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Mats Nilsson

Publications and source records attributed to Mats Nilsson.

At least 19 recordsLinked to original sources
PubMed2006

Effects of surface sorption on microbial degradation of glyphosate.

Sorption may affect the bioavailability and biodegradation of pesticides in soils. The aim of this study was to test the effect of surface sorption on microbial utilization of the herbicide glyphosate as a source of phosphorus, nitrogen, or carbon. We added goethite to a humus soil to manipulate the soil's glyphosate sorption capacity. The addition of glyphosate generally either decreased microbial CO2 production or produced no effect. Additions of glyphosate, in combination with glucose and N, did not change the respiration rate in comparison with the same treatment but without glyphosate. In contrast, glyphosate additions combined with glucose and P decreased microbial growth, whereas the combination with goethite counteracted the negative effect. The different treatments were examined using attenuated total reflectance Fourier transform (ATR-FTIR) spectroscopy; the results suggest that glyphosate was de-carboxylated in the sorbed state. Stimulating microbial growth by the addition of glucose and nitrogen resulted in further oxidation of glyphosate and only phosphate was detectable on the goethite surface after 13 days incubation. Our results show that sorbed glyphosate is microbially degradable, and it retards microbial activity. This study emphasizes the importance of combining quantitative measurements with a molecular-level examination, to better understand biogeochemical processes.

Biodegradation, Environmental↗
PubMed2006

Lock and roll: single-molecule genotyping in situ using padlock probes and rolling-circle amplification.

In this review I will describe the development of a technique that enables genotyping of individual DNA molecules in the context of morphologically preserved fixed cells, from the fundamental concept published in 1994 to the present status. The review describes enzyme-assisted histochemistry approaches to achieve highly specific molecular identification reactions coupled to efficient signal amplification. The primary molecular identification is accomplished through circularization of oligonucleotide probes, called padlock probes. The circularization reaction is catalyzed by a DNA ligase, which provides robust distinction between single-nucleotide variants under standard reaction conditions. To generate a detectable signal from individual circularized probe molecules, a DNA polymerase is added that replicates probe circles, generating a long tandem-repeated DNA product, easily visualized using a standard epi-fluorescence microscope. Individual signals are recorded as bright dots, providing digital information about the abundance of specific sequences and opportunities for simultaneous detection of several targets using spectral multiplexing. The importance of strictly target-dependent signal amplification will be discussed.

Animals↗
PubMed2006

Organic material: the primary control on mercury methylation and ambient methyl mercury concentrations in estuarine sediments.

Estuarine environments that have no direct sources of mercury (Hg) pollution may have sediment concentrations of methylmercury (MeHg) as high as those of polluted marine environments. In this study we examined the biogeochemical factors affecting net methylation and sediment MeHg concentrations in an unpolluted estuarine environment, the Ore River estuary, which discharges into the Bothnian Bay (20-120 ng total Hg g(-1) dry sediment, salinity 3-5% per hundred). We analyzed the spatial and temporal differences in surface sediment profiles of MeHg concentration, Hg methylation, MeHg demethylation, and concentrations of sulfide and oxygen between accumulation and erosion type bottoms. The main difference between the bottoms studied was in the proportion of organic material (OM) in the sediment, ranging between 0.8% and 10.8%. The pore water sulfide concentration profiles also differed considerably between sites and seasons, from 0 to 20 microM, with 100 microM as the extreme maximum. The sediment MeHg concentration profiles (0-10 cm) mostly varied between 0.1 and 7 ng g(-1) dry weight (dw, as Hg). The MeHg demethylation rates were relatively low and the depth profiles of the rates were relatively constant over season, site, and depth. In contrast, both rates and depths of maximum Hg methylation differed between the bottoms. The results indicate that the amount of OM accumulated at the bottoms was the main factor affecting net MeHg production, while the total amount of Hg had little or no influence on the amount of MeHg in the sediment.

Environmental Monitoring↗
PubMed2006

Digital quantification using amplified single-molecule detection.

We describe a scheme for biomolecule enumeration by converting nanometer-scale specific molecular recognition events mediated by rolling-circle amplification to fluorescent micrometer-sized DNA molecules amenable to discrete optical detection. Our amplified single-molecule detection (SMD) approach preserves the discrete nature of the molecular population, allowing multiplex detection and highly precise quantification of molecules over a dynamic range of seven orders of magnitude. We apply the method for sensitive detection and quantification of the bacterial pathogen Vibrio cholerae.

