Testing the sensitivity and specificity of diagnostic PCR primers for detecting novel strains of SARS-CoV-2
Duration: 01.05.2021 − 31.12.2022
Program: Research and Development projects in collaboration with companies.
Vastutav täitja: Maido Remm
Tellija: Solis Biodyne OÜ
Abstract: We will perform in-silico validation of diagnostic Sars-CoV-2 PCR primers used by Solis Biodyne. The test will include computational analysis of primer specificity against a predetermined list of organisms and computational analysis of primer sensitivity against new and widely spreading viral strains (UK strain, SA strain, Indian strain, omikron strain, etc.).

Diagnostic test for fast identification of Listeria monocytogenes sequence types
Duration: 01.09.2021 − 31.08.2022
Program: ETAg experimental development grant
Abstract: The aim of the project is to develop a diagnostic test for fast identification of all major Listeria monocytogenes MLST types (multilocus sequence types). The tests will be based on multiplex-PCR technology. The availability of such tests would allow faster actions in a situation where Listeria-contaminated food is discovered in a food processing factory or food stores. The potential clients for such a diagnostic test would be all kind of raw food-producing and/or selling companies and potentially also government control organs responsible for food safety.

Routs for development and spread of antibiotic resistance and resistance containment measures
Duration: 01.07.2019 – 30.06.2022
Program: Riigi Teadus- ja Arendusprogramm RITA
Project leader: Tanel Tenson
Abstract: The level of antibiotic resistance is continuously increasing. Antibiotics are used for treating infections in humans and this group of pharmaceuticals is also heavily used in animal husbandry. Independent of the segment where antibiotics are consumed the usage selects for resistance of bacteria. The resistant microorganisms will be occasionally released to the environment and spread thereby. In addition, antibiotic residues released from the organisms treated are entering waste water treatment plants or applied to the fields with sludge. To combat the resistance problem the potentially critical nodes must be approached in integrated manner. We propose to characterize the antibiotic resistant infectious bacteria in Estonia in fine detail through whole genome sequencing. We will also determine the concentrations of antibiotics in samples taken from the environment. The inputs from previous data and from the new information collected will be integrated to provide recommendations.

European Venom Network
Duration: 06.10.2020 – 05.10.2024
Program: The European Cooperation in Science and Technology (COST)
Project leader in Estonia: Maido Remm
Abstract: The overarching aim of the EUVEN COST Action is to foster venom investigation at the European level. The Action will identify priority targets and promising innovative approaches, develop best practice pipelines ensuring consistency across Europe and providing international standards in venom research. Further, it provides a novel platform to promote synergistic interactions between academia, industry and society, and to nurture a new generation of venom researchers with a multidisciplinary expertise. Building a gender, age and geographically balanced network involving all the relevant stakeholders will be the fundamental prerequisite to leverage the extraordinary biochemical warfare enclosed in animal venoms, with an enduring scientific, technological and socioeconomic impact.

Centre of Excellence in Genomics and Translational Medicine
Duration: 01.01.2016 − 01.03.2023
Program: Centers of Scientific Excellence in Estonia
Project leader: Andres Metspalu

Faster and more reliable methods for analysing genomic sequence data
Duration: 01.01.2015 – 31.12.2020
Program: Institutional grant
Project leader: Maido Remm
Abstract: We will develop k-mer based methods for detection of variants in human personal genomes and develop methods for DNA-based detection of pathogenic bacteria, viruses, resistance genes, food allergens, etc.

