Mid-infrared supercontinuum-based Fourier transform spectroscopy for plasma analysis.

Broadband mid-infrared (MIR) spectroscopy is a well-established and valuable diagnostic technique for reactive plasmas. Plasmas are complex systems and consist of numerous (reactive) types of molecules; it is challenging to measure and control reaction specificity with a good sensitivity. Here, we demonstrate the first use of a novel MIR supercontinuum (SC) source for quantitative plasma spectroscopy. The SC source has a wide spectral coverage of 1300-2700 cm-1 (wavelength range 3.7-7.7 µm), thus enabling broadband multispecies detection. The high spatial coherence of the MIR SC source provides long interaction path lengths, thereby increasing the sensitivity for molecular species. The combination of such a SC source with a custom-built FTIR spectrometer (0.1 cm-1 spectral resolution) allows detection of various gases with high spectral resolution. We demonstrate its potential in plasma applications by accurate identification and quantification of a variety of reaction products (e.g. nitrogen oxides and carbon oxides) under low-pressure conditions, including the molecular species with overlapping absorbance features (e.g. acetone, acetaldehyde, formaldehyde, etc.).

Mid-infrared dual-comb spectroscopy with absolute frequency calibration using a passive optical reference.

We demonstrate an absolute-frequency-calibrated mid-infrared dual-comb spectrometer by using a reference absorption cell. The source is based on a singly-resonant OPO containing two MgO:PPLN crystals in a common ring cavity, synchronously pumped by two mode-locked Yb-fiber lasers. The repetition-rate of the two pumps are stabilized while their offset frequencies and the OPO cavity length are not actively controlled. The reference spectrum is used to correct the frequency fluctuations in the sample spectrum providing a high-quality averaged spectrum with spectral resolution of 6 GHz and calibration precision of 120 MHz, without adding any complexity to the experimental setup or signal processing.

Detection of Staphylococcus aureus in cystic fibrosis patients using breath VOC profiles.

Staphylococcus aureus (S. aureus) is a common bacterium infecting children with cystic fibrosis (CF). Since current detection methods are difficult to perform in children, there is need for an alternative. This proof of concept study investigates whether breath profiles can discriminate between S. aureus infected and non-infected CF patients based on volatile organic compounds (VOCs). We collected exhaled breath of CF patients with and without S. aureus airways infections in which VOCs were identified using gas chromatography-mass spectrometry. We classified these VOC profiles with sparse partial least squares discriminant analysis. Multivariate breath VOC profiles discriminated infected from non-infected CF patients with high sensitivity (100%) and specificity (80%). We identified the nine compounds most important for this discrimination. We successfully detected S. aureus infection in CF patients, using breath VOC profiles. Nine highlighted compounds can be used as a focus point in further biomarker identification research. The results show considerable potential for non-invasive diagnosis of airway infections.

Identification of Pseudomonas aeruginosa and Aspergillus fumigatus mono- and co-cultures based on volatile biomarker combinations.

Volatile organic compound (VOC) analysis in exhaled breath is proposed as a non-invasive method to detect respiratory infections in cystic fibrosis patients. Since polymicrobial infections are common, we assessed whether we could distinguish Pseudomonas aeruginosa and Aspergillus fumigatus mono- and co-cultures using the VOC emissions. We took headspace samples of P. aeruginosa, A. fumigatus and co-cultures at 16, 24 and 48 h after inoculation, in which VOCs were identified by thermal desorption combined with gas chromatography - mass spectrometry. Using multivariate analysis by Partial Least Squares Discriminant Analysis we found distinct VOC biomarker combinations for mono- and co-cultures at each sampling time point, showing that there is an interaction between the two pathogens, with P. aeruginosa dominating the co-culture at 48 h. Furthermore, time-independent VOC biomarker combinations were also obtained to predict correct identification of P. aeruginosa and A. fumigatus in mono-culture and in co-culture. This study shows that the VOC combinations in P. aeruginosa and A. fumigatus co-microbial environment are different from those released by these pathogens in mono-culture. Using advanced data analysis techniques such as PLS-DA, time-independent pathogen specific biomarker combinations can be generated that may help to detect mixed respiratory infections in exhaled breath of cystic fibrosis patients.

