working feedstock costs would be minimal, using we are more likely to be successful.
derivatives
has provided Dr Jenkinson and her team is ground breaking work, and is likely with bacteria that are not standard waste that would otherwise be burnt or
with a breakthrough technology capable to change the world as we know it. The lab strains therefore we had lots of left to breakdown naturally. However With the recent purchase of a
of expanding and diversifying their ability to develop a diverse range of challenges to overcome and that was right now, the sugars contained in these manufacturing plant in America, will
what drew me in. lignocellulosic feedstocks are generally Green Biologics continue to expand
product range. Using this innovation, products using Green Biologics’ methods
inaccessible to our strains and the in the future?
clostridial microbes can be effectively will not only help the environment, but it Why is finding green alternatives pre-treatment processes are either not That is the idea. Our first commercial
converted into small chemical factories will also provide a platform Formulated to products typically derived from efficient or economic to use at scale. As plant at Little Falls, Minnesota
which, with the application of genomic
editing and synthetic biology techniques,
on which further beneficial
research can take place.
products fossil fuels so important to you?
There is a need to find alternative
these technologies mature, the costs of
production will come down and in the
began production in 2016. We are
currently producing butanol and
can develop more products than the ways of making these chemicals. Using future it is feasible that bio-butanol could acetone and selling them to chemical
microbial fermentation is one way to be used as a fuel to power our cars. companies and directly blended into
do this whereby we can take waste consumer products. Our first product,
The emergence of CLEAVETM Consumers and convert it into something useful.
Ultimately these processes can be both
Why did you choose to use Clostridium
as the bacterium in the fermentation
Greenflame™ charcoal lighter fluid
is now available in stores in the US
technology as a potential, renewable and sustainable, they can
reduce greenhouse gas emissions,
process?
Solventogenic Clostridia have previously
(www.greenflame.com). Over the next
12–18 months, production of acetone
scientifically-proven, and they can provide some security
regarding supply chains.
been used as industrial microbes for the
production of ABE; therefore, we know
and butanol will be ramped up and
in the meantime we are looking for
alternative method to How likely is it that your technology
they are robust enough to be scaled up.
The process itself, however, fell out of
potential new plants in the US or
Europe. Ultimately, we will introduce
fossil fuels is ground- could replace fossil fuels as a power
source (rather than as a source of
favour when it could no longer compete
economically with petrochemical-derived
new products developed through
CLEAVETM to develop biorefineries
breaking work, and is chemicals to use in products) in the
future?
products. In the last 15–20 years our
understanding of these microbes, the
making a range of renewable
chemicals.
likely to change the world Right now the challenge with using
the bio-butanol from our process as a
advances made in genomics and in
genetic manipulation technologies and
as we know it
60 www.researchoutreach.org www.researchoutreach.org 61
Thought Leader
T
he European Society for useful suggestions and help implement student meetings every two years. In
Evolutionary Biology (ESEB) has all our decisions. addition to this, we provide special topic
approximately 1,400 members networks if people want to develop a
mainly from across Europe. From How has ESEB evolved over the years new topic and so, they have a meeting
students to professors, members of the since its inception back in 1987, and to do that which we will also sponsor.
society share a passion for evolutionary what are the society’s current main
biology. Since it began 30 years ago, strategic focuses? Do you think research for evolutionary
the society has shaped the direction There has been a large increase both biology receives as much funding and
of research into evolution throughout in our membership and our finances. attention as it should?
Europe. It has helped researchers We receive more money now, which I’d say it depends on which countries. In
by providing a networking platform, has allowed us to develop quite a some countries, there are good funding
conferences and funding and introduced few different products. For example, opportunities like here in Switzerland,
two academic journals. At the forefront ESEB is financing outreach projects for for instance. However, there are many
of the ESEB is Professor Laurent Keller a more than five years. This has turned countries in the world that tend to
Swiss evolutionary biologist. out to be one of our most successful fund more applied research. In these
and popular initiatives, through which countries, it’s more difficult to get
Research Outreach spoke to Prof Keller members are proposing highly creative money to conduct evolution-based
about all things evolution, from what concepts to bring the topic of evolution research than in other countries.
it is like to be president of the society to the general public.
to where the future of evolutionary The ESEB produces the wonderful
biology is heading. He discusses why A more recent and related activity is Journal of Evolutionary Biology. What
evolution should play a part in medical called the Global Training Initiative. difference does it make in terms of What do you make of the open perfect. However, the worst case can be Award in which you have a large say in
research, and the countries that are This is slightly different. It is designed spreading ideas and data? access movement? journals which are not open access but whom the award goes to. How difficult
leading the way in evolutionary biology. more for scientists, but for countries The original aim of this journal was to That is a difficult issue but a very allow authors to pay to have their articles is it making that decision?
where there is little research on aid the development of evolutionary important one. Editors and publishers open access. Although they claim the The Presidents’ Award is a new award,
Hi Laurent! Could you please describe evolution or a bad perception of biology research in Europe as this was of scientific journals make a lot of contrary, I believe those journals get paid so there’s only been one person who has
for us your role as President within evolution. We try to help scientists more underdeveloped in comparison profit. I truly believe in the concept twice (by libraries which subscribe to the received it. We have our next meeting in
the European Society for Evolutionary in these countries to meet and to the US. While evolutionary biology of open access and the movement journal and by authors who want to make the summer of 2018 in Montpelier where
Biology? communicate together. This will research was prevalent in some itself. Although, at some point, people their article open access). In my opinion, myself, the previous president and the
The society has an executive typically be in countries where the countries in Europe, like the UK, it was must pay to publish and you have two it should be either those publishing or president-elect must select a researcher
committee, which consists of a topic of evolution and its research is very limited or non-existent in other options. The first option is where the those reading who pay – not both. for the award.