DNA, Bacterial↗
PubMed2006

Detection of Alu sequences and mtDNA in comets using padlock probes.

Single cell gel electrophoresis, or the comet assay, is widely used to measure DNA damage and repair. However, the behaviour of the DNA under the conditions used for the comet assay is not fully understood. In developing a method for studying specific gene sequences within comets, using 'padlock probes' (circularizable oligonucleotide probes), we have first applied probes that hybridize to Alu repetitive elements and to mitochondrial DNA (mtDNA). During the sequence of stages in the comet assay, mtDNA progressively disperses into the surrounding agarose gel, showing no tendency to remain with nuclear DNA in the comets. In contrast, Alu probes remain associated with both tail and head DNA.

Alu Elements↗
PubMed2005

Analyzing genes using closing and replicating circles.

During the past two years, significant breakthroughs have been achieved in genetic analyses through the application of technologies based on analytical DNA-circularization reactions. Padlock probes and molecular inversion probes have enabled parallel, high-throughput single nucleotide polymorphism (SNP) genotyping at increased scales, whereas, at the other end of the analysis spectrum, DNA molecules in individual cells have been genotyped, in situ, using padlock probes and rolling-circle amplification (RCA). This review describes the recent developments in the technologies that use specific DNA circularization, coupled to DNA amplification through PCR or rolling-circle amplification, and addresses the great potential of these tools.

Animals↗
PubMed2005

Thermoplastic microfluidic platform for single-molecule detection, cell culture, and actuation.

We have developed a multipurpose microfluidic platform that allows for sensitive fluorescence detection on inexpensive disposable chips. The fabrication scheme involves rapid injection molding of thermoplastics, followed by silica deposition and covalent attachment of an unstructured flexible lid. This combines the virtues of elastomer technology with high-throughput compact disk injection molding. Using this technique, the time to produce 100 chips using a single master can be lowered from more than 1 week by standard PDMS technologies to only a couple hours. The optical properties of the fabricated chips were evaluated by studying individual fluorescence-labeled DNA molecules in a microchannel. Concatemeric DNA molecules were generated through rolling circle replication of circular DNA molecules, which were labeled by hybridization of fluorescence-tagged oligonucleotides. Rolling circle products (RCPs) were detected after as little as 5 min of DNA polymerization, and the RCPs in solution showed no tendency for aggregation. To illustrate the versatility of the platform, we demonstrate two additional applications: The flexible property of the lid was used to create a peristaltic pump generating a flow rate of 9 nL/s. Biocompatibility of the platform was illustrated by culturing Chinese hamster ovary cells for 7 days in the microfluidic channels.

Animals↗
PubMed2005

ProbeMaker: an extensible framework for design of sets of oligonucleotide probes.

BACKGROUND: Procedures for genetic analyses based on oligonucleotide probes are powerful tools that can allow highly parallel investigations of genetic material. Such procedures require the design of large sets of probes using application-specific design constraints. RESULTS: ProbeMaker is a software framework for computer-assisted design and analysis of sets of oligonucleotide probe sequences. The tool assists in the design of probes for sets of target sequences, incorporating sequence motifs for purposes such as amplification, visualization, or identification. An extension system allows the framework to be equipped with application-specific components for evaluation of probe sequences, and provides the possibility to include support for importing sequence data from a variety of file formats. CONCLUSION: ProbeMaker is a suitable tool for many different oligonucleotide design and analysis tasks, including the design of probe sets for various types of parallel genetic analyses, experimental validation of design parameters, and in silico testing of probe sequence evaluation algorithms.

Algorithms↗
PubMed2005

Production of milligram quantities of affinity tagged-proteins using automated multistep chromatographic purification.

A new chromatography system, AKTAxpress (GE Healthcare, Amersham Biosciences, Uppsala, Sweden) has been designed to meet the demand for high-throughput purification of proteins in structural genomics and drug discovery. The system offers a number of automated multistep purification protocols for affinity-tagged proteins. All protocols start with affinity chromatography followed by combinations of desalting, ion exchange chromatography and gel filtration. As an option, tag removal can be included in the purification protocols. Up to 16 proteins can be purified per day and the yield can be as high as 50 mg of each protein at > 90% purity. To highlight the versatility of the system, this paper presents several case studies; purifications of hexahistidine- and glutathione S-transferase-tagged proteins using different protocols, automated on-column tag cleavage and optimization studies for a hexahistidine-tagged kinase.