Detection of ampicillin and clindamycin resistance genes in Lactobacillus brevis strain TAK 124-1 AerobEst® NCIMB42149
Duration: 01.04.2016 − 30.09.2016
Program: Research and Development projects in collaboration with companies.
Partner: Bio-Competence Centre of Healthy Dairy Products
Project leader: Maido Remm

Development of biotechnology-based food allergen surveillance methods
Duration: 01.12.2012-31.08.2015
Project leader: Mart Ustav, Institute of Technology
Partners: Tartu University Hospital, Icosagen Cell Factory OÜ, The Association of Estonian Food Industry, Naxo OÜ

Molecular Multiplex Diagnostics of Antimicrobial Resistance
Duration: 1.11.2011−31.12.2014
Project leader: Siiri Kõljalg, University of Tartu, Faculty of Medicine, Department of Microbiology
Abstract: Find determinants of antibiotic resistance from 1200 fully sequenced genomes of Klebsiella pneumoniae and Escherichia coli strains.

Estonia’s Integration to the European Bioinformatics Infrastructure (ELIXIR)
Duration: 01.11.2012 – 31.08.2015
Project: SMTAT12017T/1
Project leader: Jaak Vilo, UT Institute of Computer Science
Partners: Tallinn University of Technology, Estonian Biocenter, National Institute of Chemical and Biological Physics, University of Tallinn
Abstract: 1. Maintenance, upgrade and integration of bioinformatics tools and databases produced by Estonian research community (g:Profiler for gene list characterisations, MEM for large scale gene expression data analysis and queries, ESCDb – Embryonic stem cell database, etc.)
2. Interfacing with BBMRI through partnering with Estonian Biobank (Estonian node has expertise in data management solutions for health data, and Estonian medical records) and e-health data
3. Developing, offering, and intermediating training on bioinformatics and infrastructure that goes beyond standard university course offering
4. Developing Estonian node to match the future needs of bioinformatics data analysis, e.g. in next generation sequencing and respective service offering – building links to high-performance computing facilities in Estonia and through ELIXIR, porting bioinformatics solution on the cloud and more cost effective hardware (FPGA).

CTG – Centre of Translational Genomics
Duration: 2011 – 2015
Project: SP1GVARENG
Program: Development Fund of the University of Tartu
Abstract: The activities of the project are focused on discovering the genetic, epigenetic, transcriptomic, proteomic and metabolomic components lying behind common and complex diseases. The project will facilitate a systemic approach to the translation of genetic information from the DNA variations to the metabolic variations including also the RNA, epigenetic and proteomic levels.
www.ctg.ut.ee

Computational studies of genome sequences
Duration: 01.01.2009-31.12.2014
Project: SF0180026s09
Program: SF 2009
Abstract: Current grant application is focused to analysis and comparison of genome sequences of various organisms, mainly human genome. Throughout the project mainly bioinformatics and statistical methods are used for research. Experimental data is obtained from public databases or from collaborating partners. Firstly, we plan to analyze novel types of variations in human genome – gene copy number variations, inversions and traces of integrated viral genomes. Secondly, we plan to participate in larger projects which search for correlations between genes and human traits or diseases. Our part would be creation and use of novel statistical and bioinformatics methods for analyzing genomic data. Third part of the project will be devoted to comparison of non-human genome sequences. Our aim in this part of the project is discovery of novel universally conserved functional DNA elements. Our first target is to identify conserved upstream Open Reading Frames (uORFs) in bacterial genomes.

Centre of Excellence in Genomics
Duration: 01.02.2008-31.08.2013
Project: TK10, 3.2.0101.08-0011
Financer: Archimedes Foundation
Abstract: The Centre of Excellence in Genomics is based on three workgroups from University of Tartu, and Estonian Biocentre, with its focus on basic and applied research of human as well as other genomes. The main objective of this consortium is to achieve, through dedicated collaboration, an added value, to be materialized and manifested in high-level scientific publications, enhanced international collaboration, creation of intellectual property and promotion of entrepreneurship in biotechnology. A particular goal will lie in applications in healthcare and in enhancement of the value of Estonian Biobank as a valuable national asset. It is an interdisciplinary research consortium with a scope extending from creating tools to analyse genomic, proteomic and metabolomic information and search for “disease genes”, to the understanding of the origin of genetic structure variation in humans.

