Life sciences (LIFE) // Life Sciences (LIFE)

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https://odr.chalmers.se/handle/20.500.12380/10

Vi bedriver forskning och utbildning − och driver innovation − för att möjliggöra ett biobaserat samhälle och förbättra människors hälsa. Våra områden innefattar både grundläggande och tillämpad forskning inom life sciences.
På institutionen för life sciences, LIFE, (tidigare biologi och bioteknik) utforskar vi hur biologiska system och innovativa teknologier kan användas för att omvandla biomassa till livsmedel, läkemedel, material, kemikalier och bränslen. Vi utvecklar och använder avancerade experimentella tekniker och beräkningsmodeller för att undersöka hur biomolekyler, levande celler och organismer fungerar och interagerar. Vi banar väg för nya metoder för att förutse, förebygga, diagnosticera och behandla sjukdomar.

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För forskning och forskningspublikationer, se https://research.chalmers.se/organisation/biologi-och-bioteknik/

We conduct research, innovation, and education to enable a biobased society and improve human health. Our topics cover both basic and applied aspects of life sciences.
At the Department of Life Sciences, LIFE, (former Biology and Biological Engineering) we explore how biological systems and innovative technologies can be used to convert biomass into foods, pharmaceuticals, materials, chemicals and fuels. We develop and apply advanced experimental and computational technologies to discover how biomolecules, living cells and organisms function and interact. We pioneer new methods for the prediction, prevention, diagnostics and treatment of diseases.

Studying at the Department of Life Sciences at Chalmers

For research and research output, please visit https://research.chalmers.se/en/organization/biology-and-biological-engineering/

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A CRISPR approach to manipulating NK cell receptor ligand expression
(2018) Kristensson, Linnea; Chalmers tekniska högskola / Institutionen för biologi och bioteknik; Chalmers University of Technology / Department of Biology and Biological Engineering
Natural killer (NK) cells are important innate lymphocytes in the immune system and have been considered to be vital in fighting cancer, virus infections as well as regulating immune responses. The activity of NK cells is regulated via a complex signaling between inhibitory and activating receptors. Ligands for most of the ac-tivating receptors have been discovered but no endogenous ligand for one of the important natural cytotoxicity receptors, NKp46 has been identified. Therefore, the long term aim of this thesis project was to define ligand candidates for the acti-vating receptor NKp46 with intermediate aims to manipulate expression of NK cell activating receptor ligands in the K562 cell line using a CRISPR approach. The result from the performed cytotoxicity assays demonstrated the importance of the activating receptors NKp30 and DNAM-1 in elimination of K562 cells and the expression of the complementary ligands NCR3LG1, PVR and NECTIN2 was confirmed using RT-qPCR. The successful creation of a Cas9-expressing K562 cell line was demonstrated, including verification of Cas9 protein expression using both flow cytometry and western blot. Following that, a constructed plasmid with the gRNA for the B7-H6 gene, NCR3LG1, was generated and shown to create a cleavage and mutation within the gene. The engineered cell line was ultimately shown to have a reduced expression of the B7-H6 protein, indicating the successful knockout of the NCR3LG1 gene.
A kinetically-constrained FBA-model of the synthesis of aromatic amino acid-derived products in Saccharomyces cerevisiae
(2015) Janasch, Markus; Chalmers tekniska högskola / Institutionen för biologi och bioteknik; Chalmers University of Technology / Department of Biology and Biological Engineering
During the last decades the research interest for creating a more sustainable and environmentallyfriendly society and industry has increased dramatically. The employment of icroorganisms to create valuable compounds such as fuels and chemicals from renewable resources has gained high popularity. With directed modifications in the metabolism of these microorganisms, metabolic engineering seeks to optimize the properties of these organisms for an efficient bioprocess to produce valuable compounds. One characteristic of metabolic engineering is the extensive use of computational models to predict the behavior of the metabolism and thereby identifying suitable targets for genetic interventions in an in silico to in vivo progress. Flux Balance Analysis (FBA) is a popular analysis method for metabolic models, as it only requires the underlying stoichiometric network of the metabolism modelled. With FBA the optimal flux distribution, given a certain objective to be maximized, can be calculated with linear programming algorithms. As FBA only takes the stoichiometry and reaction directionality into account, further physiological constraints have to be included in the framework to increase the predictive strength of the simulations. In this thesis, an expanded form of FBA, that includes kinetic enzyme parameters as additional constraints on the system, was used to analyze a metabolic model of the popular industrially-used organisms Saccharomyces cerevisiae, that included, additionally to the native metabolism, also recombinant enzymatic steps to form the plant secondary metabolites resveratrol and naringenin from the aromatic amino acids phenylalanine and tyrosine. Resveratrol and naringenin have been found to be beneficial to human health by offering anti-inflammatory, anti-carcinogenesis and anti-oxidant properties. The kinetically-constrained model was successfully used to estimate the impact of introducing recombinant pathways on the protein pool in the cell as well as to identify the enzymatic steps offering the highest control over the flux towards these products. This might be used in metabolic engineering to estimate the efficiency of metabolic pathways in the context of the whole metabolism form a protein cost point of view.
