Radboud Honours Academy FNWI Yearbook 2013 2014 · 2017-02-01 · Preface 4 RHA ‐ FNWI Preface...
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Radboud Honours Academy
FNWI
Yearbook
2013‐2014
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 1
Radboud Honours Academy
FNWI
Yearbook
2013‐2014
C o n t a c t
2 R H A ‐ F NW I
RHA FNWI Contact
Programme Director:
Drs Hay Geurts
Tel: 024‐3652575
E‐mail: [email protected]
Secretary:
Nicolette Poelen
Tel: 024‐3653313
E‐mail: [email protected]
Postal address:
RHA FNWI
Faculty of Science
Radboud University Nijmegen
PO Box 9010
6500 GL Nijmegen
Visiting address:
Heyendaalseweg 135
6525 AJ Nijmegen
Website:
http://www.ru.nl/rha/fnwi/
V o o r w o o r d
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 3
Voorwoord
Met grote trots bieden we U het jaarboek aan van Disciplinaire programma van de Radboud
Honours Academy aan de faculteit Natuurwetenschappen, Wiskunde, en Informatica: het
RHA FNWI Year Book 2013 ‐ 2014. Het is intussen ons vijfde Honours jaar, hetgeen op 24
oktober a.s. met gepaste aandacht zal worden gevierd! Met onze disciplinaire RHA biedt de
faculteit haar 25 meest getalenteerde en gemotiveerde bachelor studenten een uitdagend,
interdisciplinair academisch programma van twee jaar aan. Op deze manier maken de RHA
studenten al vroeg in hun studie kennis met het belang van het werken in teamverband in
modern interdisciplinair natuurwetenschappelijk onderzoek. De studenten leren daarnaast
om kritisch te reflecteren op natuurwetenschappelijke vraagstellingen, en op het belang en
de impact daarvan voor grote maatschappelijke vraagstukken.
In het eerste jaar van het programma werken de studenten onder begeleiding van een
mentor in vijf interdisciplinair samengestelde groepjes aan een zelfgekozen
natuurwetenschappelijk vraagstuk. Halverwege het jaar gaan de studenten op excursie om
bij internationaal gerenommeerde laboratoria meer te weten te komen over hun specifieke
onderwerp. In maart van dit jaar is de groep naar Oxford geweest, wat een groot succes was.
Dit jaarverslag presenteert de vijf verschillende onderzoeksprojecten van cohort 2013 in
korte samenvattingen van elk twee pagina’s. U zult hieruit onmiddelijk de grote breedte en
reikwijdte van de projecten kunnen appreciëren: van biomedische vragen rondom specifieke
neurologische of stofwisselingsziekten, of het belang van man‐vrouw verschillen bij
medicijnonderzoek, tot de zoektocht naar duurzame oplossingen voor het energieprobleem.
In het tweede RHA jaar gaan de studenten elk hun eigen weg om een individueel,
zelfgekozen onderzoeksproject uit te voeren, samen met een gerenommeerde onderzoeker
(de ‘meester’). In dit jaarverslag zijn de samenvattingen van de 22 onderzoeksprojecten van
cohort 2012 gebundeld.
Als voorzitter van de Programmaraad ben ik bevoorrecht om het enthousiasme en de
creatieve geesten van onze meest getalenteerde studenten van nabij mee te mogen maken
(ook in Oxford mocht ik er bij zijn!), en verder helpen te ontplooien. Het bewijs van het
succes van ons programma treft U op de hierna volgende pagina’s aan.
Veel leesplezier toegewenst,
Prof. dr. John van Opstal
Voorzitter Programmaraad RHA FNWI
P r e f a c e
4 R H A ‐ F NW I
Preface
With due pride we present to you the yearbook of the disciplinary programme of the
Radboud Honours Academy at the Faculty of Science, Mathematics and Information
Sciences: the RHA FNWI Yearbook 2013 ‐ 2014. This is our fifth year running, an occasion
that will be marked on the 24th of October this year with a lustrum symposium. Through our
disciplinary RHA the Faculty offers an ambitious, and foremost fascinating academic
programme of two years to 25 of our most talented and motivated bachelor students.
Already in an early stage of their study the students learn the importance of working in
interdisciplinary teams in the natural sciences. Moreover, they learn how to critically reflect
on research questions that arise from the natural sciences, and on the importance and
impact of this research for society.
In the first year of their RHA programme the students work under the supervision of a
mentor on a self‐chosen research problem. Halfway through the year the students visit
laboratories of international renown to inform themselves further on the specific subject. In
March this year the group visited Oxford which was a great success. This yearbook presents
the five different research projects from cohort 2013 in short two‐page summaries. The
reader can immediately appreciate the enormous range of topics: from biomedical research
questions concerning particular neurological or metabolic diseases, to the search for a
sustainable energy source to solve the global energy problem.
In their second RHA year each of the students defines his/her own research project, to
be performed under the guidance of a renowned researcher. This yearbook bundles the 22
summaries of the research projects from cohort 2012.
As the chairman of the Programme Committee I feel privileged to be so close to the
enthusiastic and creative minds of our most talented students (this year I was able to join in
the visit to Oxford!) and to to help them to develop their scientific ambitions. I am sure that
the next pages will demonstrate the success of our programme.
I hope you will enjoy reading this yearbook,
Prof. dr. John van Opstal
Chairman Programme Committee RHA FNWI
C o n t e n t s
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 5
Inhoud/Contents
Voorwoord .............................................................................................................................................. 3
Preface .................................................................................................................................................... 4
Acknowledgements ................................................................................................................................. 6
The Radboud Honours Programme of the Science Faculty .................................................................... 7
Het Radboud Honours Programma FNWI ............................................................................................... 9
1st Year ................................................................................................................................................... 11
Het gemeenschappelijke deel van het honoursprogramma FNWI in het tweede studiejaar .......... 12
1st Year RHA FNWI Research Projects ............................................................................................... 17
Excerpts from the jury review reports of the 2013 ‐2014 Faculty of Science Honours Projects ...... 28
2nd Year .................................................................................................................................................. 29
Het individuele deel van het honoursprogramma FNWI in het derde studiejaar ............................ 30
2nd Year RHA Research Projects ........................................................................................................ 33
Scientific Output .................................................................................................................................... 57
Leden RHA Programma Raad 2012‐2013 .............................................................................................. 59
About this yearbook
This yearbook is about the Radboud Honours Academy of the Science faculty and concerns
students who have started the Science Honours programme in the 2012‐2013 academic year
(cohort 2012) and those who have started in the 2013‐2014 Academic year (cohort 2013). All
project proposals and research projects are written in English but include an abstract in
Dutch. An overview of the Radboud Honours Programme of the Science faculty is given both
in English as well as in Dutch and the detailed description of both the 1st and 2nd year of the
programme is in Dutch only.
Dr Ernst R.H. van Eck
A c k n ow l e d g em e n t s
6 R H A ‐ F NW I
Acknowledgements
Without the help of a lot of people, this programme would not be the programme it is now.
The RHA FNWI would therefore like to acknowledge all the researchers and research groups
who have helped our first year RHA students with their projects, be it in giving advice or in
enabling preliminary experiments to be performed. The research groups in England who
have so kindly received our students this year, have showed them around their facilities and
had fruitful discussions with them to help them along with their projects are also thanked
warmly (and thanks Muriel for the report). The efforts of the jury members who have so
expertly judged the 1st year RHA research projects and examined the students during the
RHA 1st year symposium are deeply appreciated. Our 2nd year honours students have spent
time abroad as part of their programme. We are indebted to the research groups and people
that have welcomed them and thus made their time abroad an enervating experience.
Finally all the academic supervisors who guided the honours students throughout the
programme (the ‘mentors’ and “meesters’) are recognised for their efforts.
R H A – F NW I P r o g r amm a
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 7
The Radboud Honours Programme of the Science Faculty
The Radboud Honours Programme of the Science Faculty of the Radboud University
Nijmegen is a programme of excellence for 2nd and 3rd year Science Bachelor students. The
top students of the Science faculty (Faculteit der Natuurwetenschappen, Wiskunde in
Informatica, FNWI) are offered the opportunity to enroll in this programme in addition to
the programme of their 2nd and 3rd year Bachelor degree. Selection and admission to this
programme is based on the marks attained in the first year in addition to their intrinsic
motivation and ambition. The workload of the programme is 30 ECTS spread out over 2
years (for comparison: 1 years’ worth of study is 60 ECTS). During these 2 years students
participate in the honours programme in addition to their regular Bachelor programme, both
of which should be completed at the end of their 3rd year. Having successfully finished the
Science Honours programme the students will receive a special certificate: the so‐called
“honoursbul” (honours diploma)
The Science honours programme aims to cater to the desires and ambitions of excellent and
motivated students who wish to be challenged above and beyond their regular degree
programme. They are expected to enrich themselves within their own discipline as well as
within the context of the sciences in general. Attention is also given to the acquisition of
concomitant academic skills. The ultimate goal is to enable students who excel in their
studies to develop to their full potential during their degree programme. Here we strive to
reach a level, already at the Bachelor phase, where students can participate in scientific
research and in some cases, even in publications in the peer reviewed scientific literature.
A dm i s s i o n t o t h e h o n o u r s p r o g r amme
( F i r s t y e a r B S c )
Based on the results attained in the first semester of their Bachelor degree the best 25% of
the students of each Science degree are invited by the rector magnificus of the university to
apply for a place in the Science honours programme. Selection and admission to this
programme is competitive and based on their motivation and ambition, which they have to
show in a letter of motivation followed by an interview. Only 25 places are available in this
programme. Students that have been selected are asked to give suggestions for a research
project/theme. Ultimately access is granted if the first year of their Bachelor degree
(propedeuse) is attained within 1 year.
1 s t y e a r h o n o u r s p r o g r amme : I n t e r d i s c i p l i n a r y r e s e a r c h p r o j e c t .
( S e c o n d y e a r B S c )
In the first year of the FNWI honours programme, the process of writing of a joint research
proposal is central to that year, meriting 12 ECTS. The students will work together in small
groups (4‐5 students) and in the end produce a research proposal. Students of various
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scientific disciplines collaborate, investigating an interdisciplinary research theme. Each of
the students contributes from the perspective of their own degree programme. An
experienced member of the academic research staff will supervise the group. During regular
progress meetings each group will report to all other groups and the programme committee.
Part of the programme is a visit to a foreign top university/institute where leading experts
on their chosen subject will be consulted. This year is also used to develop their academic
skills and the students will receive training in giving presentations, scientific writing etcetera.
At the end of this year each group writes their research proposal, which should include a
suggested course of investigation and in certain cases some preliminary experiments. The
proposals will be sent to an expert jury who will judge the proposals on their merit. The
students will be given the opportunity to present their proposal and will be questioned by
the jury panel who will give the groups feedback on their contribution. All reporting, in
writing or orally, is expected to be in English.
2 n d y e a r h o n o u r s p r o g r amme : I n d i v i d u a l r e s e a r c h p r o j e c t .
( T h i r d y e a r B S c )
During this year the students will do the individual part of the honours programme: a
research project and extra courses totaling 18 ECTS. The student will choose a research
group and will be supervised by an academic researcher. Usually the internship is combined
with the regular Bachelor research internship, effectively doubling the time that can be
spend on a specific topic, allowing the student to fully engage in academic research. A stay
abroad, for research, for attending a conference or taking part in a course is part of this
internship. At the end of the internship a written report is produced and a presentation to
the research group is given and assessed. The 2nd year honours programme is finalised with a
symposium which is open to the general public. Here, every student will pitch their honours
research in just 2 minutes preceding a poster session where discussions ensue. The
symposium concludes with the awarding of the “honours bul” to the students.
P r o g r amme c o u n c i l
The board of the Science faculty has established the RHA FNWI programme council to
develop and execute the honours programme within the Science faculty as well as for
continual improvement and quality assurance of the programme. Members of the council
also partake in the board of examiners which who audit the compliance of individual
students with the guidelines of the programme.
R H A – F NW I P r o g r amm e
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 9
Het Radboud Honours Programma FNWI
De beste bachelorstudenten van de faculteit Natuurwetenschappen, Wiskunde en
Informatica (FNWI) wordt de mogelijkheid geboden om in het tweede en derde jaar van hun
bacheloropleiding een disciplinair excellentieprogramma te volgen: het honoursprogramma
FNWI. Selectie voor toelating tot dit programma vindt plaats op basis van studieresultaten
behaald in het eerste studiejaar, in combinatie met motivatie en ambitie. De totale omvang
van het tweejarige excellentieprogramma bedraagt 30 EC. Studenten volgen dit programma
naast hun reguliere bacheloropleiding. Daarbij is het uitgangspunt dat de deelnemende
studenten zowel hun honoursprogramma als hun reguliere bachelorprogramma in drie jaar
afronden. Studenten die het honoursprogramma FNWI succesvol doorlopen, ontvangen
hiervoor een speciale bul, de honoursbul.
Het honoursprogramma FNWI beoogt in te spelen op de wensen en ambities van excellente
en gemotiveerde studenten die zoeken naar extra uitdagingen. Het gaat hierbij om
verdieping binnen zowel de eigen discipline als binnen een interdisciplinaire bètacontext.
Daarnaast is er aandacht voor het verwerven van de bijbehorende academische
vaardigheden. Uiteindelijk doel is om excellente studenten in staat te stellen om zich
gedurende hun opleiding zo goed mogelijk te ontwikkelen. Daarbij is het streven om al in de
bachelorfase een niveau te bereiken waarbij participatie in ‐ en soms ook publiceren van ‐
wetenschappelijk onderzoek mogelijk is
H e t e e r s t e s t u d i e j a a r : d e s e l e c t i e
Op basis van de studieresultaten gedurende het eerste semester worden de beste studenten
van de verschillende opleidingen van FNWI door de rector magnificus van de universiteit
uitgenodigd om te solliciteren naar deelname aan het honoursprogramma FNWI. Selectie
vindt plaats op grond van motivatie en ambitie via een schriftelijke en mondelinge
selectieronde. De geselecteerde studenten wordt gevraagd om zelf met suggesties te
komen voor een bepaald onderzoeksthema of onderzoeksgebied. Voorwaarde om
uiteindelijk deel te mogen nemen aan het honoursprogramma FNWI is dat de propedeuse in
1 jaar behaald wordt.
H e t t w e e d e s t u d i e j a a r : d e i n t e r d i s c i p l i n a i r e o n d e r z o e k s v r a a g
In het tweede studiejaar staat het gemeenschappelijke onderzoeksvoorstel/project met een
omvang van 12 ec op het programma. Studenten van verschillende opleidingen werken in
kleine projectgroepen (4‐5 studenten) samen aan een interdisciplinaire probleemstelling,
waarbij ieder vanuit zijn eigen discipline bijdragen levert. Een ervaren wetenschappelijk
onderzoeker treedt op als mentor en begeleidt een dergelijke projectgroep. Tijdens
voortgangsavonden geeft iedere projectgroep gedurende het jaar een update van de stand
van zaken. Een gezamenlijk werkbezoek aan een buitenlandse topuniversiteit maakt deel uit
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van het programma. Daarnaast zijn er trainingen, gericht op het verder ontwikkelen van een
aantal academische vaardigheden. Aan het eind van het jaar wordt per projectgroep een
verslag geschreven van het onderzoeksproject, inclusief voorstellen voor nader onderzoek.
Over dit verslag wordt een mondelinge presentatie gegeven op een afsluitend symposium.
Hierbij krijgen de groepen feedback van een jury van externe experts op het gebied van de
thema's. Alle verslaglegging en presentaties vinden plaats in het Engels.
Een uitgebreide beschrijving van het gemeenschappelijk deel van het honoursprogramma
FNWI in het tweede studiejaar staat in het gedeelte van het 1ste jaars honourprogramma.
H e t d e r d e s t u d i e j a a r : d e i n d i v i d u e l e v e r d i e p i n g
Tijdens het derde studiejaar doorloopt de student het individuele onderzoeksproject met
een omvang van 18 ec. Dit bestaat uit een inhoudelijke verdieping binnen een zelfgekozen
onderzoeksrichting in de vorm van een onderzoeksproject. De student kiest hiervoor zelf een
onderzoeksgroep en een begeleider, de "meester". De student wordt aangeraden dit
onderzoeksproject te combineren met de reguliere bachelorstage om zo voldoende omvang
voor een verdiepend onderzoek te verkrijgen. Een verblijf in het buitenland, voor onderzoek,
congresbezoek of een cursus, maakt deel uit van dit gedeelte.
Een uitgebreide beschrijving van het individuele deel van het honoursprogramma FNWI in
het derde studiejaar staat in het gedeelte van het 2de jaars honourprogramma.
P r o g r amma r a a d
Het faculteitsbestuur heeft een programmaraad ingesteld om de opzet en uitvoering van het
honoursprogramma FNWI vorm te geven en toe te zien op de kwaliteit van het programma.
Leden van deze programmaraad treden ook op als examencommissie, die toetst of het
programma van individuele studenten voldoet aan de richtlijnen.
