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Johan Nilsson

Publications and source records attributed to Johan Nilsson.

At least 19 recordsLinked to original sources
PubMed2005

Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125.

A considerable fraction of life develops in the sea at temperatures lower than 15 degrees C. Little is known about the adaptive features selected under those conditions. We present the analysis of the genome sequence of the fast growing Antarctica bacterium Pseudoalteromonas haloplanktis TAC125. We find that it copes with the increased solubility of oxygen at low temperature by multiplying dioxygen scavenging while deleting whole pathways producing reactive oxygen species. Dioxygen-consuming lipid desaturases achieve both protection against oxygen and synthesis of lipids making the membrane fluid. A remarkable strategy for avoidance of reactive oxygen species generation is developed by P. haloplanktis, with elimination of the ubiquitous molybdopterin-dependent metabolism. The P. haloplanktis proteome reveals a concerted amino acid usage bias specific to psychrophiles, consistently appearing apt to accommodate asparagine, a residue prone to make proteins age. Adding to its originality, P. haloplanktis further differs from its marine counterparts with recruitment of a plasmid origin of replication for its second chromosome.

Adaptation, Physiological↗
PubMed2005

Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes.

We have performed a comparative analysis of amino acid distributions in predicted integral membrane proteins from a total of 107 genomes. A procedure for identification of membrane spanning helices was optimized on a homology-reduced data set of 170 multi-spanning membrane proteins with experimentally determined topologies. The optimized method was then used for extraction of highly reliable partial topologies from all predicted membrane proteins in each genome, and the average biases in amino acid distributions between loops on opposite sides of the membrane were calculated. The results strongly support the notion that a biased distribution of Lys and Arg residues between cytoplasmic and extra-cytoplasmic segments (the positive-inside rule) is present in most if not all organisms.

Amino Acids↗
PubMed2005

Flow-through microdispenser for interfacing micro-HPLC to Raman and mid-IR spectroscopic detection.

A flow-through microdispenser has been coupled to a micro HPLC separation system and used as a solvent elimination interface for Fourier transform infrared (FTIR) and Raman spectroscopic detection of the separated compounds. Using the microdispenser picoliter sized droplets can be generated and deposited on an appropriate target placed on a computerized x, y-stage. Evaporation of volatile solvent and buffer is rapid and allows analysis of the obtained dry deposits by various techniques. Due to the destruction free character of Raman and FTIR spectroscopy they can be applied sequentially to interrogate the same deposit. In the reported application five phenolic acids typically present in wine have been separated on a C-18 column technique using a mixture of water, methanol and acetic acid as mobile phase. For spectrum acquisition infrared and Raman microscopes have been used. The spectra recorded from the dried deposits of the separated compounds agreed well with the reference spectra of corresponding components.

Chromatography, High Pressure Liquid↗
PubMed2005

Clinical outcome after poststernotomy mediastinitis: vacuum-assisted closure versus conventional treatment.

BACKGROUND: The conventional treatment for poststernotomy mediastinitis usually involves surgical revision, closed irrigation, or reconstruction with omentum or pectoral muscle flaps. Recently, vacuum-assisted closure has been successfully used in poststernotomy mediastinitis. The aim of the present study was to compare the clinical outcome and survival in 101 patients undergoing vacuum-assisted closure therapy or conventional treatment for poststernotomy mediastinitis. METHODS: One hundred one consecutive patients underwent treatment for poststernotomy mediastinitis: vacuum-assisted closure therapy (January 1999 through December 2003, n = 61) or conventional treatment (July 1994 through December 1998, n = 40). Follow-up was made in April 2004 and was 100% complete. Actuarial statistics were used to calculate the survival rates. RESULTS: The 90-days mortality was 0% in the vacuum-assisted closure group and 15% in the conventional treatment group (p < 0.01). The failure rate to first-line treatment with vacuum-assisted closure and conventional treatment were 0% and 37.5%, respectively (p < 0.001). There was no statistically significant difference in the recurrence of sternal fistulas after vacuum-assisted closure therapy or conventional treatment: 6.6% versus 5.0%, respectively. Overall survival in the vacuum-assisted closure group was significantly better (p < 0.05) than in the conventional treatment group: 97% versus 84% (6 months), 93% versus 82% (1 year), and 83% versus 59% (5 years). CONCLUSIONS: Our findings support that vacuum-assisted closure therapy is a safe and reliable option in poststernotomy mediastinitis with excellent survival and a very low failure rate compared with conventional treatment.

Aged↗
PubMed2005

The impact of vacuum-assisted closure on long-term survival after post-sternotomy mediastinitis.

