Molecular biology and microbiology
Molecular biology and microbiology
Molecular biology focuses on various aspects of cellular and biological function, from how DNA is replicated, repaired and expressed, how cells are built and function, and how complex organisms develop from a single cell.
The main research areas within the Institute are topics like
- How do neurons and glial cells develop and influence diseases? (SRF)
- What is the role of hedgehog signalling in development of bones and osteaoarthridis? (SS)
- Can the innate immunity be activated as a therapeutic intervention? (GHG)
- Which genetic factors influence the diversity of breast cancer subtypes? (LV)
- How do sequence variants affect protein structure and function? (GR)
- What are the main roles of pontin and reptin in neuronal cells? (SRF, ZOJ)
- Which factors influence microbial diversity in geothermal regions? (SB)
- Is the fish gut microbiome a good tool for stock identification? (HR, SP)
- Which genes and pathways associate with recent adaptations and rapid divergence? (SRF, ZOJ, AP, SP)
- How do the regulatory systems of development evolve? (AP)
Research projects
Supervision
About the project
Clearing of misfolded or damaged proteins in cells is important for all organisms. Long-lived neurons depend on efficient surveillance of excess proteins. Failure to remove protein aggregates underlies several neurological diseases and is an important factor in aging. Pontin and Reptin are proteins of the AAA+ ATPase family. They serve as chaperones in complex assembly, have diverse roles in cellular processes and were recently found to be required for aggresome formation and aggregate clearing. In this project, we expand on our ongoing research on Pontin and Reptin in the Drosophila melanogaster nervous system. Both proteins are expressed in neurons, with prominent microtubule-like distribution in motor neuron axons. Loss of either protein leads to speckles and beading in neurites and progressive loss of adult fitness. Using genetic tools and endogenous protein tags in Drosophila, we will investigate the role of Pontin and Reptin in preventing the accumulation of misfolded proteins in axons; their interaction with proteasomes and proteasome function; their relationship with neuronal autophagy in the clearance of protein aggregates; and their role in aggresome formation and clearance. This we do by LSM and RESOLFT imaging of live and stained samples, electron microscopy, co-IP and immunoblotting. Five graduate students will receive training in the project and the results have relevance for research on neurodegenerative disorders as well as neurobiology and basic cell biology.
Supervision
About the project
Host directed therapy (HDT) has been highlighted as an alternative or supplementary treatment to classical antibiotics against infections. HDT can include induction of AMPs expression against infection. Therefore, signal pathways for AMP expression and regulation of innate immunity is of importance. As a proof of concept induced AMPs expression works against infections both in animal infection models and in human clinical trials. In this proposal novel inducers of AMP expression are included, called aroylated phenylene-diamines (APD). The APD inducers are nontoxic to cells in culture and negative in Ames test. We have concentrated on two APDs designated HO53 and HO56. The compounds induce several AMP genes in human bronchial epithelial cell lines. Moreover, bacterial load was significantly reduced in a cell cultures upon APD induction. Our results warrant further analyses and the proposal includes studies on the detailed mechanism to find the cellular target for APDs. Furthermore, upon induction we will study autophagy, that has been indicated relevant for clearance of bacteria. Bacterial escape from autophagy has been indicated important for persistent bacteria and is relevant to medicine. The proposal also includes studies on a novel signal pathway recently found linked to an uncharacterized antimicrobial response of special interest to cystic fibrosis. Finally, we will use our recent compounds in animal infections for efficacy and toxicology measurements.
Supervision
About the project
Antimicrobial peptides (AMPs) made by epithelia contribute to the defense barrier. Several pathogens downregulate AMP in epithelia to enter tissues. Such downregulation may be counteracted by small molecular inducers of AMP expression. In animal models these AMP inducers can inhibit infectious pathogens and promote host recovery. We have identified inducers that can counteract AMP downregulation and/or strengthen the epithelial barrier. In this project novel inducers will be tested with reference to lung epithelial barrier i.e. expression of AMP and integrity functions. Detailed effects of the inducers will be resolved by transcriptome analyzes. Furthermore, we will study transcription factor, HIF1alpha (hypoxia-inducible factor) for involvement in innate immunity of lung epithelium. We will use knockdown cell lines and screen for altered functions of the epithelial barrier. Finally, we analyze the effects of a defined toxin from Bordetella on lung epithelial cells to advance our understanding on the mechanisms of respiratory pathogen-host cell interactions in general. These bacteria are exclusively human pathogens and their interaction with airway epithelia remain poorly explored due to the lack of suitable experimental models. We will analyze the Bordetella adenylate cyclase toxin in relation to innate immune genes and barrier integrity. The project is expected to enhance our understanding of innate immunity and have impact on treatment alternatives against infections.
