mobilitas - sihtasutus eesti teadusagentuurterviews with media companies in estonia and germany to...

Mobilitas

COMPASS

Grantees

Tallinn

2015

Estonian Research Council

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Estonian Research Council

(Eesti Teadusagentuur)

Soola 8, 51013 Tartu, Estonia

Representation in Tallinn:Lauteri 5, 10114 Tallinn, Estonia

Mobilitas Programme Manager: Tiina LoitProofreading: Pille PõiklikCover image: Shutterstock.comEditing and layout: Meediaseire MTÜ

ISBN 978-9949-9512-7-7 (in print)ISBN 978-9949-9512-8-4 (pdf)Print: Ecoprint AS

Phone +372 [email protected]

http://www.etag.ee

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3Grantees

Dear reader

The researcher mobility programme Mobilitas,

co-funded from the European Social Fund, is run-

ning from 2008 until the end of 2015. The pro-

gramme aims to activate the international ex-

change of researchers and knowledge and is tar-

geted at postdoctoral and top-level researchers.

Based on the profiles recognised by the European

Framework for Research Careers, this means Rec-

ognised Researcher (R2) through Established Re-

searcher (R3) to Leading Researcher (R4).

The Estonian Research Council has awarded 127

postdoctoral grants, the majority of which are for

incoming grants, but there are also 28 outgoing

grants and 12 grants for mobility within Estonia.

The postdocs who have received grants work in 7

different R&D institutions – 73 in the University

of Tartu, 27 in the Tallinn University of Technol-

ogy, 10 in Tallinn University, 8 in the National In-

stitute of Chemical Physics and Biophysics, 7 in the

Estonian University of Life Sciences, and one in

both the Estonian Literary Museum and Protobios.

18 top researchers have received funding for cre-

ating their own research group. 6 of the research

groups are working in the area of material technol-

ogy, 5 investigating topics related to biotechnolo-

gy, and the others are concerned with environmen-

tal technology (3 groups), energy (3 groups) and

information and communication technology (1

group).

The grants are divided between 4 R&D institu-

tions: the University of Tartu and the Tallinn Uni-

versity of Technology (both have 6 grants), the

National Institute of Chemical Physics and Bio-

physics (4 grants), and Tallinn University (2 grants).

In 2014, we published the booklet – “Mobilitas

Compass 2013” containing a collection of popular

narrative texts on research conducted by the Mobi-

litas postdocs and top researchers in order to present

the outcome of the programme to the public. The

booklet was co-authored by 52 grantees.

By the end of 2014, 68% of all the grantees

had finished their project work. This booklet in-

troduces 37 grantees – 3 top researchers and 34

postdocs – who completed their research projects

during 2014. I would like to thank all of them for

their kind cooperation.

Tiina Loit

Mobilitas Programme Manager

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4 Mobilitas Compass 2014

Partner Institutions

University of Tartu

Tallinn University of Technology

Tallinn University

National Institute of Chemical Physics and Biophysics

Estonian University of Life Sciences

Estonian Literary Museum

Protobios LLC

Ministry of Education and Research

SA Archimedes

Intermediate Body

Implementing Agency

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5

‘‘

Grantees

Top Researcher in the field of material technology

� Title: Manufacturing, processing and characterization of

graphene-based nanostructures

� Grant: MTT1, 1 Mar 2009 – 28 Feb 2014

� Partner institution: University of Tartu

Harry Alles

[email protected]

”

The top researcher Mobilitas grant allowed me to set up graphene

studies in the University of Tartu that is now a partner of a large-scale

European Graphene Flagship project.

Towards Graphene-based Gas SensorsGraphene, a single atomic layer of carbon, has

been a star in materials science in the last ten yearsdue to its extraordinary properties like very goodelectrical and thermal conductivities. At the sametime, it is the thinnest known material and thestrongest one ever measured.

In the Institute of Physics at the University ofTartu (IPUT), our goal was to prepare graphenesheets of the size and quality suitable for deviceapplications, in particular, for the development ofgas sensors based on graphene. Thus, one of thehighlights of this project was that we were able toshow that, under ambient conditions, the graphene

sensors, initially insensitive to oxygen gas, can beactivated with relatively weak ultraviolet light.These results were published in the top class jour-nal Applied Physics Letters. Since 1 Oct 2014, ourresearch group studies the application of this prin-ciple in the case of other gases under the large-scale European Graphene Flagship project.

In fact, the initial results, obtained within thisproject, already allowed the material scientists inTartu to join the international network of researchgroups working on graphene. In addition to theMobilitas project, two European graphene researchprojects were running in IPUT during 2010–2013.

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‘‘

Anna Karin Borg Karlson

[email protected]

’’

Top Researcher in the field of environmental technology

� Title: Chemical Ecology

� Grant: MTT2, 1 Nov 2009 – 31 Dec 2014


A successive integration of the students in chemistry and biology by offering

courses in chemical ecology and natural product chemistry followed by funded

research projects in chemical ecology would be the basis for building up compe-

tence in the research of sustainable and organic cropping and forestry.

Chemical EcologyThe aim of the project “Chemical Ecology” was

to initiate education and support the ongoing re-search in Estonia.

Chemical ecology is an interdisciplinary researchfield dealing with the isolation, identification, syn-thesis and evaluation of the biological effects ofnaturally occurring chemicals in various organisms.Knowledge in this area can help replace toxic bio-cides with nontoxic degradable compounds to fa-cilitate the development of sustainable pest con-trol in agriculture and forestry.

During the five years, we developed a PhD coursein Chemical Ecology with Estonian teachers andguest lecturers from Lithuania, Norway and Swe-den. The goal was to initiate a network with PhDstudents with research topics in chemistry or biol-

ogy. The course was taught twice and attracted 20master and PhD students both from the chemis-try and biology faculties at the University of Tartuand from the Estonian University of Life Sciences.

The research in chemical ecology is focussed onstate of the art methods in the identification andsynthesis of biologically active compounds such asinsect pheromones, complex flower scents and mi-crobial compounds. Knowedge of the active chemi-cal signals can be used in the development of sus-tainable control methods in agriculture and for-estry in Estonia and elsewhere. The project hasgenerated 9 publications in international scientificjournals and 13 manuscripts so far.

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Grantees

Shinya Sugita

I continue working as a senior scientist at the Institute of Ecology,

Tallinn University. I am currently leading a six-year IUT project that

evaluates the impacts of the Holocene storminess changes on the coastal

landforms and [email protected]

’’

Top Researcher in the field of environmental technology

� Title: Dynamic Landscape Analysis in Southern Estonia (DYLAN-

Estonia): Spatial Dynamics of Vegetation and Land Cover through Time

� Grant: MTT3, 1 Sept 2009 – 1 Sept 2014

� Partner institution: Tallinn University

Landscape-scale Change in

Holocene VegetationThe Holocene records of vegetation and climate

provide baseline information for plausible scenarios

of the future changes in land cover. The Haanja

Heights area in SE Estonia is unique in NW Eu-

rope because of the availability of many small de-

pressions 10–20 m in diameter, from which the past

changes of vegetation in the landscape-scale (10–

20 ha) can be reconstructed using fossil pollen pre-

served in sediments 1–2 m deep. The sediment

records from 15 study sites in the area reveal that

the spatial structure of vegetation shifted signifi-

cantly when late-successional trees such as spruce

and lime became dominant in the region about 9000

years ago. The regional climate between 7000–2000

years ago was probably drier than today, causing

sediment hiatuses at most of the sites. Although

human activities affected the vegetation composi-

tion over the last 2000 years, the spatial scale of

the vegetation mosaic has not been dramatically

altered. The site-to-site variation of the vegeta-

tion composition has been large through time. Spa-

tial patterns of soils and topography may have

played a role, affecting the vegetation structure;

however, the correlations between the species com-

position and those factors have not always been

significant, suggesting that other factors such as

species interactions and local climate variations

have been important. In view of human-induced

global warming, palaeo-records such as ours are

informative for the future planning of natural re-

source management and conservation locally and

globally.

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‘‘

In now work as a researcher in Finland, and I find that the results of

my postdoctoral research are essential to my ongoing and future research

career.

Ulrike Rohn

[email protected]

� Title: Economic and cultural implications of Social Network

Sites – A case study of Estonia and Germany

� Supervisor: Halliki Harro-Loit

� Grant: MJD18, 1 Oct 2009 – 31 Dec 2014


’’

Social Network Sites – Between

Culture and BusinessIn my research project, I studied social network

sites (SNSs), such as Facebook, from two perspec-tives: the user and the company perspective.

