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University of Helsinki
 
Biocentrum Helsinki
General information:

Contact information:

Professor Pekka Lappalainen
Director
Tel. +358 9 191 59499
E-mail:
pekka.lappalainen -at- helsinki.fi


Sari Tojkander
Coordinator
Tel. +358 9 191 59505
E-mail:
sari.tojkander -at- helsinki.fi



Riitta Smahl-El Hamraui
Administration secretary
Tel. +358 9 191 25408
E-mail:
riitta.smahl-elhamraui -at- helsinki.fi



BIOCENTRUM HELSINKI RESEARCH GROUPS

The current Biocentrum Helsinki groups carry out research in the Faculties of Medicine, Biological and Environmental Sciences, Pharmacy, and at the Institute of Biotechnology, FIMM, Neuroscience Center, and at Aalto University. The main emphasis of the work performed in Biocentrum Helsinki is devoted to cell and molecular biology, cancer biology, molecular neurobiology, developmental biology, human molecular genetics, plant biotechnology, structural biology and biophysics, systems biology, and bioinformatics.

The current Biocentrum Helsinki groups appointed for 1.1.2014-31.12.2016 are:

Biotechnology and Bioinformatics

Sampsa Hautaniemi:
Systems Biology and Bioinformatics

short description and contact information

Olli Kallioniemi:

short description and contact information

Samuel Kaski:
Machine learning for multi-omics cumulative biology

short description and contact information

Mauri Kostiainen:
Macromolecular Engineering of Biohybrid Materials
short description and contact information

Markus Linder:
Biomolecular materials

short description and contact information

Cell and Molecular Biology

Mikko Frilander:
Minor spliceosome as the regulator of gene expression

short description and contact information

Ville Hietakangas:
Nutrient sensing

short description and contact information

Elina Ikonen:
Intracellular Cholesterol Transport; Development of New Imaging Techniques to Study Cholesterol Cell and Tissue Biology 
short description and contact information

Pekka Katajisto:
Stem cells and aging
short description and contact information

Liisa Kauppi:
Mechanisms of genome stability in mammalian cell
short description and contact information

Pekka Lappalainen:
Regulation of actin and plasma membrane dynamics in cell migration and morphogenesis   
short description and contact information

Tomi Mäkelä:
Kinase signaling in tumor suppression and transcription   
short description and contact information

Timo Otonkoski:
Biomedicum Stem Cell Center; Human pluripotent stem cells for biomedical research
short description and contact information

Kalle Saksela:
Protein interactions in cellular signaling and virus-host cell interplay
short description and contact information

Maria Vartiainen:
Actin as an organizer of gene expression
short description and contact information

Developmental Biology

Jukka Jernvall:
Evolutionary developmental biology of mammalian dentition
short description and contact information

Marja Mikkola:
Epithelial morphogenesis
short description and contact information

Macromolecular Structure and Biophysics

Dennis Bamford:
Virus Universe; from theoretical considerations
to practical applications
short description and contact information

Sarah Butcher:
Macromolecular structure and assembly  
short description and contact information

Markku Varjosalo: home page: http://www.biocenter.helsinki.fi/bi/protein

Molecular Cancer Biology

Akseli Hemminki:
Cancer immunotherapy utilizing oncolytic viruses
short description and contact information

Satu Mustjoki:
Immunotherapy and discovery of novel drug targets in hematological malignancies
short description and contact information

Molecular Genetics

Lauri A.Aaltonen:
Tumor Genomics Group

short description and contact information

Hannes Lohi:
Canine and feline models of human inherited disorders

short description and contact information

Päivi Peltomäki:
Hereditary Cancer; Epigenetic mechanisms of predisposition to common human cancers
short description and contact information

Samuli Ripatti:
Statistical and translational genetics

short description and contact information

Molecular Neuroscience

Eero Castrén:
Role of TrkB and p75 Neurotrophin receptors in mood disorders and antidepressant treatments
    
short description and contact information

Kai Kaila:
Control of neuronal signaling and plasticity by ion-regulatory proteins during brain development and seizure disorders   
short description and contact information

Mart Saarma:
Structure, biology and therapeutic potential of neurotrophic factors 

short description and contact information

Anu Wartiovaara:
Molecular basis of mitochondrial dysfunction in human disease

short description and contact information

Pharmaceutical Nanotechnology and Drug Delivery

Hélder A. Santos:
Biodegradable nanoporous silicon nanomaterials for controlled drug delivery and targeted cancer therapy

short description and contact information

Plant Biotechnology and Molecular Biology

Yrjö Helariutta:
Genetic control of wood development
short description and contact information

Jaakko Kangasjärvi:
Reactive Oxygen Species signaling in plant stress
 
short description and contact information

Translational Cancer Biology

Kari Alitalo:
Targeting of endothelial growth factor pathways and cancer stem cells
short description and contact information

Tumor Genomics Group

 

Lauri Aaltonen
M.D., Ph.D.
Academy Professor

Genome Scale Biology Research Program & Department of Medical Genetics
Biomedicum Helsinki
P.O. Box 63 (Haartmaninkatu 8)
FI-00014 University of Helsinki, Finland

Tel. 358-9-191 25595
Fax 358-9-191 25105

e-mail: lauri.aaltonen -at- helsinki.fi

home page: http://research.med.helsinki.fi/gsb/aaltonen/

The research of the group – a member of the Academy of Finland’s Center of Excellence in Cancer Genetics -focuses on human tumor susceptibility. A particular focus of interest has been hereditary colorectal cancer, where the group has contributed to several key discoveries; see the link for selected publications. Molecular background events in microsatellite unstable colorectal cancer is one of our long term interests. We have also identified and characterized novel tumor predisposition syndromes, hereditary leiomyomatosis and renal cell cancer (HLRCC), and pituitary adenoma predisposition (PAP), and identified the respective susceptibility genes. Another gene discovery relates to the molecular basis of common colorectal cancer predisposition; we have contributed to identification of the respective genetic loci, as well as to mechanistic studies to unravel the biological basis of such predisposition.