president, a vice president, a secretary, limited, like in Turkey. countries. I think the journal and the researcher will pay to publish or the
and so forth. This executive committee society have been very useful and second option being that the readers ESEB offers several award initiatives We also have the Maynard Smith’s
is key to the central decisions of the We provide the opportunity to develop successful in further developing the pay an article access or subscription fee. to show recognition for evolutionary Award, which is given to young
society. As president, I try to make different meetings and we also sponsor field of evolutionary research in Europe. I think neither of these two options are biologists, including the Presidents’ researchers, and this has been quite
62 www.researchoutreach.org www.researchoutreach.org 63
Thought Leader
64 www.researchoutreach.org www.researchoutreach.org 65
Biology ︱ Dr Mauricio Rodriguez-Lanetty
Development of
is expected that they will encounter
the same pathogens at several points
during their lives. Therefore, it is
believed that, through repeated low-
level exposure, corals may build up
a resistance against disease-causing
immunity in basal
pathogens. However, this area of
science is highly under-researched.
ANEMONES AS MODELS
To further our understanding of disease
metazoans
resistance in corals, Dr Rodriguez-
Lanetty studies the immune response
of anemones as a model system.
Anemones are easier to cultivate
in laboratories, where they also
have symbiotic algae and undergo
bleaching, making them suitable
replacements for coral species in
research.
C
The brown anemone, called Exaiptasia
Dr Mauricio Rodriguez- oral reefs are one of the most cause. Dr Mauricio Rodriguez-Lanetty pallida, is used in the “CAREER:
Lanetty from Florida important ecosystems on the is currently leading a programme Exploring the Immunological Priming
International University (FIU), is planet as they support a wide and to research immunological priming in a Basal Metazoan (Anthozoan)”
currently conducting research diverse array of organisms and human in anthozoans and determine if programme. This species is found in
that focuses on immunological activities. Unfortunately, however, they are these animals can be inoculated the western Atlantic Ocean, sharing
priming in corals and anemones, also one of the most vulnerable. against disease. His programme the same waters as Caribbean reefs.
a process by which an animal will also provide educational and It is likely to encounter the same
can resist pathogens through Corals are categorised as anthozoans, research experiences to high school, pathogens as corals in this area, making
repeated, non-lethal exposure. a class shared by anemones, and are undergraduate, and postgraduate it susceptible to certain diseases
As corals are at risk due to made up of small, colonial animals students to inspire the next generation that allow it to be used in place of In his initial research proposal for the immune responses such as this are not
climate change, this is an which come together to create reefs. As of scientists. corals in this research. By studying CAREER programme, Dr Rodriguez- limited to complex vertebrates. As a
important project to help further coral tissues contain symbiotic algae, immunological priming in brown Lanetty hypothesised that sub-lethal result, this has opened many doors for
our understanding of their they can only live within a “goldilocks CORAL DISEASE anemones, our understanding of the exposure to a pathogen could result further research into the immunological
immunology. The project also zone”, where the waters are suitably Not only are corals very visually processes behind immunological in anthozoans establishing a defensive processes of anthozoans.
includes an outreach programme warm and where the algae receive appealing, attracting thousands defence in anthozoans, and the response that they will be able to
to motivate minority students to
enough light to photosynthesise and of tourists every year, they provide evolution of immunity in basal express more effectively when they Differences in proteins between
pursue science as a career.
support their coralline hosts. Climate numerous services to local populations. metazoans (species that diverged early encounter the pathogen again in the unexposed and exposed anemones
change has reduced the size of the They act as nurseries for fish, support on in evolution and have remained future. were also identified, suggesting that
area habitable by corals due to ocean fisheries, and protect coastlines from relatively unchanged since) will expand. this defensive mechanism is controlled
warming, and has caused further issues facing the full force of storms. They To determine if this is the case, brown at a molecular level. The identified
that include ocean acidification and an are also home to thousands of animals IMMUNOLOGICAL PRIMING anemones were repeatedly exposed proteins were similar to genes
increased prevalence of coral diseases. and are areas of high biodiversity. As Immunological priming is a process to Vibrio coralliilyticus – a bacterial associated with immune responses
As such, swathes of reef are being lost such, it is vital that we find ways to by which the immune response of an species known to cause morbidity and in other organisms. One in particular
organism is strengthened by repeated bleaching in both corals and anemones. was similar to inotropic glutamate
Research suggests that immunological exposure to a pathogen. This is
common in more advanced species,
It was found that three days of exposure
to the bacterium could be considered
receptors (iGluR), which are associated
with neurotransmissions in animals with
priming could have developed much such as humans and other vertebrates, “sub-lethal”, and anemones exposed a nervous system, and are common
66 www.researchoutreach.org www.researchoutreach.org 67
Behind the Bench
Binding of peptides HSP Dr Mauricio Rodriguez-Lanetty
to HSPs
3
E: rodriguezlanetty@gmail.com; rodmauri@fiu.edu T: +1 337 254 7136 W: http://imageslab.fiu.edu
W: http://biology.fiu.edu/portfolio/mauricio-rodriguez-lanetty/
TLR Increased expression
of pro-inflammatory
1
HSP mediators Research Objectives Collaborators in Marine Studies from the University of
2 Dr Rodriguez-Lanetty’s research The work and experiments of cnidarian Queensland (Australia) and is now the
programme will elucidate the specificity, immunology is being conducted in Principal Investigator of the IMAGES lab at
memory and molecular basis of the collaborations with Biologists from Florida FIU.