Affinity Labels↗
PubMed2005

Multiplex amplification enabled by selective circularization of large sets of genomic DNA fragments.

We present a method to specifically select large sets of DNA sequences for parallel amplification by PCR using target-specific oligonucleotide constructs, so-called selectors. The selectors are oligonucleotide duplexes with single-stranded target-complementary end-sequences that are linked by a general sequence motif. In the selection process, a pool of selectors is combined with denatured restriction digested DNA. Each selector hybridizes to its respective target, forming individual circular complexes that are covalently closed by enzymatic ligation. Non-circularized fragments are removed by exonucleolysis, enriching for the selected fragments. The general sequence that is introduced into the circularized fragments allows them to be amplified in parallel using a universal primer pair. The procedure avoids amplification artifacts associated with conventional multiplex PCR where two primers are used for each target, thereby reducing the number of amplification reactions needed for investigating large sets of DNA sequences. We demonstrate the specificity, reproducibility and flexibility of this process by performing a 96-plex amplification of an arbitrary set of specific DNA sequences, followed by hybridization to a cDNA microarray. Eighty-nine percent of the selectors generated PCR products that hybridized to the expected positions on the array, while little or no amplification artifacts were observed.

Base Sequence↗
PubMed2005

PieceMaker: selection of DNA fragments for selector-guided multiplex amplification.

We describe PieceMaker, a software tool for the design of applications of selector probes-oligonucleotide probes that direct circularization of target nucleic acid molecules. Such probes can be combined in parallel to circularize a selection of fragments from restriction digested total genomic DNA. These fragments can then be amplified in a single PCR using a common primer pair, yielding substrates for subsequent analyses, such as parallel genotyping or sequencing. However, designing multiplex selector assays is a laborious task. The PieceMaker program alleviates this problem by selecting restriction enzymes to generate suitable fragments for selection, and generating the output data required to design the selector probes.

Computational Biology↗
PubMed2005

Analysis of T-cell receptor V beta gene repertoires after immune stimulation and in malignancy by use of padlock probes and microarrays.

BACKGROUND: Detection of expanded T-cell clones, identified by their receptor (TCR) repertoires, can assist diagnosis and guide therapy in infectious, inflammatory, and autoimmune conditions as well as in tumor immunotherapy. Analysis of tumor-infiltrating lymphocytes often reveals preferential use of one or a few TCR V beta genes, compared with peripheral blood, indicative of a clonal response against tumor antigens. METHODS: To simultaneously measure the relative expression of all V beta gene families, we combined highly specific and sensitive oligonucleotide reagents, called padlock probes, with a microarray read-out format. T-Cell cDNA was combined with a pool of V beta subfamily-specific padlock probes. Reacted probes were selectively amplified and the products hybridized to a microarray, from which the V beta subfamily distribution in each sample could be determined relative to a control sample. RESULTS: In lymphocytes stimulated with the superantigen staphylococcal enterotoxin B, we detected expansions at the mRNA level of TCR subfamilies previously shown to respond to staphylococcal enterotoxin B. Expansions of the same V beta families could also be detected by flow cytometry. In samples from two bladder cancer patients, we detected predominant representations of specific V beta subfamilies in both tumor-infiltrating lymphocytes and in the draining lymph nodes, but not in non-tumor-draining lymph nodes or peripheral blood. Several expression profiles from draining lymph nodes in patients with malignant melanoma were divergent from profiles seen in non-tumor-draining lymph nodes. CONCLUSION: Padlock probe-based parallel analysis of TCR V beta gene distributions provides an efficient method for screening multiple samples for T-cell clonal expansions with reduced labor and time of analysis compared with traditional methods.

Adenocarcinoma↗
PubMed2004

In situ genotyping individual DNA molecules by target-primed rolling-circle amplification of padlock probes.