1 s t Y e a r R H A – F NW I
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1st Year
Radboud Honours Academy
FNWI
1 s t Y e a r R H A – F NW I D e s c r i p t i o n
12 R H A ‐ F NW I
Het gemeenschappelijke deel van het honoursprogramma FNWI in
het tweede studiejaar
Het tweede studiejaar bestaat uit gemeenschappelijke onderzoeksvoorstel/project met een
omvang van 12 ec, waarvan 10 ec toegekend worden aan het onderzoeksvoorstel en 2 ec
aan het onderdeel academische vorming. De start van het programma bestaat uit een
verplicht introductieblok in de week direct voorafgaand aan het begin van het tweede
studiejaar. Binnen deze introductie van drie dagen komen onder meer aan de orde:
kennismaking (studenten, mentoren, leden programmaraad)
informatie over opzet en inhoud van de verschillende programma‐onderdelen
inleiding en eerste afbakening van de te kiezen onderzoeksthema's (mentoren)
kennismaking met toegepast multidisciplinair onderzoek (lezingen en excursie TNO
Soest)
sessies waarin de studenten samen met de mentoren werken aan keuze van de
thema's en de indeling van de multidisciplinaire projectgroepen
eerste inhoudelijke verkenning en werkafspraken (projectgroep en mentor)
sociaal programma
H e t g eme e n s c h a p p e l i j k e o n d e r z o e k s v o o r s t e l / p r o j e c t
Binnen het gemeenschappelijke onderzoeksproject werken studenten in een
multidisciplinaire groep gezamenlijk aan de uitwerking van een uitdagende
wetenschappelijke vraagstelling. Het dient hierbij te gaan om een thema waarbij voor de
uitwerking een interdisciplinaire bèta‐aanpak noodzakelijk is. De groepen hebben een
omvang van ongeveer vijf studenten, afkomstig van verschillende opleidingen. De uitwerking
van het thema in de vorm van een gezamenlijk onderzoeksproject vindt plaats in de periode
van september tot juni van het tweede studiejaar. Indien mogelijk kunnen experimenten
deel uit maken van het project. Met het oog op een effectieve en doelmatige aanpak kent
deze periode een aantal ondersteunende vaardigheidstrainingen en voortgangsrapportages.
Onderdelen die bij de vaardigheidstrainingen (2 ec) aan de orde komen zijn:
presentatie‐ en debating‐technieken
professioneel samenwerken in multidisciplinaire groepen
projectmatig werken
Tijdens de voortgangsrapportages geven de projectgroepen een overzicht van hun
vorderingen, zodat de programmaraad het verloop van ieder onderzoeksproject kan
beoordelen aan de hand van tussenresultaten of "milestones".
1 s t Y e a r R H A – F NW I D e s c r i p t i o n
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Op z e t e n v o o r t g a n g
De programmaraad beoogt aan de hand van enkele algemene richtlijnen de voortgang van
de onderzoeksprojecten te ondersteunen. Bij de voortgangsrapportages hanteert de
programmaraad als milestone de volgende criteria:
Tijdens de eerste voortgangsrapportage in oktober presenteert elke projectgroep
hoe het oorspronkelijke thema is afgebakend tot een onderwerp met duidelijke
vraagstelling en doelstelling.
Tijdens de tweede voortgangsrapportage in december presenteert elke projectgroep
een helder overzicht van wat bekend is uit de relevante literatuur met betrekking tot
hun onderzoeksvraagstelling en bijbehorende aanpak.
Tijdens de derde voortgangsrapportage in april biedt elke projectgroep een eerste
overzicht van de behaalde resultaten inclusief voorstellen tot vervolgonderzoek en
eventuele aanbevelingen.
We r k b e z o e k b u i t e n l a n d
In het voorjaar van het tweede studiejaar wordt er gezamenlijk een tweedaags werkbezoek
gebracht aan een buitenlandse topuniversiteit (afgelopen jaren respectievelijk Oxford,
Cambridge, de ETH in Zürich, Berlijn). Het is de bedoeling dat dit bezoek de afzonderlijke
projecten ondersteunt en daarom dienen de projectgroepen met hun mentor vooraf contact
te leggen met een afdeling of instituut ter
plekke, waarvan het onderzoek goed
aansluit bij de vraagstelling van het project.
Het spreekt voor zich dat een gedegen
voorbereiding (o.a. het opstellen van
duidelijke vragen aan de afdeling/instituut)
voorwaarde is voor een succesvol bezoek.
Dit jaar werd Oxford bezocht, waar
natuurlijk Oxford University werd bezocht
naast uitstapjes naar King’s College London
en de University of Cambridge.
H e t e i n d p r o d u c t
Het gemeenschappelijke onderzoeksproject leidt tot een werkstuk met raakvlakken aan
meerdere wetenschapsgebieden binnen de natuurwetenschappen, vanuit een duidelijke
wetenschappelijke probleemstelling alsmede een aantoonbare maatschappelijke relevantie.
In het werkstuk wordt een helder overzicht gegeven van de stand van zaken in de literatuur.
Daarnaast dient ook de creativiteit van de groep zichtbaar te zijn o.a. doordat voorstellen
worden gedaan voor specifieke maatregelen of verder onderzoek. Het niveau en de stijl van
het werkstuk komen overeen met die van een wetenschappelijke notitie. Men kan denken
aan een projectvoorstel voor NWO of STW, of een wetenschappelijk onderbouwd advies, et
Oxford, March 2014: RHA students and accompanying staff pose
inside of St Johns college.
1 s t Y e a r R H A – F NW I D e s c r i p t i o n
14 R H A ‐ F NW I
cetera. De taal is Engels, net zoals bij alle andere officiële producten van het
honoursprogramma FNWI. Omvang van het werkstuk: 10 tot maximaal 25 pagina's.
B e o o r d e l i n g e n a f s l u i t i n g
Het werkstuk wordt beoordeeld door een lid van de programmaraad en een externe
deskundige. Het gemeenschappelijke gedeelte van het RHA programma wordt afgesloten
met een symposium in juni. Daarin presenteren de projectgroepen hun resultaten aan een
breed, niet per se wetenschappelijk publiek (o.a. ouders/vrienden/medestudenten) en een
(externe) jury. De taal van de presentaties is Engels. Na afloop van deze presentatie zal de
jury met de groepsleden van gedachten wisselen, waarbij gericht vragen gesteld kunnen
worden aan individuele studenten. Na afloop zal de voorzitter van de jury voor elke groep
het jury‐rapport voorlezen.
Group picture of the 2013 cohort and their supervisors. The picture was taken at the 3 day introduction period to the FNWI RHA.
1 s t Y e a r R H A – F NW I D e s c r i p t i o n
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 15
Research Visit to Oxford
Each year in early spring all students in their first year of the RHA get the chance to visit research
groups in and experience a world‐renown academic centre. Each RHA‐group arranged meetings with
research departments that were doing research related to their own project. In these meetings we
exchange thoughts with the researchers and ask them questions about their subjects. This year the
destination of the research visit was Oxford, UK.
Thursday the 6th of March the journey started early in the morning
when we left Schiphol by plane to London Heathrow and
subsequently by bus to Oxford. This day was full of different
experiences of university life at the colleges. Our first destination
was one of the larger colleges of Oxford: St. John’s College. We
were kindly greeted by our tour guides who both live and study in
St. John’s. They showed us the gardens, library (with books from
the 15th century as well as modern scientific books) and dinner‐
halls and talked about student life in Oxford and the colleges. The
oldest buildings of the college were built in the 15th century. It was
a beautiful college to look at and
learning about the system of
universities in England was also
very interesting. The tour was
followed by a lecture given by
professor Grahame Lock, professor of philosophy, in which he
explained the system of the University of Oxford with regard to the
application procedure and the use of colleges to educate the
students. Another talk was given by Charlotte Koolstra, president
of the NWS Oxford (a society for Dutch students abroad), about
the general process of studying abroad, with a particular emphasis
on Oxford and practicalities of admittance and doing a master. In
the evening we got the chance to join a formal dinner at St John’s
College, where the students and professors wore their traditional
gowns. This was a
very impressive experience and also a very good
dinner. The day was concluded by a nice evening at
Chequers, where we could meet some other Dutch
students studying in Oxford organized by NWS.
On the Friday each group of students discussed their
projects with one or multiple research groups doing
research on related topics. In two cases, the day
brought us outside of Oxford; the group of Paul
Kouwer travelled to King’s College London (Institute
of Pharmaceutical Science), after a morning visit to
the Chemical Biology group in Oxford, and the group Nicole and Marijn presenting the project of Nicole van
Dam’s group
Group of Paul Kouwer enjoying London
Formal dinner in St. John’s college.
1 s t Y e a r R H A – F NW I D e s c r i p t i o n
16 R H A ‐ F NW I
of Alexandra de Silva spent the entire day at the University of Cambridge (Department of Plant
Science). During the visits, we presented our project to the researchers and had informal discussions
with professors, post‐docs and PhD students.
Often, the discussion about the research proposals led to
an eye‐opener. Our visit made us realize that the process
to come up with a research proposal is harder than it
seems and you’ll have to adjust your research question
often to come to final one. Of course, much information
was gathered regarding the topics. In one of the visits, our
host immediately after our presentation began drawing a
concept, something very much along the lines of our idea,
but with the actual expertise of someone working in the
field. Things we had thought about, but weren’t sure were
actually possible, were made explicit, molecules and
mechanisms named instead of staying conceptual. With seven heads thinking about the same
problems, solutions and ideas came quite quickly. She seemed to
enjoy it as much as we all did. We also had the opportunity to look
around in the labs and research facilities and heard about which
research is being done: we managed to see research that hasn’t
even been published. All in all the visits were really instructive and
much fun. After the visits and before travelling back on the
saturday there was some time to look around in Oxford (and for
the group of Paul Kouwer also in London).
In general, we all had a great time visiting Oxford. We enjoyed all of
these experiences that we otherwise would have never had. It
definitely helped us with our research proposal by introducing us to
new methods and helping us with problems we otherwise might
not have solved.
Group of Uli Zeitler in an informal
discussion with prof. Armstrong
Group of Gerard Martens waiting for their visit
1 s t Y e a r R H A – R e s e a r c h P r o j e c t s
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 17
1st Year RHA FNWI Research Projects
Flux‐balance analysis of vinblastine production
Nicole van Buuringen Sharon Janssen
Marijn Man Lisa Noorlander
Supervisor: Prof. Dr. Nicole van Dam
Medicine release mechanisms in artificial organs applied to the administration of insulin
Roel Maas Eline Meijer
Roel Oldenkamp Jelle Piepenbrock
Lonneke Slenders
Supervisor: Dr. Paul Kouwer
Sex‐specific metabolism and effect of
Yvonne Bartels Charlotte Hoogstraten
Krijn Reijnders Felix Tönisen
Lina Wübbeke
Supervisor: Prof. Dr. Gerard Martens
SALMON – Superformulas And L‐systems: MOdelling Nature
Joery den Hoed Stijn Peeters
Bren Schaap Noor Smal
Luuk Verhoeven
Supervisor: Alexandra Silva
Improving CMC electrodes for use in enzymatic fuel cells
Gijs Franken Alexandra Hohnen
Sander Lemmens Ferdia Sherry
Berend Visser
Supervisor: Dr Uli Zeitler
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18 R H A ‐ F NW I
Abstract: Vinblastine is a compound of a medicine that is frequently used to treat cancer and is produced in the
plant Catharanthus roseus. For this purpose, vindoline and catharanthine get extracted and isolated out of C.
roseus and are transformed into vinblastine. Unfortunately, this is still an expensive process. At this point, the
process of research can be made far more efficient. We propose to make a genome scale model of the pathway
of vinblastine/vindoline and catharanthine. After some research we decided to use flux balance analysis (FBA)
to analyse the model. This method can help us to determine the most promising sites for modification in the
pathway. The model will be made by using an already existing model of the primary metabolism of Arabidopsis
thaliana. On top of this model the secondary metabolism of C. roseus will be build. When constraints are
brought on and the model is interpreted, the best places of alteration can be found.. This allows us to
genetically modify the plant efficiently and perform knockouts to increase the produced amount of vindoline
and catharanthine.
Samenvatting: Vinblastine is een veelgebruikt medicijn voor de behandeling van verschillende type kanker. Deze
stof wordt geproduceerd in de plant Catharanthus Roseus. Helaas is de productie hiervan nog erg duur. Ons
onderzoeksvoorstel heeft dan ook als doel de productiehoeveelheid van vinblastine te verhogen. Dit willen we
doen met behulp van een model van de pathway van de voorlopers van vinblastine: vindoline en catharanthine.
Na het bouwen van het model gebruiken we flux balance analysis (FBA) om veelbelovende plaatsen in de
pathway te vinden voor modificatie. We beginnen met een al bestaand model van het primaire metabolisme
van de plant Arabidopsis thaliana en bouwen hier bovenop het secundaire C. roseus model. Met het model
kunnen de beste plekken voor veranderingen aan de plant worden gevonden en kan er met behulp van
genetische veranderingen de productie van vindoline en catharantine verhoogd worden.
Introduction: In our society, cancer is a huge problem. Not every type of cancer can be treated and the
medicines that do exist are very expensive. One of these medicines contains the substance vinblastine. It is
widely used in treatments against lymphomas, leukemia’s and solid tumors. Vinblastine is an alkaloid produced
by the plant Catharanthus roseus, better known as the Madagascar Periwinkle.
In order to be able to use vinblastine in medicines,
it has to be extracted from the plant. Figure 1
shows the ‐ rather simplified ‐ last part of the
pathway of vinblastine in Catharanthus roseus. A
pathway is a chain of chemical reactions that
occur within a cell, often with a certain end
product. In this case, you can see that vinblastine
is created from the substances vindoline and
catharanthine. These two substances are available
in larger quantities in the plant than vinblastine,
so vindoline and catharanthine are extracted from
the plant and in the laboratory transformed into
Flux‐balance analysis of vinblastine
production
Nicole van Buuringen, Sharon Janssen, Marijn Man, Lisa
Noorlander
Supervisor: Prof. Dr. Nicole van Dam
Figure 1: The important steps of the biosynthesis of vinblastine and vincristine (Schröder 2010).
From left to right: Lisa Noorlander, Marijn Man, Sharon Janssen and Nicole van Buuringen
1 s t Y e a r R H A – R e s e a r c h P r o j e c t s
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 19
vinblastine. Still, naturally, one plant does not produce a large amount of vindoline and catharanthine. It would
therefore be convenient if there was a way to increase the amount of vinblastine that the plant produces.
Research Proposal: The main goal of the experiment is to increase the amount of vindoline and catharanthine
in the plant Catharanthus roseus. To achieve this, we have proposed to make a flux‐balance model of the
secondary metabolism of C. roseus. The model will be made on top of an already existing model of the primary
metabolism of Arabidopsis thaliana from Cheung et al. (Cheung and others 2014) This model is the most recent
and takes the day‐night cycle of the plant into account, which is important for the production of certain
metabolites. The reactions of the pathway of vinblastine are obtained from the database CathaCyc
(www.cathacyc.org) and added to the model, including all other pathways that are connected to that of
vinblastine. Then the model will be made more realistic by adding constraints to the model, such as the input
and the output. These constraints can be found in literature, can be measured or – as a last option ‐ educated
guesses can be made.
The reconstructed model can then be analysed by simulating knock‐outs of genes. Certain gene knock‐outs will
change the fluxes in the plant and we can investigate which knock‐outs lead to the highest production of
vindoline and catharanthine. There are three major methods to simulate these knockouts: FBA, ROOM
(Regulatory On/Off Minimization) or MOMA (Minimization Of Metabolic Adjustment). With FBA it is possible to
model knock‐outs by constraining the value of the reaction speed. The computer then calculates the new flux‐
distribution by maximising the fluxes again. MOMA is based on the same constraints as FBA, but it assumes
that the new flux distribution, after the knock‐out, remains as close as possible to the wild‐type distribution.
(Segre and others 2002) At last, ROOM minimizes the total number of significant flux changes from the wild‐
type flux vector, under the same constraints as FBA and MOMA. (Shlomi and others 2005) For our research we
propose to use MOMA, because it is not reasonable that genetically modified organisms function optimal:
these mutants are not subjected to the same evolutionary pressure that shaped the wild type. (Segre, Vitkup et
al. 2002) It is also the method that is most used with models of plants.
After the analysis has been done and the best places for alteration in the pathway are known, C.
roseus can be genetically modified to efficiently increase the amount of produced vindoline. There are different
ways by which the genes of C. roseus can be silenced. One way to do this is the use of RNA interference (RNAi),
a permanent method. (Hannon 2002) Another technique for silencing is called Virus induced gene silencing
(VIGS), a transient method. (Lu and others 2003).
Outlook: This model seems a promising method to efficiently improve medicine production. Now the model
needs to be made and tested with in vivo results. With this information, the model can be made more accurate
and hopefully improve the efficiency of research.
References
Cheung CM, Poolman MG, Fell D, Ratcliffe RG, Sweetlove LJ. 2014. A diel flux‐balance model captures interactions between
light and dark metabolism during day‐night cycles in C3 and CAM leaves. Plant Physiology:pp. 113.234468.
Hannon GJ. 2002. RNA interference. Nature 418(6894):244‐251.
Lu R, Martin‐Hernandez AM, Peart JR, Malcuit I, Baulcombe DC. 2003. Virus‐induced gene silencing in plants. Methods
30(4):296‐303.
Schröder J. 2010. Fig. 1 Overview of the pathway to the bisindole alkaloids vinblastine and vincristine. . In: The bisindoles
vinblastine and vincristine amiVaV, editor.
Segre D, Vitkup D, Church GM. 2002. Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci
U S A 99(23):15112‐7.
Shlomi T, Berkman O, Ruppin E. 2005. Regulatory on/off minimization of metabolic flux changes after genetic perturbations.
Proc Natl Acad Sci U S A 102(21):7695‐700.