defence response of corals upon repetitive International University. Graduate students:
Complement
encounters with pathogens. Understanding Tanya Brown and Ellen Dow. Postdoctoral Contact
system
4 how the immune system of these organisms
responds to pathogens may offer insights
Fellow: Dr Anthony Bellantuono. Dr Mauricio Rodriguez-Lanetty
Associate Professor and Director
into the resilience of these ecosystems, and Bio QBIC Programme (Quantifying Biology in
6 Transcription factors potentially may inform remediation of them. Dr Mauricio Rodriguez-Lanetty is an the Classroom)
NF KappaB Associate Professor at Florida International Department of Biological Sciences
Funding University (FIU, Miami). After obtaining a Florida International University
National Science Foundation (NSF) bachelor degree in Biology in Venezuela, 11200 SW 8th St; Miami, FL 33199
Pathogen taken up HSP 7 Dr Rodriguez-Lanetty achieved a PhD USA
by Phagocytosis
Lyosome TLR
8
Capthesin
Q&A in need. Over the last ten years, several
of us in the field of coral biology have
proposed and are actively working using
of sea anemones display some degree of
acquired immunity with a mechanism yet
to be fully understood. Also, anemones
What first sparked your interest in the sea anemone Exaiptasia pallida, as and humans share many components of
5 corals?
Coral reefs encompass one if not the most
a model organism to study corals. The
important features considered in this
first line of defence, the innate immune
system, composed of conserved Pathogen
? productive and diverse ecosystems within selection were attributed to the fact that Recognition Receptors (PRRs) that sense
the marine realms, housing hundreds these anemones engage symbiotically and distinguish large groups of Pathogen-
of thousands of species from single-cell with similar microorganisms as corals do Associated Molecular Patterns (PAMPs)
DAMP iGluR microorganisms to spectacular colourful and therefore, make them good proxies found on many infectious microbial
fish vertebrates. What is incredible, is that to study coral biology and ecology. pathogens.
a symbiotic association between reef- Furthermore, these anemones are fast
building coral hosts and photosynthetic growers and easy to culture in captivity Is there much crossover between the
microalgae living inside the corals and in laboratory conditions. A great pathogens encountered by anemones
powers the foundation of such ecological advantage of this system is that clonal and corals?
Based on these findings, future research Proposed model of Heat Shock Proteins (HSP), Capthesin and Glutamate Receptor (iGluR) roles in success. The mysteriously intricate cellular populations of anemones can be raised We do not know yet the degree in which
cnidarian molecular defense priming: (1) HSP are up regulated and some are extracellularly secreted communication of these mutualistic from a dozen of individuals to a population natural populations of sea anemones are
will assess whether host responses to where bind to peptides and act as DAMPs; (2) as DAMPs, HSP help with a faster activation of the innate associations in which both host and of hundreds in a matter of a months in the affected by the same pathogens causing
repeated infectious agent exposure are complement system, and/or (3) interact and cause a quicker activation of outer host cell membrane
symbionts benefit from each other, caught lab. All these features make the anemones infections on corals, and this type of
pathogen-specific, and how symbiotic TLRs; (4) intracellularly, up-regulated HSP proteins can be delivered into lysosomes in which they
my research interest early on during my the right ‘laboratory mouse’ to study research exploration is currently being
can also interact and activate endosomal cell membrane TLRs; (5) higher production of Capthesin
microbes respond to immunological are delivered into lysosomes in which they can also interact and activate endosomal cell membrane career as scientist. Unfortunately, coral reef corals. undertaken. Having said that, we have
priming. These are exciting areas that TLRs; (6) activated TLRs either from the outer membrane or endosomal membranes will trigger cell ecosystems are in decline because of the shown that many identified infectious
with further improve our understanding signaling pathways that will converge in the activation of transcription factors (likely NF-kappa β) that will threats of local man-made disturbances How similar are the immune responses pathogens affecting coral species also
ultimately induce the expression of immune-related genes (7) resulting in the production of potential and global climate factors such as ocean of anemones to our own immunological cause disease sign development on E.
of disease resistance in anthozoans. pro-inflammatory molecules; (8) Higher expression of iGluR expressed on the outer membrane will also warming and acidification. Many maladies priming mechanisms? pallida anemones, which adds strength to
facilitate a faster sensing of potential DAMPs upon secondary exposure of pathogens. Adapted from a linked to these stressors such a coral In many cellular and molecular aspects, our model system for studying cnidarian
CAREER DEVELOPMENT figure originally published in SCIENTIFIC REPORTS under the Creative Commons CC BY 4.0 license. bleaching and diseases are on the rise. there are considerable differences immunology.