Extended nitric oxide analysis may improve personalized anti-inflammatory treatment in asthmatic children with intermediate F(E)NO50.

Exhaled nitric oxide (F(E)NO) is elevated in asthma, and a clinical practice guideline has been published with recommendations for anti-inflammatory treatment. It summarizes that a F(E)NO at an expiratory flow rate of 50 ml s(-1) (F(E)NO50) above 35 ppb in children indicates eosinophilic inflammation, and the most likely response is to use inhaled corticosteroids. Intermediate F(E)NO50 between 20-35 ppb should be interpreted cautiously. The aim of the study was to investigate this guideline in a small group of asthmatic children. Thirty-seven asthmatic children; 23 boys and 14 girls, visited the outpatient clinic, and provided exhaled breath samples for offline NO measurement. These samples were analysed with chemiluminescence techniques. Three flow rates, namely 16, 90 and 230 ml s(-1) were used for the extended NO analysis (Högman-Meriläinen algorithm, HMA) to estimate the alveolar concentration (C(A)NO), diffusion rate of the airway wall (D(aw)NO) and airway wall content (C(aw)NO). For accuracy of the HMA, the estimated value of F(E)NO at 50 ml s(-1) (F(E)NO50) was compared with measured F(E)NO50. In nine children the difference was more than 5 ppb and the data were therefore excluded. Five children with F(E)NO50 <20 ppb had no known allergy and their F(E)NO50 geometrical mean (25th; 75th percentile) was 11 (10;14) and CawNO was 32 (20;43) ppb. Ten children with F(E)NO50 > 35 ppb had an allergy and had F(E)NO50 of 56 (47;60) ppb and C(aw)NO of 140 (121;172) ppb. Thirteen children with allergies, with intermediate F(E)NO50, had F(E)NO50 of 27 (25;30) ppb with a wide range of C(aw)NO. In five of these children, values were comparable to healthy children, 44 (43;50) ppb while eight children had elevated C(aw)NO values of 108 (95;129) ppb. Our data indicate the clinical potential use of extended NO analysis to determine the personal target value of F(E)NO50 for monitoring the treatment outcome. Furthermore, for children with intermediate F(E)NO50 more than half of them could possibly benefit from an adjustment of inhaled corticosteroids if the C(aw)NO value was considered.

Broadly, independent-tunable, dual-wavelength mid-infrared ultrafast optical parametric oscillator.

We demonstrate a two-crystal mid-infrared dual-wavelength optical parametric oscillator, synchronously pumped by a high power femtosecond Yb:fiber laser. The singly-resonant ring cavity, containing two periodically poled lithium niobate crystals, is capable of generating two synchronized idler wavelengths, independently tunable over 30 THz in the 2.9 - 4.2 µm wavelength region, due to the cascaded quadratic nonlinear effect. The independent tunability of the two idlers makes the optical parametric oscillator a promising source for ultrafast pulse generation towards the THz wavelength region, based on different frequency generation. In addition, the observed frequency doubled idler within the crystal indicates the possibility to realize a broadband optical self-phase locking between pump, signal, idler and higher order generated parametric lights.

External cavity diode laser-based detection of trace gases with NICE-OHMS using current modulation.

We combine an external cavity diode laser with noise-immune cavity-enhanced optical heterodyne molecular spectroscopy (NICE-OHMS) using current modulation. With a finesse of 1600, we demonstrate noise equivalent absorption sensitivities of 4.1 x 10(-10) cm(-1) Hz(-1/2), resulting in sub-ppbv detection limits for Doppler-broadened transitions of CH(4) at 6132.3 cm(-1), C(2)H(2) at 6578.5 cm(-1) and HCN at 6541.7 cm(-1). The system is used for hydrogen cyanide detection from sweet almonds.

Sensitivity enhancement in off-axis integrated cavity output spectroscopy.

We report on a detailed model of an improved three mirror off-axis integrated cavity output spectroscopy (OA-ICOS) setup, which re-injects the light reflected by the optical cavity. The model simulates the impact of design parameters on instrument sensitivity and can be used for any off-axis configuration. We demonstrate the application of this model for the real-time detection of ethylene with a pulsed quantum cascade laser (QCL). The three mirror OA-ICOS scheme provides a 10 times increase in signal-to-noise ratio as compared to standard OA-ICOS, resulting in a noise equivalent absorption sensitivity of 1.5 x 10(-8) cm(-1) Hz(-1/2).