Estonian Scientific Computing Infrastructure
Duration: 2011-2013
Project: The High Performance Computing Center
Abstract: The High Performance Computing Center is a consortium of UT and it’s purpose is to build and develop the necessary infrastructure for scientific computing. It also manages and coordinates the use of said computing equipment. This computing resource is open for use to any research groups inside the university. Users from other Estonian science- and research institutions are also welcome.
http://www.hpc.ut.ee/

Designing primers and hybridization samples suitable for complex diagnostics
Duration: 15.04.2010-31.12.2012
Project: LLOMR 10049
Financer: Quattromed HTl Laborid OÜ
Abstract: HPV detection panel. Amplifing scheme for 42 different human papillomavirus (HPV) strain with the minimum number of universal primers, and 2-5 samples of strain-specific Luminex samples for each starin. Preferably, use regions E6/E7, if necessary, add LNA or other modified nucleotides.
Cervical pathogens primer panel. Designing PCR primers and Luminex hybridization samples for STD causing bacteria and viral pathogens. In total we will design primer pairs for about 14 different kinds / types of pathogens. For each pathogen we design 2-5 primers and 2-5 Luminex samples for testing purposes. If necessary, other modified nucleotides or LNA will be added to primers.
Panel of diarrhea pathogens. Designing PCR primers and Luminex hybridization samples for diarrhea causing bacteria and viral pathogens. In total we will design primer pairs for about 20 different kinds / types of pathogens. For each pathogen we design 2-5 primers and 2-5 Luminex samples for testing purposes. If necessary, other modified nucleotides or LNA will be added to primers.
Offering bioinformatic support services for the above-mentioned activities and for the activities related to EAS project” Enhancing complex diagnostics based on biotechnological platforms for healthcare system.

Design of PCR primers and Luminex hybridization probes
Duration: 01.01.2010-30.06.2010
Project: LLOMR 10018
Financer: Quattromed HTl Laborid OÜ
Abstract: In the first step, species-specific PCR primers consisting only DNA nucleotides are designed for 6 bacterial pathogens. For each species 2-5 PCR primer pairs are designed. The species under investigation areChlamydia trachomatis, Ureaplasma urealyticum, Ureaplasma parvum, Mycoplasmagenitalium and Trichomonas vaginalis. Luminex hybridization probes are designedfor PCR products that are amplified by previously designed PCR primers. In thisstep, Luminex probes consist only DNA nucleotdes also.For each PCR product 2-5 hybridization probes are designed. Thereafter the sequences are tested in the lab.
Oligos, designed in the first step, are redesigned. Into the PCR primer sequences 2-3 LNA nucleotides are added, so that PCR primers preserve similar melting temperature and temperature appropriatefor PCR. In the case of Luminex probes, different sites in probes are considered for inserting LNA nucleotides. After insertion of LNA nucleotides, melting temperatures are recalculated.

Modular Education for Interdisciplinary Systems Biology
Duration: 01.11.2007-31.12.2009
Project: MBGMR07249
Program: Leonardo

Applied venomics of the cone snail species Conus consors for the accelerated, cheaper, safer and more ethical production of innovative biomedical drugs (CONCO)
Duration: 01.02.2007-31.01.2012
Project: LSHB-CT-2007-037592
Program: FP6
Abstract: CONCO is an innovative post-genomic project dedicated to the discovery and development of novel biopharmaceuticals generated by the broad biodiversity of cone snails. The project aims at characterising from the genomic up to potential therapeutic properties all putative bioactive compounds that can be synthesised by a cone snail species. The genome and transcriptome of Conus consors will be exhaustively studied. Large amounts of venom will be fractionated and submitted to proteomic studies to generate a biochemically characterised “”natural library”" of compounds. Large scale synthesis of each identified candidate will be achieved to form a “”synthetic library”" of compounds. The biological activity of these two libraries will be investigated on a panel of physiological targets that are recognised of therapeutic value. Selected hits will be optimised and validated in vivo. A publicly accessible web-based database will be developed and annotated to integrate and share all the knowledge generated by the project.
www.conco.eu