BACKGROUND: Post-sternotomy mediastinitis after coronary artery bypass grafting is reported to be a strong predictor for poor late survival when using conventional wound-healing therapies. The aim of this study was to compare the long-term survival after vacuum-assisted closure treated mediastinitis following coronary artery bypass grafting with that of patients without mediastinitis. Another objective was to identify risk factors for developing mediastinitis. METHODS: Forty-six patients were treated for mediastinitis, with vacuum-assisted closure but without additional tissue flaps, after isolated coronary bypass grafting between January 1999 and September 2004. During this period, 4,781 patients underwent isolated coronary bypass grafting without mediastinitis. Actuarial survival was compared with the log-rank test. Univariate and multivariate analysis were used to identify risk factors for mediastinitis. RESULTS: There was no difference in early or late survival between the mediastinitis group treated with vacuum-assisted closure and the control group (p = not significant). The survival at 1, 3, and 5 years was 92.9% +/- 4.0%, 89.2% +/- 5.2%, and 89.2% +/- 5.2%, respectively, in the vacuum-assisted closure group; and 96.5% +/- 0.3%, 92.1% +/- 0.5%, and 86.9% +/- 0.8%, respectively, in the control group. Diabetes mellitus, low left ventricular ejection fraction, obesity, renal failure, and three-vessel disease were identified as risk factors for developing mediastinitis. CONCLUSIONS: This study suggests that patients with vacuum-assisted closure treated mediastinitis may have similar long-term survival as patients without mediastinitis after coronary artery bypass grafting. The independent risk factors identified were similar to those found in previous studies. Our data support that vacuum-assisted closure therapy minimizes the negative effects of mediastinitis on late survival after coronary artery bypass grafting.

Aged↗
PubMed2004

Trapping of microparticles in the near field of an ultrasonic transducer.

We are investigating means of handling microparticles in microfluidic systems, in particular localized acoustic trapping of microparticles in a flow-through device. Standing ultrasonic waves were generated across a microfluidic channel by ultrasonic microtransducers integrated in one of the channel walls. Particles in a fluid passing a transducer were drawn to pressure minima in the acoustic field, thereby being trapped and confined at the lateral position of the transducer. The spatial distribution of trapped particles was evaluated and compared with calculated acoustic intensity distributions. The particle trapping was found to be strongly affected by near field pressure variations due to diffraction effects associated with the finite sized transducer element. Since laterally confining radiation forces are proportional to gradients in the acoustic energy density, these near field pressure variations may be used to get strong trapping forces, thus increasing the lateral trapping efficiency of the device. In the experiments, particles were successfully trapped in linear fluid flow rates up to 1mm/s. It is anticipated that acoustic trapping using integrated transducers can be exploited in miniaturised total chemical analysis systems (microTAS), where e.g. microbeads with immobilised antibodies can be trapped in arrays and subjected to minute amounts of sample followed by a reaction, detected using fluorescence.

Journal Article↗
PubMed2004

High-energy in-fiber pulse amplification for coherent lidar applications.

An Er:Yb codoped fiber amplifier chain for the generation of pulses for coherent lidar applications at a wavelength near 1.5 microm is reported. The final 1.8-m-long power amplification stage had a 50-microm core diameter and yielded a 23-dB energy gain, resulting in 0.29-mJ, 100-ns pulses at a repetition rate of 4 kHz with no Brillouin scattering and an M2 of 2.1.

Journal Article↗
PubMed2004

Autonomous protein sample processing on-chip using solid-phase microextraction, capillary force pumping, and microdispensing.

A capillary force filling microsystem consisting of a chip-integrated solid-phase microextraction (SMEC) array and a microdispenser for sample purification and trace enrichment of peptides is described. The microextraction array was loaded with solid-phase media (50 microm Poros R2 beads) for purification and enrichment of proteomic samples. Samples bound to the SMEC were eluted in a volume of 200 nL. A piezo-electric microdispenser was docked to the array and the samples bound to the SMEC were eluted in a volume of 200 nL using capillary forces. The purified and enriched samples were dispensed onto the matrix-assisted laser desorption/ionization (MALDI) target, providing quality data from samples in the picomolar range. The nanoproteomic platform was compared to corresponding commercial preparation protocols, showing higher mass spectrometry (MS) signal intensities for peptides generated from an alpha-casein digest. The platform was also evaluated with regards to two-dimensional (2-D) gel-derived protein digests from both fibroblast and epithelial target cells.

Electrophoresis, Gel, Two-Dimensional↗
PubMed2004

New directions of miniaturization within the biomarker research area.