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Medicine release mechanisms in artificial
organs applied to the administration of
insulin
Roel Maas, Eline Meijer, Roel Oldenkamp, Jelle
Piepenbrock and Lonneke Slenders
Supervisor: Dr. Paul Kouwer
Abstract: Artificial organs create the possibility to restore lost organ functions, for instance by regulating the
concentrations of hormones, proteins or other important molecules. The goal of this research project was to
design a generic structure or system that can act as a template for treatment. The insulin production system in
the human body was used as a model system. After consideration of various artificial organ compositions, we
propose a mechanism involving a polymer membrane encapsulating a source of insulin, carbon nanotubes, a
rotaxane acting as a gate molecule and a non‐enzymatic glucose sensor. This system, in principle, seems to be
a promising treatment for diabetes type 1. We propose further research in this field.
Samenvatting: Kunstmatige organen maken het mogelijk om verloren orgaanfuncties te herstellen. Het doel
van dit onderzoeksproject was het ontwerpen van een kunstmatig orgaan dat gebruikt kan worden als een
blauwdruk voor het behandelen van verscheidene ziektes die ontstaan door de absentie van regulatie van een
bepaalde molecuulconcentratie in het bloed. Na het in beschouwing nemen van verscheidene samenstellingen
van kunstmatige organen, stellen wij een mechanisme voor met een polymeermembraan dat een insulinebron
omsluit, carbon nanotubes, een rotaxaan dat dienst doet als poortmolecuul en een niet‐enzymatische
glucosesensor. Dit lijkt in principe een veelbelovende manier om diabetes type 1 te behandelen. Wij stellen
verder onderzoek hiernaar voor.
Introduction: The demand for the replacement of defect organs has steeply increased in recent years. The loss
of function can be the cause of different diseases by the creation of insufficient or dysfunctional proteins. To
overcome this, a donor organ replaces this dysfunction.
Although transplantation sounds promising, this procedure faces many problems. The most challenging issue is
the initiation of an immune response by the host. This will ultimately lead to the degradation of the whole
implanted organ. A lot of research has been done on the prevention of this immune response, but a successful
organ implantation still requires chronic immunosuppression.
The immune response can be prevented by microencapsulation of cells. Microencapsulation is a process that
envelops cells in a selectively permeable membrane, creating an “artificial organ”. The membrane prevents the
host’s adaptive immune system from initiating an immune response by preventing the influx of
immunoglobulins and antibodies into the interior cells. In our research, we will focus upon what we have
identified as the main bottleneck: a release mechanism to accompany functional cell microencapsulation. This
mechanism releases a pharmaceutical product in an appropriate concentration, for instance insulin release,
proportional to the glucose concentration. The main research question is the following: In what way can a
controlled insulin release mechanism be created, that can stay in the human body for prolonged periods of time
and release insulin proportional to the blood glucose level?
Research Proposal: To make such an artificial organ function properly, three different components are needed.
The first component is responsible for the production of insulin. To make this possible, we want to encapsulate
insulin producing cells in a hydrogel [1]. The second component is responsible for the survival of these cells,
providing a way to control the matrix in which cells can thrive and to control the influx and efflux of nutrients
London, March 7th 2014. From left to right: Eline Meijer (Chemistry), Roel Maas (MLS), Roel Oldenkamp (Biology), Jelle Piepenbrock (MLS), Lonneke Slenders (Biology)
1 s t Y e a r R H A – R e s e a r c h P r o j e c t s
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 21
and waste products. The latter function is important to let the cells produce insulin on a long‐term base. Cell
protection is governed by a combination of a polymer membrane and carbon nanotubes. The last component
is the controlled release mechanism, a way to release insulin at a concentration proportional to the glucose
concentration. This mechanism itself can be divided into two subcomponents. The first of these is the actual
mechanism of release, a gate molecule [2]. The second subcomponent is a sensor which can measure the
glucose concentration and produces a signal proportional to the glucose concentration [3]. This sensor is
therefore responsible for the controlled release of insulin.
Our proposed release mechanism consists of a bistable
[2]rotaxane that changes conformation through a redox
reaction. The electrons for this reaction are supplied by
a glucose sensor.
A bistable [2]rotaxane consists of two different π‐
electron rich groups. Next to these, it contains an
electron‐deficient ring. This ring prefers binding to one
of the electron rich groups over the other one. When
this preferred group is oxidized, the ring switches to the
other π‐electron rich group due to the Coulombic
repulsion between the oxidized group with the ring.
After reducing the oxidized group the ring slowly moves
back to the originally preferred group [2]. This shuttling
mechanism can be used to open and close a carbon
nanotube channel that is fixed in a polymer membrane.
Outlook: Theoretically, this mechanism could prove very useful in fighting various diseases. Preliminary
literature research suggests it is viable, but precisely how useful it is in practical applications needs to be
determined in a large scale research trajectory, carefully reviewing and modulating each single component and
in a second stage all components together.
References
[1] Murua, A., A. Portero, et al. (2008). "Cell microencapsulation technology: towards clinical application." Journal of
Controlled Release 132(2): 76‐83.
[2] Dey, S. K., A. Coskun, et al. (2011). "A redox‐active reverse donor–acceptor bistable [2] rotaxane." Chemical Science 2(6):
1046‐1053.
[3] Jiang, Y., S. Yu, et al. (2013). "Improvement of sensitive Ni (OH)2 nonenzymatic glucose sensor based on carbon
nanotube/polyimide membrane." Carbon 63: 367‐375.
Figure 1: A schematic overview of the setup of our
proposed membrane. (A) multi‐walled carbon
nanotubes, (B) single‐walled carbon nanotubes, (C)
polymer membrane, (D) insulin molecules and (E)
molecular valve which shuttles position when electrons
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Abstract: Drugs are differently handled by male and female bodies, but surprisingly little attention is paid to this
phenomenon in research on and the prescription of drugs. Therefore, in this research proposal we aim to
explore the sex‐specific differences in the pharmacokinetics of drugs. An unbiased genome‐wide study will
examine which mRNAs and proteins are sex‐specifically expressed in human hepatocytes from males and
females. Further experiments, in vitro and in vivo, will be performed to examine these differences more
specifically. These results will be used to build a computational model. Together, our results may lead to an
improvement of the efficiency and efficacy of drug use.
Samenvatting: Het lichaam van een man reageert anders op medicijnen dan het lichaam van een vrouw, maar
hier wordt verrassend weinig rekening mee gehouden bij het doen van onderzoek naar en het voorschrijven van
medicijnen. Daarom zullen wij onderzoek doen naar de sekse‐specifieke verschillen in de farmacokinetiek. Er zal
een studie naar het gehele genoom worden gedaan, waarbij geen verwachtingen mee zullen spelen, om te
bepalen welke mRNA’s en eiwitten verschillend tot expressie komen in levercellen van mannen en vrouwen.
Verdere experimenten, in vitro en in vivo, zullen worden gedaan om deze verschillen beter in kaart te brengen.
Met deze resultaten zal een model worden gebouwd, welke kan leiden tot een verhoogde efficiëntie en
werkzaamheid van de medicijnen.
Introduction: Sex‐related differences in pharmacokinetics of the liver contribute to differences in drug efficacy
and toxicity profiles in men and women [1]. Drug metabolism in the liver has been well studied and appears to
consist of three phases. The first phase is the phase of oxidation, which is brought about by the substrate‐
oxidizing enzyme cytochrome P450 (CYP450). The second phase is a phase of conjugation reactions, which are
effected by transferases. The last phase is the phase of excretion, in which drug efflux transporters excrete the
drugs. All three phases and the contribution of CYP450 have been well studied. [2] However, the contributions
of proteins other than CYP450 to the sex‐related differences in pharmacokinetics have not been described yet.
Therefore, the aim of our proposed research is to determine the differences in sexual dimorphic gene
expression in the liver that may explain the sex‐specific differences in pharmacokinetics.
Research proposal: Our study design is
unbiased because we will first perform
genome‐wide expression analysis to
determine which mRNAs and proteins
are sex‐specifically expressed in vitro in
human hepatocytes from males and
females. In addition, we will analyze
human hepatocytes from males and
females treated with various
concentrations of different hormones
(growth hormone, estradiol,
testosterone) and with the
immunosuppressant drug cyclosporin,
which is mainly metabolized in the liver.
From left to right: Felix Tönisen, Lina Wübbeke, Krijn Reijnders, Yvonne Bartels and Charlotte Hoogstraten
Sex‐specific metabolism and effect of
Yvonne Bartels, Charlotte Hoogstraten, Krijn Reijnders, Felix
Tönisen, Lina Wübbeke
Supervisor: Prof. Dr. Gerard Martens
Figure 1:Model of drug metabolism in the liver. K1, k2 and k3 represent the different rate values for the various steps. K1 is a constant rate value, and k2 and k3 are Michaelis‐Menten rate values; c is cyclosporin.
1 s t Y e a r R H A F NW I R e s e a r c h P r o j e c t s
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 23
The top list of differentially expressed genes will be validated, and selected genes will be further analyzed in
mice with transplanted human ectopic artificial livers (HEALs). [3] In these humanized mice, also the plasma
clearance of cyclosporin will be measured using liquid chromatography‐mass spectrometry. Short hairpin RNAs
will be used in vitro to downregulate the sex‐specifically expressed top‐list genes in order to determine the
effect of their downregulation on the cyclosporin clearance efficiency between human hepatocytes from male
and female. To evaluate the validity of the mouse model, we will measure the clearance of cyclosporin in male
and female human blood samples as well. Finally, based on our experimental results we will build a
computational model (see figure 1) to predict the sex‐specific pharmacokinetics of cyclosporin and other drugs
in the liver.
Outlook: The outcome of this research project may improve the efficiency and efficacy of the use of drugs.
Increased efficiency and efficacy are important to reduce adverse effects and improve overall medication and
thus the healthiness of patients. However, it also reduces costs on drug use as well as on treating adverse
effects. Furthermore, it will lead to lower drug usage.
References
[1] Franconi F, Campesi I. 2014. Pharmacogenomics, pharmacokinetics and pharmacodynamics: interaction with biological
differences between men and women. Br. J. Pharmacol.
[2] Anzenbacher P, Anzenbacherova E. 2001. Cytochromes P450 and metabolism of xenobiotics.
[3] Chen AA, Thomas DK, Ong LL, Schwartz RE, Golub TR, Bhatia SN. 2011. Humanized mice with ectopic artificial liver
tissues. Proc. Natl. Acad. Sci. U. S. A.
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Abstract: This project aims to unify two potent methods of describing shapes in nature, namely L‐systems and
the Superformula. Combining these models will yield a powerful way of modelling and describing shapes as they
complement each other beautifully, L‐systems being very good at representing branches and branchlike
structures and the Superformula being excellent at floral and leaf like shapes. We will approach this unification
from two angles. We will try to include key properties of L‐systems in the capabilities of the Superformula by
making the Superformula time dependent and extending it to cover branching structures. We will also
investigate the possibilities of incorporating the Superformula into the existing framework that L‐systems
provide.
Samenvatting: In dit project proberen we twee methodes voor het bestuderen van natuurlijke vormen te
combineren. Deze twee methoden zijn het L‐systeem en de Superformule. De L‐systemen zijn erg geschikt om
vertakte structuren te beschrijven, terwijl de Superformule erg geschikt is om de vorm van bloemen en bladeren
weer te geven. Het verenigen van deze twee methoden zullen we op twee manieren aanpakken. Aan de ene
kant zullen we proberen om de belangrijkste eigenschappen van L‐systemen over te brengen op de
Superformule. Aan de andere kant zullen we onderzoeken wat de mogelijkheden zijn om de Superformule in het
huidige systeem van L‐systemen te gebruiken.
Introduction: For centuries mankind has been intrigued by the enormous variety of patterns and shapes in
nature. Flowers, snowflakes and starfish are examples of symmetrical shapes. Some succulent plants, shells and
horns show spiral patterns. Honeycombs, scales and peels form tiling patterns and water surfaces and deserts
show wave patterns. This diversity of complex shapes and patterns creates an urge to comprehend them.
Different disciplines use different approaches to obtain a better understanding. Biology explains this wealth of
patterns and shapes with the theory of evolution. Millions of years of natural selection have created many
intricate patterns and shapes. A chemical approach to understand patterns is to look at morphogens, special
signalling molecules responsible for pattern formation. Mathematicians and physicists study all kinds of
abstract and natural shapes and are therefore also interested in those we find in nature. Relatively new is the
discipline of Computer Science, which tries to capture patterns and shapes in computational models.
Figure 1: Different patterns and shapes found in nature (source: Google images)
Significant events in the history of studying patterns and shapes in nature are, among others, the following. In
1952, Alan Turing published The Chemical Basis of Morphogenesis. Turing was a mathematician and described a
mechanism that can explain a great variety of patterns, like stripes and spots, based on diffusing and reacting
morphogens [1]. In 1967, Mandelbrot published an article that discusses fractals, self‐similar shapes we also
find in nature (e.g. snowflakes, crystals and flowers) [2]. In 1968, Aristid Lindenmayer developed the L‐system,
SALMON – Superformulas And L‐systems:
MOdelling Nature
Joery den Hoed, Stijn Peeters, Bren Schaap, Noor Smal,
Luuk Verhoeven
Supervisor: Alexandra Silva From left to right: Bren Schaap, Stijn Peeters, Alexandra Silva, Joery den Hoed, Luuk Verhoeven and Noor Smal
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Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 25
a model to recreate branching patterns and to describe plant growth [3]. And finally in 2003, Johan Gielis
invented the Superformula to model closed shapes, like flowers, leaves and starfish [4].
Research Proposal: In this proposal, we will present a plan for the combination of two existing formalisms for
modelling shapes into one, more powerful, formalism. One of these formalisms is the Lindenmayer system, a
computational method that is already very prevalent in biological research and provides an intuitive and simple
way for the modelling of branching structures. However, this method is not very well suited to model closed
shapes like flowers and leaves. The other one is the Superformula, a mathematical formula that can describe an
incredibly wide variety of shapes with a very limited number of parameters.
L‐systems and the Superformula are two formalisms with different properties that are important for a good
model. Combining these formalisms will yield a powerful model, as they complement each other’s strengths.
However, achieving this combination is a difficult task. In order to complete it we shall focus on the following
mutually related research goals:
G1: Ageing Gielis’ Superformula: time‐dependent modelling.
Modelling the development of plants over time is a challenging task. The difficulty in modelling biological
systems, and in particular growth, stems from their complexity and diversity. We explored the capability of the
Superformula to model shapes over time and its advantages and disadvantages in comparison with L‐systems.
By modelling the same shape with both an L‐system and a time dependent Superformula, we expect to draw
parallels between both L‐system and Superformula. These parallels could provide insights on how to unify the
distinct model systems.
G2: Branching meets Buds: incorporating Superformulas in an L‐system.
L‐systems are good in describing branching structures. However, a shortcoming of L‐systems is that modelling
closed shapes like leaves and flowers with L‐systems is a laborious task and requires complicated methods.
Therefore we proposed to implement the possibility of drawing Superformulas within L‐systems by expanding
existing software so scientists and other users will be able to use the Superformula in an L‐system in an easy
and convenient way.
G3: Branching the Superformula: incorporating L‐system properties into Superformular shapes.
One of the greatest weaknesses of the Superformula compared to L‐systems is its inability to capture
branching. Therefore, to incorporate this important feature into the Superformula, we have explored the
possibility of extending it by combining different Superformulas into one single shape with the aid of R‐
functions.
Outlook: Combining the two formalisms into one biological model will create a new bridge between Biology,
Computer Science and Mathematics. The new model could be used to more accurately replicate the shapes of
biological systems, especially plants, for research purposes and to improve existing computer graphics in both
realism and storage efficiency.
References
[1] Turing, A. M. (1952). The chemical basis of morphogenesis. Bulletin of mathematical biology, 52(1):153–197.
[2] Mandelbrot, B. B. (1967). How long is the coast of britain. Science, 156(3775):636–638.
[3] Prusinkiewicz, P. and Lindenmayer, A. (1990). The Algorithmic Beauty of Plants. Springer‐Verlag New York, Inc., New
York, NY, USA.
[4] Gielis, J. (2003). A generic geometric transformation that unifies a wide range of natural and abstract shapes. American
journal of botany, 90(3):333–338.
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Abstract: Compacted mesoporous carbon (CMC) electrodes have applications in enzymatic fuel cells, where they
can be used to, among other things, greatly increase the effective surface area of electrodes. We propose an
experiment which is a first step towards optimising CMC electrodes for use in enzymatic fuel cells. For this, we
describe a method for varying the pore size of CMC electrodes and testing the effect that this variation has on
the power output and lifetime of a fuel cell which uses these electrodes.
Samenvatting: In biologische brandstofcellen worden redox‐reacties die een elektrisch vermogen kunnen
leveren gekatalyseerd door organisch materiaal. Biologische brandstofcellen kunnen grofweg worden
opgedeeld in microbiële en enzymatische brandstofcellen. Wij hebben ons gericht op enzymatische
brandstofcellen, omdat onze interesses lagen in toepassingen op kleine schaal (bijvoorbeeld in het lichaam) en
deze soort brandstofcel daarvoor bijzonder geschikt is. De twee belangrijkste nadelen van enzymatische
brandstofcellen is hun relatief lage vermogen en hun korte levensduur, die wordt veroorzaakt door de inherente
instabiliteit van enzymen. Recent onderzoek [1] heeft aangetoond dat het gebruik van een bepaalde soort
elektrode, de compacted mesoporous carbon (CMC) elektrode, kan leiden tot een groter vermogen. In dit
onderzoek zijn CMC elektrodes gebruikt met een standaard poriegrootte. Wij stellen daarom voor om de invloed
van de poriegrootte op de prestatie van de brandstofcellen (zowel de levensduur als het vermogen) te
onderzoeken door CMC elektrodes te maken met verschillende poriegroottes en de verschillen in prestatie waar
te nemen.