One current aim is to utilize registry-based approaches to identify unique cancer family materials, for sequencing based analysis and disease gene identification. Finland provides excellent resources for this work, and an effort to systematically utilize the National Cancer Registry (operating since 1953) and Population Registry databases in cancer gene identification is in progress.

Our main focus at present is characterization of colorectal cancer and uterine leiomyoma genomes by exome and whole genome sequencing and other high-throughput methods. Thus our work ranges from epidemiology and genealogy to molecular work, and meaningful analysis and interpretation of the massive amounts of data derived is a key interest area for us. Our works have been published in journals such as Nature, Science, New England Journal of Medicine, and Nature Genetics.

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Targeting of endothelial growth factor pathways and cancer stem cells

 

Photo: Aleksi Poutanen

Kari Alitalo
M.D., Ph.D.
Academy professor

Translational Cancer Biology Program
Biomedicum Helsinki
P.O.B. 63 (Haartmaninkatu 8)
FI-00014 University of Helsinki, Finland

Phone: +358-9-191 25511
FAX: +358-9-191 25510

E-mail: kari.alitalo -at- helsinki.fi

home page:
http://research.med.helsinki.fi/cancerbio/alitalo/

Solid tumors require blood vessels for growth and dissemination, and use lymphatic vessels as additional conduits for metastatic spread. The identification of growth factor receptor pathways regulating angiogenesis has led to clinical approval of the first anti-angiogenic molecules targeted against the vascular endothelial growth factor (VEGF) pathway. However, in many cases resistance to anti-VEGF-VEGFR therapy occurs, and thus far the clinical benefit has been limited to only modest improvements in overall survival. Therefore, novel treatment modalities are required. We are interested in the other members of the VEGF family, as well as the angiopoietin growth factors and their receptors as targets for the inhibition of tumor angiogenesis, lymphangiogenesis and metastasis. This work has led us also to putative targets in cancer stem cells. Combinatorial targeting of multiple vascular growth factor pathways shows promise for improving the efficacy of anti-angiogenic tumor therapy.

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Virus Universe; from theoretical considerations to practical applications

 

Dennis Bamford
Academy Professor

Institute of Biotechnology and Department of Biosciences
P.O. Box 56 (Viikinkaari 5)
FI-00014 University of Helsinki, Finland

tel +358-9-191 59100

E-mail: dennis.bamford -at- helsinki.fi

homepage: http:// www.helsinki.fi/molecularvirology

We investigate viruses containing protein, nucleic acid and lipid 
constituents that infect prokaryotic (bacterial and archaeal) hosts. 
These viruses are used as model organisms in understanding structure, 
assembly and function of biological macromolecular complexes. These 
studies have also shed light on the evolution and origin of viruses. 
We propose that seemingly unrelated viruses infecting hosts in all 
three domains of life may have a common origin.

Furthermore, we have a keen interest in elucidating the structure and 
function of RNA-dependent RNA polymerases originating from dsRNA 
bacteriophages. Such polymerases, in addition to providing insight 
into the mechanisms of initiation, elongation and termination of the 
polymerization reaction, are valuable tools in biotechnology due to 
their capacity to produce dsRNA of practically unlimited length or 
amount for gene silencing.

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Macromolecular Structure and assembly

 

Sarah Butcher
Professor
Academy of Finland Centre of Excellence in Virus Research (2006-2011)
Structural Biology and Biophysics Program

Institute of Biotechnology
P.O.Box 65 (Viikinkaari 1)
FI-00014 University of Helsinki, Finland

Tel.+358-9-191 59563
Fax +358-9-191 59930

E-mail: sarah.butcher -at- helsinki.fi

home page: http://blogs.helsinki.fi/butcher/introduction/

Our work aims to understand the structure, assembly and function of
biological macromolecule complexes using cryo-electron microscopy
integrated with other approaches such as X-ray crystallography,
biochemistry and genetics. Our major interests are the structural basis
of virus assembly, replication, host recognition and entry. Currently we
are studying: capsid structure and host cell recognition by
picornaviruses, archaeal and dsRNA viruses. The results may have
implications in the prevention of viral diseases.

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Role of TrkB and p75 Neurotrophin receptors in mood disorders and antidepressant treatments 

 

Eero Castrén
M.D.
Professor, Director

Neuroscience Center
P.O. Box 56 (Viikinkaari 4)
FI-00014 University of Helsinki, Finland

Tel.+358-9-191 57626
Fax +358-9-191 57620

E-mail:: eero.castren -at- helsinki.fi

home page: http://www.helsinki.fi/neurosci/groups/castren.html

Brain-derived neurotropic factor (BDNF) acts by binding to two receptors producing functionally opposite effects, TrkB promoting survival, growth and plasticity while p75 mediates apoptosis, pruning and synaptic depression. We have previously shown that antidepressant drugs rapidly activate TrkB mediated signaling and thereby reactivate juvenile-like plasticity in adult rodent brain. Given the opposite functional role of TrkB and p75 we hypothesize that stress and depression might promote p75 expression and signaling.  Our aim is to investigate the role of neurotrophin receptors TrkB and p75 in mood and anxiety disorders, and in antidepressant treatments used for therapy of these disorders.