Studying users, I was interested in if, how, andto what extent the increasing global success ofSNSs leads to an increasing cross-cultural connec-tivity. For this, I conducted focus group interviewsas well as an online survey (n=1,464) with Esto-nian, Russian-Estonian, and German users ofSNSs. The results showed that, on SNSs, users areless directly connected with users from other coun-tries and cultures through their personal lists ofcontacts than they are indirectly connectedthrough the increasing use of the same SNS:Facebook. Furthermore, the study found that Rus-sian-Estonians tend to have fewer contacts with

people with the same mother tongue than Germansand Estonians do. A the same time, however, theyare more connected with users outside their coun-try of residence. The survey also showed that thereis only a small amount of connectivity betweenEstonian and Russian-Estonian SNS users.

Studying companies, I conducted in-depth in-terviews with media companies in Estonia andGermany to find out how they use SNSs for thedistribution and promotion of their content. Theinterviews conducted between 2010 and 2014yielded insight into how the use of social mediaplatforms has led to organizational changes andincreasing professionalization over the years.

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‘‘

Grantees

Eve Avel

In the future, I would like to proceed with palaeoecological research,

using different microorganisms and pollen assemblage data.

� Title: Testate amoebae and water-table level fluctuation in NE

Estonian bogs

� Supervisor: Margus Pensa

� Grant: MJD31, 4 Aug 2009 – 3 Oct 2014

� Partner institution: Tallinn University

[email protected]’’

Testate Amoebae and Water

in NE Estonian BogsTestate amoebae are a group of protists living in aquatic to

moist habitats and are known as good indicators of soil and peatmoisture levels and water chemistry. Because of their well pre-serving external shells (tests) in sediments, they are used inpalaeoecolgical studies.

During the project, modern testate amoebae assemblages werestudied from five NE Estonian bogs to relate their distributionto local environmental variabilities. The data was collected intoa transfer function for water table depth which enabled to re-construct water level change in Selisoo bog during the last 5000years. Using macrofossils, pollen and testate amoebae assemblagesin the study, it was possible to reveal the natural development ofthe bog (including two major fires in Selisoo bog – 4200 years BPand 130 years BP) and human impact (since 550 years BP) on itduring the last five millennia.

Nebela carinata is one of the largest species

of testate amoebae and prefers wet living

conditions.

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‘‘

Michal Cagalinec

� Title: Mitochondrial Dynamics in Models of Neurodegenerative

Diseases

� Supervisor: Allen Kaasik

� Grant: MJD35, 1 Sept 2009 – 31 May 2014


[email protected]

Currently applying for new funding, I hope I will be able to continue

with my research focused on mitochondrial dynamics and ultrastructure in

neurons and myocytes.

’’

Mitochondrial Dynamics and

NeurodegenerationPerturbations in mitochondrial functioning is a

common characteristic of neurodegenerative dis-eases. Mitochondrial dynamics, involving the move-ment, fusion and fission of mitochondria has beenobserved to be impaired for a long time before theenergetic deficit appears. Therefore perturbationsin mitochondrial dynamics are considered an earlymarker of the disease. Neurons as highly polarizedcells are critically dependent on proper energy and,thus, mitochondrial distribution. However, the de-tails of how mitochondria are distributed, transport-ed and maintained when located far from the cellbody are not well understood. We have shown bythe use of mitochondria-targeted photoconvertibleproteins that mitochondrial fusion and movementin neuronal axons happen in highly sophisticated

Fusion detection in axons. Mitochondria expressing photo-convertible protein KikumeGR1 were converted to red. Fusionbetween red and green mitochondria is indicated by an arrow.

patterns. These were negatively influenced in exper-imental conditions, mimicking neurodegenerativediseases of interest.

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11

‘‘

Grantees

Liisi Keedus

� Title: The Making of the Scientific Imagination: Debates on

American Political Science, 1945–1965

� Supervisor: Vello Andres Pettai

� Grant: MJD48, 1 Apr 2010 – 31 Oct 2014


[email protected]

As of January 2015, I am a Marie Curie research fellow at the Erik

Castrén Institute of International Law and Human Rights at the University

of Helsinki. My main research fields are the history of twentieth century

political thought and intellectual history in Europe in the inter-war period.

’’

The project carved out a historical perspectiveon the debates on the relation between scientific ob-jectivity and social values by reassessing the devel-opment of political science in the United States af-ter World War II. This was a period of dramatictransformation for American political science, whichlater became the model for the studies of politicsaround the world.

In the mainstream of the discipline, political sci-entists sought to transform their field into a “rigor-ous”, “analytic”, and “theoretical” science. At thesame time, this attempt was constantly challengedby the integration of European émigré scientists –not only in the field of political science but also in“sister-disciplines” such as philosophy, sociology andlaw. The antagonisms between these currents gave

birth to a myriad of new ideas, concepts, debatesand problems.

What were the historical, epistemological anddiscursive dimensions of the intersections betweenscience, values and politics in the aftermath of WorldWar II? How did the newly “scientific” science as-sert itself as science, and what conceptual tools didit use – and how did it instrumentalise or clash withthe newly imported “European” debates – to con-struct and legitimate its fields? How were the hori-zons of scientific imagination and language shapedand re-shaped in political science? How can this his-torical knowledge contribute to a critical perspec-tive on our contemporary scientific-axiologicalchoices?

The Making of the Scientific Imagination

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‘‘

Maria Mälksoo

The Politics of Mnemonical

Security in Europe

My next project zooms in further on the impact of the failure of transi-

tional justice in post-communist Russia on its foreign policy discourse and

practice.

� Title: The Power Politics of Memory in Eastern Europe: Securitis-ing the Legacy of Communism in the Baltic states, Poland, Ukraine,and Russia� Supervisor: Andres Ilmar Kasekamp� Grant: MJD60, 1 Mar 2010 – 21 Apr 2014� Partner institution: University of Tartu

[email protected]

’’

The Polish plane crash on the way to commemo-rate the victims of Katyn in the spring of 2010 andthe violent events in Ukraine four years later, ladenwith historical (mis)perceptions, provided the con-textual starting and end points of my researchproject. My general aim was to explore the conflictsover historical remembrance of communism be-tween Poland, Ukraine, the Baltic states and Rus-sia. With the toolkit of Critical Security Studies, Iexamined the calls to politically and legally condemnthe communist regimes at a pan-European level.

By seeking recognition for the inclusion of theirexperiences and assessment of communism into theestablished European mnemonical narrative and anormative verdict on twentieth-century totalitar-ianisms, the East European actors concurrently seek

recognition for their agency as Europeans. In turn,Russia’s State Duma’s recent passing of the mem-ory law, targeted specifically against the ’dissemi-nation of false information on the activities of theSoviet Union during WWII’ and the ’rehabilitationof Nazism’ is another example of politically orches-trated attempts to secure a particular ’nationalmemory’ by means of law.

My inquiry into the sources and meanings of thenascent pan-European remembrance of totalitar-ian communist regimes points to the various EastEuropean struggles for mnemopolitical emancipa-tion, competitive claims on the security of memorywithin the wider Europe, and the gradually chang-ing mnemonic identity of the EU.

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‘‘

Grantees

Lili Milani

The next step is to incorporate these pharmacogenetic markers into a

database of genetic variants relevant for the implementation of personalized

medicine in Estonia.

� Title: In-depth genetic and epigenetic analysis of the cyto-

chrome P450 system by next-generation sequencing

� Supervisor: Andres Metspalu

� Grant: MJD71, 1 Mar 2011 – 28 Feb 2014


[email protected]

’’

Drug Prescription Based on GeneticsInterindividual variability in drug metabolism

and response is extensive. The drug levels in plasmacan vary more than 1000-fold between two indi-viduals having the same weight and given the samedrug dosage. This is a result of variation inreceptors and the activity of enzymes in charge ofdrug metabolism. The variation is caused by com-binations of genetic, physiological, and environ-mental factors, which are usually not accountedfor when prescribing drugs.

The aim of this research project was to identifygenetic signatures that control interindividual vari-ation in drug metabolism. We used modern DNAsequencing technology to identify genetic and epi-genetic variation in major genes involved in drugmetabolism in a unique collection of liver samples.In collaboration with scientists from Karolinska

Institutet, Sweden, we developed a novel methodto study the genetic and epigenetic regulation ofgenes. Next, we used a genome-wide approach toexplore the regulation of gene expression in thehuman liver. Combining genetic and epigenetic in-formation, up to 80% of the variation in gene ex-pression could be determined for hundreds of genesrelevant to liver function. Many of the genes havealso been associated with different metabolic dis-eases or traits.