Introduction: Enzymatic fuel cells are an interesting alternative energy source. Because of the substrate
specificity of enzymes, membranes are not always necessary, which implies that cells can be miniaturised and
can be made at lower costs than comparable fuel cells which do not use enzymatic catalysts. However there
are limitations to the use of enzymatic fuel cells. The two main issues are the short lifetimes of enzymes and
relatively low power output density. The first issue is caused by a large number of different factors and seems
to be the most difficult to overcome. The power output density of enzymatic fuel cells is limited by the electron
transfer rate of enzymes, which is related to the
geometry of the enzymes. A straightforward way of
increasing power output density of these cells could
be to increase the effective surface area of the
electrodes.
We propose to explore the use of compacted
mesoporous carbon (CMC) electrodes, which may
provide a partial solution to both of the main issues.
The main goal of the proposal, however, is to suggest
a method for increasing the power output density of
enzymatic fuel cells which use CMC electrodes. To
achieve this goal, we suggest looking at the effect of
the pore size of the mesoporous carbon which is used
in the CMC electrodes.
Improving CMC electrodes for use in
enzymatic fuel cells
Gijs Franken, Alexandra Hohnen, Sander Lemmens, Ferdia
Sherry, Berend Visser
Supervisor: Dr Uli Zeitler
Figure 1: A schematic diagram of a fuel cell
From left to right: Uli Zeitler, Berend Visser, Sander Lemmens, Alexandra Hohnen, Ferdia Sherry, Gijs Franken
1 s t Y e a r R H A F NW I R e s e a r c h P r o j e c t s
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 27
Research Proposal: In order to investigate
the effects of pore size on the lifetime and
power output, we will have to create
mesoporous carbon with different pore
sizes. Using the method described in [2]
we can relatively easily create graphitised
mesoporous carbon with different pore
sizes. We would like to investigate pore
sizes in the region between 5 and 25 nm.
When we have successfully
synthesised and measured our
mesoporous carbon with the desired pore
sizes we will turn the material into fuel
cells. The mesoporous carbon can be made
into an electrode and [NiFe] Hydrogenase‐
1 enzymes extracted from a certain strain
of E. coli can be loaded onto the electrode. This enzyme is used because of its extraordinary oxygen tolerance.
This electrode will be used as the anode and for consistent comparisons a platinum electrode will be used as
the cathode. The electrodes are mounted inside a chamber which is kept at an atmosphere of 80% H2 to 20%
normal air. The reactions powering the cell are oxidation of hydrogen at the anode and reduction of oxygen at
the cathode. Using LabVIEW the power outputs and lifetimes of the fuel cells with the CMC electrodes with
different pore sizes can be monitored. This allows us to decide what pore size is optimal.
Outlook: After the experiment we can compare our findings to those of Xu and Armstrong [1], and also to
platinum fuel cells, which are already in a state of practical application. If we can get the power output of an
EFC to be comparable to that of a platinum cell, whilst still retaining a somewhat respectable lifetime, that
would imply that commercial applications are viable in situations where the size of a fuel cell is of importance.
We will therefore after the experiment attempt to create a fuel cell with optimised pore size that can compete
with a commercial platinum fuel cell.
References
[1] Lang Xu and Fraser A. Armstrong. “Optimizing the power of enzyme‐based membrane‐less hydrogen fuel cells for
hydrogen‐rich H2–air mixtures”. In: Energy & Environmental Science 6 (2013), pp. 2166–2171.
[2] Haifeng Yang et al. “A Simple Melt Impregnation Method to Synthesize Ordered Mesoporous Carbon and Carbon
Nanofiber Bundles with Graphitized Structure from Pitches”. In: Journal of Physical Chemistry B 108 (2004), pp. 17320–
17328.
Figure 2: A schematic diagram of the experimental setup
1 s t Y e a r R H A R e s e a r c h P r o j e c t s
28 R H A ‐ F NW I
Excerpts from the jury review reports of the 2013 ‐2014 Faculty of
Science Honours Projects
Flux‐balance analysis of vinblastine production; Nicole van Buuringen, Sharon Janssen, Marijn Man, Lisa
Noorlander, group van Dam:
This proposal aims at making a flux model for alkaloid biosynthesis in the medicinal plant Catharanthus roseus,
with the ultimate aim to use it for optimizing the production of valuable compounds such as the anti‐cancer
agent vinblastine. The proposal has a relatively short incomplete introduction of the biological model. The
exact biological model to be used is not defined, but appears to be plants. Most of all, it is not made clear how
a flux model will contribute exactly to the goal, i.e. production of more vinblastine.
Jury member: Prof. Dr. J. Memelink Institute of Biology Leiden University
Medicine release mechanisms in artificial organs. Applied to the administration of insulin; Roel Maas, Eline
Meijer, Roel Oldenkamp, Jelle Piepenbrock, Lonneke Slenders, group Kouwer:
By being maybe a bit too ambitious the proposal has lost a bit of focus which could possibly have been avoided
by immediately taking the proposed research out of its direct context and concentrate on an adaptive release
device for insulin. Having said that I still regard this proposal very good showing where opportunities for
research projects are on the way towards the higher goal of artificial organs to improve healthcare.
Jury member: Dr. D.W.P.M. Löwik Bio‐organic Chemistry Radboud Unversity
Sex‐specific metabolism and effects of drugs; Yvonne Bartels, Charlotte Hoogstraten, Krijn Reijnders, Felix
Tönisen, Lina Wübbeke, group Martens
One of the remarks: I have my doubts about the value of the in vivo model with HEAL mice. To use such a
rather invasive and drastic model there should be a better motivation to use this model. Nevertheless, I
consider this a very good research proposal that, after some modifications, might be even successful in grant
application programmes.
Jury member: Prof. Dr. B.Blaauboer Institute for Risk Assessment Sciences University of Utrecht
SALMON: Superformulas and L‐systems modeling nature; Joery den Hoed, Stijn Peeters, Bren Schaap, Noor
Smal, Luuk Verhoeven, Group da Silva
Well‐written research project with many challenges. One of the difficulties is that it goes beyond mainstream
mathematics (and mainstream / biological) thinking. On the other hand, when successful, this may or will
result in various technological applications and can certainly result or expanded into a number of papers. The
project benefits from the interplay of students with various backgrounds. The presentation and defense was
very good. The following comments may help the students in refine and shape their thoughts further.
Jury member: Dr. J.Gielis University of Antwerp
Improving CMC electrodes for use in enzymatic fuel cells; Gijs Franken, Alexandra Hohnen, Sander Lemmens,
Ferdia Sherry, Berend Visser, Group Zeitler
The proposal is well written but I would expect more detail especially on the enzyme‐containing fuel cells.
Some schemes and examples would help the reader. In addition I would like to see paragraphs on feasibility
and societal relevance of the proposal.
Jury member: Dr. H.J.M. op den Camp Microbiology Radboud University
2 n d Y e a r R H A – F NW I
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 29
2nd Year
Radboud Honours Academy
FNWI
2 n d Y e a r R H A – F NW I D e s c r i p t i o n
30 R H A ‐ F NW I
Het individuele deel van het honoursprogramma FNWI in het derde
studiejaar
In het derde studiejaar maakt iedere student tijdens het individuele deel actief kennis met
het wetenschappelijk onderzoek binnen een afdeling of onderzoeksgroep van FNWI of (met
toestemming van de examencommissie) daarbuiten. Hiertoe kiest de student in de loop van
zijn tweede studiejaar een wetenschappelijk begeleider, de "meester". Student en meester
komen in onderling overleg tot de inrichting van het individuele onderzoeksproject; een en
ander wordt vastgelegd in een Persoonlijk Opleidingsplan, dat moet worden goedgekeurd
door de examencommissie van het honoursprogramma FNWI . Voor dit opleidingsplan is dit
formulier beschikbaar.
P e r s o o n l i j k Op l e i d i n g s p l a n
Het Persoonlijk Opleidingsplan voor het honoursprogramma FNWI van het derde studiejaar
omvat 18 ec en beschrijft de verschillende onderdelen met hun omvang en een tijdpad:
Een projectvoorstel voor een onderzoeksproject met daarin opgenomen een
uitgewerkt overzicht van de voor het project relevante literatuur; omvang 3 ec.
Een onderzoeksproject met een omvang van minimaal 9 ec. Uitbreiding van het
onderzoeksproject met de reguliere bachelorstage is met het oog op de diepgang aan
te bevelen.
Een overzicht van te volgen cursussen op het gebied van de specialisatie tot een
maximum van 6 ec.
Een invulling van de buitenlandcomponent, bijvoorbeeld in de vorm van (een deel
van) het onderzoeksproject, een cursus, een summer school, een congres of een
werkbezoek.
Een tijdpad waarin de diverse honoursactiviteiten/cursussen, alsmede de onderdelen
van het reguliere bachelorcurriculum, vermeld staan.
Eventuele aanvullende werkafspraken. Gedurende het project maakt de student deel
uit van de onderzoeksgroep met de bijbehorende rechten en plichten (o.a. deelname
aan werkbesprekingen, colloquia).
H e t o n d e r z o e k s p r o j e c t
Het zwaartepunt van het individuele deel is een wetenschappelijk onderzoeksproject met
veel ruimte voor eigen initiatief, zelfstandigheid en creativiteit. Projectdoelen moeten
dusdanig geformuleerd worden dat zij met relatief geringe achtergrondkennis en van de
andere kant veel inzet en creativiteit haalbaar zijn. De overige onderdelen (onderwijs,
buitenlandcomponent) worden afgestemd op het onderzoeksproject. Met het oog op een
doelmatige studieplanning kunnen voor projectvoorstel, cursussen en buitenlandcomponent
ook al de zomermaanden tussen het tweede en derde studiejaar benut worden.
2 n d Y e a r R H A – F NW I D e s c r i p t i o n
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 31
U i t b r e i d i n g me t b a c h e l o r s t a g e
Bij een combinatie van het onderzoeksproject met de bachelorstage wordt de omvang van
het project met 12 tot 15 studiepunten uitgebreid (afhankelijk van de omvang van de
bachelorstage bij de reguliere opleiding). De beoordeling van het bachelorverslag of de
bachelorscriptie zal dan plaatsvinden op basis van het gehele project. Over het
onderzoeksproject uitgebreid met de bachelorstage dient één eindverslag geschreven te
worden, in het Engels.
C u r s u s s e n
Deze cursussen mogen geen deel uitmaken van het reguliere bachelorprogramma. Bij de
extra cursussen kan wel gedacht worden aan doelgerichte uitbreiding van reguliere
cursussen in overleg tussen student, meester en de docent van de betreffende cursus.
B u i t e n l a n d
Een verblijf in het buitenland maakt deel uit van het individuele programma. De student
bezoekt in overleg met de meester een relevante wetenschappelijke bijeenkomst in het
buitenland (bijvoorbeeld een conferentie) of doet (een deel van) de onderzoekstage in het
buitenland.
De student regelt de aanvraag en organisatie, alsmede de financiële en administratieve
afhandeling van het buitenlandverblijf met (de afdeling van) de meester en dient zich zelf
ook in te spannen om subsidies te verkrijgen voor de buitenlandcomponent. Hij stuurt ter
informatie een begroting van de kosten naar het secretariaat van de programmaraad.
E i n d p r o d u c t
Het eindproduct dient te bestaan uit een geschreven verslag van het onderzoek, conform de
criteria voor wetenschappelijke publicaties. Daarnaast dient het resultaat van het onderzoek
op de een of andere manier naar buiten kenbaar te worden gemaakt, bijvoorbeeld in de
vorm van een poster op een conferentie, een voordracht op een summer school, een
bijdrage aan een extern colloquium, of een artikel in een populair‐wetenschappelijk
tijdschrift. In een aantal gevallen kan het onderzoeksproject leiden tot een
wetenschappelijke publicatie.
A f s l u i t i n g e n Ho n o u r s b u l
Het individuele onderzoeksproject wordt afgesloten met een gezamenlijk symposium van
alle honoursstudenten FNWI. Op dit symposium geeft elke student een korte presentatie
van de resultaten van zijn onderzoeksproject. Deze presentatie is gericht op een breed
publiek. Daarnaast presenteert de student een poster, waarop de wetenschappelijke
resultaten centraal staan. Tijdens het symposium wordt ook de honoursbul uitgereikt.
2 n d Y e a r R H A – F NW I D e s c r i p t i o n
32 R H A ‐ F NW I
C o n t a c t t u s s e n RHA s t u d e n t e n
Op verzoek van de studenten worden ook tijdens het derde studiejaar avondbijeenkomsten
georganiseerd waar academische vaardigheden centraal staan. In het voorjaar presenteren
de studenten hun vorderingen aan hun medestudenten, de programmaraad en de meesters.
Verder kunnen de studenten zelf initiatieven nemen voor gezamenlijke activiteiten; de
programmaraad zal deze waar mogelijk faciliteren.
On September 17 2014: the Honours diplomas were awarded to the 2ndyear RHA Science students (cohort 2012)
2 n d Y e a r R H A R e s e a r c h P r o j e c t s
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 33
2nd Year RHA Research Projects
Marloes van den Akker bi Dr. Marnix H.A.G. Gorissen Organismale dierfysiologie
Janine Arts mlw Prof. dr. Gert Jan J.C. Veenstra Molecular Developmental Biology,
Koen van Asseldonk sci Dr. Anouk M. Rijs Molecular and Biophysics
Marilen Benner bi Dr. J. van der Vlag Nierziekten
Maarten Broekman bi Prof dr. H. Siepel Dierecologie en ecofysiologie
Lotte Eilander mlw Prof. dr. Ger Pruijn Biomolecular Chemistry
Lisanne Gommers bi Prof.dr. Iris D. Nagtegaal Pathologie UMCN
Carolin Heller bi Dr. Leonie M. Kamminga, Molecular Biology
Niels Hesp na&st Dr. Alix McCollam High Field Magnet Laboratory
Wouter Hetebrij wi, na&st Prof. dr. Hans D.M. Maassen Toegepaste Stochastiek,
Serge Horbach wi Dr. Bernd Souvignier Algebra & Topologie
Shauni Keller sk Dr. Daniela Wilson Bio‐organic Chemistry
Luc van Kessel na&st Dr. Jörg R. Hörandel Astrophysics
Alex Kolmus sk Dr. Bas Y.T. van de Meerakker, Molecular and Laser Physics
Yvonne Lasarzewski bi Dr. Jo Huiqing Zhou Molecular Developmental Biology
Niels Neumann wi, na&st Dr. Walter D. van Suijlekom, Mathematical Physics
Elias Post sk Prof. dr. Floris P.J.T. Rutjes Synthetic Organic Chemistry
Christian Pruefert sk Dr. Martin C. Feiters Synthetic Organic Chemistry,
Freek Roelofs na&st Prof. dr. Heino D.E. Falcke Astrophysics
Suzanne Timmermans mlw Prof. dr. Wilhelm T.S. Huck Physical Organic Chemistry
Milo Vermeulen na&st Prof. dr. Wim J. van der Zande Molecular and Biophysics
Rebecca Wallrafen mlw Dr Dirk Schubert CNS donders
2 n d Y e a r R H A R e s e a r c h P r o j e c t s
34 R H A ‐ F NW I
Figure 2:. In‐situ hybridisation of lepa and NKA (which marks the ionocytes) in gills of SW acclimated
Atlantic salmon (parr). No overlay could be observed in the merged image.
Abstract: During saltwater acclimatisation of fish an adjustment of ion‐transporters in the gills takes place. For
this process a lot of glucose is needed. In this experiment the role of leptin in the energy regulation associated
with the regulation of osmosis in the Atlantic salmon is demonstrated.
Samenvatting: Tijdens zoutwater acclimatie vindt er een aanpassing van iontransporters in de kieuwen plaats,
waarvoor veel glucose nodig is. In dit experiment is de betrokkenheid van leptine in de energie regulatie
aangetoond tijdens het proces van osmoregulatie in de Atlantische zalm.
Leptin is a key hormone in regulation of feeding behaviour, energy homeostasis and high energy consuming
processes, like osmoregulation. In this study, we examined the potential role of leptin in energy (re)distribution
in liver and gills after an acute hyperosmotic challenge in smolt stage Atlantic salmon. During such a challenge,
the environmental salinity increases which influences the internal ion balance. By changing their
osmoregulatory system (e.g. different ion transporters), salmon are able to maintain homeostasis.
Atlantic salmon were acclimated to fresh water and transferred to salt water, or to fresh water as a
control. Fish were sampled at 0, 1.5, 4, 12, 24 and 72 h after transfer. qPCR analyses on lepa1, lepa2, lepr1 and
lepr2 were performed on gill and liver samples. In‐situ hybridisation with lepa and NKA was performed for
cellular localisation of lepa expression in the gills.
Figure 1. mRNA expression levels of (A) gill lepa1 and (B) liver lepa2 relative to elf1αa/20S of anadromous Atlantic salmon (smolts)
followed over time after fresh water – fresh water transfer (closed circles) and fresh water – salt water transfer (open circles). Values are
means ± SE (n=8). An asterisk indicates a significant difference between fresh water and salt water treatment at a given time as
determined by a Student’s t test. Different small and capital letters indicate significant differences between time points in respectively fresh
water and salt water treated salmon as determined by a one‐way ANOVA and a pairwise Tukey test. The significance level for all statistical
tests was P<0.05.
Plasma osmolality increased till 24 h after FW‐SW transfer, as did the expression of branchial lepa1 mRNA (transiently at 1‐3 h) and hepatic lepa2 mRNA (transiently at 4‐12 h). By in‐situ hybridisation we localised lepa1 in glycogen‐rich cells adjacent to ionocytes (mitochondrion‐rich cells). Gill lepa expression site and time of mRNA upregulation suggest involvement in glycogenolysis of the glycogen rich cells for energy supply during osmoregulation.
