Electron cyclotron resonance ion source plasma chamber studies using a network analyzer as a loaded cavity probe.

A method and first results utilizing a network analyzer as a loaded cavity probe to study the resonance properties of a plasma filled electron cyclotron resonance ion source (ECRIS) plasma chamber are presented. The loaded cavity measurements have been performed using a dual port technique, in which two separate waveguides were used simultaneously. One port was used to ignite and sustain the plasma with a microwave source operating around 11 GHz and the other was used to probe the cavity properties with the network analyzer using a frequency range around 14 GHz. The first results obtained with the JYFL 14 GHz ECRIS demonstrate that the presence of plasma has significant effects on the resonance properties of the cavity. With plasma the frequency dependent behavior is strongly damped and this trend strengthens with increasing microwave power.

Increased incidence of Mycoplasma pneumoniae infection in Finland, 2010-2011.

The number of cases of Mycoplasma pneumoniae infection detected by laboratory-based surveillance increased in Finland in late 2010. During 2011, the number of cases was four times higher than during the previous epidemic in 2005. The 2011 epidemic affected mostly school-age children. The increased number of cases was probably not due to changes in laboratory procedures, but public interest may have had an effect, since the number of Google queries followed closely the epidemic curve.

Invited article: Electric solar wind sail: toward test missions.

The electric solar wind sail (E-sail) is a space propulsion concept that uses the natural solar wind dynamic pressure for producing spacecraft thrust. In its baseline form, the E-sail consists of a number of long, thin, conducting, and centrifugally stretched tethers, which are kept in a high positive potential by an onboard electron gun. The concept gains its efficiency from the fact that the effective sail area, i.e., the potential structure of the tethers, can be millions of times larger than the physical area of the thin tethers wires, which offsets the fact that the dynamic pressure of the solar wind is very weak. Indeed, according to the most recent published estimates, an E-sail of 1 N thrust and 100 kg mass could be built in the rather near future, providing a revolutionary level of propulsive performance (specific acceleration) for travel in the solar system. Here we give a review of the ongoing technical development work of the E-sail, covering tether construction, overall mechanical design alternatives, guidance and navigation strategies, and dynamical and orbital simulations.

Recurrent Sphingomonas paucimobilis -bacteraemia associated with a multi-bacterial water-borne epidemic among neutropenic patients.

A cluster of septicaemias due to several water-related species occurred in a haematological unit of a university hospital. In recurrent septicaemias of a leukaemic patient caused by Sphingomonas paucimobilis, genotyping of the blood isolates by use of random amplified polymorphic DNA-analysis verified the presence of two distinct S. paucimobilis strains during two of the separate episodes. A strain of S. paucimobilis identical to one of the patient's was isolated from tap water collected in the haematological unit. Thus S. paucimobilis present in blood cultures was directly linked to bacterial colonization of the hospital water system. Heterogeneous finger-printing patterns among the clinical and environmental isolates indicated the distribution of a variety of S. paucimobilis clones in the hospital environment. This link also explained the multi-microbial nature of the outbreak.

Nosocomial Legionella pneumophila serogroup 5 outbreak associated with persistent colonization of a hospital water system.

An outbreak of infections caused by Legionella pneumophila serogroup 5 was detected in a university hospital, and nosocomial reservoirs of the legionella epidemic were examined. Clinical isolates from two patients who had been affected by the L. pneumophila serogroup 5 outbreak, and from another patient with a legionella infection caused by the same serogroup 3 years later, were compared to L. pneumophila serogroup 5 isolates from the hospital water supply by two molecular methods, amplified fragment length polymorphism (AFLP) analysis and random amplified polymorphic DNA analysis (RAPD). Genotyping confirmed the epidemiological linkage of the first two patients, and linked their infections with the hospital water supply. The third clinical strain, which was also linked to the hospital water, was very similar to the epidemic strain. Even though the water distribution system was sanitized (superheat and flush sanitation), the epidemic strain was shown to be persisting in the hospital water outlets several years after its initial discovery.

Comparison of a new immunochromatographic rapid test with a commercial EIA for the detection of Puumala virus specific IgM antibodies.