Our laboratory uses a wide range of biochemical, genetic and imaging methods to investigate the role of neurotrophic factors and neuronal plasticity in mood disorders and the mechanisms of drug action.

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Minor spliceosome as the regulator of gene expression


Mikko Frilander
Ph.D.
Group Leader

Institute of Biotechnology
Program in Genome biology
P.O.Box 56 (Viikinkaari 9)
FI-00014 University of Helsinki, Finland

Tel.+358-9-191 59509
Fax +358-9-191 59366

E-mail: mikko.frilander -at- helsinki.fi

home page: http://www.biocenter.helsinki.fi/bi/SPLICING/index.html

Post-transcriptional processing of nascent primary transcripts to mature mRNA molecules is an essential step in eukaryotic gene expression pathway, but provides also important regulatory step to control gene expression. Pre-mRNA splicing is the most significant nuclear RNA processing step and is responsible of the removal the noncoding intron sequences from the pre-mRNA molecules to yield mature protein-coding mRNAs. In alternative splicing  multiple mRNA variants can be produced from a single gene. This leads to formation of protein isoforms with different biological properties. Alternatively, mRNA variants can differ in their stability or cellular distribution. Defects in the pre-mRNA processing are one of the most common cause of human congenital diseases.

In most multicellular organisms there are two separate pre-mRNA splicing machineries, or spliceosomes. Our research focus on so called minor spliceosome. This spliceosome can regulate processing of a subset of genes through slower splicing that leads to nuclear retention and decay of the mRNAs. We use various methods in RNA biology and biochemistry to investigate the function and components of this machinery. Furthermore, we use genome-wide methods (RNAseq) to investigate global regulation of through minor spliceosome.



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Systems Biology and Bioinformatics

 

Sampsa Hautaniemi
D.Tech.
Professor

Genome-Scale Biology Research Program
P.O. Box 63 (Haartmaninkatu 8)
FI-00014 University of Helsinki, Finland

Tel.+358-9-191 25419
Fax 358-9-191 25610 

E-mail: sampsa.hautaniemi -at- helsinki.fi

home page: http://research.med.helsinki.fi/gsb/hautaniemi/default.html

With the rapid development of technologies that allow molecular level quantitative measurements with unprecedented quantity and resolution, computer science, engineering techniques and mathematics have become an integral part of modern medicine. The overall goal of the Systems Biology group is to develop computational approaches that allow translation of the multidimensional molecular and clinical data into knowledge. Our main focus is on achieving systems level understanding on key cell decision processes driving cancers resistant to therapeutics.

The research in the Systems Biology group concentrates on two topics. Firstly, in order to efficiently analyze large-scale and multilevel molecular data, we have developed a computational ecosystem called Anduril. Our approach provides a modular and open source workflow framework for data analysis, and it is the backbone that enables efficient analysis and interpretation of biomedical data. Secondly, we actively develop and apply approaches to integrate genetics, transcriptomics, proteomics, epigenetics and clinical data to gain understanding of cancer progression and resistance to anti-cancer treatments. Currently, we focus mainly on lymphoma, ovarian cancer and breast cancer.

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Genetic control of wood development

 

Ykä (Yrjö) Helariutta
Ph.D.
Professor

Institute of Biotechnology
P.O.Box 65 (Viikinkaari 1)
FI-00014 University of Helsinki, Finland

Tel.+358-9-191 59422
Fax +358-9-191 59366
E-mail: yhelariu -at- mappi.helsinki.fi

home page: http://www.biocenter.helsinki.fi/bi/Helariutta/

We investigate the molecular basis of wood development and its 
diversity. Wood, also called secondary xylem, is derived from an 
actively dividing cylindrical lateral meristem, vascular cambium. 
Periclinal cell divisions produce secondary phloem (transports 
carbohydrates) outwardly, and secondary xylem (conducts water and 
minerals) inwardly. The cambial activity varies seasonally in trees 
from the temperate-zone, giving rise to annual rings. Our topic is an 
example of a plant developmental problem.

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Cancer immunotherapy utilizing oncolytic viruses

 

Akseli Hemminki
M.D., Ph.D.
Docent
Research director

Haartman Institute
P.O. Box 21 (Haartmaninkatu 3)
FI-00014 University of Helsinki, Finland

Tel: +358-9-191 25464
Fax: +358-9-191 25465

e-mail: akseli.hemminki -at- helsinki.fi

Home page http://www.hi.helsinki.fi/cgtg/index.htm

Work in the Cancer Gene Therapy Group focuses on utilization of oncolytic viruses for immunotherapy of cancer lacking currently available effective modalities. Oncolytic viruses kill cancer cells by replicating in them (oncolysis), but they also induce danger signals in the tumor reducing immunosupression. Immunotherapeutic effect can be boosted by arming the virus with immunostimulatory molecules encoding genes, e.g. CD40L or GMSCF, that recruits T-cells to the tumor. Recently, our group has studied the use of oncolytic viruses in enhancing the efficacy of adoptive T-cell therapy, which is potential form of therapy but in its current form still has some obstacles to overcome. The emphasis in our group is on translating the most promising preclinical approaches into treatments for patients.