Supervision
Denis Warshan
About the project
Cyanobacteria in symbioses with fungi (cyanolichens) and mosses contribute nearly 30% of the dinitrogen-fixation on land, establishing these symbioses as major players of biogeochemical cycles. Despite its ecological importance, molecular understanding of the establishment of cyanolichen symbioses lags far behind many other symbiotic systems, and little is known about the cyanobacterial gene repertoire needed to form the association.
The proposed work will provide additional characterization of these associations at unique levels:
- Evolutionary history of cyanobacteria forming cyanolichens.
- Metabolomics of cyanolichen partners during the early step of symbiosis formation.
- Genetic analysis of candidate genes involved in establishing and maintaining the interaction.
The objectives of the project are to:
- Determine what gene acquisitions are associated with the evolution of cyanobacteria forming lichens by comparative genomic and by symbiosis reconstruction experiments with lichen hosts.
- Deciphering signaling exchange between lichen partners during symbiosis formation
- Characterize the function of cyanobacterial symbiotic candidate genes by using targeted knockouts of genes retained in the symbiotic cyanobacteria.
The proposed work will create the first model system of molecular interaction between partners for the cyanolichen symbiosis and it will design new methods and molecular tools to monitor adaptation and health of these symbioses and their ecosystems.
Supervision
Kalina Hristova Kapralova and Michael Blair Morrissey
About the project
The Arctic charr (Salvelinus alpinus) of Lake Thingvallavatn are ideally suited for studies of the ecology and genetics of adaptive diversification: i) it is an extraordinarily well-characterised system, ii) it has young evolutionary history, iii) it has diverged into four morphs with distinct variation in life history characteristics, behavior and trophic morphology, suggesting rapid adaptive diversification. This system thus represents an extremely compelling case of rapid adaptive differentiation. However, to date, the system has been under-used to answer fundamental questions about the genetic basis of this diversification, due in large part to a lag in the development of genomic resources, and the long generation time. These issues have recently been overcome, and it is now possible to get at some long-outstanding questions. The overall aim of this project is answer fundamental questions about the genetic basis of this extraordinary case of rapid adaptive differentiation, by determining the number, genomic distribution, range of effect sizes and evidence of selection of loci contributing to adaptive diversification. We will answer these questions by deploying a series of studies, using both classical genetic study designs (QTL mapping) of carefully constructed laboratory crosses, and modern population genomic analyses of field-collected specimens.
Supervision
About the project
The White-tailed eagle (Haliaeetus albicilla) in Iceland lowered in numbers after the mid-1800s from 150 breeding pairs down to 20 pairs in 1914 when it was protected by law. Despite protection the population did not grow until 1970, mainly due to fox poisoning. The growth rate is slow and its fecundity is mucl lower than among White-tailed eagles in Scandinavia. The aim of the project is to analyse the effect of small population size and inbreeding on genomic variation and fitness, by analysing a unique sample and dataset gathered over years 2001-2016. Firstly, genomic variation of the population in Iceland today will be compared to genomic variation from before and during the bottleneck. Secondly, the genomic variation of the contemporary population in Iceland will be compared to the larger population in mainland Europe. Thirdly, inbreeding depression will be studied by comparing variation in fitness with kinship and genetic variation and telomere length, and in relation to extrinsic factors such as parasitic load and environmental information. The genomic variation gives possibility to evaluate hypotheses regarding the effects of natural selection and population bottleneck on molecular variation. The result of this study has implications for both evolutionary and conservational biology and the coservation of the White-tailed eagle in Iceland.
Supervision
About the project
Availability of fixed nitrogen is essential for primary production. We will gather information on biological nitrogen fixation (BNF) in eight defined subarctic habitats (EUNIS classification) representing nearly 90% of cryptogam (lichen, moss and biocrust) cover in uncultivated areas of Iceland; by measuring of BNF, by identification of the bacteria and nitrogen fixation systems involved, including the alternative Vnf system, and by testing hypotheses regarding the major players in laboratory experiments, making use of chemical and isotope analysis, gene sequencing technology and bioinfomatics.