BACKGROUND: Hantaviruses are associated with two human diseases: haemorrhagic fever with renal syndrome (HFRS) and Hantavirus pulmonary syndrome (HPS). Puumala virus (PUUV), which is one of the Hantaviruses, is a causative agent of nephropathia epidemica (NE), a mild form of HFRS. OBJECTIVE: a new 5 min rapid test, POC PUUMALA (Erilab Ltd, Finland), for detecting IgM antibodies to PUUV was evaluated and compared with the commercially available Hantavirus (Puumala) IgM ELISA test (Progen, Germany). Discrepant test results between the two tests were confirmed by a mu-capture reference EIA. STUDY DESIGN: Two hundred and thirty five serum samples, which had earlier been analyzed with the Progen IgM ELISA, were assayed with the POC PUUMALA rapid test. Five persons, without knowing the Progen IgM ELISA test results, interpreted independently the rapid test results. In addition, a panel of 48 serum samples was analyzed in parallel with the rapid test and the Progen IgM ELISA by one technician in daily routine diagnostics in a clinical microbiology laboratory. RESULTS: the agreement between the results of the five interpreters was 95%, and the congruence of the results between individual readers and commercial ELISA test varied from 93 to 96%. Diagnostic efficacy of the rapid test varied between 98 and 99% compared with 96% of the Progen IgM ELISA. The POC PUUMALA rapid test showed higher or similar sensitivity compared with the Progen IgM ELISA, whereas both the tests had similar levels of specificity. CONCLUSIONS: the analytical performance of the POC PUUMALA rapid test was found to be as good or even slightly better than the analytical performance of the Progen IgM ELISA. In addition, the rapid and straightforward procedure makes the POC PUUMALA a feasible tool for the diagnosis of the acute PUUV infection.

Low-resolution gas-phase FT-IR method for the determination of the limonene/carvone ratio in supercritical CO2-extracted caraway fruit oils.

A low-resolution gas-phase FT-IR method for the fast analysis of supercritical CO2-extracted caraway fruit oils has been developed. The limonene/carvone ratio of extraction product was determined within seconds, yielding a coefficient of variation of <5% (n = 10). A selection of experimental parameters is discussed on the basis of the analysis of 52 extracted samples. GC-FID was used as a reference method. A correlation of 0.983 (n = 24) between the two methods was observed. This method is suitable for the analysis of a large number of caraway fruit extracts due to its speed, repeatability, and minimum sample preparation.

PCR-based typing of Mycobacterium avium isolates in an epidemic among farmed lesser white-fronted geese (Anser erythropus).

Mycobacterium avium is an important veterinary pathogen causing avian tuberculosis in birds. The aim of the study was to evaluate the genetic relatedness in M. avium isolates from deep tissues of farmed lesser white-fronted geese with avian tuberculosis and in samples from the farm environment. The strains were analyzed by two PCR-based typing methods, inverted repeat (IR) typing and random amplified polymorphic DNA (RAPD) analysis. The primers for the inverted repeats of the insertion sequences IS1245 and IS1311 were used in IR typing, and the RAPD analysis was performed with six primers. Seven of the nine avian strains yielded an identical pattern in the IR typing, but they could be divided into two groups in the RAPD analysis. The remaining two bird isolates had an identical IR pattern (IR cluster II) which they shared with two environmental isolates. However, the RAPD analysis revealed that these environmental isolates had a RAPD pattern (RAPD cluster VI) distinct and different from either of the bird isolates (RAPD clusters II and IV). In all, four M. avium strains were verified as being inducers of avian tuberculosis in birds, and all were distinct from the three environmental strains identified. Thus, the results did not confirm the preliminary idea that a single strain had caused the epidemic. The polymorphism among M. avium strains highlighted the great biodiversity among an M. avium population even in a limited environmental setting during a short time span, and indicated the high susceptibility to avian tuberculosis of lesser white-fronted geese.

Process control of apple winemaking by low-resolution gas-phase Fourier-transform infrared spectroscopy.

Four apple wine fermentation processes have been observed by means of direct-inlet gas-phase FTIR spectroscopy. The apple juice concentrates were each fermented by two species of Saccharomyces cerevisiae starters, and the experiment was repeated. The development of the concentrations of 1-propanol, 4-methylpyridine, acetaldehyde, acetic acid, and ethyl acetate was monitored. Two different sampling methods were used--static headspace and direct injection of the must. The performance of the FTIR method is limited by the high ethanol concentration. It can be mathematically proven that the amount of sample can be selected so that any distortion due to ethanol is minimized. Headspace GC-MS was used for preliminary compound identification.

Detection and correction of instrumental line-shape distortions in fourier spectroscopy.

The detection and the correction of instrumental line-shape distortions have been studied. Some common distortion principles have been mathematically examined. A procedure for error correction is presented. In addition to a theoretical study, we also investigated simulated and experimental examples. An application for the procedure is presented.

Hospital water supply as a source of disseminated Mycobacterium fortuitum infection in a leukemia patient.

Nosocomial acquisition of Mycobacterium fortuitum led to a disseminated infection in a leukemia patient. A linkage to showerhead water was supported by molecular typing of clinical and environmental isolates. Contamination of the hospital water system with microbes that are relatively resistant to common sanitation processes poses an increased risk of infection to neutropenic patients.