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Nutrient sensing

 

Ville Hietakangas
Ph.D.
Assistant Professor

Department of Biosciences & Institute of Biotechnology
Biocenter 2
P.O. Box 56 (Viikinkaari 5)
FI-00014 University of Helsinki, Finland

Tel: +358-9-191 58001

e-mail: ville.hietakangas -at- helsinki.fi

Home page http://www.biocenter.helsinki.fi/bi/hietakangas/

Animals constantly monitor their nutrient status and adjust their physiology accordingly. Sensing and regulation of nutrient homeostasis is mediated by conserved signaling pathways and transcriptional networks. The main focus of our group is to understand the regulation of tissue growth and energy metabolism in response to carbohydrate and amino acid sensing. Our main model system is Drosophila, which is a versatile tool for genetic dissection of nutrient homeostasis regulation in vivo.

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Intracellular Cholesterol Transport; Development of New Imaging Techniques to Study Cholesterol Cell and Tissue Biology 

 

Elina Ikonen
M.D., Ph.D., Academy Professor

Institute of Biomedicine, Anatomy
Biomedicum Helsinki
P.O. Box 63 (Haartmaninkatu 8)
FI-00014 University of Helsinki, Finland

Tel.+358-9-191 25277
Fax +358-9-191 25261

E-mail: elina.ikonen -at- helsinki.fi

home page: http://www.biomed.helsinki.fi/research/cholesterol

The complete genomic sequence of over a hundred organisms, including several higher eukaryotes, has been determined. We develop and use a wide range of computational tools to make sense of this book of life. The overall goal is to model evolutionary relationships in sequence and structure data and to elucidate their functional correlates. Genome annotation is a particular application.

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Evolutionary developmental biology of mammalian dentition

 

Jukka Jernvall
Ph.D.
Academy Professor, group leader

Institute of Biotechnology
P.O. Box 56 (Viikinkaari 9)
FI-00014 University of Helsinki, Finland

Tel.+358-9-191 59352
Fax +358-9-191 59366

E-mail: jukka.jernvall -at- helsinki.fi

home page: http://www.biocenter.helsinki.fi/bi/evodevo/index.shtml

Evolutionary developmental biology (evodevo) is a field of biology aiming to uncover how developmental mechanisms and genes have changed in the evolution of phenotypes. Our aim is to construct developmental-based models that are used to explain and predict phenotypic evolution. Most of our work uses mammalian dentition as a model system in the context of both micro- and macroevolution, and methods ranging from developmental biology experiments to computer models simulating development.

Tooth phenotypes are invariably complex and difficult to fully characterize, and we are developing approaches to allow fast-throughput analysis of three-dimensional shapes. To study natural and mutant phenotypes, we have developed computational modeling tools to link experimental data with theoretical models. Our future aims include 1) finding out what regulates dental complexity during development and evolution, 2) how tooth shape is fine-tuned during development, 3) finding tooth shape specific enhancers, and 4) developing the Saimaa ringed seal as an evodevo model.

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Control of neuronal signaling and plasticity by ion-regulatory proteins during brain development and seizure disorders

 

Kai Kaila
Ph.D.
Professor, research director

Department of Biosciences & Neuroscience Center
P.O.Box 65 (Viikinkaari 1)
FI-00014 University of Helsinki, Finland

Tel.+358-9-191 59860

E-mail: kai.kaila -at- helsinki.fi  

home page: http://www.helsinki.fi/neurobiology/

The Laboratory of Neurobiology studies the role of ion-regulatory proteins (IRPs) in the control of neuronal signaling, plasticity and trauma at the single-cell and neuronal network level, both in vitro and in vivo. Specifically, our research focuses on IRPs in epileptogenesis and in the generation of seizures in vitro and in vivo in both the neonate and adult brain. The IRPs include plasmalemmal transporters such as the cation-chloride cotransporters (CCCs) as well as carbonic anhydrases (CAs) and other pH-regulatory proteins, e.g. the Na/H exchangers (NHEs).

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Olli Kallioniemi
M.D., Ph.D.
Director, Professor

Institute for Molecular Medicine Finland (FIMM)
P.O. Box 20 (Tukholmankatu 8)
FI-00014 University of Helsinki, Finland

Tel.+ 358-50-415 0363

E-mail: olli.kallioniemi -at- helsinki.fi  

home page: http://www.fimm.fi/en/research/research_groups/kallioniemi_group/

 

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Reactive Oxygen Species signaling in plant stress

 

Jaakko Kangasjärvi
Ph.D.
Professor of Plant Biology

Division of Plant Biology, Department of Biosciences
Viikki Biocenter
P.O.Box 65 (Viikinkaari 1)
FI-00014 University of Helsinki, Finland

Tel.+358-9-191 59444
Fax +358-9-191 59552

E-mail: jaakko.kangasjarvi -at- helsinki.fi

home page:
http://www.helsinki.fi/biosci/plantstress/research

Our work combines plant physiology with genetics and molecular biology and concentrates on finding out how plants sense and transmit stress signals at the cellular level.
The primary focus is on understanding the signaling networks involving reactive oxygen species (ROS) such as hydrogen peroxide, superoxide, singlet oxygen and hydroxyl radical. ROS are produced by plant cells in a variety of situations: An active burst of ROS production is a common link between nearly all biotic and abiotic stresses including ozone and pathogens but ROS also play important roles during development. Previously thought to be merely damaging agents, ROS are now understood for their roles as signaling molecules.
We utilize a variety of genetic strategies with the model plant Arabidopsis thaliana. We use forward genetics screens as a strategy to dissect ROS signalling pathways at the genetic level. To this end, we have isolated a collection of ROS sensitive mutants. This has resulted in the isolation and cloning of novel regulators of ozone, ROS, and stomatal responses.