Leptin and energy regulation during seawater acclimation in
Atlantic salmon, salmo salar
Marloes van den Akker
Supervisor: M. Gorissen, department of animal physiology, Radboud University
0 20 40 60 800.0
0.2
0.4
0.6
0.8
FWFW
FWSW*
a/A
a/BC
a/B
a/AB
a/A
a/AC
Time (hours)
lepa
1ex
pres
sion
relat
ive to
elf1a
/20S
0 20 40 60 800.0
0.2
0.4
0.6
0.8 FWFW
FWSW
**
a/A
a/Aa/B
a/BC
a/C
a/BC
time (hours)
lepa
2ex
pres
sion
relat
ive to
elf1a
/20S
2 n d Y e a r R H A R e s e a r c h P r o j e c t s
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 35
TBP TBP2
Figure 1: Schematic representation
of gene expression change. Red
downregulated genes, blue
upregulated genes.
Abstract: During development specific gene expression is required, directed by transcription factors TBP and
TBP2. We have assessed the genome‐wide dependence on TBP and TBP2 in early Xenopus laevis embryos.
Genes dependent only on TBP, only on TBP2 and on both transcription factors were identified and give insight in
the role of the two factors during developmental gene expression.
Samenvatting: Het erfelijke materiaal – het DNA – is in iedere cel hetzelfde, maar in tijdens de ontwikkeling
komen in iedere cel op ieder moment andere genen tot expressie. Dit wordt gedirigeerd door
transcriptiefactoren zoals TBP en TBP. Sommige genen worden specifiek door een van deze twee factoren
aangezet en andere genen door beide. Dit onderzoek geeft inzicht in deze twee basale factoren tijdens de
ontwikkeling van kikkerembryos (Xenopus laevis).
The development of a single cell embryo into a complex multicellular organism requires coordinated gene
expression, where transcription factors play an important role. The basal transcription factor TATA‐box Binding
Protein (TBP) directs the assembly of the transcription machinery. A vertebrate specific paralog called TBP2
(TRF3) was found [1]. Although the two factors have a different expression pattern both factors are required in
the early embryo. A specialized role and a functional redundancy were proposed for the two factors [1,2,3].
By combining an antisense directed knockdown approach with next
generation sequencing, we have investigated the genome‐wide dependence on
TBP and TBP2 during early frog (Xenopus laevis) embryogenesis (NF stage 10.5).
TBP knockdown embryos (TBP > 90 %; TBP2 70 %) show a gastrulation
arrested phenotype as described before [1,2,3]. In figure 1 all genes
significantly changed more than fourfold are depicted on the y‐axis, red colors
mean downregulation, while blue colors mean higher expression in knockdown
embryos. Expression change for both TBP as well as TBP2 knockdown is shown.
Genes dependent on TBP, TBP2 or both factors were identified.
Although Jacobi et al [3] did TBP and TBP2 knockdown experiments, till now no
genome‐wide study was performed. Here we show specialized and redundant
roles for the two transcription factors with a genome‐wide approach. Future
works directed towards a double knockdown experiment or overexpression
studies with both transcription factors will yield more knowledge to systematically dissect developmental gene
regulation at the level of basal transcription factors.
References
[1] Jallow, Z.; Jacobi, U.; Weeks, D.; Dawid, I.; Veenstra, G.; Specialized and Redundant Roles of TBP and a Vertebrate‐Specific TBP Paralog in Embryonic Gene Regulation in Xenopus, PNAS (2004) 101: 13525‐13530 [3] Veenstra, G.; Weeks, D.; Wolffe, A.; Distinct Roles for TBP and TBP‐Like Factor in Early Embryonic Gene Transcription in Xenopus, Science (2000) 290: 2312‐2315 [3] Jacobi, U.; Akkers, R.; Pierson, E.; Weeks, D.; Dagle, J.; Veenstra, G.; TBP Paralogs Accommodate Metazoan‐ and Vertebrate‐Specific Developmental Gene Regulation, EMBO (2007) 26: 3900‐3909
TBP‐Family Members and their Role in Gene Expression during Early Xenopus laevis Development
Janine Arts
Supervisors: Sarita S Paranjpe, Gert Jan C Veenstra Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen
2 n d Y e a r R H A R e s e a r c h P r o j e c t s
36 R H A ‐ F NW I
Abstract: Energy for most processes in living cells is supplied by ATP hydrolysis, catalyzed by proteins called
ATPases. Their general mechanism is studied thoroughly, but details on the atomic scale remain speculative. We
studied gas‐phase ATPase active site mimics to elucidate how ATP is selectively recognized by ATPases against
other biomolecules, and how the local structure of the ATPase active site is affected upon ATP hydrolysis.
Samenvatting: Levende cellen hebben energie nodig voor de processen die erin plaatsvinden. Deze energie is
afkomstig van ATP‐moleculen die gehydrolyseerd worden door enzymen genaamd ATPases. Hoe dit plaatsvindt,
is in grote lijnen bekend, maar details op het niveau van individuele atomen zijn nog niet opgehelderd. In ons
onderzoek hebben we de werking van ATPases op deze schaal onderzocht door bindingssterktes en lokale
structuren te bestuderen van complexen van ATP met modellen van het actieve centrum van F1‐ATPase.
Hydrolysis of adenosine 5’‐triphosphate (ATP) in the active sites of
ATPases is a vital process, yet poorly understood at the atomic level [1‐2].
In our study, we explored gas‐phase local structure and binding
characteristics of complexes consisting of ATP bound to mimics of the F1‐
ATPase active site. The complexes were fragmented in a quadrupole ion
trap using collision‐induced dissociation and infrared multiple‐photon
dissociation. All complexes show fragmentation channels in which the
non‐covalent interactions between mimic and ATP are broken; the
doubly charged anionic complex of our monopeptide arginine mimic with
ATP exhibits an additional, hydrolysis‐like fragmentation channel in which
ATP loses its γ‐phosphate in the form of PO3− (fig. 1).
Bond strengths of the complexes, determined by measuring
breakdown diagrams (fig. 2), indicate that (i) ATP binds more strongly to
our monopeptide arginine mimic than ADP and G6P, (ii) the bond strength
Figure 1: Mass spectrum of simple dissociation (purple) and hydrolysis‐like fragmentation (blue) of the doubly charged ATP monopeptide arginine complex (red).
between ATP and different mimics depends on the charge and the structures of the mimics, and (iii) in the
doubly charged anionic complex of monopeptide arginine with ATP, the β‐γ phosphate bond of ATP is weaker
than the non‐covalent interactions between ATP and arginine. A structural explanation for the latter was sought
Figure 2: Breakdown diagrams of several complexes.
employing IR spectroscopy, but the obtained IR spectra of
this complex and its fragment after PO3− release should be
improved and compared with DFT calculations in order to
identify local structural features.
Besides exploring complexes in the ion trap set‐up,
the isolated gas‐phase structure of the neutral tripeptide
mimic Ac‐Glu‐Phe‐Lys‐NH2 was determined in a molecular
beam set‐up employing IR‐UV ion dip spectroscopy [3]. At least two conformers were discovered. Their
experimental IR spectra were compared with DFT calculations and both conformers were structurally assigned.
References
[1] Boyer, P.D. Biochim. Biophys. Acta, 1140(3), 215–250, 1993.
[2] Weber, J. and Senior, A.E. Biochim. Biophys. Acta, 1458(2‐3), 300–309, 2000.
[3] Jaeqx, S., Oomens, J. and Rijs, A.M. Phys. Chem. Chem. Phys., 15(38), 16341–16352, 2013.
Exploring structures and binding characteristics of gas‐
phase complexes of ATP with ATPase active site mimics
Koen K.W. van Asseldonk
Supervisors: dr. Anouk M. Rijs, IMM, Radboud University Nijmegen &
dr. Isabelle Compagnon, Institut Lumière Matière, Université Lyon 1.
m/z
2 n d Y e a r R H A R e s e a r c h P r o j e c t s
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 37
Abstract: The effect of knocking out heparanase in mouse models for anti‐GBM and LPS‐induced
glomerulonephritis was studied.
Samenvatting: De expressie van het enzym heparanase is verhoogd tijdens bepaalde nierziektes. We hebben
gekeken welk effect het heeft als we muizen twee verschillende nierziektes induceren terwijl deze muizen geen
heparanase tot expressie kunnen brengen.
Proteins are restrained from entering the urine by the glomerular filtration barrier (GFB). The GFB is composed
of fenestrated glomerular endothelial cells covered by the glycocalyx, the glomerular basement membrane
(GBM) and podocytes with interdigitating foot processes. When one of these layers is affected, albumin can
leak into the urine. Albuminuria is an independent risk factor for progressive renal diseases [1]. Heparan
sulphate (HS) is a negatively charged polysaccharide abundantly expressed in
the GFB. Loss of glomerular HS negatively correlates with the extend of
proteinuria [2]. HS is cleaved by heparanase (HPSE), which has been shown to
be essential for the development of proteinuria in experimental diabetic
nephropathy [3].
To evaluate the role of HPSE on the development of proteinuria in other
glomerular diseases, we induced anti‐GBM and LPS‐induced
glomerulonephritis in wildtype (WT) and Hpse‐deficient mice. We collected
their kidneys, urine and blood and determined proteinuria, renal function,
HPSE expression and influx of inflammatory cells in these mice. HPSE
expression was increased in anti‐GBM and LPS‐induced nephritis in WT mice.
LPS and anti‐GBM‐induced nephritis both increased albuminuria and blood urea nitrogen (BUN) levels. Hpse KO
mice showed a better renal as they developed less albuminuria and lower BUN levels compared to the WT
mice. Fibrinogen deposition was increased in time after induction of anti‐GBM nephritis, but was lower in Hpse
KO mice compared to WT mice. Glomerular granulocyte influx was increased during anti‐GBM and LPS‐induced
nephritis, with no differences between Hpse‐deficient mice and WT mice. Significantly lower numbers of
macrophages were observed in Hpse KO mice compared to WT mice. The expression of tumor necrosis factor
alpha (TNF‐α), a pro‐inflammatory cytokine, was increased in both models, but significantly lower in Hpse‐
deficient mice compared to WT mice. The reduced TNF‐α expression of the Hpse KO mice may be attributed to
the decreased glomerular macrophage influx, as macrophages produce TNF‐α. TNF‐α also stimulates HPSE,
which in turn activates macrophages creating a positive feedback loop. Therefore, we conclude that HPSE‐
deficiency protects against the development of proteinuria and renal damage, possibly by creating a less pro‐
inflammatory milieu.
[1] Singh, A. and S.C. Satchell, Microalbuminuria: causes and implications. Pediatr Nephrol, 2011. 26(11): p. 1957‐65. [2] Vandenborn, J., et al., Distribution of GBM heparan‐sulfate proteoglycan core protein and side‐chains in human
glomerular‐diseases. Kidney International, 1993. 43(2): p. 454‐463. [3] Gil, N., et al., Heparanase is essential for the development of diabetic nephropathy in mice. Diabetes, 2012. 61(1):
p. 208‐16.
The Role of Heparanase in Experimental Glomerulo‐
nephritis and LPS‐nephritis
Marilen Benner
Supervisor: Johan van der Vlag, Department of Experimental
Nephrology, Radboud University Nijmegen
Figure 1: 2 hours after induction of anti‐GMB nephritis leukocytes infiltrate theglomerulus. This is reduced in Hpse KOmice
2 n d Y e a r R H A R e s e a r c h P r o j e c t s
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Abstract: In De Peel habitat fragmentation led to the existence of only two small isolated populations of the
endangered smooth snake (Coronella austriaca). These remaining populations are probably too small to prevent
future effects of inbreeding and decreasing genetic variation. Therefore, smooth snake populations in De Peel
have a high risk of extinction.
Samenvatting: De Peel was ooit een groot hoogveengebied waarvan nu nog slechts enkele kleinere gebieden
over zijn. De bedreigde gladde slang (Coronella austriaca) komt hierdoor nog maar in twee van elkaar
gescheiden populaties voor. Deze populaties zijn waarschijnlijk te klein om de negatieve effecten van inteelt en
het verlies van genetische variatie te voorkomen. De Gladde slangen populaties in De Peel hebben daarom een
grote kans op uitsterven
The smooth snake (Coronella austriaca) (figure 1) is an
endangered snake species that lives in most parts of Europe
and the west part of Asia [1]. De Peel is a peatland area in the
south of the Netherlands and one of the areas where this
species lives. However, a large part of this big peatland area
disappeared due to drainage for peat extraction. Now only
two areas are left where this species still occurs. It was
hypothesized that this habitat fragmentation forms an
important threat for this species, as this could lead to small
and isolated populations. Small and isolated populations are
at risk of extinction because the resulting inbreeding and loss of genetic variation can severely impact these
populations [2].
In this research the influence of habitat fragmentation on smooth snake populations in De Peel was
studied. A DNA analysis was performed to look at the degree of isolation, the loss of genetic variation and the
amount of inbreeding. To estimate the population size, a capture‐mark‐recapture (CMR) analysis was used,
accounting for the imperfect detectability of this species [3].
The results of these analyses showed that the two remaining populations are isolated from each other,
but that there is currently no loss of genetic variation nor inbreeding. However, the population size of one of
the populations was estimated to lay between the 100 and 200 individuals. This population size is too small to
prevent the negative effects of inbreeding and loss of genetic variation [4]. These effects are therefore likely to
arise in the future and could eventually led to the extinction of these populations. It is thus concluded that
smooth snake populations in De Peel have a high risk of extinction.
References
[1] Spellerberg, I.F., Phelps, T. Biology, general ecology and behaviour of the smooth snake, Coronella austriaca Laurenti.
Biological Journal of the Linnean Society, 9(2), 133‐164, 1977
[2] Frankham R. Conservation genetics. Annual review of genetics, 29(1), 305‐327, 1995
[3] Williams, B., Nichols, J., Conroy, M. Analysis and management of animal populations. Academic Press, New York, 2002
[4] Franklin, I. “Evolutionary change in small populations”, Conservation Biology: An evolutionary perspective, 1980, pp 135‐
149
The influence of habitat fragmentation on smooth
snake (Coronella austriaca) populations in De Peel
Maarten Broekman
Supervisor: Prof. dr. Henk Siepel, Department of Animal ecology and
Ecophysiology, Radboud University Nijmegen
Figure 1: the smooth snake (Coronella austriaca)
2 n d Y e a r R H A R e s e a r c h P r o j e c t s
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 39
Abstract: This study has established the association of the SNP rs10175798 with rheumatoid arthritis (RA) and
has investigated the possible regulatory function of the region wherein the SNP is located.
Samenvatting: Dit onderzoek heeft het verband tussen de aanwezigheid van een veelvoorkomende mutatie in
het DNA, rs10175798, en het hebben van reumatïode artritis vastgesteld. Er is ook gekeken naar de gevolgen
van de mutatie voor de productie van eiwitten.
Rheumatoid arthritis is an autoimmune disease that affects about 1% of the worldwide population. It causes the inflammation of the joints. At the moment, the diagnosis of RA depends on the symptoms of the patients and the presence of two biomarkers: rheumatoid factor (RF) and anticitrullinated protein antibodies (ACPA). Both of these biomarkers are far from perfect (1). Therefore, a new biomarker is welcome. This research has used the T‐Plex PCR assay (2) to determine whether the presence of one of the alleles at the locus of the rs10175798 in the cell‐free DNA of patients can be used as a biomarker of RA. It has also looked into the functional role of rs10175798 in the pathogenesis of RA. SNPs, like rs10175798, can be either linked or causative in relation to a disease. Causative genes can be located in coding or non‐coding, regulatory regions. Whether or not a SNP is indeed located in a regulatory element can be determined by a luciferase assay. This assay shows differences in expression depending on the allele that is present.
The results of the T‐Plex PCR assay (fig. 2 and 3) show that the AG genotype and the A allele are more common amongst RA patients.
During this research, the rs10175798 locus in the cfDNA of healthy controls, RA patients and RRMS patients has been genotyped. Although there seems to be an association of the AG genotype and the A allele, this is not significant.
References
[1] Scott, D. L., Wolfe, F., Huizinga, T. W. J. (2010) Rheumatoid arthritis. Lancet, 376, 1094‐1108. [2] Baris, I., Etlik, O., Koksal, V., Ocak, Z., & Baris, S. T. (2013). SYBR green dye‐based probe‐free SNP genotyping: Introduction of T‐Plex real‐time PCR assay. Analytical biochemistry, 441(2), 225‐231. [3] http://learn.genetics.utah.edu/content/pharma/snips/, retrieved on 14‐9‐2014
rs10175798 as a possible biomarker for rheumatoid
arthritis
Lotte Eilander
Supervisors: dr. M. Dunaeva and prof. dr. G.J. Pruijn,
Biomolecular Chemistry, Radboud University
Figure 2: The different kinds of SNPs in relation to disease.
Figure 3: The genotype distribution among controls (blue),all RA patients (red) and RRMS patients (green). The oddsratio (OR) calculated for the different genotypes indicatethat AG is associated with RA, while GG is the protectivegenotype. None of these results however, are significant.
Figure 3: The allele frequencies among the controls, all RA patients and RRMS patients. The OR shows that the A allele might be associated to both RA and RRMS. These results are not significant.