Mutant derivatives of the main respiratory allergen of cow are less allergenic than the intact molecule.

BACKGROUND: Allergen immunotherapy offers an alternative for drug treatment in the management of allergic diseases. Because immunotherapy often induces side-effects, less allergenic preparations would be beneficial. OBJECTIVE: The purpose of this study was to examine whether the allergenicity of a cow-derived lipocalin allergen, Bos d 2, could be diminished by substituting or deleting carboxy-terminal amino acids including the cysteine which forms a disulphide bond with a cysteine inside the molecule. METHODS: Four recombinant mutants of Bos d 2 were created by substituting or deleting the four most carboxy-terminal amino acids. The immunological characteristics of the mutant preparations were compared with the unmodified rBos d 2 by Western blotting, ELISA inhibition, skin prick tests, and the proliferative responses of allergen-specific T-cell clones. RESULTS: In Western blot, one of the two monoclonal antibodies showed reduced binding to the preparations without the terminal cysteine. In contrast, the other monoclonal antibody, human IgE and rabbit immune serum bound equally well to all the preparations. ELISA inhibition analyses revealed, however, that the preparations without the terminal cysteine bound antibody less efficiently. They were needed 15-38 times more than the unmodified rBos d 2 to cause the same level of inhibition. Surprisingly, one of the mutants with the terminal cysteine but a mutated adjacent amino acid turned out to be the weakest in inducing skin reactivity. All the preparations stimulated well allergen-specific T-cell clones. CONCLUSIONS: The results show that the allergenicity of a lipocalin allergen, Bos d 2, can be diminished by modifying the carboxy-terminal end of the molecule. Modifications in the area which encompasses a disulphide bond impaired the antibody binding without affecting the T-cell stimulatory capacity. It was also shown that in vivo tests are necessary for determining the allergenicity of a modified allergen.

Mycobacterium malmoense-specific nested PCR based on a conserved sequence detected in random amplified polymorphic DNA fingerprints.

Mycobacterium malmoense is an opportunistic human pathogen of increasing clinical importance. Since it is difficult to detect and identify the organism by conventional techniques, it was decided to seek a nucleic acid amplification method specific for M. malmoense. The method was based on detection of a conserved band in random amplified polymorphic DNA (RAPD) fingerprints of 45 M. malmoense strains. This band was a 1,046-bp product which was proven to be M. malmoense specific in dot blot hybridization analysis with a panel of mycobacterial strains belonging to 39 other species. The fragment was sequenced, and oligonucleotide primers were synthesized to evaluate the specificity of the PCR. Two primer pairs were found to be specific and sensitive in the nested PCR that was developed. All 49 M. malmoense strains analyzed produced a PCR product of the expected size. In contrast, no strains belonging to the other mycobacterial species tested produced amplicons with these primers under specified reaction conditions. The results of the electrophoresis were confirmed by the hybridization with the M. malmoense-specific oligonucleotide probe. This method could be applied to the analysis of clinical or environmental samples, permitting the rapid detection of M. malmoense.

T cell epitopes of a lipocalin allergen colocalize with the conserved regions of the molecule.

In this study we characterized the human T cell-reactive sites of the major cow dander allergen, Bos d 2, a member of the lipocalin protein family. We showed that Bos d 2 contains only a limited number of epitopes. This is in contrast to many other allergens, which usually contain multiple T cell epitopes throughout the molecule. The epitopes of Bos d 2 were primarily concentrated in the conserved regions of the molecule. One of the epitopes was recognized by all the cow-asthmatic individuals regardless of their HLA phenotype. Computer-predicted T cell epitopes on Bos d 2, other lipocalin allergens, and human endogenous lipocalins were situated in similar locations on these molecules and corresponded to experimentally identified epitopes on Bos d 2. The results suggest that human endogenous lipocalins could be involved in the modulation of immune responses against exogenous lipocalin allergens. In addition, our findings are likely to facilitate the development of new forms of immunotherapy against allergies induced by the important group of lipocalin allergens.

Probing the molecular basis of allergy. three-dimensional structure of the bovine lipocalin allergen Bos d 2.

The three-dimensional structure of the major bovine allergen Bos d 2 has been determined by using x-ray diffraction at 1.8-A resolution. Structurally Bos d 2 is a member of the lipocalin family comprising proteins with transport functions. There is a flat small cavity inside the Bos d 2 protein core suitable for ligand binding, and it is possible that Glu115 and Asn37 inside the core are able to make hydrogen bonds with the ligand. Many allergens from different animals belong to the lipocalin family. The amino acid residue similarities between these lipocalins indicate putative regions for IgE binding. Comparison with the available allergen structures from other sources suggests that these allergens are roughly the same size and that their shape is more spherical than elliptical.