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Machine learning for multi-omics cumulative biology

 

Samuel Kaski
D.Sc.
Professor, Director

Helsinki Institute for Information Technology HIIT
P.O. Box 15400 (Konemiehentie 2, Espoo)
FI-00076 Aalto University, Finland

Tel.+358-50- 305 8694
Fax +358-9- 855 0114

E-mail: samuel.kaski -at- hiit.fi

home page:
http://www.hiit.fi/samuel.kaski/

We develop new machine learning, computational inference and probabilistic modelling methods for learning from multiple data sources: data integration, prediction, retrieval, recommendation, interaction and visualization. Given the multiple omics databases, these data analysis problems are shared core challenges underneath research problems in chemical systems biology, disease association studies and personalized medicine which we work on. A particularly interesting research problem is how to relate new omics data to earlier research on the level of data, to help make the research process more cumulative.

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Stem cells and aging

 

Pekka Katajisto
Ph.D.
Group leader, Academy Research Fellow

Institute of Biotechnology
P.O. Box 56 (Viikinkaari 9)
FI-00014 University of Helsinki, Finland

Tel.+358-9-191 59402
Fax +358-9-191 59366

E-mail: pekka.katajisto -at- helsinki.fi

home page:
http://www.biocenter.helsinki.fi/bi/katajisto/index.html

Young stem cells renew tissues constantly, but old stem cells can no-longer produce cells for the function of the tissue at the required rate. The resulting decline manifests as aging. Stem cells can fail at their regenerative task due the damage they have accumulated, or if they are misinformed of the tissue's needs by the neighboring cells. Our goal is to unravel whether stem cells have developed special mechanisms to reduce damage accumulation, and if the communication between stem cells and neighbors (niche) could provide points for intervention in aging related diseases.

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Mechanisms of genome stability in mammalian cells

 

Liisa Kauppi
Ph.D.
Academy Research Fellow, Principal Investigator

Genome-Scale Biology Research Program
Faculty of Medicine
Haartmaninkatu 8, Room C501b
P.O. Box 63 (Haartmaninkatu 8)
FI-00014 University of Helsinki, Finland

E-mail: liisa.kauppi -at- helsinki.fi

home page:
http://research.med.helsinki.fi/gsb/kauppi/default.html

In healthy cells, two “genome guardian” mechanisms help prevent the propagation of cells with abnormal DNA content: the DNA damage response and the spindle assembly checkpoint. Our research addresses two basic aspects of mammalian chromosome biology: how do cells repair DNA double-strand breaks, and how do they sense misbehaving chromosomes? These processes safeguard the organism against the propagation of cells that could become malignant due to imbalances in gene dosage or expression. We are studying both somatic and germline cells, using e.g. genetics, cytological and long-range PCR approaches.

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Macromolecular Engineering of Biohybrid Materials

 

Mauri Kostiainen
Ph.D.
Assistant Professor

Biohybrid Materials Group
Department of Biotechnology and Chemical Technology
P.O. Box 16100 (Kemistintie 1)
Aalto University
FI-00076 Aalto, Finland

Tel. +358-50-530 0027

E-mail: mauri.kostiainen -at- aalto.fi

home page: http://chemtech.aalto.fi/bihy

The possibility to direct nanoscale structural order in length scales between 1 and 100 nm is an important prerequisite for the preparation of next-generation nanomaterials. Periodic nanostructures, for example nanoparticle superlattices, are particularly interesting in this respect because they can exhibit collective properties, such as coupling of localized surface plasmon resonances or magnetoplasmonic effects, which emerge from the geometrical structuring of discrete building blocks rather than their band structure or composition directly.

Biohybrid Materials Group does research at the interface of chemistry, physics and biochemistry. Our research focuses on biohybrid materials, which allow the best features of synthetic and biological material types to be combined – the versatility of synthetic matter and highly controlled assembly properties of biomolecules. We use common nanoparticle, organic and polymer synthesis methods to prepare large synthetic building blocks, which are self-assembled mainly in biocompatible aqueous environment with biomacromolecules (DNA, proteins, viruses, cellulose). Our group utilizes high-end characterisation techniques: atomic force microscopy, cryogenic transmission electron microscopy and small angle X-ray scattering to study the systems. Ultimately, such materials can be utilized for chemical analysis, catalysis or delivery applications.

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Regulation of actin and plasma membrane dynamics in cell migration and morphogenesis

 

Pekka Lappalainen
Ph.D.
Professor , research director

Institute of Biotechnology
P.O. Box 56 (Viikinkaari 9)
FI-00014 University of Helsinki, Finland

Tel. 358-9-191 59499
Fax 358-9-191 59366

e-mail: pekka.lappalainen -at- helsinki.fi

home page: http://www.biocenter.helsinki.fi/bi/lappalainen/

Coordinated polymerization of actin filaments against cellular membranes provides force for a number of biological processes, including cell morphogenesis, motility, endocytosis, and phagocytosis. In addition, actin filaments together with myosin filaments form contractile structures in muscle and non-muscle cells. Recent studies have revealed that abnormalities in actin-dependent processes, including cell motility and cytokinesis, often occur in cancer cells, and that many pathogens exploit the actin polymerization machinery of the host cell during the infection process. Thus, elucidating the mechanisms of actin dynamics will also be valuable for understanding these actin-dependent pathological states.