Array based sequencing-by-synthesis
Duration: 01.09.2005-31.08.2007
Project: MBGMR05146R
Program: FP6

Modeling of DNA-DNA interactions for PCR applications
Duration: 01.03.2005-31.05.2007
Project: IBGMR05044
Financer: EAS

Detection of conserved sequence motifs in eukaryotic genomes using comparative genomics approach
Duration: 01.01.2005-31.12.2006
Project: ETF6041
Program: ETF 2005
Abstract: The aim of the current project is to identify conserved functional elements from the mammalian genomes. Identification of evolutionarily conserved sequences helps to find a range of important functional elements that are otherwise difficult to detect, for example small RNA genes, promoters, transcription factor binding sites and other regulatory regions. For correct and efficient identification of conserved sequences we plan to test, compare and improve existing computational methods. The detection of conserved elements in studied genomes will be executed in three stages: alignment of syntenic genome regions, determination of evolutionarily conserved sequences and identification of functional sequence elements. The main emphasis is initially put into development of improved automatic methods for alignment of syntenic sequence regions, using orthologous genes as “anchors”. The conserved sequences identified within this project will be entered into dedicated database and visualized with help of the UCSC genome browser. All methods are initially tested in 3-4 well-studied genomic regions where experimental data is available as a set of positive controls. After verification the methods will be applied to the whole genome sequences.

SLIC-Biosensors in Molecular Diagnostics: Nanotechnology for the Analysis of species-specific Microbial Transcripts
Duration: 01.01.2005-31.12.2007
Project: LSHB-CT-2005-513771
Program: FP6
Abstract: The development of the novel biosensor-based device for application in molecular diagnostics was based on combining two proprietary technologies, the SLIC-Nanobiosystem, the biosensor platform and RiboSEQ, a molecular target technology. The SLIC-Nanobiosystem consists of a self-assembled lipid bilayer membrane that integrates a synthetic ligand-gated ion channel (SLIC). The SLIC comprises a capture molecule that can specifically bind a given analyte, a process that is monitored via electrical impedance spectroscopy. It was shown recently that SLIC molecules can be designed to detect with high sensitivity antibody binding to antigens on a SLIC via modulation of the SLIC ion channel conductance [Angew. Chem. Int. Ed. 40, 1740-1743 (2001)]. With this system the effect from even a few channels can be resolved thus providing an ultra-sensitive, highly stable and versatile biosensor platform. The RiboSEQ platform based on the universal bacterial genomic target tmRNA encoded by the ssrA gene is a high copy number RNA target that has conserved and variable sequence signatures that can be exploited to develop nucleic acid tests with various levels of specificity for microbial identification. S. pneumoniae was selected as the model system for the development of the biosensor-based device. Additionally, it was envisaged that a novel sample preparation device that could be integrated with the biosensor to provide a homogenous assay format would be developed.

Haplotype structure of the human genome
Duration: 01.01.2004-31.12.2008
Project: SF0182649s04
Programm: SF 2004
Abstract: Current project is focused on analysis of haplotype structure of the human genome with the aim of improving methodology of large scale association studies. The study is performed with bioinformatic methods, using genotype data from public sources and also from collaborative projects with University of Tartu, The Sanger Institute, UK and GSF, Technical University of Munich. We initially focus on methods for modelling haplotype blocks and informative SNPs for their detection. The main task is to find a mathod for modelling haplotype blocks which would be a) effective, allowing description of haplotype variants with minimum number of tag SNPs b) universal, giving comparable results over different populations. We also study relationship between haplotype blocks and different genome features (location of genes, patterns of primary sequence). In the following years we plan to initiate additional projects for improving selection of controls for association studies and methods for statistical correction of the population stratification.

IT in higher education. Establishing the bioinformatics computer cluster
Duration: 01.12.2003-01.04.2004
Project: SBGMR04008
Financer: Eesti Infotehnoloogia Sihtasutus