In conclusion, these findings are very importantfor the better understanding of interindividualvariation in drug metabolism and response, andtheir implementation in daily clinical practice willeventually lead to better drug response and lessadverse effects in patients.

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‘‘

Gemma Atkinson

My research continues on the evolution of the factors of protein biosyn-

thesis machinery. Meanwhile, predictions from the results of my Mobilitas-

funded project are being tested experimentally in collaborating laborato-

ries.

� Title: Origin and functional evolution of ribosome-associatedenvironmental response enzymes� Supervisor: Tanel Tenson� Grant: MJD99, 6 Sept 2010 – 11 Apr 2014� Partner institution: University of Tartu

[email protected]

’’

The Diversity and Molecular Evolution

of Ribosome-Interacting ProteinsThe ribosome is the molecular machine used by

the cells of all life on earth to produce the proteinsnecessary for survival and growth. Various proteinfactors interact with the ribosome to control itsfunctional cycle and to sense the state of the ribo-some. These proteins are often essential and an-cient, having evolved before the last common an-cestor of all extant life.

The project began with a comprehensive sur-vey of the diversity and functional evolution ofproteins in the RelA/SpoT Homologue (RSH) fam-ily of proteins. These factors sense starvation andother stresses by interacting with the ribosome andother molecules. We performed high-throughput

sensitive sequence searching of over 1000 genomesfrom across the tree of life, in combination withphylogenetic analyses to consolidate the previousidentification of diverse RSHs in different organ-isms and provide a much-needed unifying termi-nology for the field. We classified the RSHs into30 subgroups and carried out comparative sequenceanalysis among the subgroups to predict novel as-pects of function and intermolecular interactions.

We then expanded the research to other ribos-ome-interacting factors, identifying among otherthings a protein critical for the normal function-ing of yeast mitochondria, previously thought tobe absent in this organism.

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‘‘

Grantees

After completing this project, I will continue my research with

organosilicon and organophosphorus compounds.

Anu Ploom

� Title: Structure-reactivity relationships in reactions at atoms of

the third period elements

� Supervisor: Margus Lopp

� Grant: MJD105, 1 Sept 2010 – 30 Nov 2014

� Partner institution: Tallinn University of Technology

’’[email protected]

Reactivity of Silicon and

Phosphorus CompoundsQuantitative structure-reactivity analysis has

widely been practiced in organic chemistry for de-ducing reaction mechanisms, calculating physico-chemical parameters of molecules, and has sub-stantial importance in drug design and in materi-als science. Most often, these methods have beenfocused on reactions at carbon atom. Differentlyfrom this, I have worked with organosilicon com-pounds. During my PhD studies, I have elaborateda new algorithm, which describes structure-reac-tivity relationships in organosilicon chemistry.

This project aimed to test the applicability ofthe algorithm on the other elements of the thirdperiod, starting from organophosphorus com-pounds. This selection is partially based on the factthat organophosphorus compounds play an essen-tial role in biological processes and, therefore, have

a central role in the design of new biologically im-portant materials. The new algorithm has been suc-cessfully applied to describe the reactivity of or-ganophosphorus compounds.

In parallel to this theoretical work, I have prac-tically investigated the reactivity of the Grignardreaction with organosilicon compounds, which isthe most important method of silicon-carbon bondmaking in both laboratory practice and chemicalindustry. Despite the increasing use of the reac-tion in silicone industry, there have been no at-tempts to ascertain the structure-reactivity rela-tionships in the Grignard reaction with silanes be-fore our work. The analysis of the reactivity datagave novel and essential information about themechanism of this reaction.

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‘‘

Vinay Choubey

I am continuing Parkinson disease related research at the University of

Tartu on Grant PUT513. Big thanks to Estonian Research Council

(Mobilitas and PUT513) and the University of Tartu.

� Title: Multiple Roles Of Alpha-Synuclein In Origin of Mitochon-

drial Dysfunction And Neuronal Death

� Supervisor: Allen Kaasik

� Grant: MJD120, 1 June 2011 – 31 May 2014


[email protected]

’’

The Role of Mitochondrial Dysfunction

in Parkinson DiseaseParkinson’s disease (PD) is a major neurode-

generative disease which afflicts 1–5% of the glo-bal aged population. PD causes mobility andpsychiatric disturbances due to the degenerationof dopaminergic neurons located in the brain re-gion substantia nigra. The leading proposed causeof PD is mitochondrial dysfunction. Interestingly,several genes linked to the familial form of PDare found to be involved in mitochondrial main-tenance. The objective of my research was and isto find out the cause of mitochondria dysfunc-tion which could lead to PD.

During this project, we found that overexpressionof PD-linked mutant α-synuclein (A53T) in neu-rons induces autophagic (self-destruction) mitochon-drial degradation and net loss. That caused bioen-ergetic deficit and resulted in neuronal death. The

inhibition of mitochondrial autophagy by silencingautophagy proteins Beclin1, Atg12, and Parkin re-stored mitochondrial density and provided protec-tion. Subsequently, we investigated the role of Be-clin-1 in mitochondrial removal (mitophagy). Wefound that Beclin1 interacts with PD-linked pro-tein Parkin and regulates Parkin translocation tomitochondria, the initial step of mitophagy.

Further, we observed that the depletion of Be-clin-1 prevents Parkin translocation-induced mito-fusin loss which allowed mitochondrial fusion. Thus,Beclin-1 suppression might not only interfere withthe clearance of dysfunctional mitochondria but alsoallows the fusion of mitochondria irrespective oftheir functional status. This could contribute to themitochondrial dysfunction known to be present inPD.

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Grantees

Toomas Silla

This project is still ongoing. In collaboration between Estonian Genome

Centre, Tartu University Hospital and National Cancer Centre Singapore, we

have sequenced UCEs in familial breast cancer samples in order to link muta-

tions in UCEs to breast cancer development.

� Title: New Mutations in Old Genes: Discovering Cancer-RelatedVariations in Non-Coding Ultra-Conserved Genes� Supervisor: Mathijs Voorhoeve� Grant: MJD147, 1 May 2011 – 30 Apr 2014� Partner institution: University of Tartu� Receiving institution: Duke-NUS Graduate Medical School, Singapore

[email protected]

’’

New Mutations in Old GenesUltra-conserved genes or elements (UCGs/UCEs)

in the human genome are extreme examples of con-servation. These regions are longer than 200 basepairs and are 100% identical between human, mouseand rat reference genomes. Despite scientists’ efforts,the biological function of these regions has remainedelusive. It has been proposed that UCEs can act aslong distance enhancers and/or they can be tran-scribed to non-coding RNAs.

We were interested to see to which extent UCEscontain natural variations and whether these vari-ations could potentially impact UCE function. Wecharacterized natural variations in 2884 UCEs intwo distinct populations, Singaporean Chinese(n=280) and Italian (n=501), by using a pooled sam-ple, targeted capture, sequencing approach. This

next generation sequencing methodology allows usto analyze relatively large sets of samples in an eco-nomical way. We identified, with high confidence,in these regions the abundance of rare variations ofwhich 75% is not present in the databases. By com-bining our data with 1000 Genome Project data, weshowed in three independent datasets that preva-lent UCE variants are more often found in relativelyless-conserved nucleotides within UCEs, comparedto rare variants. Moreover, prevalent variants areless likely to overlap transcription factor binding site.All together, these results suggest that UCEs arenot under selective pressure as a stretch of DNAbut are under differential evolutionary pressure onthe single nucleotide level.

mobilitas 2014.p65 3/24/2015, 4:59 PM17


‘‘

Mithu Guha

What Regulates the Autoimmune Regulator?

� Title: What Regulates the Autoimmune Regulator?

� Supervisor: Pärt Peterson

� Grant: MJD164, 1 June 2011 – 31 May 2014


[email protected]

’’

My research project was focussed on the charac-terization of the role of AIRE for the preventionof autoimmune diseases. AIRE is a key transcrip-tional regulator in the thymus and contributes tothe negative selection of autoreactive T-cells. Mu-tations in AIRE result in the aberrant expressionof thymic autoantigens and cause autoimmune poly-endocrinopathy-candidiasis-ectodermaldystrophy(APECED).