Inspiring future generations is a vital part My current motivation is to find solutions between the immune system of anemones
and remedies to mitigate the problems and those from humans, however, we have How successful has the outreach
of the scientific process. An important
currently affecting corals. also learned they share more similarities programme been so far?
component of the CAREER programme educational aspect of the programme Aventura Cientifica is a four-week long that we once considered the long The educational summer science-
is outreach to students from high school focuses on engaging Hispanic students experience held at Florida International What must be considered when using evolutionary history separating anemones experience workshop (Aventura Cientifica)
to postgraduate levels, and particularly and other minorities. University that will involve high school anemones as proxies for studying from us. tailored for high school students has been
to minorities who are underrepresented students in subjects included in the corals? very successful. We have run it twice with
Coral species are very slow-grower Anemones, and all invertebrates lack a total of 40 students that have already
in science. This is highly important as it Conducting a summer science CAREER programme, improving their
organisms that on average, extend their of the cellular components of the participated in the programme. We even
encourages those that may not pursue programme entitled “Aventura confidence and appreciation for science. calcareous skeleton a few centimetres adaptive immune system, such as T cell have some students continuing their
careers in science to consider entering Cientifica”, Dr Rodriguez-Lanetty This is vital to ensure that people from per year, and consequently, this poses and B cells (Lymphocytes), has led to science involvement after completing the
the field. hopes to motivate minority high school all backgrounds have opportunities to a challenge to set up well replicated the assumption that evolutionary early workshop either in their high schools or in
students to consider scientific research advance their interests in science and experiments that can be conducted in diverged invertebrates do not have University research laboratories. Our plan
a reasonable timeframe to study how the capability to develop a trained or is to expand and enlarge the participation
By 2050, 60% of the US’ population as a career. This is inspired by his own ultimately pursue a career in research.
corals function and how they respond acquired immunity. Nevertheless, our of students over the next three remaining
growth is expected to originate from the experiences, attributing a large part of It will also enable the future generation to biotic and abiotic factors around recent phenomenological findings, in years of the programme.
Hispanic community, however, Hispanic his success to the positive role models to continue protecting the environment, their changing environments. Hence, a concordance with results from insects,
people are the least likely to enter he encountered throughout school and which will become increasingly more surrogate model to study corals has been have revealed that the defence system
higher education. For this reason, the extra-curricular activities. important over the coming years.
68 www.researchoutreach.org www.researchoutreach.org 69
Biology ︱ Professor Allen Liu
Synthetic cells
have senses too
B
What defines a living cell? iologists and philosophers have Foundation (NSF) project, ‘Construction
How to capture the molecular long pondered the question, of DNA Programmed Minimal Cells
essence of life? These “What are the hallmarks of life?” with Membrane Mechanosensitive
fundamental questions underpin Whilst many scientists attempt a top- Functions.’
the collaborative research down approach to the issue based on
programme led by Prof Allen the organisms we see around us, Prof Although construction of synthetic
Liu at the University of Michigan Liu and Prof Noireaux are pioneers of an biological cells now appears plausible,
and Prof Vincent Noireaux at alternative, bottom-up approach. Their no functional minimal cells have
the University of Minnesota. The long-term goal is to construct a functional, yet been constructed from basic
pair uses molecular components living cell from scratch, something that molecules. Liu and Noireaux believe
to construct prototypes of has never been done before but now that their modular approach should
synthetic cells displaying the through their efforts appears conceivable. enable the integration of multiple
minimal characteristics of life. molecular components through
Their ‘cell analogs’ shed light LIFE AT A MINIMUM carefully characterised connections,
on basic biological processes, To build a synthetic cell, Liu and to create the artificial cells capable
and also provide new tools for
Noireaux have identified three essential of incorporating multiple cellular
biotechnology and medicine.
‘modules’ that they consider define functions.
a functional living cell. Their aim is to
bring these modules together in the INFORMATION IS POWER
lab to first construct models of ‘minimal Using elements of the molecular
cell’ capable of recapitulating complex machineries of the bacterium
biological functions. It is an essential Escherichia coli, Liu and Noireaux have ORGANISATION IS KEY MAKING METABOLISM POSSIBLE osmotic pressure (the pressure created
step before moving towards a full developed a cell-free system that can In the Michigan-Minnesota system, Having encased the information by the difference in concentrations
minimal cell (a cell that displays only the transcribe and translate the information the TXTL machinery is encased in a system inside a liposome, the final, of the dissolved molecules in the
minimum requirements for life), and, in a DNA sequence into the proteins small, cell-sized compartment called and perhaps most challenging part of surrounding water and the inside of
in doing so, characterise the essential that carry out cellular functions. a liposome. Liposomes make use of building a minimal cell is to enable it to liposomes).
elements needed to sustain life. Transcription (the copying of the DNA the simple fact that fats (lipids) do communicate with the outside world.
code onto a template RNA molecule) not dissolve in water. A double layer To metabolise, grow, and reproduce, To test the function of the MscL
The three essential modules are and translation (the construction of of molecules, each comprising a the minimal cell must be able to channel, they also encoded in the DNA
information (the instructions for proteins using this RNA template) are hydrophilic (water-loving) group such take in sources of energy across its of their minimal cell an engineered
building cellular components, held both achieved in the team’s unique as a phosphate and a hydrophobic membrane, expel waste products in protein called G-GECO, which
(lipid) component, when placed in the opposite direction, and respond to fluoresces in response to calcium ions.
analogues of the membranes with the lipids pointing into the centre
of the membrane, shielded from the Liu and Noireaux’s current work is
the membrane via MscL, G-GECO
responds by fluorescing.