A Modular Toolkit to Enable Intein-mediated Enzyme Fusions
(2024) Storm, Linus; Chalmers tekniska högskola / Institutionen för life sciences; Chalmers University of Technology / Department of Life Sciences; Larsbrink, Johan; Widén, Tove
In second generation biorefineries, lignocellulosic biomass is fermented by microbes to higher-value products. Hydrolysis of the substrate is necessary to break it into fragments that the microbes can utilize. Enzymatic hydrolysis is often preferred, but a bottleneck is the high costs of enzyme cocktails since lignocellulosic polymers require several types of enzymes to be degraded. Fusion enzymes have been produced to increase conversation rates, but the methods for creating them are either complex or limited. This project aimed to circumvent some of these limitations by creating a modular toolkit to produce any fusion enzymes, where the fusion is split intein-mediated in vitro. For evaluation of the toolkit, an α-xylosidase (BoGH3B) and a β-glucosidase (BoGH31A) involved in xyloglucan (XyG) degradation, were chosen. The toolkit was developed to completion and consists of eight types of parts, excluding the protein of interest. Three assemblies were confirmed by sequencing, proving that the toolkit works. Aside from the toolkit-mediated assemblies, the enzymes on their own were expressed and tested in different combinations for XyG degradation. This was done to compare with the split intein-fused enzymes. However, when it came to expressing the protein assemblies the yield was low, and no fusion could be observed. Thus, the possibly synergistic effect of fusing BoGH3B and BoGH31A could not be investigated. A lot of research is still needed to determine the usefulness of split inteins for creating enzyme fusions. For future work, some experiments need redoing, and new experiments with different linkers and configurations of the assemblies could be performed.
A platform for Acetyl-CoA synthesis using xylose as feedstock in Saccharomyces cerevisiae
(2015) Englund Örn, Oliver; Chalmers tekniska högskola / Institutionen för biologi och bioteknik; Chalmers University of Technology / Department of Biology and Biological Engineering
Global rise in temperature and diminishing oil reserves has stimulated a market of alternative replacements to traditional petroleum based products. An alternative is the use of a bio refinery capable of converting biomass to the normally petroleum based products. The baker yeast Saccharomyces cerevisiae is an attractive cell factory as its existing large-scale infrastructures for bioethanol production. However, it cannot utilize xylose, an otherwise unusable part of the plant biomass, which represents of utmost importance in the bio-refinery development. To also have a strain capable to produce a wide range of products, it could be used as a platform to base a bio refinery upon. Therefore, the aim of this study is to generate platform strains capable of forming acetyl-CoA, an intermediate metabolite in many of the cells metabolic reactions and also for many other industrially relevant bio-chemicals. With this goal in mind, the metabolism of S. cerevisiae was engineered. The genes encoding an isomerase-based xylose assimilation pathway (RTG, XI, XKS), and a phosphoketolase pathway (XPK, PTA), were cloned into the yeast strain CEN.PK113-5D to enable the yeast to take up and convert xylose into acetyl-CoA. The functionality of this synthetic pathway were evaluated for the production of 3-hydroxypropionic acid via introduction of ACC1** and MCR genes into the engineered strains. By characterisation of all the engineered strains on glucose growth we found increase of acetate production in strains with the phosphoketolase pathway expressed, indicating the in vivo activity of this pathway. However, expression of the xylose assimilation pathway through genome integration did not render the strains able to grow on xylose, suggesting the low efficiency of the assembled xylose assimilation pathway. To overcome this adaptive laboratory evolution is recommended.
A Rolling Circle Amplification-Based Methodology for Making Long, SequenceRepeating, DNA Duplexes
(2018) Dekoning, Nora; Chalmers tekniska högskola / Institutionen för biologi och bioteknik; Chalmers University of Technology / Department of Biology and Biological Engineering
In vitro studies of sequence-specific DNA-protein interactions using techniques where long DNA molecules is needed are currently limited by the size of synthesized DNA molecules, or is restricted to the commercially available DNA. For single molecule DNA imaging techniques using for instance nanochannels confinement, the small sized molecules make the interactions difficult to detect. The commercially available DNA, on the other hand, does not allow any freedom in choosing or changing the DNA sequence. Therefore, a method for producing long DNA molecules containing a sequence of choice would alleviate these limitations and greatly improve the possibility to study DNA-protein interactions. The general concept of this paper was to create long, double-stranded DNA molecules with a sequence that is specifically designed to interact with the protein internal host factor. To make such molecules, three experimental procedures were developed, building on the single-stranded DNA products from a rolling circle amplification (RCA) reaction. The first experimental procedure was based on the presumed perfect annealing of smaller complementary strands to the single-stranded RCA product. The second experiment assumed that single-stranded gaps would be present in the duplex after annealing, hence the addition of a polymerisation reaction. In the third experiment, the RCA was run for 24 hours, to allow double-stranded product to be formed in the RCA. The DNA strands were visualized using fluorescence microscopy, with the goal of studying them and their protein interactions in nanochannels. To be able to use this detection method, an external fluorescent dye, YOYO, is used in the main aim of the project. However, as these types of dyes change the native structure of DNA, an extra aim was to use the fluorescent base analogue tC incorporated into one of the duplex strands, leaving the native structure intact. All three experimental procedures were shown to be capable of producing apparently double-stranded DNA molecules, that were larger than 100 kilo-base pairs albeit with a broad size distribution. This shows that the main aim in terms of procuing DNA molecules has been completed. The tC-containing DNA molecules were not visible under the microscope with the settings used, but appears to be promising.