One reported AIRE-interacting partner is TOP2A,and this interaction has been found to promoteTOP2A initiated double-stranded breaks. We aimedto study the possible involvement of double-strandedDNA breaks in the AIRE transcriptional activationof target genes in AIRE-expressing HEK293 cellstreated with etoposide or merbarone, the well-knowninhibitors of TOP2A.

We observed an upregulation of AIRE target

genes after treatment with etoposide that stabilizesTOP2A to cleaved DNA and prevents the religationof DNA breaks.

In contrast, treatment with merbarone, whichblocks topoisomerase-mediated DNA cleavage, didnot affect AIRE target gene expression. These spe-cific differences indicate a possible role for the dou-ble-stranded breaks in AIRE-dependent transcrip-tion. We used FAIRE-seq to map open chromatinregions in AIRE-expressing HEK293 cells. Wefound that significantly more CpG island promot-ers become accessible in the presence of AIRE.

We conclude that AIRE/etoposide enhances theupregulation of AIRE target genes through the in-volvement of DNA double-stranded breaks andrenders CpG island promoters more accessible.

After finishing my Mobilitas grant, I continued in Pärt Peterson’s group

as a researcher working on the role of the autoimmune regulator (Aire) gene

on central tolerance.

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Grantees

Eduard Aleksanyan

Innovative Scintillating Materials

� Title: Development of novel scintillators based on thin

nanocrystalline films

� Supervisor: Marco Kirm

� Grant: MJD166, 23 Sept 2011 – 22 Sept 2014


[email protected]

Currently, I work at the A. Alikhanian National Science Lab located in

Yerevan, Armenia. In cooperation with colleagues from UT, we continue the

investigation of new types of materials with their potential application in light

emitting and short wavelength radiation converting devices.

’’

Over the past several years, rapid progress in vari-ous imaging technologies facilitated an increasingdemand for new luminescence materials with im-proved performance. This motivates researchers tofind and develop such compounds for a wide rangeof applications covering fields from medicine andhigh-energy physics to homeland security.

In comparison with scintillators in use, the newadvanced luminescent materials must have a fasterand more proportional response with increased lightyield. In order to maintain a high spatial resolution,the scintillator layer has to be really thin. There-fore, my research focused on the investigation ofHfO

2 and ZrO

2 thin films. Both these materials pos-

sess suitable absorption properties, but their scin-tillating properties need further investigation.

We also synthesized nanopowders and preparedceramics in cooperation with Polish scientists. Theresults show that, by selecting different preparationmethods and process parameters, it is possible tomodify the properties of novel materials.

My research greatly benefitted from using ad-vanced time-resolved VUV spectroscopy setups un-der synchrotron radiation excitation at the DORIS(in Hamburg, Germany) and MAX-III storage rings(Lund, Sweden), built by our research group during2013–2014. Finally, my stay in Tartu deepened co-operation between Armenian and Estonian scien-tists. This is a good ground for a new postdoctoralfellow or PhD student to be engaged in research atexcellent laboratories provided in new Physicum ofthe University of Tartu.

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‘‘

Alexandr Popov

A continued research into the nanoparticles suitable for bioimaging will

be carried out in Russia by collaborating with colleagues in the Institute of

Physics, University of Tartu.

� Title: Rare-earth ions doped nanoparticles for fluorescent

medical diagnostics

� Supervisor: Ilmo Sildos

� Grant: MJD167, 1 Aug 2011 – 31 July 2014


[email protected]

’’

Inorganic Nanoparticles as Labels for

Biological SystemsThe application of luminescent inorganic nano-

particles (NPs) in medicine and biology will allowus to use the same drug simultaneously for the di-agnosis and therapy of a disease. Special NPs pre-pared can selectively penetrate diseased cells and,detecting the luminescence signal, a doctor can seethe location of diseased cells or tissue. For this, theNPs are doped with rare-earth ions which have theluminescent transitions in the near infrared rangeof the spectrum (“the transparency window” of bio-logical tissues).

The low intensity of the infrared luminescenceis one of the main problems in the applications ofNPs. Luminescence quenching occurs due to thepresence of water molecules in the NPs which arisedue to the chemical composition features and syn-thesis chemical parameters.

Our main achievement is the development of atechnique based on the analysis of the time decaycurves of NPs luminescence. This technique allowsus to determine the state and localization of watermolecules in the NPs. Water molecules may be situ-ated as an internal or surface defect of the crystalstructure or attach to the inner surface of the ultrasmall emptiness of the NPs. We used chemical meth-ods to achieve the reduction of water molecules con-centration and, thereby, increase the luminescenceintensity of the NPs.

This work was carried out in close collaborationwith scientists from chemical engineering, theoreti-cal physicists, and biophysicists. The results wouldmake a crucial contribution to the knowledge requiredfor the synthesis of high quantum yield dielectric NPsfree of water.

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Grantees

Nasir Sohail

� Title: Study of the flatness (homological) properties of S-posets in

connection with the amalgamation of partially ordered monoids

� Supervisor: Valdis Laan

� Grant: MJD198, 21 Nov 2011 – 28 Nov 2014


[email protected]

’’

Amalgamation of Partially Ordered MonoidsThe amalgamation properties of partially or-

dered monoids, briefly pomonoids, were first con-sidered by S. M. Fakhruddin in the mid 1980s. Inthe recent past, S. Bulam-Fleming and N. Sohailrekindled this study. In this project, we further in-vestigated these properties and explored their con-nections with dominions and epimorphisms. Tocharacterize the dominions of pomonoids, we firstproved an ordered analogue of the celebrated Isbellzigzag theorem.

Subsequently, we showed that dominions and(hence) epimorphisms and the special amalgama-tion of monoids are not affected by the introduc-tion of order. Together with Dr. L. Tart, I also gen-eralized these findings to partially ordered semi-groups. This work narrowed down the conjecture

that absolutely flat (inverse) pomonoids are amal-gamation bases to asking whether they are weakamalgamation bases. Together with Dr. V. Laan andDr. L. Tart, I also studied different notions relatedto pomonoid amalgams in the general setting ofordered algebras, which provided me a further in-sight into the amalgamation of pomonoids.

The amalgamation of ordered monoids is a rela-tively new research area in pure mathematics thathas many open problems which might be of inter-est to future researchers. In particular, we are in-terested in (ordered) inverse monoids, which maybe thought of as representing partial symmetries.The results obtained in this project also motivateme to study similar problems for (general) orderedalgebras and relational structures.

My future endeavor is to work in a university towards establishing my

own research agenda. Next to the amalgamation of ordered monoids, I

can now see that one can ask similar questions about quantels, in particu-

lar, and ordered algebras in general.

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‘‘

I will stay in Tartu and continue studying prompt processes in the

scintillating materials. My duties will also include the development of

optical materials for fusion reactors.

Sergey Omelkov

� Title: Electronic excitations and their dynamics in functional

fluoride and oxide based materials

� Supervisor: Marco Kirm

� Grant: MJD219, 1 Jan 2012 – 31 Dec 2014


[email protected]

’’

Electronic Excitations

in Complex Optical MaterialsThe scintillators are optical materials which con-

vert ionizing radiation into visible or UV light.However, the energy of radiation has to pass a verylong way inside a crystal to become light. The ini-tial particle transfers energy to the electrons ofthe material. “Electronic excitations” are differ-ent states of these electrons, carrying energy indifferent ways. To understand the performance ofan optical material, it is often necessary to investi-gate what happens or could happen to these exci-tations before they have a chance to release theirenergy as light. There is a good understanding ofit in simple (binary) compounds, but complex ma-terials like the ones studied in the project are much

trickier. Often, the structural properties of suchmaterials enable several entities of the same typeof excitation. The project contributed to the un-derstanding on how differently they can act.

The most interesting aspect of the researchcame out when the pulse cathodoluminescence set-up was reconstructed for the needs of the project.Its short pulses allow us to study the first stagesof energy conversion in the materials. It has beenknown that some light is emitted already at thesestages, but the setup lets us study this in detailand possibly use this prompt light in the future toincrease the time resolution of the scintillators.

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Grantees

I will further develop my career in Guatemala. In Tartu, I initiated a

collaboration with a national hospital in order to study high-risk HPVs

circulating in the country.