70 www.researchoutreach.org www.researchoutreach.org 71
osmotic
pressure
external
calcium Behind the Bench
Prof Allen Liu Vincent Noireaux
(Top left) Schematics of
dsDNA protein synthesis by TXTL
in synthetic cells. (Top
right) AND-gate output E: allenliu@umich.edu E: noireaux@umn.edu
mRNA with osmotic pressure T: +1 734 764 7719 T: +1 612-624-6589
AND and external calcium as
W: http://liulab.engin.umich.edu W: http://www.noireauxlab.org
biosensing inputs. (Bottom) Increase in
osmotic pressure triggers
mechanosensitive channel
activation leading to Research Objectives Bio Contact
membrane-active G-GECO fluorescence. Prof Liu and Prof Noireaux’s project aim is Allen Liu received his PhD in Biophysics Prof Allen Liu
Figure adapted from to construct synthetic cells, consisting of a in 2007 from the University of California- Assistant Professor of Mechanical
property Majumder, Garamella et al.,
fluorescence Chemical Communications,
cell-free expression system encapsulated Berkeley. Since 2012, he has been an Engineering
52, 7349-7352, 2017. into a cell-sized phospholipid vesicle, Assistant Professor in the Department of University of Michigan
capable of sensing the environment Mechanical Engineering at the University 2350 Hayward Street, Ann Arbor,
Lipid G-GECO
Ca2+ through its lipid bilayer by expressing
mechanosensitive channels.
of Michigan. MI 48109,
USA
Vincent Noireaux received his PhD in
Funding Biophysics in 2000 from the University Prof Vincent Noireaux
G-GECO National Science Foundation (NSF) Paris XI. Since 2005, he has been an University of Minnesota – Twin Cities
Assistant, Associate and now Full Physics and Nanotechnology
Collaborators Professor in the Physics Department at the 115 Unions Street SE
• Sagardip Majumder, PhD student, University of Minnesota. Minneapolis, MN 55455-2070
University of Michigan USA
iso-osmotic • Jonathan Garamella, PhD student,
Ca2+ Lipid G-GECO University of Minnesota
72 www.researchoutreach.org www.researchoutreach.org 73
Biology ︱ Professor Carl Johansson
Properly preserved, catalogued and One of the best ways to do this is But even the best digital records
curated, zoological specimens are a mine with high quality digital photographs, are useless if they remain isolated in
of information, both in the organisms alongside digitised label data. With individual museums where they cannot
themselves and the associated ‘label a grant from the US National Science be compared. As Prof Johansson
data’ (notes on where and when the Foundation (NSF), Prof Johansson, Dr believes, data is only valuable if it can be
animal was collected, what it looked Kimsey and their students set about accessed freely and easily by anyone,
like when alive, and so on). Sadly, the mammoth task of digitising North anywhere on the planet. For this reason,
74 www.researchoutreach.org www.researchoutreach.org 75
Behind the Bench
A new species discovered by
Johansson’s students, Oreella
chugachii. Calloway, Miller,
Johansson & Whiting, 2011 from
southern Alaska, USA.
Q&A
pushing to share their data in online The recently discovered DNA repair and probably hundreds of thousands of
databases. However, standardised protection mechanisms that tardigrades files and computer hard drives loaded
SEM of mouth with what might be very important
databases require standardised data. seem to excel at, are also obviously
and front claws of
Because museums around the world a tardigrade What attracted you to study such an hugely important. Not only that, but data that end up never being released
evolved in relative isolation until obscure group as the tardigrades? the newly uncovered glass proteins and because the researcher retired, died,
When I became eligible to apply for Trehalose will be key in extending the lost interest, or lost funding.
recently, each has their own specimen
a sabbatical, I asked myself: “What shelf life of organs or tissues – facilitating
cataloguing system, incompatible with
others, and that means investing a huge There is a real sense of community do I know absolutely nothing about?”
Tardigrades were an answer to that
a much higher transplant rate. What advice would you give to
students who want to pursue a
surrounding the project, everyone
amount of time, money and energy question, and they truly intrigued me, I am also very interested in pursuing the career in scientific research but feel
re-cataloguing specimens in a universal so I wrote an application aimed at idea that wind born Tardigrades could they are not able to?
framework. Fortunately for the water
bears, Johansson and Kimsey’s students
involved has strived to make the researching tardigrades of California.
That opened up Pandora’s box for me
be vectors for the spread of disease
globally. There is currently some poorly
If it is truly your passion, it is the
greatest career you can ever imagine.
have provided that energy, resulting in project a success – in a very good way! known research into this area that
indicates there could be an issue.
If, however, you think that it could
be your pathway to fame, wealth or
a complete specimen collection now
online, searchable and freely accessible top-level NSF-funded project, receive compared to an average graduation How might research into the stardom, don’t waste your time!
in the database iDigBio. sound training in research methods, rate of just 30%, Johansson’s is closer tardigrades make a difference to How important is it that scientific data
human health? is freely accessible to all? What does the future hold for this
database management and digital to 100%. Youngsters who once aspired
Based on John Crow’s pioneering If funding is from a public source or project?