2 n d Y e a r R H A R e s e a r c h P r o j e c t s
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Abstract: This study showed by use of immunohistochemistry that p53 expression is commonly abnormal in pancreatic ductal adenocarcinoma (PDAC), suggesting mutated TP53. However, p53 expression seemed to be normal in all patient cases of chronic pancreatitis (CP), indicating a possible discriminating factor. This difference could be used to improve clinical decision‐making. Samenvatting: Deze studie laat door middel van immunohistochemie zien dat p53 expressie vaak afwijkend is in pancreaskanker, als gevolg van een gemuteerd TP53 gen. Aan de andere kant wordt er in alle patientencasussen met chronische pancreatitis geen afwijkend p53 expressiepatroon waargenomen. Dit zou mogelijk een onderscheidende factor kunnen zijn tussen beide ziekten. Dit resultaat kan worden gebruikt om diagnosis beter en sneller te kunnen stellen.
Pancreatic ductal adenocarcinoma (PDAC)
has one of the worst prognoses of all
cancer types with only a 5‐years survival of
3‐5%. Many risk factors for pancreatic
carcinogenesis have been found of which
chronic pancreatitis (CP), an inflammatory
disease of the pancreas, is suggested as an
important factor for this development [1].
Four driver mutations are associated with
PDAC: KRAS, CDKN2A/P16, TP53 and
SMAD4 [2]. This study focused on the
prevalence of these driver mutations in patients with PDAC and CP in order to facilitate differential diagnosis.
A PALGA search identified 23 patients with PDAC and 7 patients with CP on the availability of formalin‐fixed
paraffin embedded (FFPE) tissue and corresponding clinicopathological data. Immunohistochemistry was used
to analyze the prevalence of p53 and p16 expression in both diseases. Additional DNA isolation of all patient
samples was performed for sequencing analysis. The results showed that abnormal p53 expression can be
found in 82.6% (p=0.002) in PDAC and 0% in CP respectively. Normal p16 expression is observed in 100% of the
cases in PDAC and CP. In conclusion, the prevalence of TP53 mutations might be useful in differentiating PDAC
from CP. More molecular insights in the interactions between CP and pancreatic ductal adenocarcinoma are
needed to facilitate differential diagnosis and to improve clinical decision‐making.
References [1] Rosty C, Geradts J, Sato N, Wilentz RE, Roberts H, Sohn T, Cameron JL, Yeo CJ, Hruban RH, Goggins M. p16 Inactivation in
pancreatic intraepithelial neoplasias (PanINs) arising in patients with chronic pancreatitis. Am J Surg Pathol
2003;27(12):1495‐501. [2] Yachida S, White CM, Naito Y, Zhong Y, Brosnan JA, Macgregor‐Das AM, Morgan RA, Saunders T, Laheru DA, Herman JM
and others. Clinical Significance of the Genetic Landscape of Pancreatic Cancer and Implications for Identification of
Potential Longterm Survivors. Clinical Cancer Research 2012;18(22):6339‐6347.
Prevalence of TP53, CDKN2A/P16 mutations useful in Pancreatic Adenocarcinoma and Chronic Pancreatitis differential diagnosis Lisanne Gommers
Supervisors: Prof. dr. Iris Nagtegaal, Monica van Zanten,
Department of Pathology, Radboudumc
Figure 4: Immunohistochemical analysis of p53 in PDAC and CP.
2 n d Y e a r R H A R e s e a r c h P r o j e c t s
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 41
Abstract: Using ChIPseq and RIPseq methods we investigate the possible role of RNAs during the recruitment of
Polycomb repressive complex 2 (PRC2), an epigenetic regulator involved in development.
Samenvatting: Het eiwit PRC2 onderdrukt genen, met name gedurende de vroege ontwikkeling van embryo’s.
In dit onderzoek kijken we met moderne moleculaire technieken, hoe PRC2 hun doelwit genen kan vinden.
How do cells maintain their identity? During development cells specify into different tissues and subsequently
this has to be maintained. Disruptions in this process are likely to cause malformations and loss of tissue
function. All cells in a multicellular body originate from a single cell, the zygote, and mainly have the same DNA
content. Due to this fact there have to be mechanisms that control the activation and repression of tissue and
cell specific gene sets. This happens on an epigenetic level of regulation. Epigenetics regulate gene expression
without changing the underlying DNA sequence.
Polycomb repressive complex 2
(PRC2) plays an important role in the
epigenetic regulation during
development and has histone
methyltransferase activity. Mutations
in this gene lead to early lethality in
vertebrates and cancer. Ezh2, as the
catalytic active subunit of PRC2, places
the repressive H3K27me3 mark on the
genome. A central question regarding
PRC2 is, how it is recruited to its
target genes. [1] [2]
Chromatin Immunoprecipitation
sequencing (ChIPseq) is a method
identifying all locations on the genome to which a certain protein binds. Here we adapt the ChIP protocol for
zebrafish, making it more efficient by reducing the number of embryos and finding a correct antibody for
zebrafish Ezh2. Furthermore we take the first steps to apply RNA Immunoprecipitation sequencing (RIPseq) in
zebrafish, giving all the RNAs interacting with Ezh2. By combining these two methods we can find Ezh2 binding
loci and the Ezh2 interacting RNAs to elucidate how PRC2 is recruited to the genome. Furthermore we
investigate the role of Ezh2 at the mid blastula transition in a maternal paternal zygotic nonsense mutant and
find a shift in expression of genes around MBT. This findings and earlier reports imply a model in which Ezh2
can sense the expression state of a gene by its nascent RNA transcript and repress these.
References
[1] Margueron, R. & Reinberg, D. (2011) The Polycomb complex and its mark in life. Nature, 469(7330), 343‐349
[2] Surface, L. E., Thorton, S.R., Boyer, L.A. (2010). Polycomb group proteins set the stage for early lineage commitment.
Cell Stem Cell, 7(3), 288‐298
Recruitment of Polycomb Repressive complex 2 by
RNAs in zebrafish
Carolin Heller
Supervisor: Dr. Leonie M. Kamminga, Dept. Molecular Biology, RIMLS
Figure 1: Ezh2 and H3K27me3 ChIP qPCR. 1 to 3 are known H3K27me3 targets, 4 and5 are Czb1 and ZOzb1 enhancers and 6 the irx3 promoter. Neq1 and neg2 are negative controls.
2 n d Y e a r R H A R e s e a r c h P r o j e c t s
42 R H A ‐ F NW I
Abstract: PrOs4Sb12 belongs to the class of strongly correlating electron systems. In this class of materials, the
complexity of the electronic behaviour gives rise to novel and unusual electronic and magnetic properties. In this
study, we have performed experiments at high magnetic fields to examine the strength and evolution of the
electronic interactions.
Samenvatting: In bepaalde materialen hebben de elektronen sterke interacties met elkaar. Hierdoor kunnen
interessante fenomenen als supergeleiding optreden. Echter, door de complexiteit van deze interacties is het
lastig om deze materialen volledig te begrijpen. In dit onderzoek zijn we door middel van hoge magneetvelden
meer te weten gekomen over de werking van PrOs4Sb12 , dat ook tot deze groep materialen behoort.
Strongly correlated electron systems are one of the most interesting
classes of materials, since they often exhibit intriguing phenomena such
as unconventional superconductivity, different types of magnetism and
heavy fermion behaviour. Today, there is still much unknown about the
mechanisms responsible for these phenomena, although complex
interactions between the electrons are considered to play a major role.
Since 2002, PrOs4Sb12 has been studied actively because of the presence
of unconventional superconductivity [1], an antiferro‐quadrupolar (AFQ)
ordered phase [2], and heavy fermion behaviour. The combination of
these features makes this material an interesting model to study, hoping
that it can provide more insight into similar materials.
We have performed an extensive torque magnetometry study of
PrOs4Sb12 in high magnetic fields, consisting of measurements at
different sample orientations and temperatures. Using torque
magnetometry (see figure 1), one can measure small changes in the
magnetisation of a sample. We have used this technique to measure
quantum oscillations in the magnetisation, from which the quasipaticle
masses can be determined.
These masses have been determined at high magnetic fields up to
33 T, where it was found that these masses do not change significantly
as a function of the magnetic field, see figure 2. Therefore this suggests
that the multipole fluctuations in the AFQ phase do not contribute to the
mass enhancement of the quasiparticles, as was previously suggested.
In addition to this result, we have found in one of the samples a
magnetic transition at 21 T, suggested to be a spin‐flop transition, see
figure 3. This could mean that there is antiferromagnetism present in
PrOs4Sb12 at high magnetic fields, something that may help towards a
better understanding of the various features this material exhibits.
References
[1] Bauer, E. D. et al. Superconductivity and heavy fermion behavior in PrOs4Sb12. Physical Review B, 65: 100506, 2002.
[2] Kohgi, M. et al. Evidence for magnetic‐field‐induced quadrupolar ordering in the heavy‐fermion superconductor
PrOs4Sb12. Journal of the Physical Society of Japan, 72: 1002–1005, 2003.
Torque Magnetometry Study of PrOs4Sb12 in High
Magnetic Fields
Niels Hesp
Supervisor: Dr. Alix McCollam, High Field Magnet Laboratory (IMM),
Radboud University Nijmegen
20 22 24 26 28 300
1
2
3
4
5
6
Magnetic field (T)
Eff
ecti
ve m
ass
(me)
18
β
α
Figure 2: Quasiparticle masses as functionof the magnetic field.
Magnetic field (T)
°-4°°°°°°°°
°
(i)
(ii)
(iii)
Figure 3: Measured torque as function of themagnetic field. The broad peak at 21 T issuggested to be a spin‐flop transition.
400 μm
Figure 5: One of our samples mounted on acantilever used for torque magnetometry.
2 n d Y e a r R H A R e s e a r c h P r o j e c t s
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 43
Figure 1: The non‐additivity, below 0, as function of p
Abstract: The additivity of the capacity of two quantum channels was one of the oldest problems in quantum
theory probability, which is equivalent with the additivity of the minimal output von Neumann entropy of
quantum channels. It has been shown that for the generalization, the minimal output Rényi p‐entropy, the
additivity conjecture is false for all p greater than 1, and eventually also for p=1. It will be shown that there is a
certain p0 below 1, which can be explicitly found, such that for all p>p0 the additivity conjecture for the minimal
output Rényi p‐entropy is false.
Samenvatting: In de kwantumversie van de kansrekening, waarbij kansverdelingen worden vervangen door
speciale matrices, namelijk dichtheidsmatrices, geven al deze dichtheidsmatrices een waarde aan de minimale
output Rényi p‐entropie. Deze waarde geeft als het ware aan in hoeverre een niet‐verstrengelde vector
verstrengeld raakt wanneer de dichtheidsmatrix op deze vector werkt. Er was een vermoeden dat zei wanneer
je twee dichtheidsmatrices neemt, en de minimale output Rényi p‐entropie van beide matrices bij elkaar optelt,
dat dit gelijk is aan de minimale output Rényi p‐entropie van de matrix die je krijgt wanneer je de ene matrix als
het ware invult in de andere matrix. Nu blijkt dit niet zo te zijn voor bepaalde waarden van p, waar een grens
wordt gegeven waarvan zeker is dat voor alle waarden boven deze grens die twee waarden verschillen.
Quantum information theory deals mainly about the
different properties of quantum channels, positive semi‐
definite matrices with trace 1. One of those properties is
the minimal output Rényi p‐entropy of a quantum
channel, which is derived from the Rényi p‐entropy. The
entropy itself defines a lower bound for the average
amount of bits used to encrypt a message, which still
allows a unique decoding. The output entropy can be seen
as how much a pure stat, becomes mixed as the quantum
channel acts on the pure state. The question which arose
together with the minimal output Rényi p‐entropy was
whether the quantity is additive under tensor products.
It was soon discovered that, in general, this is not the case, which was eventually brought back to non‐
additivity for all p≥1. However, using [1] together with [2], we showed that the bound of 1 can be lowered to
around 0.9964, see figure 1. To do so, the dimension of the output of the quantum channel were taken to
infinity, which made it possible to calculate a value for p0, instead of mere existence.
However, it might be possible to get an even lower bound by using [3], where the value of one half
would be the most interesting case, as it has an equivalence with the Arveson norm. However, at this time it is
not clear whether there is additivity or not for the value of p is one half.
References
[1] Guillaume Aubrun, Stanislaw Szarek, and Elisabeth Werner. Hastings additivity counterexample via Dvoretzky’s theorem.
Communications in Mathematical Physics, 305(1): 85‐97, 2011.
[2] Motohisa Fukada, Christopher King, and David K Moser. Comments on Hastings additivity counterexamples.
Communications in Mathematical Physics, 296(1): 111‐143, 2010.
[3] Patrick Hayden. The maximal p‐norm multiplicativity conjecture is false. arXiv preprint arXiv:0707.3291, 2007.
Non‐additivity of Rényi p‐entropy for p>p0
Wouter Hetebrij
Supervisor: Prof. Dr. J.D.M. Maassen, department of Applied Stochastics,
Radboud University
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Abstract: In this research we propose two new protocols in group‐based cryptography. These protocols employ
either different one‐way functions or different groups than the currently available protocols in group‐based
cryptography.
Samenvatting: In ons onderzoek stellen we nieuwe vormen van cryptografie voor. Dit met de bedoeling om een
alternatief te bieden op de huidige vormen van cryptografie die veelvuldig gebruikt worden in verscheidene
maatschappelijke toepassingen.
Traditionally cryptography is the science of writing in secret code. Its main objective is to enable
communication between two or more parties without eavesdroppers being able to intercept this
communication. Presently there is an increasing demand for secure cryptosystems due to the enormous
increase in the interest for Internet shopping, electronic financial transfers, etcetera.
The basic idea of cryptography is the use of a so‐called one‐way‐
function or trapdoor‐function: an action which is easy to perform but
hard to invert, except if one is in the position of having some ‘extra’
knowledge. In this case it should again be easy to invert to process, as
is explained in figure 1.
Over the past decades, attempts have been made in order to create
secure cryptographic protocols, based on several mathematical
structures. From these, the protocols based on number theoretic
issues have been most widely used and form the core of nearly all
contemporarily used cryptographic protocols.
In our research we have attempted to set up protocols based on the structure of non‐abelian groups and
thereby contribute to the research called group‐based cryptography. [1]
A group is a mathematical structure consisting of a set of objects and an operation on these objects, which is
invertable. Examples of groups used in our research are groups of matrices, SL(4,p), and permutation groups,
Sn.
In our research, we have designed two new protocols
based on group theoretic issues. In one of the protocols,
the novelty is that we introduce a new one‐way‐function,
conjugacy of subgroups, while in the other protocol we
use a standard one‐way‐function but implement it on a
novel class of groups which has not been used for
cryptographic purposes before.
References
[1] Myasnikov A., Shpilrain B., Ushakov A., Group‐based Cryptography. Advanced Courses in Mathematics, CRM Barcelona,
2007.
Group‐based Cryptography
Serge Horbach
Supervisor: Dr. B. Souvignier, IMAPP, Radboud University
Figure 6: trapdoor function
Figure 7: Cryptographic device
2 n d Y e a r R H A R e s e a r c h P r o j e c t s
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 45
Figure 8, Transmission electron microscopy image of azide‐functionalized polymer stomatocyte.
Abstract: The aim of this research was to prepare polymer stomatocytes, bowl‐shaped polymeric vesicles,
modified on the outer surface with a temperature responsive polymer to be able to open and close the
structure. To this end, dual‐functionalized polymer stomatocytes were prepared containing azide‐ and amine‐
functionalities and poly‐N‐isopropyl acryl amide was successfully synthesized using single electron transfer –
living radical polymerization.
Samenvatting: Het doel van dit onderzoek was om nanostructuren te maken die de vorm van een kommetje
hebben waarop een temperatuur gevoelige component aan vast gemaakt kan worden om de structuur te
openen en the sluiten. Hiervoor zijn nanostructuren gemaakt die aan de binnen en buitenkant verschillend zijn
en zijn er temperatuur gevoelige componenten gesynthetiseerd
Polymer stomatocytes, bowl‐shaped polymeric vesicles, are interesting structures for biomedical applications
and have recently been investigated as nanomotors. Their bowl‐like shape enables them to capture catalytic
platinum nanoparticles which catalyze the decomposition reaction of hydrogen peroxide into water and
propelling oxygen.[1]‐[3] Temperature‐dependent stimulus responsive polymers attached to the surface of
polymer stomatocytes were expected to allow further control over their structure and function upon a
temperature stimulus. Such a temperature‐dependent structure is achieved by self‐assembling amphiphilic
block copolymers into polymersomes followed by an induced osmotic shock to transform the shape into a
polymer stomatocyte. Functional handles were introduced to the polymers to enable further modification of
the stomatocytes with the temperature‐responsive polymer poly‐N‐isopropyl acryl amide, poly‐NIPAM.
Dual‐functionalized polymer stomatocytes were prepared by reducing
the outer surface of azide‐functionalized polymer stomatocytes into
amines. These structures were analysed using transmission electron
microscopy, figure 1, zeta‐potential measurements and fluorescence
measurements. These experiments confirmed that polymer
stomatocytes were formed and that there were amines present on the
surface of the stomatocytes.
Poly‐NIPAM was successfully synthesized using single electron transfer
– living radical polymerization, SET‐LRP [4]. Kinetics experiments were
used to determine the optimal conditions for this synthesis, which are
at 0 °C using Cu(I)Br as a catalyst.
These two parts are currently in progress to prepare poly‐NIPAM modified polymer stomatocytes.
References
[1] Wilson, D.A., Nolte, R, J. M., van Hest, J.C.M. Nature Chem. 2012, 4, 268‐274. b) Wilson, D.A., Nolte, R, J. M., van Hest,
J.C.M. J. Am. Chem. Soc., 134, 9894, (2012).