Fernando Rodriguez-Castañeda

� Title: Identification of the mammalian chromatin host factor

involved in the segregation of the human papillomavirus genome

� Supervisors: Mart Ustav

� Grant: MJD228, 10 Feb 2012 – 21 Nov 2014


[email protected]

’’

Cutaneous Papillomavirus in Skin CancerThere are hundreds of different human papillo-

mavirus (HPV) genotypes. The most studied belongto the alpha-genus. They infect the ano-genital tis-sues, and their role in the causation of anogenitalcancer (i.e., cervical cancer) is well established. Incontrast, beta-genus HPV, also known as cutaneoussince they are commensal papillomavirus of the hu-man skin, have been found in the skin lesions of indi-viduals with a rare genetic disorder, epidermodys-plasia verruciformis.

These individuals have a higher risk of developingnon-menaloma skin cancer than the general popula-tion, and both cutaneous HPV and UV radiation areconsidered risk factors for progression to cancer. Inaddition, transplant recipients undergoing immuno-suppression therapy also have an increased risk ofnon-menaloma skin cancer associated with cutaneousHPV. We use an osteosarcoma cell line U2OS to studycertain aspects of the life cycle of the human papil-lomaviruses.

Immunofluorescence of U2OS cells transfected with an

expression vector of the viral protein E2. Chromatin in

blue; beta-tubulin in red; centromeres in green; and E2 in

magenta (3D reconstruction of the confocal microscopy

images).

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I will continue to do research and write a book that reflect the probable

direction of science education in the new millennium, focusing on closing

the gap between the school curriculum and the current societal and envi-

ronmental issues within the modern society.

Sheila Gamut Oyao

� Title: Promoting multi-faceted approach to teaching and assess-ment for interdisciplinary science education incorporating cross-curricular topics� Supervisor: Miia Rannikmäe� Grant: MJD235, 1 Jan 2012 – 31 Dec 2014� Partner institution: University of Tartu

[email protected]

’’

Towards a Competence-based

Learning Framework

Many education curricula in Europe and else-where in the world are now embracing the develop-ment of competence which is seen as encapsulatinga complex amalgamation of knowledge, skills orpractices, attitudes, and values that have much rel-evance to a variety of purposes and contexts, rang-ing from the personal to social and to global spheres.

Seeing this potential for a competence approach,my research work proposes a competence-basedlearning framework that has global applicability,which is applied to the study of ‘big ideas’; viz thestudy of natural hazards and disaster risk reduc-tion. Although this domain is least taken to be akey science learning area, it provides a good exem-plar, illustrating the future science curricula which

moves towards the promotion of global compe-tence. This developed framework focuses on newvisions of competences, placing emphasis on nur-turing connectedness and behavioural actions to-ward resilience and sustainability so as to adequate-ly prepare learners to face and handle real-life chal-lenges in the 21st century.

A part of this research work is the explorationof how Estonian students in basic education viewednatural hazards, considering that Estonia is leastvulnerable to many of these natural events. Then,a cross-cultural comparison is made with the Fili-pino counterparts to gain comprehensive perspec-tives that will develop a knowledge base to sup-port global competence.

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Grantees

In collaboration with GIS and UT, I am going to continue my research

in the field of complex genetics. Furthermore, the functional role of the

genetic variants detected will be described in RA pathogenesis.

Katrin Kepp

� Title: Analysis of genetic variation in p65 binding sites in arheumatoid arthritis cohort of European descent� Supervisor: Sonia Davila� Grant: MJD236, 1 Nov 2011 – 31 Oct 2014� Partner institution: University of Tartu� Receiving institution: Genome Institute of Singapore (GIS)

[email protected]

’’

p65 Binding Sites in RA DevelopmentRheumatoid Arthritis (RA) is known as a com-

plex disease, with a high proportion of the diseaserisk to be accounted for by the genetic makeup ofthe individual as well as environmental and hormo-nal contributions. Over the recent years, genotyp-ing-based genome-wide association studies aimingto identify the genetic basis of complex diseases havedominated the genetic field. However, it is nowwidely recognized that much of this genetic contri-bution still remains unexplained. Therefore, newapproaches are needed to reveal the so-called “miss-ing genetic heritability”. A recent development insequencing technologies is one of the best ways offilling this gap in human genetics. Many complexdisease studies have shown the important role ofgenetic variations on gene expression via transcrip-tion factors (TF) bindings and, thus, they may con-tribute to the development of human disease.

In this project, I combined NGS (Next Genera-

tion Sequencing) technologies to identify sequencevariation within the previously described TF bind-ing sites (>15,000) of one of the subunits of p65,associated with susceptibility to RA in two pop-ulations (Estonia and Sweden). Chronic up regula-tion of TF p65 has been shown in the synovial fluidof RA patients, thus, indicating an important rolein disease development.

As a result of this project, a set of genes withgenetic polymorphisms within p65 binding regionswith the indication of the potential differential ac-tivation by p65 was detected. In the future, theseregions may potentially provide interesting thera-peutic targets to tackle this devastating disease. Inaddition, the whole assay build up in this project isvaluable in the case of other (autoimmune or infec-tious) diseases where inflammation and p65 havebeen shown to play an important role.

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‘‘

Vimala Huchaiah

� Title: Development of research and diagnostics tools for ZnT8,

a new autoantigenic target in type-1 diabetes

� Supervisor: Raivo Uibo

� Grant: MJD239, 1 Jan 2012 – 31 Dec 2014


[email protected]

The Presence of Autoantibodies Is an

Important Predictive Marker for T1DM

At present, I am working as a researcher at the University of Tartu.

’’

The main objective of the project was to developa diagnostic test system for screening autoantibodiesagainst ZnT8 in patients’ sera to predict type-1 dia-betes mellitus (T1DM).

T1DM is an organ-specific autoimmune disorderinvolving autoimmune destruction of the insulinproducing β-cells of pancreas, which leads to meta-bolic abnormalities. To date, this is an irreversibleprocess and, consequently, the patients depend onexogenous insulin administration to survive. The ap-pearance of autoantibodies usually precedes theonset of diabetes by months/years. These are isletcell autoantibodies, antibodies against insulin (IAA),glutamic acid decarboxylase (GADA), protein tyro-sine phosphatase (IA2A/ICA512) and Zinc trans-porter-8 autoantibodies (ZnT8A).

Autoantibody against the protein zinc trans-porter-8 (ZnT8) is the most recently reported (2007)marker which has joined the list of autoantibodiesmeasurement to confirm the T1DM manifestationclinically. Three to four autoantibody types increasethe risk of progressing to T1DM by 60–100%, asthe risk of progression to clinical disease correlateswith the number of autoantibodies rather than in-dividual titers.

Radioimmunoassay has been developed for anti-bodies directed against GADA, IA2A and IAA.ELISA staining for autoantibodies on sections of hu-man pancreas and immunofluorescence assays are alsoroutinely used. To minimize the use of radioisotopes,a luminescent marker (Gaussia luciferase) was usedin this newly developed diagnostic assay to detectZnT8A.

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Grantees

Once I have finalized all the outputs coming from this project, I will

hopefully continue my career, eventually still in Estonia.

Giuseppe Buono

� Title: Paleoecological and Isotopic investigation of the Ordo-vician-Silurian of Estonia: a key to understand the dynamic ofecosystems� Supervisor: Tõnu Meidla� Grant: MJD241, 1 Jan 2012 – 31 Dec 2014� Partner institution: University of Tartu


Worldwide Ordovician and Silurian carbon and oxygen

isotopic record brachiopods derived.

Geochemistry of Estonian Paleozoic FossilsThe main aim of the study was the investigation

of stable isotope (carbon and oxygen) fluctuationin the biogenic fossilized material of the Ordovicianand Silurian periods (approx. from 485 to 419 mil-lion years ago) in Estonia, and its meaning in a glo-bal context.

For this purpose, we collected hundreds of ma-rine invertebrate fossils, mainly brachiopods, from20 localities in Estonia (mainland and islands). Speci-mens preservation has been carefully investigatedthrough a detailed series of analyses focused on as-sessing fossil ultrastructure, mineralogical phasesand elemental composition. Stable isotopic compo-sition was analyzed only in very well preserved car-bonate shells.

Among the relevant results of the study are: (a)an isotopic signal is better preserved in the fossilshells rather than in rocks; and (b) the determina-tion of paleolatitudinal and paleobathimetric iso-

topic (and related thermal and salinity) gradientsand their shifting through time happens accordingto tectonic plates shifting.