INSPIRING A COMMUNITY imaging, and even publish peer reviewed to work in fashion, media or finance
work in the 1970’s, clinical trials are sources, it should be mandatory that We have now finished the cataloguing
One of the greatest beneficiaries of this papers naming new species; not many are now inspired to pursue advanced currently examining the effectiveness and digitisation of the collection.
those findings are released in a timely
project is not tardigrade taxonomy at undergraduates can claim that! The degrees in research biology. What’s of “Dried Blood’ preserved with manner. Many scientists believe that You can visit IDigBio to see our
all, but the community of Fresno and students work with top scientists, more, they can be proud of their part in Trehalose – a sugar used by they need to hold their research close to results. Currently we have students
beyond. California’s oldest community receiving genetic support from Byron bringing knowledge of the water bears tardigrades in their process of their chest to stop someone else from working on writing several new
college, Fresno prides itself on Adams at Brigham Young University, to researchers and enthusiasts across cryptobiosis, which plays a huge role in “scooping them”, publishing their work species descriptions, based on slides
giving economically and/or culturally databasing expertise from Ed Gilbert the world. The full benefits of this level of protecting cells from damage caused before they do. found in the database. We also have
challenged students a chance: many are of Symbiota (the software that supports accessibility, to biodiversity conservation, by dehydration. Essentially a soldier or students writing up the re-mounting
the first in their family to attend college, iDigBio), and the immense tardigrade medical research and human health, other person could carry small packets I personally find that to be a totally methodology they have now
of their blood as a dried powder and, arrogant approach. If your findings are perfected.
ninety percent receive financial aid, the knowledge of Dr William Miller at Baker remain to be seen. But one thing is
if needed, rapidly rehydrate their dried important, you need to make them
majority are from minority groups, and University, Kansas. certain: this pioneering project will
blood to give them matching blood available as soon as possible. There are
most have no scientific background. ensure the water bears are no longer available – anywhere, anytime.
Yet Johansson calls them to work on a And their success is phenomenal: overlooked.
76 www.researchoutreach.org www.researchoutreach.org 77
Biology ︱ Professor Sara Hotchkiss
78 www.researchoutreach.org www.researchoutreach.org 79
events, while deeper ones would require
more prolonged periods of drought. It
also follows that kettle lakes at higher
Behind the Bench
altitude – which are generally rainfall-
fed – would be more susceptible to
Prof Sara C. Hotchkiss Prof Robert K Booth
E: shotchkiss@wisc.edu E: rkb205@lehigh.edu
colonisation than lower altitude lakes
T: +1 808 895 0442 T: +1 610 758 6580
supplied by more reliable groundwater. W: http://www.botany.wisc.edu/hotchkiss.htm W: http://www.lehigh.edu/~rkb205
If these hypotheses are correct, they may W: http://www.botany.wisc.edu/hotchkiss/index.html
be able to predict which kettle holes are
most susceptible to peat encroachment
over coming decades. Integrated
with regional climate forecasts, their Research Objectives the Nelson Institute for the Environment’s Contact
Prof Booth and Hotchkiss’ research uses the Centers for Climatic Research and Culture, Prof Sara C. Hotchkiss, PhD
projections could help anticipate and
paleoecological record preserved in kettle History, and Environment. She earned an Department of Botany
even mitigate the effects of climate
hole ecosystems of northern Wisconsin to AB in Biology from Oberlin College and University of Wisconsin – Madison
change on these ecosystems. assess the potential for climate-induced a PhD in Ecology from the University of 132 Birge Hall, 430 Lincoln Drive,
ecosystem state shifts, as well as the Minnesota-Twin Cities. Madison, WI 53706 USA
This is important because kettle ecological effects of these events.
hole landscapes provide a range Bob Booth is an associate professor in Prof Robert K Booth, PhD
of ecosystem services including Funding the Earth and Environmental Science Earth & Environmental Science Department
National Science Foundation (NSF) Department at Lehigh University. He earned Lehigh University, 1 West Packer Ave
biogeochemical cycling, habitats for
a BS in Biology from the Pennsylvania State Bethlehem, PA 18015 USA
aquatic and wetland flora and fauna, Bio University, an MS in Biology from Georgia
areas for human recreation, and of Sara Hotchkiss is a professor in the Southern University, and a PhD in Botany
course carbon sequestration. Although Department of Botany and a member of from the University of Wyoming.
the end appearance of kettle holes is
identical regardless of whether their
Q&A
creation was slow and steady or rapid
and episodic, the contrasting paradigms explanation than one that demands How can we manage the kettle hole
have markedly different implications. a dramatic change in conditions. We ecosystem better?
examine how the plants that live there We need to think about managing
As Hotchkiss and colleagues put it in
What first drew you to the kettle now support one another physically, and for diversity of landscape features,
a recent paper, “From an ecological
hole ecosystem as somewhere both we infer a slow process of expansion of including kettles that are deep and
perspective, the important question is, at prone to the impacts of climate that support across the surface of the shallow, high and low in the local
what rate do these variables change? Are change and vital to attempts to water. To explain the kind of sudden watershed, isolated and connected to
these lake systems responding linearly mitigate it? state change that our observations other lakes and peatlands. Taking this
to peatland expansion over millennia or To be honest, we were drawn to support requires an interval of much drier approach to maintaining landscape-
do they experience abrupt, threshold kettles because they are so beautiful! conditions in the past, without which level variety can buffer our land
effects?” (Ireland et al., 2012: 996). For Figure 2: Fallison Kettle has had three major phases: a lake phase before 5300 years ago, a dynamic Scientifically, we are both interested current conditions can’t be explained. management against our ignorance
example, the aquatic communities peatland expansion phase 5300 to 2000 years ago, and isolation of the lake by peatland during the past in the effects of climate variability on Occam’s Razor is useful in science, but of how these sensitive ecosystems
2000 years. Prior to peatland establishment the basin accumulated about half as much carbon per year their development, and in the ways sometimes upon closer observation a
supported by kettle hole lakes differ respond to extreme events and
as it did during the past 2000 years.