A Step Toward Personalized Cancer Treatment Simultaneous Detection of Multiple Types of Chemotherapyinduced DNA Damage Using Single Molecule Imaging
(2022) Foss, Ebba; Chalmers tekniska högskola / Institutionen för biologi och bioteknik; Chalmers University of Technology / Department of Biology and Biological Engineering; Westerlund, Fredrik; Akwasi Aning, Obed
Chemotherapy is commonly used to treat cancer today, either alone or more commonly as part of combination therapy. Response to a certain chemotherapeutic agent is highly individual, both in terms of treatment efficacy and the extent to which healthy cells are affected. For several drugs, induced DNA damage provides the main cytotoxic effect, and a method for evaluating this damage could therefore prove a powerful tool in treatment planning. In this thesis, a single molecule imaging approach is used to assess chemotherapy-induced DNA damage, allowing visualisation of damage sites on individual DNA strands. While previous studies have focused on one damage type, or collective damage without distinction between types, a novel modification to pre-existing techniques that allows for this distinction has recently been demonstrated. In this thesis, the alkylating agent temozolomide was used to illustrate how different damage types can be distinguished with a single molecule imaging approach. This is done using repair enzymes associated with different DNA repair pathways. The repair enzymes sequentially incorporate spectrally distinct fluorescent nucleotides at the damage site which are then visualized as fluorescent spots of two different colours on individual DNA molecules. This distinction could be shown with high repeatability in terms of colour ratio. While both enzymes used separately clearly repaired the treated DNA, there appeared to be an overlap when applying them sequentially. This could suggest a problem with enzyme specificity. Further exploration of this issue is needed to verify the feasibility of single molecule imaging for the purpose of simultaneous detection of chemotherapy-induced DNA damage types.
Accelerated shelf life tests of wheat tortillas A study of microbial and textural deterioration in wheat tortilla
(2018) Nilsson, Fredrik; Chalmers tekniska högskola / Institutionen för biologi och bioteknik; Chalmers University of Technology / Department of Biology and Biological Engineering
This study tried to shorten the time required for shelf life studies in product development of wheat tortillas, by developing accelerated shelf life test (ASLT) models for microbial and textural shelf life. ASLTs speed up product degradation by exposure to extreme environmental conditions and in this case were temperature and relative humidity (RH) used. The samples were divided into four storage groups: 3°C and 70% RH, 20°C and 30% RH, 27°C and 80% RH as well as 40°C and 80% RH. Texture was determined with a fold/roll-method, an instrument and by a sensory panel. Microbial concentrations were determined by a laboratory company. Gas composition inside the bags, tortilla pH, water content and water activity were measured to determine possible links to the shelf life. It was not possible to calculate an ASLT model for the microbial growth because of unknown starting number of microbes. The microbial tests however showed that a high temperature and humidity caused the number of bacteria to rapidly increase above what is considered acceptable. Microbial ASLTs thus seem possible, but more tests with a lower detection limit are needed to create a model. To avoid bad taste from nonpathogenic bacterial growth, consumers are recommended to avoid storing the tortillas in high temperature and/or humidity. Textural ASLTs also seem possible in regards of rollability and foldability, but more tests are needed to precisely determine the accelerating factor. Stickiness and translucency seems to deteriorate much slower than rollability and foldability under normal storage conditions. It is therefore suggested to be enough to check that freshly baked tortillas meet the quality requirements of stickiness and translucency. Tortillas seemed to lose textural quality at the same rate, or slower, in refrigerator compared to room conditions. Longer shelf life studies are therefore suggested, to verify if this is the case. If so, storage in a refrigerator could possibly prolong shelf life of wheat tortillas. Changes in the modified atmosphere inside the bags seems to correlate with textural degradation. A study with atmospheric air instead would therefore be interesting as an attempt to determine if it retards textural degradation in wheat tortillas.