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After completing this project, I intend to continue studying extracellular

vesicles for exploiting their biological functions for therapeutic applications.

Imre Mäger

� Title: Targeted exosomes for the delivery of splice-switchingoligonucleotides (SSOs) to muscle and brain� Supervisor: Matthew Wood� Grant: MJD242, 1 Dec 2011 – 30 Nov 2014� Partner institution: University of Tartu� Receiving institution: University of Oxford


Mimicking Nature: Extracellular

Vesicles for Drug DeliveryCell-to-cell communication is required for normal

functioning of all multicellular organisms. Informa-tion exchange can occur via direct contacts, secre-tion of soluble molecules, and by the release of cellmembrane derived vesicles. These extracellular vesi-cles modulate the functions of their target cells byactivating signalling pathways and by deliveringtheir cargo molecules (proteins, RNA, etc.) to theintracellular environment. My project was aimed atexploiting these natural properties of the extracel-lular vesicles for the delivery of desired therapeuticoligonucleotides, designed to modulate the gene ex-pression of preselected targets.

The project required solving several problems.Firstly, methods for isolating extracellular vesiclesneeded thorough optimisation to produce vesicle

samples from complex cell secretome in an ultrapure,reliable and scalable fashion. This was solved byadopting a unique size exclusion chromatographybased workflow for vesicle isolation which enabledthe precise characterisation of vesicle contents.

Secondly, efficient strategies had to be designedand evaluated for loading the isolated vesicles withthe desired oligonucleotide cargos. This was achievedby modifying oligonucleotides in a specific way toincrease their association with extracellular vesiclesin a releasable manner so that vesicle-associatedmolecules would retain their biological activity uponentry to recipient cells. Success in both work pack-ages allowed the testing of extracellular vesicles forthe delivery of splice-switching oligonucleotides ina spinal muscular atrophy in vivo disease model.

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Grantees

I will continue with studies of forest ecosystem responses to environmen-

tal change as senior researcher in the same work group where I fulfilled my

postdoc grant at UT.

Arvo Tullus

� Title: Growth dynamics of deciduous trees under changingclimatic conditions: physiological causes and implications forforest management� Supervisor: Anu Sõber� Grant: MJD257, 1 Dec 2011 – 30 Nov 2014� Partner institution: University of Tartu

[email protected]

’’

Rising Air Humidity Affects

Northern ForestsGlobal warming will bring more precipitation in

Northern latitudes, and warmer air can hold morewater vapour, meaning that air humidity will in-crease. The current project was conducted in theFree Air Humidity Manipulation (FAHM) facility,which is the world’s first open-air experiment wherethe responses of trees and forest ecosystems to el-evated air humidity are studied. As test species, sil-ver birch and hybrid aspen are used.

As expected, under elevated humidity conditions,transpirational water flow through the trees de-creased which, on the one hand, helped to maintainsoil moisture but, on the other hand, hindered theacquisition of nutrients that are mobile in soil andmove to the roots with transpiration-driven waterflow. Especially, the uptake of nitrogen to the treeleaves was restricted which, in its turn, decreased

the photosynthetic capacity of the leaves. Conse-quently, during the first 2–3 experimental years, thegrowth rate of both tree species was significantlyslower under elevated humidity. During the follow-ing seasons, the growth rate of birches recoveredand became faster in the final study year, while thegrowth of aspen remained suppressed. As one ofthe acclimation mechanisms, birches growing un-der elevated humidity delayed their autumn leaf fallfor 2–3 weeks, which enabled them to maintain pho-tosynthetically active foliage longer.

The results suggest that, besides increasing tem-perature and CO

2 concentration, rising air humid-

ity will also become an important climate changerelated factor that is going to affect the growth andfunctioning of trees in Northern forests.

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For three years I have told a joke that Estonia is actually the last place

to study Estonian emigration. Albeit it might not be true, the study now

continues abroad.

Pauli Heikkilä

� Title: Foreign policy of exile Estonians, 1944–1972

� Supervisor: Olaf Mertelsmann

� Grant: MJD259, 1 Jan 2012 – 31 Dec 2014


[email protected]

’’

International Cooperation

During the Cold WarIn the aftermath of World War II, approximately

70,000 Estonians fled from the Soviet troops to theWest where they restarted their lives in Swedish,American, Canadian, etc. societies. They also initi-ated political campaigns to restore Estonian inde-pendence.

Although a delightfully active research commu-nity has emerged around the Estonian diaspora,there are still few studies of their political aspira-tions and organizations. Even my project is not di-rectly interested in Estonian endeavors but usesthem as a departure point to study internationalcooperation among refugees from Central and East-ern Europe.

Assembly of Captive European Nations (1954–1972) was the most important form of their mutualefforts and, although Estonians constitute only one

of the nine member organizations, revealing their par-ticipation will illustrate the history of this extensive,yet nowadays nearly forgotten, organization.

Archives are the basis of any historical research,and the study of Cold War diaspora requires visitsto Western Europe and the USA. Thanks to a Ful-bright scholarship during my project, I was able tostudy the most relevant collections in the Immigra-tion History Research Center in Minneapolis andHoover Institute at the Stanford University.

Fortunately, there is also emerging collaborationamong researchers from Central and Eastern Eu-rope. The theme carried me away, and I have moreto show from the Baltic federation during World WarII and the protests towards the Olympic sailing inTallinn in 1980, which are outside the initial timeframe.

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Grantees

After Mobilitas, I am working at UT as a senior researcher. I continue

my work to understand the mechanisms and functions of the photosynthetic

apparatus.

Juha Matti Linnanto

� Title: Time Evolution of Electronic Excitation in Photosynthetic

Complexes

� Supervisor: Arvi Freiberg

� Grant: MJD262, 15 May 2012 – 14 May 2014


[email protected]

Light Harvesting and Energy Transfer in

Photosynthetic Complexes

’’

The Sun is the main energy source of life onEarth, with nearly every organism depending onphotosynthesis or its products for energy. In photo-synthetic organisms, light harvesting (LH) antennacomplexes trap the Sun’s light and transfer lightenergy to the photosynthetic reaction centre (RC)complexes where electron and proton transportprocesses take place. And finally, series of electronand proton transfer and biochemical reactions con-vert the energy of the Sun’s photons into chemicalenergy in the form of sugars, lipids, and other com-pounds that sustain cell life.

The LH antenna and RC complexes have suchmolecule architectures that captured solar energyflows efficiently via different molecule complexestowards the RC as water flows in a river. However,the structure of a molecular complex itself does not

directly tell the direction of the energy flow as land-scape tells the direction of water flow in the river.Therefore, different spectroscopic and computationmethods are needed to study the light harvestingand energy transfer (ET) properties of photosyn-thetic complexes.

The research project focused on the spectroscopicand ET properties of LH and RC complexes. Thestudy gave new information on the vibronic transi-tions of molecules and their complex structures. Inthe project, we modelled the photosynthetic unitfor filamentous anoxygenic phototrophs (FAP). Themodel reproduces experimentally observed transi-tion rates and suggests effective excitation energytransfer via different LH antennae to the RC com-plex of FAP.

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’’

After my postdoc, I got a position as senior researcher at Tartu Observa-

tory. I am establishing my own research group in the filed of observational

cosmology.

Elmo Tempel

� Title: Dark matter search using astrophysical sources

� Supervisor: Martti Raidal

� Grant: MJD272, 1 Nov 2011 – 31 Oct 2014

� Partner institution: National Institute of Chemical Physics and

Biophysics

[email protected]

Dark Matter and Galaxy FilamentsOne of the greatest advances in cosmology has

been the discovery of how matter and light are or-ganized on scales larger than those of galaxies – themain building blocks of our Universe. Galaxies arenot uniformly distributed in space.

Instead, they are arranged into various struc-tures: groups, clusters, chains, filaments, sheets, andsuperclusters. Galactic filaments are the most strin-gent structures found in nature, containing nearlyhalf of the total mass (visible and dark) of the Uni-verse.

Today, the cold dark matter cosmological modelis established with a few percent precision. We livein a universe that is energetically dominated by darkmatter (27%) and dark energy (68%). However, themodel does not clarify the nature of these mysteri-

ous but dominant dark components. Importanthints can be found by analyzing the details of mat-ter distribution.

The aim of the postdoc project was to search forindirect dark matter signals from nearby astronomi-cal sources – our own galaxy, galaxy groups andlarge-scale cosmic filaments. An interesting resultwas the discovery of a line-like excess of gammarays from the Galactic centre and from the nearbygalaxy clusters. Whether this signal is of dark mat-ter origin or not is still debatable.