An overview of the current trends within protein expression profiling is given where multidimensional separation of both gel and liquid phase techniques linked to mass spectrometry is viewed as a major route in the global proteome mapping. A clear trend in these biochemical developments is the effort to sequence and identify low-abundant protein expressions where assay miniaturization and integrated sample processing play a central role. Two areas of miniaturization within the proteomics field are addressed: (i) sample cleanup and enrichment, and (ii) silicon microstructure developments for protein chip microarrays.

Animals↗
PubMed2004

Early mortality in coronary bypass surgery: the EuroSCORE versus The Society of Thoracic Surgeons risk algorithm.

BACKGROUND: We compare two widely used risk algorithms for coronary bypass surgery: The European System for Cardiac Operative Risk Evaluation (EuroSCORE) and The Society of Thoracic Surgeons (STS) risk stratification algorithm. METHODS: Risk factors for all adult patients undergoing heart surgery at the University Hospital of Lund between 1996 and 2001 were collected prospectively at preoperative admission. Predictive accuracy for 30-day mortality was assessed by comparing the observed and the expected mortality for equal-sized quintiles of risk by using the Hosmer-Lemeshow goodness-of-fit test. The discriminatory power was evaluated by calculating the areas under receiver operating characteristics (ROC) curves. RESULTS: The study included 4497 coronary artery bypass-only operations. The average age was 66.4 +/- 9.3 years (range 31 to 90 years). Most patients were men (77.0% versus 23.0%). The actual 30-day mortality was 1.89%. The Hosmer-Lemeshow goodness-of-fit test gave a p value of 0.81 (EuroSCORE) and 0.83 (STS), which indicates a good accuracy of both models. The area under the ROC curve was 0.84 (95% confidence interval [CI] 0.80 to 0.88) for EuroSCORE and 0.71 (95% CI 0.66 to 0.77) for STS. The discriminatory power (area under the ROC curve) was significantly larger for EuroSCORE compared with STS (p < 0.00005). CONCLUSIONS: In this large, single institution study the additive EuroSCORE algorithm had a significantly better discriminatory power to predict 30-day mortality than the STS risk algorithm for patients undergoing coronary artery bypass.

Adult↗
PubMed2004

EuroSCORE predicts intensive care unit stay and costs of open heart surgery.

BACKGROUND: This study aimed to determine whether the preoperative risk stratification model EuroSCORE predicts the different components of resource utilization in open heart surgery. METHODS: Data for all adult patients undergoing heart surgery at the University Hospital of Lund, Sweden, between 1999 and 2002 were prospectively collected. Costs were calculated for the surgery and intensive care and ward stay for each patient (excluding transplant cases and patients who died intraoperatively). Regression analysis was applied to evaluate the correlation between EuroSCORE and costs. The predictive accuracy for prolonged postoperative intensive care unit (ICU) stay was assessed by the Hosmer-Lemeshow goodness-of-fit test. The discriminatory power was evaluated by calculating the areas under receiver operating characteristics curves. RESULTS: The study included 3,404 patients. The mean cost for the surgery was 7,300 dollars, in the ICU 3,746 dollars, and in the ward 3,500 dollars. Total cost was significantly correlated with EuroSCORE, with a correlation coefficient of 0.47 (p < 0.0001); the correlation coefficient was 0.31 for the surgery cost, 0.46 for the ICU cost, and 0.11 for the ward cost. The Hosmer-Lemeshow p value for EuroSCORE prediction of more than 2 days' stay in the ICU was 0.40, indicating good accuracy. The area under the receiver operating characteristics curve was 0.78. The probability of an ICU stay exceeding 2 days was more than 50% at a EuroSCORE of 14 or more. CONCLUSIONS: In this single-institution study, the additive EuroSCORE algorithm could be used to predict ICU cost and also an ICU stay of more than 2 days after open heart surgery.

Aged↗
PubMed2004

Experimentally based topology models for E. coli inner membrane proteins.

Membrane protein topology predictions can be markedly improved by the inclusion of even very limited experimental information. We have recently introduced an approach for the production of reliable topology models based on a combination of experimental determination of the location (cytoplasmic or periplasmic) of a protein's C terminus and topology prediction. Here, we show that determination of the location of a protein's C terminus, rather than some internal loop, is the best strategy for large-scale topology mapping studies. We further report experimentally based topology models for 31 Escherichia coli inner membrane proteins, using methodology suitable for genome-scale studies.

Alkaline Phosphatase↗
PubMed2004

Modal power decomposition of beam intensity profiles into linearly polarized modes of multimode optical fibers.