Adaptive evolution of Yarrowia lipolytica
(2017) Hellgren, John; Chalmers tekniska högskola / Institutionen för biologi och bioteknik; Chalmers University of Technology / Department of Biology and Biological Engineering
We need renewable resources to allow sustainable production of fuels. By using lipid accu-mulating yeast, biodiesel can be produced in a sustainable way from resources that were previously not used, for example lignocellulose-based sources such as agricultural waste. However, for this process to be proﬁtable, the tolerance of the yeast needs to be improved. This project aims to improve the tolerance of the oleaginous yeast Yarrowia lipolytica to-wards osmotic and saline stress by using the method adaptive laboratory evolution. This method has previously been shown to be eﬃcient in constructing strains to tolerate new conditions without the need of prior knowledge. After evolving Y. lipolytica for 220 gen-eration in minimal medium containing 1.4 M NaCl, an improved performance in the same medium was observed, along with evolved cross-tolerance towards low pH. This indicates that this adaptive evolution of Y. lipolytica resulted in improved ionic tolerance rather than pure osmotic tolerance. The evolved strains were sent for whole genomic sequencing to ﬁnd out which mutations that caused this phenotype. During this project, two previous CRISPR/Cas9 strategies were combined and adapted for eﬃcient markerless reverse en-gineering. When genome data arrives, this strategy will be used for reconstruction of can-didate mutations to ﬁnd out which mutations are important for the observed phenotype. The gained knowledge from this evolution experiment can later be used for constructing a robust industrial strain that eﬃciently converts lignocellulose-based material to biodiesel, allowing sustainable production of fuels.
Adaptive laboratory evolution of Saccharomyces cerevisiae for increased tolerance towards compounds of industrial interest
(2016) Malina, Carl; Chalmers tekniska högskola / Institutionen för biologi och bioteknik; Chalmers University of Technology / Department of Biology and Biological Engineering
Over the last decades, microbial production of fuels and chemicals has become an increas-ingly attractive alternative to petroleum-based production. This has created a demand cell factories able to produce a wide range of compounds. The yeast Saccharomyces cere-visiae is widely used in biotechnology with successful applications in the production of both bulk and fine chemicals. However, in order to reach the full potential of yeast as a cell factory challanges still remain. These include creating strains tolerant to stress conditions, such as inhibition at the high product titers required in industrial production. Traits conferring these properties are often complex and encoded by several genes. In order to obtain strains with improved tolerance, adaptive laboratory evolution (ALE) is often used. This thesis was part of an ongoing project of ALE for increased tolerance towards compounds with potential industrial applications. The work in this thesis can be divided into two main parts. The first part was screening for tolerance of S. cerevisiae towards four diols and two diamines by microplate cultivation. For both the diols and diamines, clear trends of decreasing fitness as compound concentration was increased was seen. For the diols tested, it seems increasing toxicity correlates with increasing chain length and branching. The second part was characterization of pimelic acid tolerant strains from ALE, by shake flask cultivation and HPLC analysis of metabolites. In addi-tion, the genomes of 21 strains were resequenced. Results from the shake flask cultures showed that, in presence of pimelic acid, most strains have an impaired growth on non-fermentable carbon sources. Furthermore, HPLC analysis of metabolites revealed that glycerol and acetate accumulated during cultivation while ethanol was slowly consumed, implicating a defective respiratory system. Through genome resequencing, in total 47 genes were found to be mutated across all of the evolved strains.
Aggregation of α-synuclein in primary neuron models of Parkinson’s disease
(2024) Allgén, Elin; Borg, Olivia; Chalmers tekniska högskola / Institutionen för life sciences; Chalmers University of Technology / Department of Life Sciences; Esbjörner Winters, Elin; Ghaeidamini, Marziyeh; Agholme, Lotta; Esbjörner Winters, Elin