Additionally, we mapped the galactic filamentsin the nearby universe with unprecedented details.We showed that the galactic filaments have a sig-nificant role in the formation and evolution of gal-axies.

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Grantees

I continue collaboration with the supervisor of my project and search for

new funding opportunities.

Diana Santalova

� Title: Multivariate regression models in application for trans-port flows analysis and forecasting� Supervisor: Tõnu Kollo� Grant: MJD280, 1 Jan 2012 – 31 Dec 2014� Partner institution: University of Tartu


Forecasting Transport FlowsThe main objective of the project is the forecast-

ing of passenger transport flows, applying multivar-iate regression models. Special attention has beenpaid to the modified gravity model. This is a non-linear regression model for passenger correspond-ences estimation between pairs of spatial points. Thematrix of estimated correspondences is called thecorrespondence matrix. Correspondence matrix isrequired for any transport model as input informa-tion. The model contains the “traditional” gravitypart and the regression part. The gravity part con-sists of the products of populations at the pointsand distance between them. The regression part con-tains various predictors describing the correspond-ence between points more completely. The modelcontains numerous unknown parameters whichmakes the estimation of the model quite compli-cated. Unknown parameters and correspondencesare estimated using aggregated data, i.e., the totalnumbers of passenger departures at every point in

a considered time interval. The model was estimatedunder the assumption that error term is a normallydistributed random variable, and statistical proper-ties of the estimates have been verified as well. An-other assumption of the model is that estimated cor-respondences are symmetric which contradicts thereal life. This can cause loss of estimation accuracy,which can be observed as increasing the mean squareerror. Our approach for diminishing the mean squareerror is based on a hypothesis that the non-symme-try of the correspondences can violate the assump-tion about the normality of error distribution. Themodel was generalized to a model with skew-nor-mal error distribution, and a method of its estima-tion was proposed, verified and tested.

This and other models proposed within the re-search, and their estimation methods, are universaland can be successfully applied in any area of dif-ferent patterns of factors.

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‘‘

I will continue to explore how transcription factors work in the context

of chromatin and epigenetic information to ensure a properly functioning

hematopoietic system.

Tõnis Org

� Title: Mechanisms of Scl/Tal1 dependent gene activation andrepression during mesoderm diversification� Supervisor: Hanna Mikkola� Grant: MJD284, 1 Nov 2011 – 31 Oct 2014� Partner institution: University of Tartu� Receiving institution: University of California, Los Angeles

[email protected]

’’

Cell-based Therapies for Blood DisordersMy research aims to understand the mechanisms

that direct mesoderm diversification, which holdsa great potential to advance the development ofcell-based therapies for cardiovascular and blooddisorders. The bHLH transcription factor Scl isknown as the master regulator of the hematopoi-etic fate. We discovered that, in addition to its criti-cal function in promoting hematopoietic develop-ment, Scl is also required to repress cardiomyo-genesis. However, the mechanisms for this repres-sion have remained unknown.

Using ChIP-sequencing and microarray analy-sis of embryonic stem cell derived mesodermal cells,that can give rise to both hematopoietic and car-diac lineages, we show that Scl both directly acti-vates a broad gene regulatory network required forblood development and represses transcriptional

regulators required for cardiogenesis. The repres-sion of cardiac and mesodermal programs occursduring a short developmental window through Sclbinding to distant enhancers that are primed foractivation, while binding to hematopoietic regula-tors extends throughout hematopoietic develop-ment.

The analysis of cardiac transcription factorsHand1 and Gata4 binding sites in mesodermshowed that many of them overlap with Scl bind-ing sites. This suggests that Scl hampers cardio-genesis by blocking the enhancers that cardiacmaster regulators would use for gene activation.These results denote Scl as a true master regulatorof hematopoietic vs. cardiac fate choice and sug-gest a mechanism by which lineage-specific bHLHfactors direct the divergence of competing fates.

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Grantees

Antonio Racioppi

� Title: Stückelberg Z' and scalar dark matter

� Supervisor: Martti Raidal

� Grant: MJD298, 1 Oct 2012 – 30 Sept 2014

� Partner institution: National Institute of Chemical Physics and

Biophysics

[email protected]

The Dark Unknown

I am finishing my second postdoc at KBFI where I am planning then to

establish my own research group.

’’

It is a summer time night. We are in the coun-tryside, far from the city lights. The weather isbeautiful and warm. No clouds. We look up at thesky, and we see many stars shining. All the rest isdarkness (except for the moon and some planetswhich are visible because they reflect sunlight).However, such darkness is not empty. It is full ofseveral objects like planets, natural satellites, as-teroids and so on... Still, our present knowledgecan explain just a small fraction of it.

The Standard Model (the proved present de-scription of the microscopic world) can only de-scribe 5% of the mass of the universe: the stars,planets, galaxies, etc. mentioned before. The re-maining 95% of the mass of the universe is notexplained by the Standard Model and consists of

dark energy (68%) and dark matter (27%). Theorigin of the appellative “dark” is quite simple.Such a matter does not emit light, therefore, it isdark, and it cannot be directly seen. So far, the evi-dence of its existence is only indirect and gravita-tional: ordinary matter is attracted to it. Darkmatter is searched for in detectors where a darkmatter particle colliding with an atomic nucleuscould be seen. Unfortunately, we have not seen ityet, therefore, we do not know its properties.

My project consists of developing viable andtestable models of dark matter. In particular, Istudy models in which dark matter is a scalar par-ticle coupled to the Higgs boson and involved inthe stabilization of the electroweak vacuum.

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‘‘

I plan to continue my research in the chosen field, particularly working

on different approximation methods, including subdivision and parametric

interpolation.

Evely Leetma

� Title: Smoothing problems

� Supervisor: Tom Lyche

� Grant: MJD340, 1 Aug 2012 – 31 July 2014


� Receiving institution: Centre of Mathematics for Applications, Oslo

[email protected]

’’

Computer-aided Geometric DesignComputer-aided geometric design (CAGD) is a

wide research area, dealing with the computationalaspects of geometric objects — how to produce acomputer-compatible description of some shape.The main tools in CAGD are splines and differentrecursion formulas, defining smooth subdivisioncurves and surfaces. Often, there is some amountof discrete data, and the problem is how to approxi-mate the underlying continuous process. Theseproblems are called data fitting problems. Data fit-ting problems could be divided into two groups —exact and inexact data fitting (interpolation andsmoothing, respectively).

In the case of interpolation, the desired curveor surface goes through the given datapoints. Themain topic of our research is the choice of param-eter values corresponding to these datapoints. Weanalyze the family of parameterizations that de-

pends on the chord lengths of data polygon andconsider maximum local deviation and global de-viation as the measures of the badness of the ap-proximation. This gives us an approach to find areasonably good approximation with small com-putational cost which mimics the given data poly-gon maximally.

In the case of smoothing problems, the data isgiven approximately, i.e., the resulting curve/sur-face should pass ‘close enough’ to the given data-points. The most natural problem, where ‘closeenough’ means that on each datapoint the maxi-mum deviation is given, is called the smoothingproblem with obstacles. We study how to reducethe smoothing problem with obstacles to the solu-tion of smoothing problem with weights.

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Grantees

A follow-up project, hosted by Uppsala University and the University of

Vienna, will deal with the trajectory of early market reforms in the Lithua-

nian and Ukrainian SSR.

Lars Fredrik Stöcker

� Title: A gradual transition: Perestroika, opposition, secessionand transformation in Estonia in the light of the border-crossingelite networks from the mid-1980s to the early 1990s� Supervisor: Karsten Brüggemann� Grant: MJD347, 1 Oct 2012 – 30 Sept 2014� Partner institution: Tallinn University

[email protected]

’’

Early Market Reforms in Estonian SSRResearch on the economic transformation in the

USSR has mainly been focusing on the post-So-viet period and the successor republics of the So-viet Empire. The early market reforms launchedby the Soviet leadership from 1987 onwards, bycontrast, which generated a new class of ‘Sovietcapitalists’ and contributed to a considerable eco-nomic decentralization in the USSR, have so farbeen neglected by the scholarly community.