in which the small hills and valleys more complicated explanation actually unforeseen stressors.
depending on whether or not they are
in hummocky kettle landscapes can fits the data much better than the simple
peat-bordered because the presence
maintain higher levels of biodiversity one. In these cases, it can take a long How widespread do you think these
of peat has substantial biogeochemical
and hydrological effects on the lake
Their projections could help anticipate in a region. Of course, because time for the simpler explanation to fade sudden state shifts will turn out to
they leave a record of their own from popular use. be as climate change intensifies?
itself. Under the slow and gradual model, and even mitigate the effects of climate development in the form of peat and If we began to study a kettle ecosystem Will the kettle holes turn out to be
lakes would be peat-bordered for a an anomaly, or will they be the first
change on these ecosystems
lake sediments, they are particularly during a drought period, we would
considerable time, and effects on the well-suited to paleoecological studies. quickly begin to think of those of many?
aquatic ecosystem would be gradual conditions as ‘normal’, and we would be We can expect many sudden state
over many millennia. However, under What do peatlands do for us? surprised if it were suddenly inundated shifts as the frequency of extreme
the new model rapid changes would be also release carbon to the atmosphere kettle hole ecosystems will therefore Peatlands provide a vast array of with water. climatic events increases, and we
expected. if they begin to decompose. Thus, this undergo increasing numbers of abrupt ecosystem services, including flood If you expand your time frame and think may also see sudden shifts due to
control, habitat for biodiversity, and of glacial-interglacial cycles, we are quite internal feedbacks in ecosystems as
research has implications for the total community changes over coming
global climate regulation through their comfortable with thinking of our current average climatic conditions slowly
Hotchkiss and Booth’s research may net carbon that can be fixed in kettle decades – posing new challenges to
ability to sequester carbon from the interglacial conditions as normal, but drift out of the range in which those
also predict how sudden transitions hole landscapes, an urgent parameter mitigating the effects of future climate atmosphere. And of course, they also over the past million years interglacial internal feedbacks operate. As climate
from lake to peatland could alter the for those seeking to mitigate climate change. And kettle holes are unlikely to provide us with delicious cranberries! conditions have actually only lasted 10 or continues to change, there will also
whole ecosystem’s carbon storage change through maximising carbon be the only ecosystem prone to abrupt 20,000 years out of every 100,000 years. certainly be surprises.
capacity. Peatlands accumulate carbon sequestration. state shifts. Hotchkiss and Booth’s Why do you think the paradigm of We live in anomalously warm conditions,
much faster than lake sediments do, research provides a tantalising glimpse slow, gradual colonisation of kettle nested within a broader period of earth
but they occupy sensitive transition Even in regions of moderate climate, the of our potential future and a long-term hole lakes by peatlands has been so history in which it is much more normal
zones between aquatic and terrestrial future is expected to feature significantly prediction of how our actions can trigger pervasive, until now? to have major continental ice sheets
ecosystems on the landscape. Although more frequent and intense periods of rapid and permanent changes in the It’s appealing, and it’s a simpler growing.
good at storing carbon, peatlands can drought. If the new model is correct, natural world upon which we depend.
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Biology ︱ Professor Teresa Pawlowska Root with AMF. A plant root surrounded by hyphae
and spores of Claroideoglomus etunicatum.
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Behind the Bench
or beneficial bacteria are characterised
by genetic similarity, whereas parasitic
Fungal hyphae
bacteria have a greater level of diversity,
enabling them to adapt to potential
host resistance. Therefore, these results Root hair
suggest that MRE could be parasitic.
Q&A
enable the movement of DNA within and endosymbiont’s adaptive ability. In fact, However, much more research is still
between genomes. Ultimately MGEs can to acknowledge their distinctive biology, needed to fully understand the complex
introduce novel genes, or disrupt existing the team have developed a taxonomic relationship between MRE, AMF and the
ones. The movement of MGE and proposal to accommodate MRE in the host plant. Are MRE a friend or foe of Why are arbuscular mycorrhizal CaMg, is a product of an ancestral host Why is it important to study the
amplification of sequences on a single new species ‘Candidatus Moeniiplasma their fungal host? And, if the effects are fungi (AMF) so important for plant switch from animals to fungi. Present- relationship between AMF, MRE
chromosome, increases the number of glomeromycotorum’. antagonistic, how will this impact the life health? day animal-infecting mycoplasmas are and plants?