[2] Wilson, D.A., de Nijs, B., van Blaaderen, A., Nolte, R, J. M., van Hest, J.C.M., Nanoscale, 2013, 5, 1315.
[3] Abdelmohsen, L. K. E. A., Peng, F., Tu, Y. Wilson, D. A.*, J. Mater. Chem. B., 2014, DOI: 10.1039/C3TB21451F.
[4] B. M. Rosen, V. Percec, Chemical Reviews, 109, p5069‐5119, 2009.
Opening and Closing of Polymer Stomatocytes
using Temperature‐Dependent Stimulus Responsive
Polymers
Shauni Keller
Supervisor: Dr. D. A. Wilson and L. K. E. A. Abdelmohsen, Department of
Bio‐Organic Chemistry, Radboud University Nijmegen
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46 R H A ‐ F NW I
Abstract: LORA is a scintillation detector array detecting cosmic rays. LORA can reconstruct some important
shower parameters for each shower: arrival angle, core position and the number of particles. In this project, the
reconstruction uncertainties for these parameters have been determined by simulation.
Samenvatting: LORA is een meetopstelling die aan kosmische straling meet. Dat zijn deeltjes uit de ruimte, die,
als ze de atmosfeer bereiken, een hele cascade aan nieuwe deeltjes maken. LORA kan bepaalde eigenschappen
van zo'n cascade meten. In dit project zijn de onzekerheden in zo'n meting bepaald.
Cosmic rays are highly energetic (energies range from 108 to 1021 eV) charged particles travelling through the
Universe. When a cosmic ray interacts with the Earth's atmosphere, a number of new particles are created.
Each of these can create yet more particles, causing a cascade, or “air shower”.
LORA can reconstruct a number of shower parameters. These include the core position, arrival angle and the
number of charged particles. Previously, the uncertainties for such reconstructions have only been determined
by measurement, see [1]. In this project, they were determined by simulation.
LORA can reconstruct a number of shower parameters. These include the core position, arrival angle and
the number of charged particles. Previously, the uncertainties for such reconstructions have only been
determined by measurement. In this project, they were determined by simulation.
First, air showers were simulated with CORSIKA. The output of this simulation is a set of particles at
ground level. These were then fed into a simulation of the LORA detector set‐up in GEANT4. The result from
this simulation is the total energy deposit per detector, along with times of arrival.
The output from the GEANT4 simulation was
then given to the existing reconstruction
algorithm for LORA measurements. The output
from this reconstruction algorithm was then
compared to the initial values provided by
CORSIKA.
The result of this analysis can be found in Table 1. In this table, the simulated uncertainties are compared to
the measured values. For the uncertainties in core position and arrival angle, the simulation and measurement
agree very well. However, the simulated uncertainty for the number of charged particles is much lower than
the measurement.
The reason for this discrepancy is currently unknown, though we have a suspicion. In order to save
processing time, CORSIKA does not simulate full showers. Instead, some particles are left out and others are
given a weight factor. In undoing this “thinning” procedure, care is usually taken to keep average distributions
the same [2]. However, natural fluctuations in the shower may be flattened. Due to the large amount of
computing power required, it was not possible to verify this possibility.
References
[1] S. Thoudam. Propagation of Cosmic Rays in the Galaxy and their measurements at very high energies with LORA. PhD
thesis, Radboud University Nijmegen, June 2012.
[2] B.T. Stokes, R. Cady, D. Ivanov, J.N. Matthews, and G.B. Thomson. Dethinning extensive air shower simulations.
Astroparticle Physics, 35(11):759‐766, 2012.
The reconstruction uncertainties of the Lofar
Radboud Air Shower Array – LORA
Luc van Kessel
Supervisor: Dr Jörg Hörandel, department of Astrophysics, Radboud
Quantity Simulated Measured [1]
Core position (m) 5.4 ± 0.3 5 ± 0.5
Arrival direction (°) 0.9 ± 0.1 0.8 ± 0.2
Particle number (%) 11 ± 3 27 ± 2
Table 1: Reconstruction uncertainties for LORA
2 n d Y e a r R H A R e s e a r c h P r o j e c t s
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 47
Abstract: Improving upon our understanding of chemical reactions, that is the underlying goal of measuring
spikes, also known as resonances, in the interaction probability between two molecules in the gas phase.
Simulations indicate that measuring these resonances is possible when using a particular setup. During the
characterization of this particular setup a critical component exhibited weird behaviour. A closer look into this
behaviour revealed that the molecular beam generator is bouncing. This bouncing prevented a full
characterization of the setup. Future studies should be able to complete the characterization and measure the
resonances, after repair or replacement of the beam generator.
Samenvatting: Wat gebeurt er exact met moleculen in een vlam? Fysici en chemici weten dit nog niet. Om dit
beter te begrijpen wordt er gekeken naar resonanties, plotselinge toenames in reactiesnelheden, in
molecuulbotsingen bij lage temperaturen. Het observeren van deze resonanties erg lastig. Tijdens mijn stage
heb ik met behulp van simulaties bewezen dat we onder de juiste omstandigheden deze resonanties kunnen
waarnemen en een opstelling gebouwd en (deels) gekarakteriseerd waarmee het mogelijk moet zijn om
resonanties te kunnen meten.
Our understanding of chemistry at low temperatures, in
combustion processes and outer space is lacking.
Resonances in molecule – molecule collisions can be a
stepping stone to further our understanding [1]. These
resonances are a direct consequence of quantum
mechanical effects on the potential between the two
molecules. A theoretical study shows that for NH3 and H2
collisions, resonances occur below collision energies of 50
cm‐1 (10‐21 Joule) [2], see figure 1. To be able to measure
these resonances three things are required: simulations to
prove the feasibility of the experiment, an apparatus
which can collide at sufficiently low energies and the
characterization of this apparatus.
Simulations indicated that collision energies as
low as 24 cm‐1 can be reached while keeping the
resolution sufficient to observe the resonances. The
critical component in the apparatus is the Even‐Lavie valve: a small gas container which can create very neat
gas pulses at temperatures of 4 K. During the characterization of the Even‐Lavie valve, it did not function
properly. After elaborate testing it appeared that the valve was bouncing; instead of producing one single
pulse, it produced several pulses. This bouncing prevents us from having full control over the experiment and
could potentially destroy the setup when operating at low temperatures.
In conclusion, initial steps have been made to observe resonances in the NH3 – H2 system. If the valve
is repaired and can be cooled down to sufficiently low temperatures, resonances will be measured.
References
[1]. Chandler, D. W. (2010) Cold and ultracold molecules: Spotlight on orbiting resonances. The journal of Chemical physics,
132(11), 110901
[2]. Personal communications with Ad van der Avoird and Paul Dagdigian.
Towards resolving resonances in cold collisions
Alex Kolmus
Supervisor: Dr. Bas van de Meerakker, Department of Molecular and
Laser Physics, Radboud University Nijmegen
Figure 9: Top: the cross section between NH3 and H2. Thehorizontal axis is the collision energy and the vertical axis represents the cross section, a measure for interaction probability. Each strong peak indicates a resonance. Bottom left: the post‐collision angles when a resonance occurs. Bottom right: the post‐collision angles when the collision is not on a peak.[2]
2 n d Y e a r R H A R e s e a r c h P r o j e c t s
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Abstract: To study early embryonic development in vitro the technology of human induced pluripotent stem
cells (iPSC) can be used. In this project gene regulation during epithelial differentiation in an iPSC model was
studied. Since differentiation of iPSCs towards keratinocytes is heterogeneous, single cell RNA‐Seq was used to
profile gene expression in iPSCs.
Samenvatting: “Induced pluripotent stem cells” zijn cellen die op embryonale stam cellen lijken. De cellen
kunnen gebruikt worden om vroege embryonale ontwikkeling te studeren. In dit project heb ik iPSC gebruikt om
de rol van genen in de ontwikkeling van de huid te onderzoeken.
The research question addressed in this project is to understand gene regulation of epithelial differentiation
using an iPSC model. Two objectives were addressed in this project, to establish epithelial differentiation of
iPSCs and to establish single‐cell RNA‐Seq to profile gene expression in iPSCs. To study epithelial development
iPSCs can be differentiated into keratinocytes [1]. In this
work, differentiation of human iPSCs was induced with
KSFM medium supplemented with retinoic acid and
BMP4. As seen in Figure 1 cells showed soon after
induction of differentiation cobblestone morphology
which is characteristic for keratinocytes (Figure 1, A).
Expression of the early differentiation markers for
epithelial differentiation K8, K18 and Pax6 was clearly
induced. Expression of p63 and K14 that are mature
epithelial markers was slightly induced. However, cell
morphology changed when the cells were growing more
densely, and differentiation gave rise to a heterogeneous
cell population (Figure 1, B).
To be able to study the underlying gene regulation in this heterogeneous cell
population, the use of single cell RNA‐Seq is thus necessary. In this project
single iPSCs were prepared for sequencing [2]. Single cells were picked by
mouth pipetting (Figure 2) and lysed. After reverse transcription and second
strand synthesis cDNA was amplified by PCR. Then cDNA was prepared for
sequencing. Bioinformatic analysis of the RNA‐Seq data will give insight in
the underlying molecular mechanisms of epithelial differentiation.
References
[1] Itoh, M.; Kiuru, M.; Cairo, M. S.; Christiano, A. M., Generation of keratinocytes from normal and recessive
dystrophic epidermolysis bullosa‐induced pluripotent stem cells. Proc. Natl. Acad. Sci. U. S. A. 2011, 108 (21), 8797‐8802
[2] Tang, F. C., Barbacioru, C., Wang, Y., Nordman, E., Lee, C., Xu, N., Wang, X., Bodeau, J., Tuch, B.B., Siddiqui, A., Lao,
K., Surani, M.A., mRNA‐Seq whole‐transcriptome analysis of a single cell. Nature Methods 2009.
Figure 10: Morphology of cells at day 5 and 13 of the differentiation experiments. Cells show the cobblestone morphology soon after differentiation was initiated. However, cell morphology becomes more heterogeneous when cells grew more densely.
Day 5 Day 13
A B
Epithelial differentiation of human induced pluri‐
potent stem cells and single cell RNA‐Sequencing
Yvonne Lasarzewski
Supervisor: Dr Jo Huiqing Zhou, Department of Molecular Developmental
Biology, Radboud University Nijmegen
External Supervisor: Dr Fuchou Tang, Biodynamic Optical Imaging Center,
Peking University
Scale bar: 30µmFigure 11: Single cells prepared for picking with a micro‐pipette.
2 n d Y e a r R H A R e s e a r c h P r o j e c t s
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 49
Abstract: In our research we focussed on a mathematical structure defined in the context of non‐commutative
geometry. We tried to understand the structure and apply it to the Standard Model of Particle Physics.
Samenvatting: De kleinste deeltje die er bestaan op de wereld kunnen we wiskundig beschrijven. Samen met
mijn begeleider heb ik geprobeerd om deze beschrijving beter te begrijpen en daarna te verrijken.
Geometry is an ancient part of mathematics which can be traced back to the ancient Greeks and further. Euclides and Newton used geometry in their work and Einstein used geometry for his famous theory of gravity. In order to develop his general theorem of relativity he had to use some kind of geometry, more specifically Einstein used Riemannian geometry. In this way, Einstein’s theory could describe gravity. The other three fundamental forces, the weak and strong nuclear force and the electromagnetic force, could not yet be described by it despite many effort. Many have tried to generalize Einstein’s theory, but it was Alain Connes in the twentieth century who found a generalization that allows for the inclusion of the other forces as well. The result was non‐commutative geometry and it generalizes Riemannian geometry. With this generalization it was also possible to describe the Standard Model of Particle Physics at least at the classical level. In 2013 an article was published in which non‐commutative geometry was further generalized by the disposal of one of the conditions, namely the first order condition [2].
We tried to understand this generalization better. In order to do so we concretely determined the perturbation semigroup for some simple examples, after which we determined the perturbation semigroup of all matrix algebras. After this we looked at the general structure of this perturbation semigroup and how it behaved under mathematical operations, such as the direct sum and the tensor product. We also looked at the perturbation semigroup of smooth functions over an algebra. With this results combined we could determine
the perturbation semigroup of the Standard Model of Particle Physics, which can be seen in figure 2.
Eventhough this expression looks
hideous, it is in fact quite
beautiful. The entire Standard
Model is encoded in this
expression. In fact, one can even
find the famous Higgs‐boson in
this expression.
References
[1] A. Connes. Gravity coupled with matter and the foundation of non‐commutative geometry. Comm. Math. Phys.,
182(1):155–176, 1996.
[2] A.H. Chamseddine, A. Connes, and W.D. van Suijlekom. Inner fluctuations in non‐commutative geometry without the
first order condition. J. Geom. Phys., 73:222–234, 2013.
Perturbation semigroup for matrix algebras
Niels Neumann
Supervisor: Dr. W.D. van Suijlekom, department of Mathematics, IMAP,
Radboud University Nijmegen
Figure 12: The Standard Model of Particle Physics
Figure 2: The Standard Model of Particle Physics in terms of the perturbation semigroup
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Abstract: All the reaction steps in the synthetic procedure for synthesizing [n]‐ladderanes were optimized for
the use in a flow setup to make way for large scale production.
Samenvatting: Er is getracht een ladderaan, een laddervormig molecuul, te synthetiseren door elke reactie stap
te optimaliseren en toepasbaar te maken voor flow chemie, een nieuwe synthese techniek.
After the discovery that ladderanes (figure 1), ladder‐like molecules that consist of multiple fused cyclobutane
rings, are prevalent in nature, research into this molecule increased drastically. Multiple synthetic procedures
were proposed because of the scarce availability of ladderanes. However no procedure to date has been very
successful, they either have very low yields or are time consuming. Therefor this research report proposes a
different method of synthesizing ladderanes, namely with the use of flow chemistry (figure 2), an up and
coming synthetic approach that makes large scale synthesis easily attainable.
Several steps in the synthetic procedure had to be optimized: The ozonolysis
reaction, the Wittig reaction, the [2+2] cycloaddition reaction and the
reduction of an ester to an aldehyde. The optimisation entailed that all
reagents and side products had to be soluble in the same organic solvent for
each reaction step. All the side products also had to be easily purified using
aqueous extraction. Once this is achieved any size ladderane is attainable
because the cyclic setup of the synthetic procedure.
Multiple reducing agents for the ozonolysis reaction were attempted
but not a single one was both soluble in an organic solvent after oxidation and removable by aqueous
extraction. For the Wittig reaction multiple phosphine ylides were attempted, decreasing the length of the
carbon chains attached to the phosphine atom increased its reactivity drastically and increased the solubility of
the phosphine oxide byproduct in water. The negative side to making the carbon chains too short is that the
ylide becomes too reactive and easily gets hydrolyzed. The [2+2] cycloaddition reaction was only successful
when performed on a completely pure sample, making removal of the side
products mandatory. Also the cyclized product’s stereochemistry is not
influenced by which stereoisomer is used as a reagent because the
reagent isomerizes during the illumination period. For the reduction of
ester to aldehyde both LDBBA and DIBAL were used as an reducing agent
but both were unsuccessful at multiple reaction temperatures, apparently
the ester is very unreactive.
Possible alterations to the synthetic procedure could be to use tripropylphosphine as a reducing agent for the
ozonolysis reaction and as reagent for a new ylide because it is likely that tripropylphosphine oxide can be
removed with aqueous extraction. Another alternation that could make the procedure more efficient would be
remove the ozonolysis step and start differently such as with a Diels‐Alder reaction or with a metathesis
reaction.
References
[1] Xiuchun Gao, Tomislav Friscic and Leonard R. MacGillivray, Angew. Chem. (2004), 23, 232–236.
[2] Future Chemistry Home Page.
Multistep Ladderane Synthesis in Flow
Elias Post
Supervisor: Dr. Daniel Blanco Ania, Department of Synthetic Organic
Chemistry, Radboud University Nijmegen.
Figure 13: Schematic representationof a [n]‐ladderane. [1]
Figure 2: Schematic representation of aflow setup. [2]
2 n d Y e a r R H A R e s e a r c h P r o j e c t s
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 51
Abstract: This project aimed the isolation and purification of intermediate protein complexes that are present
during the assembly cascade of the nitrogenase protein complex. This complex stabilisation was done using
ADP•AlF4‐ as substrate instead of ATP. After a manifold of column purification steps the intermediate protein
complex was set up for microbatch crystallisation. After weeks of rest, three set‐ups resulted in crystal
formation.
Samenvatting: Enzymen volbrengen in de natuur chemische reacties met een ongelooflijke efficiëntie. Als
scheikundige wil je hier achter elk detail komen om de methode in het vervolg op andere gebieden kunnen
toepassen. In mijn onderzoek zijn de enzymen zodanig verandert dat men met behulp van kristallografie hier
een “Foto” van kan maken. Deze informatie kun je dan gebruiken om processen af te leiden.
Nitrogenase provides the bio‐catalytic machinery that allows nitrogen fixation under ambient conditions. Nitrogenase achieves this reaction by employing certain gene products that hold iron‐sulphur‐clusters as their active centre, see figure 1. Detailed description of the assembly steps are still under investigation. Crystallography, a cornerstones of protein function investigation, was applied to nitrogenase and elucidated the structures of all the gene products, however not of all intermediates that are present during this assembly.