Parkinson’s disease (PD) is the second most prevalent neurodegenerative disorder, characterized by the progressive loss of dopaminergic neurons, leading to impaired motor function. In PD pathology, substantial evidence suggest that the neuronal loss is caused by the protein α-synuclein (α-syn) which aggregates into insoluble amyloid fibrils Mutations in the SNCA gene, encoding α-syn, can accelerate disease progression by enhancing the protein’s propensity to aggregate. Synthetic amyloid fibrils called pre-formed fibrils (PPFs) have recently been developed as a valuable tool for studying disease progression in vitro, by effectively induce endogenous aggregation in cells. In this project, five α-synuclein variants were studied: wild-type (WT) and pathological mutants A30P, E46K, H50Q, and A53T. The study aimed to characterize the biophysical properties of PFFs, identify differences among the variants, and assess their ability to induce endogenous α-syn aggregation and potential neurotoxicity. PFFs were generated and characterized using atomic force microscopy (AFM), circular dichroism (CD), and Thioflavin T fluorescence spectroscopy (ThT Assay). Cellular assays with primary cortical cultures from rat and mouse were then employed to evaluate cellular health, viability, and α-syn aggregation. This thesis demonstrated that within a given experiment PFFs could be generated and sonicated in a reproducible manner. Biophysical characterization revealed differences among the α-syn variants, including distinct morphologies, variations in monomer conversion to PFFs, and differences in fluorescence intensity and molar ellipticity. Furthermore, all α-syn variants induced endogenous aggregation in both cell models, with distinct aggregation patterns observed across variants and between models. E46K PFFs caused the highest level of aggregation in the mouse model without affecting cellular health, whereas A53T PFFs led to the highest aggregation in the rat model and impaired dendritic networks. H50Q induced minimal aggregation in both models, but negatively affected dendritic networks, suggesting potential neurotoxicity. Notably, aggregates induced by E46K displayed a distinct morphology compared to other variants. These findings highlight the complexity of α-syn pathology and suggest that different α-syn variants contribute uniquely to PD progression
Antimicrobial silk
(2016) Floderus Savonen, Lotta; Chalmers tekniska högskola / Institutionen för biologi och bioteknik; Chalmers University of Technology / Department of Biology and Biological Engineering
Spider silk has shown potential for use as a biomaterial. If fused to antimicrobial peptides (AMPs), recombinant spider silk could be used for medical applications and reduce the need to use conventional antibiotics to battle infections. Recombinant spider silk 4RepCT was fused to the AMPs Magainin I, Lactoferricin and a synthetically derived AMP referred to as WGR. Polystyrene disks were coated with the AMP-silk fusion proteins and the disks were incubated with cultures of Staphylococcus aureus and Escherichia coli, to test the AMP-silks antimicrobial activity. All AMP-silk fusion proteins significantly decreased bacterial adhesion of S. aureus to the disks after 48 hours of incubation compared to uncoated disks. The Mag- and WGR-silks were e↵ective already after 24 hours. The recombinant silk itself seemed to have an antimicrobial e↵ect by reducing bacterial adhesion of both bacterial strains to the polystyrene disks. Results indicated that addition of the AMPs improved this e↵ect on S. aurues, but not on E.coli.
Assessment of fermentability of steam-pretreated spruce tips, needles and branches for bioethanol applications
(2018) Asp, Tobias; Chalmers tekniska högskola / Institutionen för biologi och bioteknik; Chalmers University of Technology / Department of Biology and Biological Engineering
The production of bioethanol from fermentation-based bioprocesses utilizing ligno-celluosic feedstocks is an option for replacing fossil based fuels. By using genetically modified yeasts that co-consume glucose and xylose, it is possible to ferment lingo-cellulosic materials such as spruce for bioethanol production. In this project the fermentability of spruce tips, needles and branches, pretreated by acid-catalyzed steam explosion according to a design of experiments plan, was evaluated in terms of ethanol titer, rate and yield as well as cell viability. In order to ferment the spruce tips, needles and branches, suÿcient cell concentrations are needed. A preculture method was developed where enough cells were produced and harvested in the same physiological state in di˙erent batches for simultaneous saccharification and co-fermentation. A anaerobic shake flask system was used to ferment the spruce tips, needles and branches. Final ethanol titers of up to 10 g l-1, average volumetric ethanol production rates of up to 0.35 g l-1 h-1 and final yields of ethanol on available glucose and on available glucose together with xylose of up to 0.19 gEthanol gGlucose-1 and 0.16 gEthanol gGlucose+Xylose-1 respectively were observed. The final cell concentrations, colony forming units and growth rates observed were all fairly low values of up to 3.00 x 105 cells ml-1, 1.19 x 107 CFU ml-1 and 2.36 x 10-2 h-1 respectively. Even though there may be some indications on preferable pretreatment conditions in terms of fermentability, more testing and experiments are required to make statisti-cally significant recommendations.However, trends observed in this project points to either high temperature and short time or low temperature and long time as prefer-able pretreatment process conditions. Materials pretreated under these conditions showed the highest final titers and yields.