Methods are needed to study single molecules to reveal variability, interactions and mechanisms that may go undetected at the level of populations of molecules. We describe here an integrated series of reaction steps that allow individual nucleic acid molecules to be detected with excellent specificity. Oligonucleotide probes are circularized after hybridization to target sequences that have been prepared so that localized amplification reactions can be initiated from the target molecules. The process results in strong, discrete detection signals anchored to the target molecules. We use the method to observe the distribution, within and among human cells, of individual normal and mutant mitochondrial genomes that differ at a single nucleotide position.

DNA Mutational Analysis↗
PubMed2004

Quantifying unfrozen water in frozen soil by high-field 2H NMR.

To understand wintertime controls of biogeochemical processes in high latitude soils it is essential to distinguish between direct temperature effects and the effects of changes in water availability mediated by freezing. Efforts to separate these controls are hampered by a lack of adequate methods to determine the proportion of unfrozen water. In this study we present a high-field 2H2O NMR method for quantifying unfrozen water content in frozen soil. The experimental material consisted of the humic layer of a boreal spruce forest soil mixed with varying proportions of quartz sand and humidified with deuterium-enriched water. The relative standard deviation of unfrozen water content (measured as NMR signal integral) was less than 2% for repeated measurements on a given sample and 3.5% among all samples, based on a total of 16 measurements. As compared to 1H NMR, this 2H NMR method was found to be superior for several reasons: it is less sensitive to field inhomogeneity and paramagnetic impurities, it gives a bigger line shape difference between the ice and liquid signal, it shows a sharper response to water fusion, and it excludes the possibility of hydrogen in the organic material interfering with the measurement.

Deuterium↗
PubMed2004

Circle-to-circle amplification for precise and sensitive DNA analysis.

We present a tightly controlled process for strand-specific amplification of circularized DNA molecules. Tandem repeated complements of DNA circles are generated by rolling-circle replication, and converted to monomer circles of opposite polarity to that of the starting material. These circles are then subjected to one more round of rolling-circle replication and circularization, and the process can be further repeated. The method can be directed to produce single-stranded circular or linear monomers, or linear concatemers of the desired polarity. The reaction is not product inhibited, and can yield approximately 100-fold higher concentrations of monomer products than PCR. Each generation of the amplification process proceeds in a linear fashion, ensuring precise quantification. The procedure is suitable for parallel amplification of large numbers of DNA circles, because the few cycles and the robust reaction mechanism preserves the proportion of amplified molecules. We demonstrate the utility of the method for multiplexed genotyping of polymorphic loci and for quantitative DNA analysis.

Base Sequence↗
PubMed2004

Involvement of RFX proteins in transcriptional activation from a Ras-responsive enhancer element.

The B10.RRE element has previously been shown to mediate induced transcription in response to an activated Ha- ras gene and epidermal growth factor in keratinocytes but not in fibroblasts. We report the identification of regulatory factor for X box 3 (RFX-3) as a B10.RRE-binding protein, using the yeast one-hybrid assay. We showed that in vitro-translated RFX3, as well as RFX1 and RFX2, was able to bind B10.RRE in a sequence-specific manner. Furthermore, RFX proteins are part of the protein complex in HeLa and HepG2 cells that binds the B10.RRE element. Functional analysis in cell culture demonstrated that a truncated version of RFX1 (*RFX1) lacking the repressor domain was able to activate transcription from B10.RRE. Conversely, a dominant-negative form of RFX1 was able to block Ras-induced transcription. Taken together, these results suggest a novel role for the RFX family of transcription factors as modulators of Ras signalling in epithelial cells. Such an interaction is of potential relevance for cell growth and carcinogenesis in the skin.

Antibodies↗
PubMed2004

Homogeneous detection of single rolling circle replication products.

We describe a simple and straightforward approach for homogeneous and isothermal detection of individual rolling circle replication (RCR) products, which represent individual padlock probe circularization events. The RCR products constitute tens of kilobases long single-stranded tandem repeated copies of the probe sequence, and in solution, they fold into micrometer-sized random coils. The method is based on the local enrichment of fluorescence-labeled probes that hybridize to the coiled RCR products compared to the concentration of free probes in solution. We present a detailed characterization of the fluorescence-labeled products using a highly sensitive and fast microscopy setup. At a 10(4)-fold excess of free label, we were able to detect and follow individual RCR products at a signal-to-background noise ratio of 27. This high signal-to-background noise ratio leaves room for analysis in a simple detection device at higher speeds or at lower labeling ratios.

Animals↗