We calculate the modal power distribution of a randomly and linearly polarized (LP) multimode beam inside a cylindrical fiber core from knowledge of spatial-intensity profiles of a beam emitted from the fiber. We provide an exact analysis with rigorous proofs that forms the basis for our calculations. The beam from the fiber end is collimated by a spherical lens with a specific focal length. The original LP-mode basis is transformed by the spherical lens and forms another orthogonal basis that describes the free-space beam. By using this basis, we calculate the modal power distribution from the mutual-intensity profile. This is acquired by adopting a well-known mutual-intensity-profile-retrieving technique based on measurements of the intensity patterns several times after two orthogonal cylindrical lenses with varying separation. The feasibility of our decomposition algorithm is demonstrated with simulations.

Journal Article↗
PubMed2003

On-line monitoring of airborne chemistry in levitated nanodroplets: in situ synthesis and application of SERS-active Ag-Sols for trace analysis by FT-Raman spectroscopy.

We report a new strategy for on-line monitoring of chemical reactions in ultrasonically levitated, nanoliter-sized droplets by Raman spectroscopy. A flow-through microdispenser connected to an automated flow injection system was used to dose picoliter droplets into the node of an ultrasonic trap. Taking advantage of the flow-through characteristics of the microdispenser and the versatility of the automated flow system, a well-defined sequence of reagents could be injected via the microdispenser into the levitated droplet placed in the focus of the collection optics of the Fourier transform Raman spectrometer. In that way, chemical reactions could be carried out and monitored on-line. The developed system was used for fast, reproducible, in situ synthesis of a highly active surface enhanced Raman scattering (SERS) sol resulting from the reduction of silver nitrate with hydroxylamine hydrochloride in basic conditions. With this chemical system, SERS substrate preparation could be achieved at room temperature and in short time. The in situ prepared silver sol was used for trace analysis of several organic test molecules that were injected into the levitated SERS-active droplet again using the microdispenser. The concentration dependence of the SERS spectra was studied using 9-aminoacridine, revealing that down to the femtogram region high-quality SERS spectra could be obtained. Additionally, SERS spectra of 6-mercaptopurine, thiamine, and acridine were recorded in the levitated drop as well.

Journal Article↗
PubMed2003

Screening of nucleation conditions using levitated drops for protein crystallization.

The growth of suitable protein crystals is an essential step in the structure determination of a protein by X-ray crystallography. At present, crystals are mostly grown using trial-and-error procedures, and protocols that rapidly screen for the crystal nucleation step are rare. Presented here is an approach to minimize the consumption of precious protein material while searching for the nucleation conditions. Acoustically levitated drops of known protein concentration (0.25-1.5-microL volumes) are injected with crystallizing agents using piezoelectric flow-through dispensers (ejecting 50-100-pL droplets at 1-9000 droplets/s). A restricted number of crystallizing agents representing three classes are used: poly(ethylene glycol), salts, and the viscous alcohol 2-methyl 2,4-pentanediol. From a digitized picture of the levitated drop volume, calculations are performed giving the concentrations of all components in the drop at any time during a "precipitation experiment". Supersaturation is the prerequisite for crystal nucleation, and protein precipitation indicates high supersaturation. A light source illuminates the levitated drop, and protein precipitation is monitored using right-angle light scattering. On the basis of these intensity measurements and the volume determination, precipitation diagrams for each crystallizing agent are constructed that give the protein/crystallizing agent concentration boundaries between the minimum and the maximum detectable protein precipitation. Guided by the concentration values obtained from such plots, when approaching the supersaturation region, separate crystallization drops are mixed and allowed to equilibrate under paraffin oil. At conditions in which microcrystals can be observed, the nucleation tendency of the macromolecule is confirmed. Optimization of crystallization conditions can then follow. Proteins tested include alcohol dehydrogenase and D-serine dehydratase. Alcohol dehydrogenase, known to crystallize easily, was used to evaluate whether the ultrasonic field inhibits nucleation. Details are given for the screening procedure of D-serine dehydratase, an enzyme earlier found to be difficult to crystallize reproducibly. The time and material-saving qualities of this method are emphasized, since a range of conditions can quickly be screened using small amounts of protein to roughly determine solubility characteristics of a protein before crystallization trials are initiated.

Alcohol Dehydrogenase↗
PubMed2003

New directions of miniaturization within the proteomics research area.

An overview of the current trends within protein expression profiling is given where multidimensional separation of both gel- and liquid-phase techniques linked to mass spectrometry is viewed as a major route in the global proteome mapping. A clear trend in these biochemical developments is the effort to sequence and identify low-abundant protein expressions where assay miniaturization and integrated sample processing plays a central role. Two areas of miniaturization within the proteomics field are addressed: (i) sample cleanup and enrichment, and (ii) silicon microstructure developments for protein chip microarrays.

Miniaturization↗