Attempted Isolations of Cholesterol-to-Coprostanol Reducing Bacteria in the Human Gut
(2023) Antonsson, Selma; Chalmers tekniska högskola / Institutionen för life sciences; Chalmers University of Technology / Department of Life Sciences; Landberg, Rikard; Tremaroli, Valentina
Atherosclerotic cardiovascular disease (ASCVD) is the leading cause of death globally. In early development of atherosclerosis, retention of cholesterol in artery walls is a key step. Cholesterol both endogenously produced and absorbed from the diet ends up in the gut, where bacteria may reduce it to coprostanol. Unlike cholesterol, coprostanol cannot be reabsorbed into circulation from the intestines, leading to long-standing hypotheses that high cholesterol-to-coprostanol conversion may lower blood cholesterol and thus the risk of ASCVD. Metagenomic evidence for both conversion being health-associated and ASCVD being a microbiota-modulated disease is mounting, emphasising the potential importance of microbial cholesterol metabolism in the gut. This project thus aimed to isolate cholesterol-converting bacteria from the human gut to further characterise them. Conversion was initially studied in a pure Eubacterium coprostanoligenes culture as a positive control. However, the type strain was quickly outcompeted by a contaminant whereupon culturing of faecal samples from two healthy donors was initiated. Over four sample series, several media compositions and cultivation approaches were investigated. Coprostanol was not observed in any culture. Pathway intermediates could not be analysed and as such it is possible, although improbable, that partial conversion took place. There was also no way of detecting the potential presence coprostanoligenic but non-converting bacteria. Altogether, these results reiterate on the previously established fastidiousness of coprostanoligenic bacteria. Further attempts would benefit from more research determining the conditionssupporting cholesterol conversion, as a better understanding of those conditions is a first step in characterising the bacteria performing conversion. Eventually, this might enable research on supporting their growth using prebiotics or the feasibility of their application as next-generation probiotics for improved cardiovascular health.
Biofilm Reduction Modelling in a Drip-flow Reactor. Developing a Method for Growing Biofilms in a Laboratory Setting, to Evaluate the Effects of an Anti-fouling Product Used in Paper Machines.
(2020) Frithiofson, Emil; Chalmers tekniska högskola / Institutionen för biologi och bioteknik; Norbeck, Joakim; W. Janco, Emma
Bacterial biofilms naturally form in paper machines, causing problems in production. Reducing the amount of biofilm formed is therefore of interest to the paper industry. To model biofilm reduction, a method was developed for growing biofilms in a laboratory setting at BIM Kemi Sweden AB. The goal was for the method to be used to evaluate effect of the anti-fouling product Bimogard produced by the company, a non-biocidal agent that reduces formation of process disrupting biofilms in paper machines. Initial experiments were carried out using petri dishes for cultivation, but the main part of the work was carried out using a drip-flow biofilm reactor. The biofilms were quantified by staining with safranin and measuring absorbance. Different process parameters for running the reactor were examined and improved, including what medium concentration to use and whether to inoculate with a mono-culutre of Pseudomonas fluorescens or a co-culture where Bacillus subtilis was also added. The final method, using the mono-culture and 7.5% of standard medium concentration, was used to evaluate the effects of adding Bimogard to the nutrient medium. The addition of Bimogard significantly reduced the amount of biofilm formed, but only at low concentrations.
Biophysical approaches in a structure-guided SMYD3 ligand discovery
(2019) Talu, Martin Johannes; Chalmers tekniska högskola / Institutionen för biologi och bioteknik; Norbeck, Joakim; Talibov, Vladimir O.
In eukaryotic cells, DNA is wrapped around nucleosomal cores formed of protein heterooctamers, which consist of core histones. Nucleosomes are the main units of chromatin organization. Chromatin exist in two states - either as eu- or heterochromatin, which either promotes or silences gene expression as a consequence of its packing states. Eukaryotic cells have developed epigenetic regulation to control the chromatin state, and to guarantee a high level of differentiation. The basis of epigenetic regulation are patterns of post-translational modifications of the nucleosomal proteins. These modifications are performed by epigenetic enzymes. This thesis focuses on one of these enzymes - the human lysine methyltransferase SMYD3. SMYD3 is also capable of interacting with certain cytosolic proteins, such as the molecular chaperone HSP90 - the human Heat Shock Protein 90. Both proteins are of high interest in the drug research and development landscape, as a drastic change in their activity and expression levels have both been shown to be related to several cancers or neurodevelopmental diseases. In this work, various truncated forms of HSP90 were produced and probed for their interactions with SMYD3 using surface plasmon resonance-based biosensor technology. A previously reported interaction of SMYD3 with the C-terminal domain of HSP90 was confirmed, with an affinity discovered to be KD = 1.3 × 10−5M. Additionally, the biosensor-based assay was used to test potential ligands of SMYD3, including low affinity fragment-like organic molecules. To complement the study, extensive crystallization and co-crystallization trials were carried out with SMYD3. As a result, conditions for the formation of various crystal forms of SMYD3 were mapped, with the best crystal form found to have high stability and good diffraction properties. A set of experiments presented herein develops expertise in the tools one can use for an efficient and rational ligand discovery campaign targeting SMYD3 histone methyltransferase.