The objectives are:
- Obtain reliable estimates of BNF in major cryptogam habitats using ARA (acetylene reduction assay) standardized with 15N uptake.
- Characterize nitrogen fixing bacteria and main components in the selected habitats using methods of microbiology and gene sequencing.
- Carry out field observations, plus field and laboratory experiments to quantify cyanobacteria and environmental factors controlling BNF.
- Establish the contribution of the alternative Vnf system to nitrogen fixation in the cryptogam communities, both in the field and in the laboratory.
For this we will a) determine 15N isotope discrimination by mass spectrometry (greater with Vnf than Nif), and b) determine levels of vnf and nif gene expression by reverse transcript quantitative PCR. 5) Extend findings to habitats with same EUNIS classification elsewhere, model BNF and assess global relevance.
Supervision
About the project
The interaction of evolution and development lies at the core of morphological adaptation. To understand this interaction it is helpful to study natural populations that show signs of strong selection for and even repeated evolution of particular traits. An interesting example of this is found in Iceland, where small benthic morphs of Arctic charr have evolved in multiple lakes and four distinct morphs have evolved within the Lake Þingvallavatn in the last ~10,000 years. We have studied mRNA and miRNA expression in Þingvallavatn charr and found interesting clues as to what lies behind their different head-shapes. Those clues include gene networks that are differentially expressed between morphs during development. We now want to take the logical next step and identify regulators of the pathways and polymorphisms of functional significance that give rise to those differences. We will use next generation sequencing in three different ways to generate three important datasets for synthesis. We will start by obtaining genomic sequence data for Arctic charr. We will use reduced representation bisulfite sequencing to take a snapshot of methylation states during development and analyze their association with expression differences. We will use targeted resequencing to compare genomic regions of interest in the Þingvallavatn morphs to other populations of charr. Finally, we will perform studies in cell culture and in zebrafish to address the functional relevance of our findings.
Supervision
Sigurður Sveinn Snorrason og Kalina Hristova Kapralova
About the project
The Arctic charr (Salvelinus alpinus) of Lake Thingvallavatn is ideally suited for studies of divergence and evolution of reproductive barriers: i) it has a short evolutionary history in the lake, ii) yet it has diverged into four morphs with distinct variation in life history characteristics, behavior and trophic morphology, suggesting rapid adaptive diversification, possibly followed by or causing build-up of reproductive barriers. We will focus on the two smallest morphs, a planktivorous (PL) and small benthic charr (SB), which have diverged along the limnetic-benthic ecological axis. The central hypothesis underlying our investigation is that reproductive isolation between SB and PL charr is partly due to strong negative selection against hybrid offspring and/or differences in the exact timing of spawning (i.e. time of the day), precise spawning location and mating behavior. The project consists of 4 Work packages (WP). In WPI we will establish hybrid and pure crosses and compare fitness related traits such as survival, hatching time, body size and craniofacial morphology between hybrid and pure progeny. In WPII we will investigate putative incompatibilities detected in WPI by comparing the expression of essential developmental genes between hybrids and pure morphs. In WPIII and WPVI we will study the exact timing and spawning location and their mating behavior by conducting observations in the wild and laboratory experiments.
Supervision
About the project
Symbiosis is a major theme in the evolution of life. Worldwide, biotas are challenged by environmental stress due to climate change, with especially severe effects on fine-tuned, intimately interacting symbioses such as the lichen symbiosis. Survival can be achieved by tolerating stressful conditions, through specific adaptations which often rely on modulating gene expression. How organisms tolerate stress can dictate their capacity to respond to climate changes, yet the mechanisms of stress alleviation are understudied in fungal symbioses. We propose to study ecological genomics and phenotypic traits of two lichen symbioses representing abundant species in northern ecosystems. These lichens co-occur in many sites, but associate with primary photobionts belonging to different kingdoms. First, we will expand a RAD sequencing study of population structure in Peltigera membranacea to P. leucophlebia. Second, we plan to study gene expression (RNAseq, qPCR) and trait response to thermal stress in a controlled laboratory setting. The data and analyses enable us to partition the effect of genetic background from environmental acclimatization, and point to putative adaptive systems that influence acclimation and trait differences of symbiotic systems, thus being of broad relevance to the community of researchers studying symbiotic systems.