| 1. |
- Clausson, Carl-Magnus, 1985-, et al.
(författare)
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Compaction of rolling circle amplification products increases signal integrity and signal–to–noise ratio
- 2015
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 5, s. 12317:1-10
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Tidskriftsartikel (refereegranskat)abstract
- Rolling circle amplification (RCA) for generation of distinct fluorescent signals in situ relies upon the self-collapsing properties of single-stranded DNA in commonly used RCA-based methods. By introducing a cross-hybridizing DNA oligonucleotide during rolling circle amplification, we demonstrate that the fluorophore-labeled RCA products (RCPs) become smaller. The reduced size of RCPs increases the local concentration of fluorophores and as a result, the signal intensity increases together with the signal-to-noise ratio. Furthermore, we have found that RCPs sometimes tend to disintegrate and may be recorded as several RCPs, a trait that is prevented with our cross-hybridizing DNA oligonucleotide. These effects generated by compaction of RCPs improve accuracy of visual as well as automated in situ analysis for RCA based methods, such as proximity ligation assays (PLA) and padlock probes.
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| 2. |
- Guala, Dimitri, et al.
(författare)
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Experimental validation of predicted cancer genes using FRET
- 2018
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Ingår i: METHODS AND APPLICATIONS IN FLUORESCENCE. - : IOP PUBLISHING LTD. - 2050-6120. ; 6:3
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Tidskriftsartikel (refereegranskat)abstract
- Huge amounts of data are generated in genome wide experiments, designed to investigate diseases with complex genetic causes. Follow up of all potential leads produced by such experiments is currently cost prohibitive and time consuming. Gene prioritization tools alleviate these constraints by directing further experimental efforts towards the most promising candidate targets. Recently a gene prioritization tool called MaxLink was shown to outperform other widely used state-of-the-art prioritization tools in a large scale in silico benchmark. An experimental validation of predictions made by MaxLink has however been lacking. In this study we used Fluorescence Resonance Energy Transfer, an established experimental technique for detection of protein-protein interactions, to validate potential cancer genes predicted by MaxLink. Our results provide confidence in the use of MaxLink for selection of new targets in the battle with polygenic diseases.
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| 3. |
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| 4. |
- Guala, Dimitri, 1979-
(författare)
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Functional association networks for disease gene prediction
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Mapping of the human genome has been instrumental in understanding diseasescaused by changes in single genes. However, disease mechanisms involvingmultiple genes have proven to be much more elusive. Their complexityemerges from interactions of intracellular molecules and makes them immuneto the traditional reductionist approach. Only by modelling this complexinteraction pattern using networks is it possible to understand the emergentproperties that give rise to diseases.The overarching term used to describe both physical and indirect interactionsinvolved in the same functions is functional association. FunCoup is oneof the most comprehensive networks of functional association. It uses a naïveBayesian approach to integrate high-throughput experimental evidence of intracellularinteractions in humans and multiple model organisms. In the firstupdate, both the coverage and the quality of the interactions, were increasedand a feature for comparing interactions across species was added. The latestupdate involved a complete overhaul of all data sources, including a refinementof the training data and addition of new class and sources of interactionsas well as six new species.Disease-specific changes in genes can be identified using high-throughputgenome-wide studies of patients and healthy individuals. To understand theunderlying mechanisms that produce these changes, they can be mapped tocollections of genes with known functions, such as pathways. BinoX wasdeveloped to map altered genes to pathways using the topology of FunCoup.This approach combined with a new random model for comparison enables BinoXto outperform traditional gene-overlap-based methods and other networkbasedtechniques.Results from high-throughput experiments are challenged by noise and biases,resulting in many false positives. Statistical attempts to correct for thesechallenges have led to a reduction in coverage. Both limitations can be remediedusing prioritisation tools such as MaxLink, which ranks genes using guiltby association in the context of a functional association network. MaxLink’salgorithm was generalised to work with any disease phenotype and its statisticalfoundation was strengthened. MaxLink’s predictions were validatedexperimentally using FRET.The availability of prioritisation tools without an appropriate way to comparethem makes it difficult to select the correct tool for a problem domain.A benchmark to assess performance of prioritisation tools in terms of theirability to generalise to new data was developed. FunCoup was used for prioritisationwhile testing was done using cross-validation of terms derived fromGene Ontology. This resulted in a robust and unbiased benchmark for evaluationof current and future prioritisation tools. Surprisingly, previously superiortools based on global network structure were shown to be inferior to a localnetwork-based tool when performance was analysed on the most relevant partof the output, i.e. the top ranked genes.This thesis demonstrates how a network that models the intricate biologyof the cell can contribute with valuable insights for researchers that study diseaseswith complex genetic origins. The developed tools will help the researchcommunity to understand the underlying causes of such diseases and discovernew treatment targets. The robust way to benchmark such tools will help researchersto select the proper tool for their problem domain.