available recombination sites, thereby of the plant? Dependence on AMF for soil mineral entirely dependent on host metabolites. Once rock phosphate deposits, which
further promoting genetic diversity. The team also discovered that within a nutrients appears to be an ancestral Availability of costly metabolites from are the source of phosphate fertilisers,
Furthermore, the team showed that single AMF host, CaMg can coexist with Understanding this complex relationship feature of terrestrial plants. Some the host reduces selective pressures on are exhausted, AMF with their ability to
a significant part of the MRE genome another endobacterium, ‘Candidatus is vital for the future of agriculture. Soil plants, such as brassicas, have evolved genes responsible for their biosynthesis. translocate phosphorus from the soil
encodes proteins mainly used for Glomeribacter gigasporarum’ (CaGg). tilling disrupts delicate mycorrhizal to be independent of AMF but most These genes accumulate deleterious into plant roots will become critical to
interacting with AMF – for example, This was the first study to highlight the networks, necessitating the increased use other plants relay on AMF for mineral mutations and, in bacteria, they are food production.
the SUMO protease, which controls co-existence of two endosymbionts of chemical fertilisers such as phosphates. nutrition. Mineral nutrient deficiencies eliminated from the genome, leading to
postranslation modifications of host within a single fungal host. CaGg is However, researchers predict that are debilitating to plant growth permanent dependency on the host. It has been suggested that MRE
proteins. This provides evidence for entirely nutritionally dependant on the the world’s phosphate supply will be and development. Plants deficient could be a parasite of AMF. How
horizontal gene transfer; whereby genetic fungal host, and in return, primes host exhausted within the next 100 years. AMF, in phosphorus, the key element In what ways are MRE different from could this impact both the fungi and
material is exchanged between organisms energy metabolism. Unlike MRE, CaGg as a natural biofertiliser, could be the translocated by AMF, experience other endobacteria? the plant hosts?
of different species or populations. In fact, populations have a much lower level of answer. However, we will need to greatly stunting. CaMg is vertically transmitted and yet As a parasite, CaMg would inflict
genes that originate from AMF represent genetic diversity, which suggests that increase the prevalence of sustainable it retains mechanisms that generate a metabolic cost on AMF, which
3-5% of the total coding DNA sequences these two endosymbionts may have farming practises before this becomes a How did endobacteria, such as genetic diversity in its populations, themselves are obligately dependent
in the three different MRE populations. distinctly different lifestyles. Interestingly, viable option. mycoplasma-related endobacteria such as recombination and MGE. These on plants for energy. Consequently,
in all samples, MRE was much more (MRE) evolve to become so mechanisms are lost in other heritable mycorrhizal symbioses involving CaMg
A NEW SPECIES? abundant than CaGg, further supporting dependent on their fungal host? endobacteria. would become costlier to plants.
Overall, the research conducted differences between their biologies. Our data suggest that MRE, or better
by Professor Pawlowska and her Furthermore, results indicated both
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COMMUNICATION
The media’s manipulation
of scientific perception
Take your mind back to 1998 – the year the two-pound coin was introduced in Britain, the year DVDs made their debut and
the year Andrew Wakefield was involved in one of the most scandalous examples of science journalism to date. Take your Social Media
for Scientists
mind back to 1998 – the year the two-pound coin was introduced in Britain, the year DVDs made their debut and the year
Andrew Wakefield was involved in one of the most scandalous examples of science journalism to date.
D
uring the late 1990s, Andrew By the time the truth was revealed fact, viable – 19 years after it first came
Wakefield and 12 other about his research, following a thorough out, and 13 years after it was proved false.
researchers published fraudulent
research highlighting an apparent link
investigation by Brian Deer at The
Sunday Times, the media’s influence This kind of ignorance and refusal of
RSM was born out of multiple
between the measles-mumps-rubella
(MMR) vaccine and autism.
in broadcasting Wakefield’s claims had
almost irreversibly damaged the public’s
scientific expertise is so damaging.
conversations with researchers who
This ‘research’ sent mainstream news
perception of vaccines. Vaccines have proved over and over
again that they offer a vital, fundamental
see a real benefit in connecting
media into overdrive, publishing
the falsified results extensively and
Even to this day, the public remain
distrustful of vaccines, which has caused
defence against disease. Without them,
the global population as a whole would
with a broad audience over an
encouraging parents to avoid vaccinating
their children with the MMR vaccine. This
a potential re-emergence of certain
previously controlled diseases, including
only be more susceptible to disease.
ongoing basis. Social Media can
had the desired effect and resulted in a
substantial decline of vaccination rates
tuberculosis. If we and our leaders, as an international
society, cannot understand that for
now be considered one of the
amongst children – leading to several
preventable deaths from subsequent
Science and the media can therefore be
enemies to each other: scientists can make
ourselves, and learn to appreciate
scientific, peer-reviewed evidence, then
most prominent and important
mumps and measles epidemics. fabricated claims that the media broadcast
to the public, while the media can
we risk exposing ourselves to increasing
epidemics of fatal, yet avoidable, diseases.
engagement tools of the modern
AN INJECTION OF DISTRUST
Wakefield’s research was in fact highly
misrepresent research through sensational
claims, tarnishing public perception. It is
era. We help you get the ball rolling
biased, featuring only a small sample of
12 autistic children throughout his study.
important to overcome this and ensure
that science is received by the public in an
and can even provide long term
He also subjected the children involved
to unnecessary, painful invasive medical
accessible and accurate format.
Social Media Management support.
procedures without any ethical approval. THE TRUMP CARD
Rather worryingly, despite the numerous
The aim of his falsified research was to failed attempts to replicate Wakefield’s
create an association between vaccines work and prove the damaging reputation
and autism, to gain publicity and further of vaccines, large numbers of people,
his medical funding – and boy, did the including the President of the USA,
media fall for it. remain convinced that his research is, in
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