Bioprospecting for novel laminarin-degrading enzymes in marine microorganisms - A step towards the use of macroalgae in bioprocesses
(2015) Olsson, Joakim; Chalmers tekniska högskola / Institutionen för biologi och bioteknik; Chalmers University of Technology / Department of Biology and Biological Engineering
Currently, efforts are being made to find alternative biomasses for biofuel production, which are not competing with food production. Several kelp species have potential for large-scale cultivation, harvest and biorefinery processes. On the Swedish west coast, Laminaria digitata and Saccharina latissima are two such species. These kelps can contain up to 33% of the storage carbohydrate laminarin (dry weight), which can be hydrolysed to glucose and subsequently converted into bioethanol by for instance yeast. Enzymes able to digest the β-1,3 or β-1,6 bonds of the laminarin, to release glucose, are in large unknown and this project has been about finding microorganisms expressing such enzymes, known as laminarases. Samples from partly decomposed L. digitata and S. latissima specimens were streaked on nutrient agar plates for proliferation and isolation of surface microorganisms. Isolated organisms were subsequently screened for growth on laminarin and promising strains were identified through 16s/18s rRNA sequencing. After growth experiments on liquid medium with different carbon sources, two bacterial strains, Pseudoalteromonas ssp., were selected for further characterisation. The two strains were grown in algae extract and the sugar composition was monitored over time. In the extract, mainly mannitol and laminarin were present but glucose was formed during the cultivation, indicating the presence of hydrolytic enzymes, after which the hydrolytic activity on pure laminarin was investigated. The supernatants of one of the strains showed in vitro activity, further indicating the presence of extracellular hydrolytic enzymes. More investigations are needed on whether the enzymes can be used in any type of process. This thesis work has been successful in isolating marine organisms with laminarin-degrading activity.
Catalytic Activity of α-Synuclein Amyloid Fibers
(2024) Rehnberg, Nikita; Chalmers tekniska högskola / Institutionen för life sciences; Chalmers University of Technology / Department of Life Sciences; Wittung-Stafshede, Pernilla; Horvath, Istvan
Amyloid fibers play a significant role in neurodegenerative diseases such as Alzheimer’s Disease (AD) and Parkinson’s Disease (PD). They have for long been considered nonreactive dead-end products of protein aggregation. Recent research show that amyloid fibers, but not monomers, exhibit enzymatic catalytic activity in vitro. This project investigates the catalytic activity of α-Synuclein (aS) amyloid fibers. First, homogeneous aS amyloid fibers were made in a two-step seeding process and amyloids confirmed through ThT-fluorescence, far UV circular dichroism (CD) and atomic force microscopy (AFM). Then, an already established esterase activity assay, in vitro, was used to study ester bond cleavage of WT and A53T (disease-causing mutant) aS amyloid fibers. Another in vitro enzymatic assay was developed to study ATPase activity of WT, A53T and H50A (model of disease-causing mutants with altered residue 50) aS amyloid fibers. Results indicate that there is catalytic activity when aS amyloid fibers are incubated with both ester-bond and ATP substrates. However, the results are only qualitatively interpreted due to large variability in obtained kinetic parameters. To draw firm conclusions regarding the difference between the investigated aS mutants, additional experiments are needed.
Characterization of non-homologus end joining in Mycobacterium tuberculosis using nanofluidics
(2023) Persson, Elin; Chalmers tekniska högskola / Institutionen för life sciences; Chalmers University of Technology / Department of Life Sciences; Westerlund, Fredrik; Budida, Anusha; Pavlova, Evgeniya
DNA, the building block of all life, is constantly exposed to various pressures that can damage this vital molecule. These damages, if not repaired correctly, can result in mutations, disease and possibly cell death; why the cell has developed several ways to defend itself from the inevitable occurrence of DNA damages. The most dangerous form of DNA damage is double stranded breaks, for which the cell has only two repair mechanisms. One of these, non-homologous end joining, is especially important due to the fact that it repairs these dangerous breaks in situations where no template is available. However, the bacterial non-homologous end joining system lacks comprehensive understanding, especially on the level of individual molecules. Hence, the primary objective of this thesis is to explore the mechanisms of the two key players of this system. While the human system is a complex interplay of numerous proteins, the bacterial system primarily consists of two proteins that are homologous to their eukaryotic counterparts: the homodimer Ku and DNA ligase D. This project aimed to express, purify and utilize these two proteins from Mycobacterium tuberculosis to investigate their interaction with DNA in both bulk phase and with single molecule assays, especially a nanofluidic device based on confinement of DNA. Our findings reveal that the C-terminal arm of the Ku protein, as well as the nature of the double-stranded break, plays a critical role of DNA binding and bridging. The Ku from Mycobacterium tuberculosis was also found to have the ability to bridge blunt ended DNA, a characteristic not observed in other bacterial species such as Bacillus subtilis. Further, it was proven by single molecule methods that the ligation of double stranded breaks is directly dependent on efficient bridging of the DNA by the Ku homodimer.