Pulmonary infection, and not systemic inflammation, accounts for increased concentrations of exhaled nitric oxide in patients with septic shock.

Nitric oxide (NO) is a key mediator in the pathophysiology of septic shock that can be measured in exhaled breath. To assess whether a pulmonary infection itself or systemic inflammation is responsible for NO production, we determined exhaled NO in ventilated patients with respiratory and non-respiratory septic shock and compared it with the concentration in ventilated intensive care patients without systemic inflammation. In addition, the change of NO production over time and correlations with haemodynamic instability were evaluated. The controls without systemic inflammation, as witnessed by the absence of systemic inflammatory response syndrome criteria and low levels of interleukin-6, had similar concentrations of NO as the patients with non-respiratory septic shock. The respiratory sepsis patients exhaled more NO than the non-respiratory sepsis patients (p = 0.05), and a time dependent decline in time in both groups (p = 0.04). Exhaled NO did not correlate with markers of disease severity, systemic inflammation and haemodynamic instability. These data indicate that the infected lungs are the source of exhaled NO.

Methods of NO detection in exhaled breath.

There is still an unexplored potential for exhaled nitric oxide (NO) in many clinical applications. This study presents an overview of the currently available methods for monitoring NO in exhaled breath and the use of the modelling of NO production and transport in the lung in clinical practice. Three technologies are described, namely chemiluminescence, electrochemical sensing and laser-based detection with their advantages and limitations. Comparisons are made in terms of sensitivity, time response, size, costs and suitability for clinical purposes. The importance of the flow rate for NO sampling is discussed from the perspective of the recent recommendations for standardized procedures for online and offline NO measurement. The measurement of NO at one flow rate, such as 50 ml s(-1), can neither determine the alveolar site/peripheral contribution nor quantify the difference in NO diffusion from the airways walls. The use of NO modelling (linear or non-linear approach) can solve this problem and provide useful information about the source of NO. This is of great value in diagnostic procedures of respiratory diseases and in treatment with anti-inflammatory drugs.

ABA-deficiency results in reduced plant and fruit size in tomato.

Abscisic acid (ABA) deficient mutants, such as notabilis and flacca, have helped elucidating the role of ABA during plant development and stress responses in tomato (Solanum lycopersicum L.). However, these mutants have only moderately decreased ABA levels. Here we report on plant and fruit development in the more strongly ABA-deficient notabilis/flacca (not/flc) double mutant. We observed that plant growth, leaf-surface area, drought-induced wilting and ABA-related gene expression in the different genotypes were strongly correlated with the ABA levels and thus most strongly affected in the not/flc double mutants. These mutants also had reduced fruit size that was caused by an overall smaller cell size. Lower ABA levels in fruits did not correlate with changes in auxin levels, but were accompanied by higher ethylene evolution rates. This suggests that in a wild-type background ABA stimulates cell enlargement during tomato fruit growth via a negative effect on ethylene synthesis.

Potential biomarkers for identification of mycobacterial cultures by proton transfer reaction mass spectrometry analysis.

RATIONALE: Several mycobacterial species can produce serious infections in humans, and the treatment required depends on the infecting species. Fast identification, ideally with minimal manipulation of the infecting species, is therefore critical; here, we propose a method potentially allowing cultures to be identified by headspace analysis and use it to screen for differences between mycobacterial species based on the volatiles released during growth. METHODS: Short-chain volatile organic compound emissions from two non-tuberculosis slow growing mycobacterial species, Mycobacterium avium and Mycobacterium kansasii, and a non-pathogenic fast growing species, Mycobacterium smegmatis, in Middlebrook M7H9 culturing media were followed online with a proton transfer reaction quadrupole mass spectrometer. RESULTS: Measurable differences between the headspace of the two slow growing mycobacteria M. kansasii and M. avium were found, as well as differences with respect to the faster growing mycobacteria M. smegmatis. Three compounds, attributed to sulfur-containing volatiles--dimethyl sulfide, propanethiol and dimethyl disulfide--were found to be specific to M. avium. CONCLUSIONS: Clear differences were detected in the low molecular weight volatile emissions compounds of the mycobacterial species under study, without the need for sample manipulation. Further studies with other mycobacterial species will reveal if the differences observed are specific to the species studied here. Furthermore, the use of an ion trap as a mass analyzer with the same ionization technique, allowing molecular detection over a wider molecular range, could allow the detection of additional biomarkers thus capturing a wider molecular range.