Our laboratory uses a wide range of biochemical, cell biological, and genetic methods to reveal how the structure and dynamics of the actin cytoskeleton are regulated during various cellular and developmental processes. We also aim to elucidate how membrane phospholipids regulate actin dynamics, and how the I-BAR domain family proteins deform PI(4,5)P2-rich membranes to coordinate actin and plasma membrane dynamics during cell motility and morphogenesis.

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Biomolecular materials

 

Markus Linder
Ph.D.
Professor

Aalto University
Department of Biotechnology and Chemical Technology
P.O. Box 16100 (Kemistintie 1)
FI-00076 AALTO , Finland

Tel. 358-50-431 5525

e-mail: markus.linder -at- aalto.fi

home pages: http://chemtech.aalto.fi/en/research/groups/biomolecularmaterials/
http://hyber.aalto.fi/en/

Biomolecular materials research aims at a molecular understanding of how materials in biology work. Biological materials are interesting since they can show very high performance (e.g. silk, nacre, adhesives, biomineral structures, etc) and achieve this high performance by molecular architectures based in specific interactions, self-assembly, and hierarchical ordering.  Exactly these questions form a central part of modern materials science.  In our group we use biotechnical approaches such as protein engineering to construct precise molecular building blocks and biophysical techniques to understand their functions as components and as parts in the final assembled materials. Synthetic biology approaches are used to study dynamic and non-equilibrium aspects of materials assembly.

We collaborate closely with other groups at Aalto and at VTT, especially within the Centre of Excellence in Molecular Engineering of Biosynthetic Hybrid Materials, HYBER.

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Canine and feline models of human inherited disorders

 

Hannes Lohi
Ph.D.
Professor in Veterinary Molecular Genetics

Research Programs Unit, Molecular Neurology
Faculty of Medicine
Department of Veterinary Biosciences
Faculty of Veterinary Medicine
Folkhälsan Institute of Genetics
Biomedicum 1, Room C323b
P.O.Box 63 (Haartmaninkatu 8)
FI-00014 University of Helsinki, Finland

phone +358-9-191 25085
fax +358-9-191 25073

Email: hannes.lohi -at- helsinki.fi 

Home pages:
http://research.med.helsinki.fi/neuro/

http://www.koirangeenit.fi

Our research focuses on the canine and feline models of human complex diseases. This novel approach takes advantage of an experiment initiated by man 15,000 years ago, taming of the wolf and, more recently, generating 400 strictly inbred pure dog breeds.  Canine purebreeding has resulted in highly uniform genomes within each breed, in which the “noise” of background genetic variation is reduced making it easier to detect genetic “signals” that contribute to disease.  As a result 10 to 100-fold fewer individuals are needed in canine studies than in human studies to map genes for the same polygenic trait. That information alone would not be very helpful without the fact that several of the essential components of morphological, behavioral and disease phenotypes can be found and measured in dogs. Dogs develop biologically analogous, if not homologous in some cases, conditions to human disorders including idiopathic epilepsies, ataxias, various anxieties such as fears/phobias and obsessive-compulsive disorder (OCD), eye disorders and many developmental problems which are all actively being investigated in my laboratory.

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Epithelial morphogenesis

 

Marja Mikkola
PhD
Team leader

Institute of Biotechnology
Research Program in Developmental Biology
P.O.Box 56 (Viikinkaari 9)
FI-00014 University of Helsinki, Finland

phone +358-9-191 59344
fax +358-9-191 59366

Email: marja.mikkola -at- helsinki.fi 

Home page:
http://www.biocenter.helsinki.fi/bi/mikkola

One of the key questions in developmental biology is: how do cells of the embryo get organized into tissues and organs? Many events that shape developing animal embryos involve rearrangements of simple epithelial sheets into more complex three-dimensional structures, a process termed epithelial morphogenesis. We investigate the molecular and cellular basis of epithelial morphogenesis using skin appendages, in particular the hair follicle and mammary gland as model organs. Skin appendage development is regulated by conserved signaling pathways that mediate inductive interactions between two tissue types, the epithelium and the mesenchyme. We strive to understand the details of this tissue crosstalk and in particular how the signaling activities are translated into coordinated changes in cell behavior that ultimately drives epithelial morphogenesis. We are particularly interested in how the numbers, patterns, and shapes of organs are determined.

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Immunotherapy and discovery of novel drug targets in hematological malignancies

 

Satu Mustjoki
Adjunct professor
Academy Researcher

Hematology Research Unit
Biomedicum Helsinki
Department of Hematology
University of Helsinki and
Helsinki University Central Hospital Cancer Center
P.O. Box 700
Haartmaninkatu 8
FI-00290 Helsinki, Finland

phone +358-9-471 71898
mobile +358-40-552 1606
fax +358-9-471 71897

Email: satu.mustjoki -at- helsinki.fi 

Homepage:
http://www.helsinki.fi/hematology

Hematology Research unit Helsinki is a translational research group, which aims to understand the pathobiology of malignant blood diseases (such as leukemia) and find novel therapy targets and modes of action. We combine basic cancer research with clinical drug studies and our long-term goal is to develop curative treatment strategies for leukemia patients. Our research group is affiliated both with the Helsinki University Central Hospital and with the University of Helsinki and has close connections with the clinical patient care and basic science in Finland as well as abroad.
Currently we are working with many different types of leukemia, and with the modern sequencing techniques accompanied by the in vitro functional assays we aim to understand molecular pathways driving the malignant growth in these diseases. One of our model diseases, LGL leukemia, is also closely related to our other specific research interest-immunology and anti-leukemia immune responses. During the recent years it has become evident that the immune system plays a significant role in cancer. Thus, our goal is to understand how current targeted therapies affect the immune system, and how are we able to reverse the immune cell anergy typically found in cancer patients.