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| 5. |
- Jalilian, Ehsan, et al.
(författare)
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Luminescence properties of the Cu4I62- cluster
- 2011
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Ingår i: CrystEngComm. - : Royal Society of Chemistry (RSC). - 1466-8033. ; 13:14, s. 4729-4734
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Tidskriftsartikel (refereegranskat)abstract
- Two new solvates were prepared in the system Cu(I) I using a solvolysis reaction. The structures for both of them were solved by X-ray crystallography, showing that they constitute two modifications of the same compound with the net formula [Cu4I6](P(C6H5)(4))(2)center dot 2OC(CH3)(2). Both types of crystals show vivid fluorescence when exposed to UV light. The formation of the first modification (I) seems to be preferred by kinetics and on ageing in the mother liquor it converts to modification (II). The Cu positions in (I) are disordered while those in (II) are fully ordered. The luminescent properties of both crystals were characterized using a confocal microscope and an excitation wavelength of 405 nm, resulting in fluorescence spectra with the intensities of 1.22 and 0.52 relative to the reference (fluorescein 10 mu M). Density functional theory calculations on the ordered Cu4I62- core of modification (II) show that the de-excitation from LUMO to HOMO is responsible for the luminescence. The calculated emission spectrum has a maximum at 531 nm in good agreement with the results from confocal microscopy.
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| 6. |
- Johansson, Henrik J., et al.
(författare)
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Breast cancer quantitative proteome and proteogenomic landscape
- 2019
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Ingår i: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- In the preceding decades, molecular characterization has revolutionized breast cancer (BC) research and therapeutic approaches. Presented herein, an unbiased analysis of breast tumor proteomes, inclusive of 9995 proteins quantified across all tumors, for the first time recapitulates BC subtypes. Additionally, poor-prognosis basal-like and luminal B tumors are further subdivided by immune component infiltration, suggesting the current classification is incomplete. Proteome-based networks distinguish functional protein modules for breast tumor groups, with co-expression of EGFR and MET marking ductal carcinoma in situ regions of normal-like tumors and lending to a more accurate classification of this poorly defined subtype. Genes included within prognostic mRNA panels have significantly higher than average mRNA-protein correlations, and gene copy number alterations are dampened at the protein-level; underscoring the value of proteome quantification for prognostication and phenotypic classification. Furthermore, protein products mapping to non-coding genomic regions are identified; highlighting a potential new class of tumor-specific immunotherapeutic targets.
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| 7. |
- Ng, Jovice Boon Sing, 1975-, et al.
(författare)
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Intraparticle transport and release of dextran in silica spheres with cylindrical mesopores
- 2010
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 26:1, s. 466-70
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Tidskriftsartikel (refereegranskat)abstract
- The transport of oligomeric molecules in silica spheres with cylindrical mesopores has been quantified and related to the structural features of the spherical particles and the interactions at the solid-liquid interface. An emulsion-solvent evaporation method was used to produce silica spheres having cylindrical mesopores with an average pore diameter of 6.5 nm. The transport of dextran molecules (fluorescently tagged) with molecular weights of 3000 and 10,000 g/mol was quantified using confocal laser scanning microscopy (CLSM). The intraparticle concentration profiles in the dextran-containing spheres were flat at all times, suggesting that the release is not isotropic and not limited by diffusion. The release of dextran into the solution is characterized by an initial burst, followed by long-term sustained release. The release follows a logarithmic time dependency, which was rationalized by coupling concentration-dependent effective diffusion constants with adsorption/desorption.
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| 8. |
- Ng, Jovice Boon Sing, 1975-, et al.
(författare)
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Release and molecular transport of cationic and anionic fluorescent molecules in mesoporous silica spheres.