Molecular and crystal properties of Bos d 2, an allergenic protein of the lipocalin family.

The relationship between the molecular structure of allergenic proteins and the allergenic determinants is one of the central issues in allergology. We report here that the natural preparation of Bos d 2, a mammalian lipocalin allergen, comprises three molecular variant proteins of 17,829, 17,781, and 17,800 Da. When cDNA of Bos d 2 (Genome Sequence Data Base No. L42867) was recloned and expressed in Pichia pastoris, two proteins were produced. One of the proteins (17,831 Da) and the proteins in the natural preparation had pyroglutamate as the N-terminal residue; in the other (17,849 Da) the N-terminal residue was glutamine. Recombinant Bos d 2 protein was crystallized and the native data set was collected at 1.8 A resolution.

Random amplified polymorphic DNA (RAPD) analysis of Escherichia coli strains: comparison of urinary and concomitant blood isolates of urosepsis patients.

The discriminatory power of random amplified polymorphic DNA (RAPD) analysis was assessed for detection of intraspecies variation in Escherichia coli strains of clinical origin. Three primers (OPF 5, OPF 7 and OPF 8) were preselected from commercial 10-mer primers by the number of distinct bands obtained. These primers were used in testing 26 urinary and 13 blood isolates from 26 patients and E. coli ATCC 25922, OPF 5, OPF 7 or OPF 8 alone separated the strains into 15 to 21 RAPD types. A combination of the results of the three primers gave 25 RAPD types. When blood and urine isolates of each patient were analysed in parallel, all blood-urine pairs were found identical, and with one exception they were also unique. RAPD analysis had a high discriminatory power. It separated the strains equally well or better than ribotyping, and obviously better than serotyping which grouped the urine strains into 8 serogroups leaving 18 strains untypable or incompletely typed. Thus, to verify the identity or non-identity of isolated E. coli strains, RAPD analysis was shown to be a sensitive and reproducible technique which is technically less demanding, more rapid and more economical than either serotyping or ribotyping. However, in its present application, this technique cannot fully replace determination of the serotype or virulence factors which may show correlations with different manifestations of infection.

Human papillomavirus in vulvar and vaginal carcinoma cell lines.

A number of reports associate human papillomavirus (HPV) with cervical cancer and cancer cell lines derived from this tumour type. Considerably fewer reports have focused on the role of HPV in carcinomas from other sites of female anogenital squamous epithelia. In this study we have tested for the presence of HPV in eight low-passage vulvar carcinoma cell lines and one extensively passaged cell line, A431. One cell line from a primary vaginal carcinoma was included. The presence of the HPV was evaluated by the polymerase chain reaction (PCR), by Southern blot analysis and by two-dimensional gel electrophoresis. General primer-mediated PCR was applied by using primers from the L1 region, E1 region and HPV 16 E7 region. Southern blot hybridisation was performed under low-stringency conditions (Tm = -35 degrees C) using a whole genomic HPV 6/16/18 probe mixture and under high stringency conditions (Tm = -18 degrees C) with the whole genomic probes of HPV 16 and 33. HPV 16 E6-E7 mRNA was assessed by ribonuclease protection assay (RPA). HPV was found in only one vulvar carcinoma cell line, UM-SCV-6. The identified type, HPV 16, was integrated in the cell genome and could be amplified with all primers used. Also E6-E7 transcripts were found in these cells. Five original tumour biopsies were available from the HPV-negative cell lines for in situ hybridisation. All these were HPV negative with both the HPV 6/16/18 screening probe mixture under low stringency and the HPV 16 probe under high stringency. The results indicate that vulvar carcinoma cell lines contain HPV less frequently than cervical carcinoma cell lines and suggest that a significant proportion of vulvar carcinomas may evolve by an HPV-independent mechanism.

Isolation of potentially pathogenic mycobacteria in the Finnish environment.

Atypical mycobacteria have become more common in clinical samples, and their reservoirs, known to be in the environment, are poorly identified. In the Finnish natural environment, mycobacteria can be cultivated from surface waters in a mean of 1500 CFU/l and from soil samples in a mean of 3.6 x 10(5) CFU/g dry weight. The majority of isolates are not pathogenic to man. Less than 10% of cultivable mycobacteria belong in species which are also found in human samples, either as infectious agents or as harmless colonizers of human epithelia. The two most important potentially pathogenic atypical mycobacteria in Finland, the Mycobacterium avium-intracellulare-scrofulaceum (MAIS) complex and M. malmoense, were detected in 40% and 4%, respectively, of the examined waters.