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Kinase signaling in tumor suppression and transcription

 

Tomi Mäkelä
Ph.D.
Director, Professor

Institute of Biotechnology
P.O. Box 56 (Viikinkaari 9)
FI-00014 University of Helsinki, Finland

Tel.+358-9-191 59359
Fax +358-9-191 59366

E-mail: tomi.makela -at- helsinki.fi
 

home page: http://www.biocenter.helsinki.fi/bi/makela/

The Makela lab studies signaling pathways regulating mammalian cell growth and how these impinge on transcriptional responses in human disease. We focus on signaling by the LKB1 tumor suppressor kinase and on transcriptional CDK kinases.

We have contributed significantly to current knowledge of the tumor suppressor kinase LKB1 in vivo functions and molecular mechanisms as a critical activating kinase for AMPK, PAR1, NUAK and several less known kinases. Current studies focus on understanding how LKB1 deficiency alters stromal-epithelial interactions with an ultimate goal to define the molecular mechanisms by which LKB1 suppresses tumorigenesis. In transcription, our discoveries include identification of cyclin H as a partner of Cdk7 and component of basal transcription factor TFIIH. Current studies focus on understanding how the Cdk7 kinase is involved in transcriptional buffering, i.e. mediating information from transcriptional activity to mRNA stability.

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Biomedicum Stem Cell Center; Human pluripotent stem cells for biomedical research

 

Timo Otonkoski
M.D., Ph.D.
Professor

Research Program of Molecular Neurology & Children’s Hospital
Biomedicum Helsinki
P.O.Box 63 (Haartmaninkatu 8)
FI-00014, University of Helsinki, Finland

Tel. 358-9-191 25692

e-mail: timo.otonkoski -at- helsinki.fi

home page http://research.med.helsinki.fi/neuro/Otonkoski/

The development of cellular reprogramming technologies has made it possible to generate stem cell models to study the development of almost any cell type. This can be done using cells from patients with a defined genetic disease background, allowing the modelling of pathogenetic mechanisms and the exploration of therapeutic posibilities. Furthermore, genomic engineering technologies have made it possible to efficiently correct or induce specific mutations also in human cells, further increasing the value of the approach.

Our laboratory focuses on cellular reprogramming for the experimental modelling of disease processes in relevant cell types. One part of the research focuses on basic mechanisms of reprogramming into either pluripotent cells or directly into other types of cells. Pancreas and liver differentiation is our special area of interest. Various forms of monogenic neonatal diabetes are studied to understand causes of beta-cell failure and to develop a new platform for experimental diabetes research.

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Hereditary Cancer; Epigenetic mechanisms of predisposition to common human cancers  

 

Päivi Peltomäki
M.D., Ph.D.
Professor in Biomedical Cancer Research

Department of Medical Genetics, Haartman Institute
P. O. Box 63 (Haartmaninkatu 8)
FI-00014 University of Helsinki, Finland

Tel. +358-9-191 25092
FAX +358-9-191 25105


E-mail: paivi.peltomaki -at- helsinki.fi

Home page: http://www.helsinki.fi/haartman/lgo

 

 

Dysregulation of cellular growth can be achieved by genetic and epigenetic mechanisms. We focus on the interplay between genetic and epigenetic factors in familial and sporadic forms of common human cancers. Somatic inactivation of tumor suppressor genes frequently occurs by promoter methylation and in familial cancers follows tissue-specific patterns similar to sporadic cancers. Supported by the European Research Council, studies are in progress to dissect the critical steps in colorectal and endometrial tumorigenesis taking advantage of human and mouse models of Lynch syndrome and Familial Adenomatous Polyposis. Occasionally, promoter methylation underlies constitutional silencing of tumor suppressor genes (e.g., the DNA mismatch repair gene MLH1) and predisposes the affected individuals to early-onset colorectal and endometrial cancer. A majority of familial colorectal and endometrial cancers still remain without a known predisposition, and studies are underway to identify the predisposing defects, genetic or epigenetic, in such families.

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Statistical and translational genetics

 

Samuli Ripatti
Professor

Hjelt Institute & Institute for Molecular Medicine Finland (FIMM)
Biomedicum 2U
P. O. Box 20 (Tukholmankatu 8)
FI-00014 University of Helsinki, Finland

Tel. +358-9-191 25862

E-mail: samuli.ripatti -at- helsinki.fi

Home page: http://www.fimm.fi/en/research/research_groups/group_ripatti/

 

 

The Ripatti group studies genome-wide variation and its relation to complex traits and diseases, with a particular focus, but not limited to, on cardiovascular diseases and metabolism. We build on our understanding of genome-wide variation, Finnish genetically and epidemiologically well-profiled cohorts and knowledge and development of statistical and computational tools, and aim at identifying variants, genes and genetic loci modifying complex disease risks. We also study ways to translate the findings into potential intervention targets and comprehensive disease risk assessments.