Characterization of PlyAZ3aT
(2018) Sundström, Clara; Chalmers tekniska högskola / Institutionen för biologi och bioteknik; Chalmers University of Technology / Department of Biology and Biological Engineering
Antibiotic resistance among bacteria is a growing problem all around the world. Hence, new alternatives to antibiotics are demanded for. Bacteriophages (phages) represent such an alternative, as they are viruses that naturally affect bacteria. After infecting a bacterium, the phage uses enzymes to escape the host cell and kill it. Endolysins are one group of enzymes used in this step to cut open the bacterial peptidoglycan. A future perspective on antimicrobial agents is the direct usage of endolysins to treat bacterial infections. In the lab of Grégory Resch (Lausanne University, Switzerland) a new endolysin, PlyAZ3aT, was identified within the genome of Streptococcus tigurinus AZ3aT and its activity was evaluated in a series of experiments. In this report the explorative work on PlyAZ3aT have been continued by means of comparison with the formerly known endolysin Cpl-1 and chimeric enzymes (chimeras) constructed by domain swapping between the two native enzymes (PlyAZ3aT and Cpl-1). Six chimeras were purified from crude extract using Fast Protein Liquid Chromatography (FPLC). Thereafter, the activity of all enzymes was evaluated in vitro on S. pneumoniae D39 and S. tigurinus AZ3aT using turbidity, Minimal Inhibitory Concentration (MIC) and time-kill experiments. While all enzymes showed similar activity in poor medium (NaCl 0.9%), enzymes harbouring the Cell Wall Binding Domain (CWBD) of PlyAZ3aT performed significantly better on both strains in rich medium. Whether these first interesting results reflect a negative medium effect on Cpl-1 or an activity improvement provided by the PlyAZ3aT CWBD on dividing cells remains to be determined. In addition, to further evaluate the potential of PlyAZ3aT and/or any of the chimeras as antimicrobial agent, their activity should be verified in vivo.
Characterization of the antibacterial properties of human amyloid proteins and antimicrobial peptides based on bacterial membrane-binding domains.
(2023) Qvist, August; Chalmers tekniska högskola / Institutionen för life sciences; Chalmers University of Technology / Department of Life Sciences; Wenzel, Michaela; Wenzel, Michaela
Antibiotic resistance is one of the largest current threats to public health and food security, being directly responsible for 1.27 million deaths worldwide in 2019 and is estimated to rise to 10 million deaths per year by 2050. Therefore, there is an urgent need to find new treatments against resistant infections. This can be done by finding new antibiotic compounds with new mechanisms of action or through optimizing and potentiating existing antibiotics. The antimicrobial mechanisms of action for the human proteins S100A12 and α-synuclein, and 18 peptides derived from peripheral membrane proteins of Mycobacterium tuberculosis were investigated. Antimicrobial activity of each protein and peptide was assayed by determining the minimal inhibitory concentration (MIC). The 18 peptides derived from M. tuberculosis were screened for outer membrane permeabilization effects on Gram-negative bacteria (Escherichia coli) and mycobacteria (Mycolicibacterium smegmatis and Mycobacterium marinum) using the fluorescence probe 1-N-phenylnaphtylamine (NPN). The NPN assay was adapted from the E. coli protocol and investigated for use in mycobacteria. The fluorescent probe 3,3′- dipropylthiadicarbocyanine (DiSC35) was used in a single cell fluorescence microscopy assay to investigate effects on membrane polarization, which can indicate activity toward the plasma membrane. To determine the resistance frequency of the peptides a disk diffusion assay was used. The disk diffusion plates were checked for colonies inside of the inhibition zone after 24 and 48 hours. For S100A12 and α-synuclein-treated Bacillus subtilis grown in a minimal medium, no MIC or significant change in growth could be observed at the tested concentrations. Addition of calcium ions or copper ions to the proteins did not change the growth or MIC. This suggests that these proteins do not have any antimicrobial effect on B. subtilis under the tested conditions. However, some older batches of the S100A12 protein showed a decrease in growth rate suggesting some antimicrobial activity, likely caused by a degradation product or toxic oligomer formation. The antimicrobial activity of the OMPPs ranged from no activity to relatively high activity. The NPN assay in E. coli showed that out of the eighteen peptides, six showed no outer membrane permeabilization, and six peptides showed outer membrane permeabilization of 20% or higher at 10 μg/ml. With the DiSC35 assay, treating E. coli with the peptides for 15 minutes before imaging, an increase in fluorescence emission could be seen for the peptides that also showed a higher outer membrane permeabilization. However, no significant change in fluorescence of the dye could be seen for most peptides. The increased fluorescence of DiSC35 is likely caused by an increase in uptake of the dye due to increased permeability of the outer membrane. The disk diffusion assay showed no colonies within the inhibition zone after 24 or 48 hours indicating low frequency of resistance development towards the peptides. The collective results of the screenings in E. coli showed that two peptides may be selective outer membrane permeabilizers and should be investigated further at different concentrations. The rest of the peptides showed other or unspecific modes of action that may be of interest as antimicrobials and should also be investigated further. In mycobacteria, using NPN to assess outer membrane permeabilization needs to be further developed and optimized to produce proper results, as no reliable positive control is known. Further assays should be used to evaluate the activity of these peptides in mycobacteria.

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