The project focused on the implementation ofeconomic reforms in the Estonian SSR, which soonbecame a Soviet forerunner of marketization. Re-formers among the political elite, but also first pri-vate entrepreneurs, profited especially from thecooperation with Estonian émigrés in Sweden and

North America, which developed after the liber-alization of the border regime. Émigrés soon cameto play a leading role as business partners for So-viet Estonian joint ventures, economic advisers andmediators between Estonia and Western compa-nies and organizations. Their commitment laid theground for Estonia’s first business schools and com-panies that still exist today and culminated in theformation of an expert group that offered economicadvice to several Estonian governments. Thistransnational network considerably accelerated theintegration of Estonia into Western markets evenbefore political independence was achieved andsheds an interesting new light on the reasons forEstonia’s post-1991 economic success.

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‘‘

Jaanis Juhanson

� Title: Spatial patterns of denitrifying microorganisms for improvedmitigation strategies for nitrous oxide emissions from arable land� Supervisor: Sara Hallin� Grant: MJD376, 1 Jan 2013 – 31 Dec 2014� Partner institution: University of Tartu� Receiving institution: Swedish University of Agricultural Sciences

[email protected]

Spatial Patterns of Denitrifiers

For the next couple of years, I will continue working at the Swedish

University of Agricultural Sciences where I conducted my research study

financed by Mobilitas during years 2013–2014.

’’

Nitrous oxide (N2O) is a major greenhouse gas

contributing to 6% of the anthropogenic green-house effect, and N

2O emissions from terrestrial

environments represent up to 70% of global N2O

sources. The biological emission of N2O from soil

is mainly controlled by denitrification, an anaero-bic respiratory process that reduces soluble NO

3

–

and NO2

– to the nitrogen gases NO, N2O and N

2

via four enzymatic complexes. A key step in regu-lating N

2O emissions is the reduction of N

2O to

N2, which is catalyzed by the nitrous oxide reduct-

ase encoded by the nosZ gene.To date, two different type of nosZ genes are

known. The current project studies the composi-tion and field-scale spatial patterns of microbial

communities possessing either nosZ clade I or cladeII genes in relation to edaphic factors and poten-tial N

2O reduction activity. Results showed that

the diversity, abundance and community compo-sition of the microorganisms capable of N

2O re-

duction were influenced by different soil factors,indicating niche differentiation between the differ-ent types of nosZ communities in agricultural soil.

Further investigations of the predicted spatialpatterns of denitrifier community regulating N

2O

emissions will give insight into the mechanismsshaping these communities, which could provideus with knowledge-based land management strat-egies for mitigating N

2O emissions.

mobilitas 2014.p65 3/24/2015, 5:02 PM38

39

‘‘

Grantees

After completing my postdoc project in Estonia, I plan to continue

comparative legal research on competition law and market regulation in

Asia.

Alexandr Svetlicinii� Title: Transplantation of the EU competition rules and stand-ards in a small market economy: the case of Estonia from re-gional, EU and international perspective� Supervisor: Tanel Kerikmäe

� Grant: MJD437, 1 Oct 2012 – 30 Sept 2014

� Partner institution: Tallinn University of Technology

[email protected]

’’

Competition Rules for Small MarketsThe enforcement of competition rules is one of

the most important EU policies contributing to thefunctioning of the EU Internal Market, strength-ening the competitiveness of the EU economies andindividual Member States and according widerchoice and lower prices to the consumers. Compe-tition law is also one of the areas where EU insti-tutions, rules, and standards significantly affectedthe development of the national competition rulesof Member States.

Despite the obvious differences in market reali-ties of various Member States, the rules and stand-ards for the competition law of the EU have beencontinuously copied from the EU level onto thenational level of individual Member States. Mypostdoc project explored the problems of apply-

ing of the EU-modelled competition rules (usedfor the protection of competition on the InternalMarket comprised of 28 countries) in a small mar-ket economy such as Estonia.

The study revealed that, although Estoniancompetition rules mirror the EU model, their en-forcement practice differs significantly due to thespecifics of the domestic markets and a complexprocedural framework in which the competitionrules are applied (including administrative, misde-meanour, criminal and civil procedures).

These findings have contributed to the discus-sion on the efficiency and uniformity of the EUcompetition rules and their enforcement by EUMember States.

mobilitas 2014.p65 3/24/2015, 5:02 PM39


‘‘

My next project is at the University of Technology in Vienna (Austria)

where I work on the application of DFT and DMFT-based methods to

strongly correlated materials.

Oleg Janson

� Title: Microscopic modeling of magnetic materials using DFT+Uand hybrid functionals� Supervisor: Alexander Tsirlin� Grant: MJD447, 1 Jan 2013 – 31 Dec 2014� Partner institution: National Institute of Chemical Physics andBiophysics

[email protected]

’’

The Microscopic Modeling

of Magnetic MaterialsThe recent burst of activity on quantum mag-

nets delivered an impressive number of exotic groundstates and magnetic behaviors. Manifestations ofthese phenomena can be directly probed by modernexperimental techniques.

However, the underlying physics can be very com-plicated, turning the interpretation of the experi-mental data into a challenging task. Ab initio cal-culations based on density functional theory pro-vide a rare opportunity to dive into the microscopicroots of magnetism – exchange interactions betweenthe atoms. These interactions cannot be directlymeasured, yet, they govern the experimentally ob-served behavior. Hence, a microscopic magneticmodel is a crucial piece of information in under-standing the experiment.

In this project, microscopic magnetic modelingwas carried out for several magnetic insulators basedon 3d elements. A highlight of this research is thestudy of Cu

2OSeO

3, the compound known as the

only to-date known insulator showing the emergenceof skyrmions – topological magnetic defects with awhirlpool-like structure. Using a multi-scale ap-proach, we were able to trace the formation ofskyrmions to the microscopic exchange interactionsthat operate on completely different length scales.This is a first example of such an ab initio analysisfor a bulk skyrmionic material.

The ongoing improvement of computationaltechniques allows us to envisage future applicationsof microscopic modeling to further ambitious tasks.

mobilitas 2014.p65 3/24/2015, 5:02 PM40

41

‘‘

Grantees

After Mobilitas, I will continue my studies in joint projects on the same

multidisciplinary venue with archaeologists and research laboratories in

Sweden, Germany and Estonia.

Uwe Sperling

� Title: Research in the metalwork of Bronze Age Estonia –

archaeometric and experimental methods applied

� Supervisor: Valter Lang

� Grant: MJD458, 1 Jan 2013 – 31 Dec 2014


[email protected]

’’

Archaeometry of Bronze Age MetalworkMy studies focussed on bronze production in

prehistoric Estonia, which is about 800 BC (LateBronze Age) when the region had active connec-tions with distant European regions for the ex-change and import of copper and tin (e.g., the Alpsand Britain). The project addressed challengingquestions on the archaeological remains frombronze casting workshops (e.g., Asva): How hastechnical knowledge moved? Have (few) specialistsonly been involved in contact and travel? Whatabout the social role and function of precious met-als? I tested various hypotheses with experiments,replicating processes (fabrication of clay moulds;melt, cast of bronzes), and with methods of mate-rials science (archaeometry). The interesting resultsdo not only point to a complex and multi-tieredorganisation of this exclusive branch of craft butalso to entire households involved in these techno-logical practices.

The concept of the interdisciplinary nature of the study,

and the technological (‘embodied’) know-how to be

decrypted from archaeological finds such as the disc-

pin of Kaali meteorite-crater.

mobilitas 2014.p65 3/24/2015, 5:03 PM41


Index of Grantees

Eduard Aleksanyan 19

Harry Alles 5

Gemma Atkinson 14

Eve Avel 9

Anna Karin Borg Karlson 6

Giuseppe Buono 27

Michal Cagalinec 10

Vinay Choubey 16

Mithu Guha 18

Pauli Heikkilä 30

Vimala Huchaiah 26

Oleg Janson 40

Jaanis Juhanson 38

Liisi Keedus 11

Katrin Kepp 25

Evely Leetma 36

Juha Matti Linnanto 31

Lili Milani 13

Imre Mäger 28

Maria Mälksoo 12

Sergey Omelkov 22

Tõnis Org 34

Sheila Gamut Oyao 24

Anu Ploom 15

Alexandr Popov 20

Antonio Racioppi 35

Fernando Rodriquez-Castañeda 23

Ulrike Rohn 8

Diana Santalova 33

Toomas Silla 17

Nasir Sohail 21

Uwe Sperling 41

Lars Fredrik Stöcker 37

Shinya Sugita 7

Alexandr Svetlicinii 39

Elmo Tempel 32

Arvo Tullus 29

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