 

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Structure, biology and therapeutic potential of neurotrophic factors

 

Mart Saarma
Ph.D.
Professor

Institute of Biotechnology
P.O.Box 56 (Viikinkaari 9)
FI-00014 University of Helsinki, Finland

Tel.+358-9-191 59378
Fax +358-9-191 59366


E-mail: mart.saarma -at- helsinki.fi

home page: http://www.biocenter.helsinki.fi/bi/saarma/

The group is investigating structure, signaling, biology and therapeutic potential of the new neurotrophic factor CDNF that they discovered. Main focus is to find the receptor for CDNF, elucidate its mode of action and develop CDNF-based drug for the treatment of Parkinson’s disease. The group is also investigating signaling and biology of GDNF family ligands. They discovered a novel receptor for GDNF and charcaterize GDNF and its receptor GFRa1 conditional knockout mice.

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Protein interactions in cellular signaling and virus-host cell interplay 

 

Kalle Saksela
M.D., Ph.D.
Professor of Virology

Haartman Institute, Department of Virology
P.O. Box 21 (Haartmaninkatu 3)
FI-00014 University of Helsinki, Finland

Tel.+358-9-191 26770
Fax +358-9-191 26491

E-mail: kalle.saksela -at- helsinki.fi

home page: http://www.hi.helsinki.fi/saksela/

Virus replication depends on the protein machinery of the host cell, which viruses have evolved to regulate and exploit in numerous and elaborate ways. Molecular understanding of these interactions is a key challenge in modern research in virology, and can provide valuable insights into the basic mechanism that regulate normal and pathological cellular behavior.

The HIV Nef protein has been a key subject of our research, Nef modifies host cell physiology to better support viral replication by binding to proteins involved in cellular signal structures via their SH3 domains. SH3 domains are the most ubiquitous class of modular protein binding units found in the nature. SH3 domains mediate many key regulatory processes in normal cells and are involved the pathomechanisms of many important diseases. It appears that many other viral proteins also share the capacity of Nef to utilize binding to host cell SH3 proteins in order to mediate their functions. Identification of normal SH3-mediated cellular protein interaction networks as well as SH3-interactions that take place between cellular and pathogenic viral proteins, and elucidation of the molecular basis of binding affinity and specificity involved in these interactions are the main topics goals of our research.

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Biodegradable nanoporous silicon nanomaterials for controlled drug delivery and targeted cancer therapy

 

Hélder A. Santos
D.Sc. Tech., Docent
Head of Unit
Academy Research Fellow / Group Leader
ERC StG grantee (2013–2017)

Division of Pharmaceutical Chemistry and Technology
Pharmaceutical Nanotechnology and Chemical Microsystems Unit
P.O. Box 56 (Viikinkaari 5E)
FI-00014 University of Helsinki, Finland

Tel.+358-9-191 59661
Fax +358-9-191 59144

E-mail: helder.santos -at- helsinki.fi

home page: http://www.helsinki.fi/~hsantos/

Our research aims to develop nanotechnology (nanoparticles/nanomedicines) for biomedical and healthcare applications. Our current work makes the bridge between engineering, pharmaceutical and medical research. Our major focus and interest is in the use of biodegradable and biocompatible nanoporous silicon nanomaterials for simultaneous controlled drug delivery, diagnostic and treatment of cancer, diabetes, and cardiovascular diseases. Our long term goal is to translate any of these nanotechnologies and nanomedicines into the clinic.

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Actin as an organizer of gene expression

 

Maria Vartiainen
Ph.D.
Group leader

Institute of Biotechnology
P.O. Box 56 (Viikinkaari 9)
FI-00014 University of Helsinki, Finland

Tel.+358-9-191 59419
Fax +358-9-191 59366

E-mail: maria.vartiainen -at- helsinki.fi

home page: http://www.biocenter.helsinki.fi/bi/vartiainen

Actin cytoskeleton plays essential roles for example in cell motility and morphology. Actin is also present in the cell nucleus, where it has been linked to many processes related to gene expression, such as RNA polymerase function and chromatin remodeling. In addition, actin regulates the activity of specific transcription factors, including SRF. However, the molecular mechanisms by which actin functions during these essential gene expression processes are largely unclear, and therefore the main aim of our lab is to reveal these mechanisms and their biological significance. To achieve this, our lab uses a wide range of cell biological and biochemical methods, combined with advanced microscopy and genomic techniques, in both mammalian cells and the fruit-fly. 

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Molecular basis of mitochondrial dysfunction in human diseases

 

Anu Suomalainen Wartiovaara
M.D., Ph.D.

Sigrid Juselius Professor of Clinical Molecular Medicine
Research Program of Molecular Neurology
r. c523B P.O.Box 63 (Haartmaninkatu 8)
FI-00014 University of Helsinki, Finland

Tel. +358 9 471 71965
Fax +358 9 471 71964
E-mail anu.wartiovaara -at- helsinki.fi  

Home page: http://research.med.helsinki.fi/neuro/
Wartiovaara/default.htm

Mitochondrial dysfunction has shown out to be a common cause on human inherited disease, with amazing clinical variability, from neonatal fatal multisystem disorders to diabetes, neurodegeneration, dysfertility or tumorigenesis of adult age. Mitochondrial disorders are typically progressive with little means of effective treatment. Our research group focuses in clarifying the molecular basis of mitochondrial disorders, with a special emphasis on neurodegeneration. We search for disease genes in human sample materials, characterize disease phenotypes, create disease models based on identified gene defects and utilize these models to study molecular pathogenesis and to test potential treatments.

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