- 2008
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 24:19, s. 11096-102
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Tidskriftsartikel (refereegranskat)abstract
- We describe here a method for study of bulk release and local molecular transport within mesoporous silica spheres. We have analyzed the loading and release of charged fluorescent dyes from monodisperse mesoporous silica (MMS) spheres with an average pore size of 2.7 nm. Two different fluorescent dyes, one cationic and one anionic, have been loaded into the negatively charged porous material and both the bulk release and the local molecular transport within the MMS spheres have been quantified by confocal laser scanning microscopy. Analysis of the time-dependent release and the concentration profiles of the anionic dye within the spheres show that the spheres are homogeneous and that the release of this nonadsorbing dye follows a simple diffusion-driven process. The concentration of the cationic dye varies radially within the MMS spheres after loading; there is a significantly higher concentration of the dye close to the surface of the spheres (forming a "skin") compared to that at the core. The release of the cationic dye is controlled by diffusion after an initial period of rapid release. The transport of the cationic dye within the MMS spheres of the dye from the core to near the surface is significantly faster compared to the transport within the surface "skin". A significant fraction of the cationic dye remains permanently attached to the negatively charged walls of the MMS spheres, preferentially near the surface of the spheres. Relating bulk release to the local molecular transport within the porous materials provides an important step toward the design of new concepts in controlled drug delivery and chromatography.
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| 9. |
- Nilsson, Linnea, et al.
(författare)
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RNA-seq reveals altered gene expression levels in proximal tubular cell cultures compared to renal cortex but not during early glucotoxicity
- 2020
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Ingår i: Scientific Reports. - : Springer Nature. - 2045-2322. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Cell cultures are often used to study physiological processes in health and disease. It is well-known that cells change their gene expression in vitro compared to in vivo, but it is rarely experimentally addressed. High glucose is a known trigger of apoptosis in proximal tubular cells (PTC). Here we used RNA-seq to detect differentially expressed genes in cultures of primary rat PTC, 3 days old, compared to cells retrieved directly from rat outer renal cortex and between PTC exposed to 15 mM glucose and control for 8 h. The expression of 6,174 genes was significantly up- or downregulated in the cultures of PTC compared to the cells in the outer renal cortex. Most altered were mitochondrial and metabolism related genes. Gene expression of proapoptotic proteins were upregulated and gene expression of antiapoptotic proteins were downregulated in PTC. Expression of transporter related genes were generally downregulated. After 8 h, high glucose had not altered the gene expression in PTC. The current study provides evidence that cells alter their gene expression in vitro compared to in vivo and suggests that short-term high glucose exposure can trigger apoptosis in PTC without changing the gene expression levels of apoptotic proteins.
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| 10. |
- Ygberg, Sofia, et al.
(författare)
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A missense mutation converts the Na+,K+-ATPase into an ion channel and causes therapy-resistant epilepsy.
- 2021
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Ingår i: Journal of Biological Chemistry. - : Elsevier. - 0021-9258 .- 1083-351X. ; 297:6
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Tidskriftsartikel (refereegranskat)abstract
- The ion pump Na+,K+-ATPase is a critical determinant of neuronal excitability; however, its role in the etiology of diseases of the central nervous system (CNS) is largely unknown. We describe here the molecular phenotype of a Trp931Arg mutation of the Na+,K+-ATPase catalytic α1 subunit in an infant diagnosed with therapy-resistant lethal epilepsy. In addition to the pathological CNS phenotype, we also detected renal wasting of Mg2+. We found that membrane expression of the mutant α1 protein was low, and ion pumping activity was lost. Arginine insertion into membrane proteins can generate water-filled pores in the plasma membrane, and our molecular dynamic (MD) simulations of the principle states of Na+,K+-ATPase transport demonstrated massive water inflow into mutant α1 and destabilization of the ion-binding sites. MD simulations also indicated that a water pathway was created between the mutant arginine residue and the cytoplasm, and analysis of oocytes expressing mutant α1 detected a nonspecific cation current. Finally, neurons expressing mutant α1 were observed to be depolarized compared with neurons expressing wild-type protein, compatible with a lowered threshold for epileptic seizures. The results imply that Na+,K+-ATPase should be considered a neuronal locus minoris resistentia in diseases associated with epilepsy and with loss of plasma membrane integrity.
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