This work focuses on stabilising the NifEN1‐Iron‐complex, an intermediate of the nitrogenase assembly, crystallise the complex and prepare it for further crystallographic analysis. The first step for this investigation is the production of nitrogenase assembly related proteins in sufficient qualities and quantities. This was done by culturing a Azotobacter vinelandii strain for 24hours. After that a 6 day long cascade of purification and analytical steps were done in order to achieve these requirements. This included Ion‐exchange, size‐exclusion and salt‐gradient columns. SDS‐PAGE and Bradford assays were used to determine quality and quantity of the proteins. Now, the actual reaction of the different complex components was accomplished by
For this the complexation matrix was provided with ADP•AlF4‐ substrate, where the gamma‐phosphate is
replaced by an AlF4‐ moiety, which cannot deliver the gamma‐hydrolysis energy for dissociation of the
intermediate protein‐complex. Therefore this intermediate is stabilised and can be prepared for subsequent studies.
For the cyrstallisation screening various buffer exchanges were performed. These included alterations in matrix composition and pH values of the buffer. For each individual set‐up a 10μL batch was used to mix mother solution and protein solution. This set‐up the rested for weeks at room temperature.
The results showed, that a complete protein‐solution matrix and high protein concentrations delivered crystals and microcrystals, see figure 2. The crystals are going to be harvested and analysed, in order to derived structural information of the protein complex. References
[1] ‐ Hu, Fay, Lee, Wiig, and Ribbe. Dual functions of NifEN insights into the evolution and mechanism of nitrogenase. Dalton Trans, 39:2964–2971, 2009. [2] ‐ Ribbe. Nitrogen Fixation. Humana Press, 2011.
1 A nitrogenase gene product associated with the EN‐protein expression.
Employment of altered Substrates for Stabilisation of Nitrogenase Assembly Intermediates for Crystallographic Characterization Christian Prüfert Supervisors: MC Feiters, IMM, Radboud University, Nijmegen
MW Ribbe, MBB, University of California, Irvine
Figure 14: Majorcatalytic centre forthe nitrogen fixa‐tion reaction.
Figure 2: A single crystal surrounded by microcrystals
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Figure 1: Average image of all
movie frames
Figure 2: Result of observing the
movie for eight days with the EHT
Abstract: The Event Horizon Telescope (EHT) is a Very Long Baseline Interferometry (VLBI) array aiming to
image Sagittarius A* (Sgr A*), the radio source associated with the supermassive black hole at the center of the
Milky Way, on event horizon scales. General relativistic magnetohydrodynamic (GRMHD) simulations show that
radio emission from Sgr A* exhibits variability on timescales of minutes, whereas VLBI observations typically
take several hours. One of the key assumptions needed for radio interferometry to theoretically work is that the
source does not change during the observations, which is clearly violated for Sgr A*. In this research project,
simulated EHT observations of a GRMHD movie of Sgr A* (made by Hotaka Shiokawa) have shown that an
image of the average quiescent emission, featuring the characteristic black hole shadow and photon ring
predicted by general relativity, can nonetheless be obtained.
Samenvatting: De Event Horizon Telescope is een project waarbij radiotelescopen over de hele wereld
gecombineerd worden tot een telescoop die effectief ongeveer even groot is als de aarde. Hiermee kan een
resolutie bereikt worden die hoog genoeg is om een foto te maken van Sgr A*, het superzware zwarte gat in het
centrum van de Melkweg. Dit zwarte gat is voor onze telescopen te zien door de (radio)straling die ontstaat
door materie die het zwarte gat in valt. Echter, deze straling is variabel op een tijdschaal van minuten, terwijl
een meting met de radiotelescopen een paar uur duurt. In dit project is een methode ontwikkeld om alsnog een
foto van het zwarte gat te kunnen maken.
EHT observations of Sgr A* have been simulated with the MIT Array
Performance Simulator (MAPS). This package generates interferometric
data sets (complex visibilities) from an input brightness distribution (the
model movie of Sgr A*) and some observational parameters, such as the
locations and properties of the antennas and the observing time and
duration. The visibilities can then be used to reconstruct an image of the
source under observation.
It has been shown that for Sgr A* the reconstruction quality
increases as it is observed for multiple days, over which the visibilities are
averaged. Also, it is necessary to normalize the visibilities by the total flux
density of the currently observed movie frame. Furthermore, the image
quality increases as a smoothing algorithm (a moving average with Gaussian
weight function) is applied to the complex visibilities as a function of time.
This method can be combined with an existing method to mitigate the
effects of interstellar scattering [1].
Figure 1 shows the average image of all movie frames, which is
what one would see in an ideal situation. Figure 2 shows the result of the
simulated EHT observation of the movie, made with eight telescopes over a
period of eight days. It still shows the black hole shadow and photon ring as
predicted by the GRMHD simulations, despite the variability of the source.
References
[1] V. L. Fish et al. Imaging an event horizon: mitigation of scattering toward
Sagittarius A*. Submitted to The Astrophysical Journal, June 2014.
Observing time‐variable black holes with the Event
Horizon Telescope
Freek Roelofs
Supervisor: Prof. dr. Heino Falcke, Dept. of Astronomy, RU Nijmegen
2 n d Y e a r R H A R e s e a r c h P r o j e c t s
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 53
Abstract: In this project a 3D hMSC culture system was developed comprising strain‐stiffening hydrogels
consisting of fibrinogen and polyisocyanopeptide (PIC) and this system was used to evaluate the effect of strain‐
stiffening properties on hMSC behaviour in 3D. It was found that the relative amount of round cells increased
with increasing PIC:fibrinogen ratio.
Samenvatting: In dit project is een systeem ontwikkeld om (stam)cellen te kweken in 3D gels. De gels bestonden
uit twee materialen die harder worden naarmate er meer kracht op wordt uitgeoefend door bijvoorbeeld de
erin aanwezige cellen. Er is gebleken dat het veranderen van de verhouding van de twee gel‐componenten ertoe
leidt tot een verandering in het aantal ronde en gespreide cellen.
Human mesenchymal stem cells (hMSCs) are known to respond to physical cues from their extracellular
environment in determining what lineage to commit to during differentiation [1]. Much of the work that has
been done in investigating the role of physical parameters on cellular behaviour has been done on linearly
elastic systems with cells being cultured on top of a hydrogel. Such systems are far from the natural
environment of most cells, including hMSCs, as their in vivo environment is made out of a 3D network of strain‐
stiffening fibres, called the extracellular matrix (ECM). So a system in which hMSCs are being cultured and
studied inside a 3D hydrogel that is composed of strain‐stiffening materials would mimic the in vivo
environment more closely and could lead to new insights into a stem cell’s natural behaviour. Therefore, the
aim of my project was to develop such a system using fibrinogen and polyisocyanopeptide (PIC) [2] and to use
it to evaluate the effect of strain‐stiffening properties on hMSC behaviour in 3D.
To develop a protocol for 3D culture and evaluation of hMSCs, first a suitable cell concentration, hydrogel
thickness, hydrogel formation rate and cell staining procedure were evaluated using NIH 3T3 fibroblasts. Next,
the proposed protocol was validated using hMSCs to find out whether individual hMSCs could be visualised
throughout multiple layers of the hydrogel and to make sure that hMSCs were viable inside their 3D
environment.
Using the newly established protocol, the effect of strain‐stiffening properties on hMSC behaviour was
evaluated by analysis of the morphology of these cells after 24 hours inside PIC‐fibrinogen hydrogels of
different compositions. It was found that the relative amount of rounded cells increased with increasing
PIC:fibrinogen ratio. This could be caused by either a decrease in the fibrinogen concentration or an increase in
the critical strain or both, caused by the increase of the PIC:fibrinogen ratio. So further experiments are needed
to find out which of both factors plays a role.
While further research is needed to unravel the mechanisms through which physical cues of the
extracellular environment can affect cellular behaviour in 3D, an interesting dependency of hMSC morphology
on hydrogel composition has been found. So it would be interesting to look further into the physical cues
underlying this process and to focus more on other processes, like hMSC differentiation, that might also be
affected by hydrogel composition in the 3D system used here.
References
[1] Engler, A.J., et al. Matrix elasticity directs stem cell lineage specification. Cell, 126: 677‐689, 2006
[2] Kouwer, P.H.J, et al. Responsive biomimetic networks from polyisocyanopeptide hydrogels. Nature, 493: 651‐655, 2013
The influence of strain stiffening properties on hMSC
morphology inside 3D PIC‐fibrinogen hydrogels
Suzanne Timmermans
Supervisor: Prof. dr. W.T.S. Huck, Department of Physical Organic
Chemistry, Radboud University Nijmegen
2 n d Y e a r R H A R e s e a r c h P r o j e c t s
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Abstract: This bachelor internship deals with operational aspects of FLARE, a terahertz free‐electron laser. It
reports on calculations on the propagation of light in the cavity of FLARE in a search for the origin of so‐called
gaps in the scanning range of the laser. This internship also investigates a method of transforming the output of
FLARE, which is prescribed by the operational mechanism, into pulses of a certain length and shape. This
process uses laser driven switchable mirrors to select light pulses of tuneable length.
Samenvatting: Deze bachelorstage heeft zich beziggehouden met twee onderwerpen. Allereerst is de vrije
elektronenlaser FLARE onderzocht. Deze vijftien meter lange laser produceert niet al het licht dat het zou
moeten en het is onduidelijk wat de reden voor dit defect is. Daarnaast is de mogelijk van pulsknippen
onderzocht. Dit gebeurt met spiegels die heel snel aan‐ en uitschakelen met behulp van een sterke laser.
FLARE is a free‐electron laser designed by the Radboud university [1]. It is a special kind of laser in that its
output wavelength can be scanned continuously, an attribute that aids spectroscopy considerably. However,
upon the completion of the machine it became clear that the laser could only produce light effectively at a few
wavelengths.
Multiple experiments were carried out over the course of the project to collect data on the most basic
operations of FLARE. Taking one of the laser cavity mirrors out, the spontaneous emission of the laser could be
investigated spectrally and temporally to see whether the problem lies at the very root of the lasing
mechanism. In the end, sadly, no clear correlation between spontaneous emission and lasing could be found. In
addition to practical experiments, both the propagation of light in FLARE’s waveguide and the effects of
irregular electron bunches were mapped as a function of laser parameters. These investigations have brought
new insights to light concerning possible disruptions in FLARE’s
lasing process, such as a disadvantageous electron bunch
shapes.
As a more personal project, the feasibility of THz pulse
slicing using silicon‐on‐insulator plasma switches was
investigated. FLARE’s light pulses are 2‐15 μs long [1], making
them inconvenient to use on physical processes that work on
much shorter timescales. In order to produce shorter pulses of
light, a strong laser can be fired at a thin layer of silicon to
produce a short‐lived plasma and make it reflective for THz light
for a brief period of time [2]. In this project, the reflectivity of
several mirrors with varying thicknesses was measured with
nanosecond resolution. THz pulses on the order of tens of
nanoseconds could be created with these switchable mirrors.
References
[1] Jongma, R.T., van der Zande, W.J., van der Meer, A.F.G., Lehnert, U., Michel, P., Wünsch, R., van der Geer, C.A.J., Dunkel,
K., Piel, C., van der Slot, P.J.M. Design of the Nijmegen High‐Resolution THz‐FEL. Proceedings of FEL08, 2008
[2] Doty, M.F., Cole, B.E., King, B.T., Sherwin, M.S. Wavelength‐specific laser‐activated switches for improved contrast ratio
in generation of short THz pulses.Review of Scientific Instruments, 75(9), 2921‐2925, September 2004
The Scanning Problem of FLARE and THz Pulse Slicing
Milo Vermeulen
Supervisor: Prof. dr. W. J. van der Zande, Molecular Biophysics within
FELIX Facility within the Institute for Molecules and Materials
Figure 1: The reflectivity of the plasma switches asa function of time. A swift rise time is followed byslow decay.
2 n d Y e a r R H A R e s e a r c h P r o j e c t s
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 55
Abstract: In this project we looked at the output morphology of heterozygous knockout mice for EHMT1, and
found that the axonal properties are altered in the knockout mice. They show fewer long‐range connections and
more connectivity in their home column.
Samenvatting: Wij hebben in dit project naar de morfologie van cellen in de hersenen van muizen met het
Kleefstra Syndroom gekeken en hebben uitgevonden, dat er verschillend zijn in de cellen tussen deze en gewone
muzien.
The Kleefstra Syndrome (KS) is an intellectual development disorder, which is also
classified under the umbrella of autism‐spectrum disorders. Besides severe
intellectual disability (ID) with an IQ below 50, patients with KS show a wide variety
of different symptoms. Most prominent are the characteristic facial features (fig.1).
These facial characteristics are a tool for the diagnosis of KS, even though they make
the distinction between KS and other ID syndromes, such as Down‐Syndrome, more
difficult. A definite diagnosis can only be made by using genetic tools. Also
associated with KS are childhood hypotonia, developmental delay, speech
impairment and an autism‐like phenotype. Causes for KS lie in mutations or
deletions of a part of the 9th chromosome, where the gene for the epigenetic factor
Euchromatin Histone‐lysine N‐Methyltransferase 1 (EHMT1) is located.
Previous research on autism models showed that the basic neuronal
morphology in the part of the brain that processes somatosensory input
– the somatosensory cortex – is altered. We therefore did 3D neuronal
reconstructions of layer II/III pyramidal neurons of the somatosensory
cortex in wild type mice and also in heterozygous knock out mice
(Ehmt1+/‐).
We found that the basic axonal morphology of the Ehmt1+/‐ neurons is
altered in a way that there are fewer long‐range connections, that
means connections outside of the home column, as compared to wild
type cells.
Since we were only able to reconstruct 4 cells per genotype, more research needs to be done, but the results
are promising, and, combined with the results of other projects concerning Kleefstra Syndrome, may lead to
the understanding of the underlying causes.
References
[1] Kleefstra, T., Brunner, H. G., Amiel, J., Oudakker, A. R., Nillesen, W. M., Magee, A., Bokhoven, H. Van. (2006). Loss‐of‐
Function Mutations in Euchromatin Histone Methyl Transferase 1 ( EHMT1 ) Cause the 9q34 Subtelomeric Deletion
Syndrome, 79(August), 370–377
Structural and functional connectivity in the
somatosensory system of a mouse‐model for
Kleefstra Syndrome
Rebecca Wallrafen
Supervisor: Dr Dirk Schubert, department of cognitive neuroscience, Donders
Center for Brain, Cognition and Behavior
Figure 1: 5 patients with
Kleefstra Syndrome. Picture
from Kleefstra et al.(2006)[1]
Figure 2: Overlay of the reconstructed cells.
The axon is always depicted in red, the
receptive surface is always blue. Barrels are
depicted in grey. Left: overlay of
reconstructed wild type cells. Right: Overlay
of reconstructed Ehmt1+/‐ cells.
56 R H A ‐ F NW I
R H A – F NW I S c i e n t i f i c O u t p u t
Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 57
Scientific Output
The scientific output listed here is work that has appeared in the peer‐reviewed scientific
literature in 2013‐2014. All contributions contain (part of) the work that the RHA Science
students have done as part of their research project. Because writing and publishing does
take time, some of the papers are from previous year’s RHA Science students that have
appeared in the literature 2013‐2014 and some of the output from the 2013‐2014 RHA
Science students, who figure in this yearbook, will appear later and will be included in next
year’s yearbook.
J o u r n a l p a p e r s †
Smits, F. C. M., Casteleijns, W. W. A. and van Hest, J. C. M.; “Crosslinked ELP‐based
nanoparticles, using the strains promoted azide‐alkyne cycloaddition.” European
Polymer Journal, in press, DOI: 10.1016/j.eurpolymj.2014.07.004
Teun Dings, Erik Koelink; “On the Mathieu conjecture for SU(2)” Indagationes
Mathematicae, accepted for publication
C o n f e r e n c e C o n t r i b u t i o n s a n d P r o c e e d i n g s †
Paul H.J. Kouwer, Matthieu Koepf, Alan E. Rowan, Roeland J.M. Nolte, Maarten Jaspers,
Zaskia H. Eksteen‐Akeroyd, Mathijs Mabesoone, Vincent A.A. Le Sage. "Responsive
biomimetic Hydrogels", 5‐5‐2014, St. Petersburg State University.
† the names of the RHA science students presenting/concerned have been underlined
58 R H A ‐ F NW I
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Y e a r b o o k 2 0 1 3 ‐ 2 0 1 4 59
Leden RHA Programma Raad 2013‐2014
Prof dr John van Opstal (voorzitter, natuurkunde, DCC)
Drs Hay Geurts (secretaris, onderwijscentrum)
Drs Jan van den Broek (vaardigheden training, onderwijscentrum)
Wilke Castelijns (studentlid moleculaire levenswetenschappen)
Teun Dings (studentlid wiskunde)
Dr. Ernst van Eck (scheikunde, IMM)
Dr. Leonie Kamminga (Biologie, NCMLS)
Prof. dr. Klaas Landsman (wiskunde, IMAPP)
Dr. Elena Marchiori (informatica, ICIS)
Nicolette Poelen (ondersteuning, onderwijscentrum)
Drs Muriel van Teeseling (PhD studentlid biologie)
From left to right: Ernst van Eck, Jan van den Broek, Nicolette Poelen, Teun Dings, Hay Geurts, Elena Marchiori, Muriel vanTeeseling, Klaas Landsman, Leonie Kamminga and John van Opstal
60 R H A ‐ F NW I
Colofon
Productie, Design & Layout Ernst R.H. van Eck
Photography cover: Dick van Aalst
Print: Rikken print bv
Postal address:
RHA FNWI
Faculty of Science
Radboud University Nijmegen
PO Box 9010
6500 GL Nijmegen
Visiting address:
Heyendaalseweg 135
6525 AJ Nijmegen
www.ru.nl/rha/fnwi/