Stress responses of duckweed (Lemna minor L.) and water velvet (Azolla filiculoides Lam.) to anionic surfactant sodium-dodecyl-sulphate (SDS).

Surfactants are used for several purposes and recently they have attracted the attention for their ability to modify the behavior of other preexistent or co-disposed contaminants, although their use or discharge in wastewaters can represent a real or potential risk for the environment. Lemna minor L. and Azolla filiculoides Lam. are floating aquatic macrophytes, very effective in accumulating several pollutants including sodium dodecyl sulphate (SDS). In this work we evaluated the effects of SDS on these species by determining the stress ethylene production via laser-based trace gas detection, and the activities of enzymes involved in stress response, such as guaiacol peroxidase (G-POD), phenylalanine ammonia-lyase (PAL) and polyphenol-oxidase (PPO). Phenolics content was also determined. The macrophytes were treated with different concentrations of SDS for one week. SDS affected duckweed enzymatic activities and phenol content. While in the fern phenolics amount, PAL, G-POD and PPO activities were not affected by SDS except for 100 ppm SDS, the only concentration that was taken up and not completely degraded. Stress ethylene production was induced only in the fern treated with 50 and 100 ppm SDS.

Screening for emphysema via exhaled volatile organic compounds.

Chronic obstructive pulmonary disease (COPD)/emphysema risk groups are well defined and screening allows for early identification of disease. The capability of exhaled volatile organic compounds (VOCs) to detect emphysema, as found by computed tomography (CT) in current and former heavy smokers participating in a lung cancer screening trial, was investigated. CT scans, pulmonary function tests and breath sample collections were obtained from 204 subjects. Breath samples were analyzed with a proton-transfer reaction mass spectrometer (PTR-MS) to obtain VOC profiles listed as ions at various mass-to-charge ratios (m/z). Using bootstrapped stepwise forward logistic regression, we identified specific breath profiles as a potential tool for the diagnosis of emphysema, of airflow limitation or gas-exchange impairment. A marker for emphysema was found at m/z 87 (tentatively attributed to 2-methylbutanal). The area under the receiver operating characteristic curve (ROC) of this marker to diagnose emphysema was 0.588 (95% CI 0.453-0.662). Mass-to-charge ratios m/z 52 (most likely chloramine) and m/z 135 (alkyl benzene) were linked to obstructive disease and m/z 122 (most probably alkyl homologs) to an impaired diffusion capacity. ROC areas were 0.646 (95% CI 0.562-0.730) and 0.671 (95% CI 0.524-0.710), respectively. In the screening setting, exhaled VOCs measured by PTR-MS constitute weak markers for emphysema, pulmonary obstruction and impaired diffusion capacity.

Proton Transfer Reaction Mass Spectrometry detects rapid changes in volatile metabolite emission by Mycobacterium smegmatis after the addition of specific antimicrobial agents.

The metabolic activity of plants, animals or microbes can be monitored by gas headspace analysis. This can be achieved using Proton Transfer Reaction Mass Spectrometry (PTR-MS), a highly sensitive detection method for trace gas analysis. PTR-MS is rapid and can detect metabolic responses on-line as they occur. Here, we study the headspace of actively growing cultures of paired ciprofloxacin sensitive and resistant bacterial strains (Mycobacterium smegmatis in Middlebrook M7H9 liquid media) after the addition of the antibiotics ciprofloxacin and gentamicin in real time. Following the emission patterns of the mycobacteria over time allowed volatile markers specific for the bacterial response to each antibiotic to be detected. A proportion of the measured responses were very rapid, occurring within three hours after the addition of the compounds and varied between isolates with different resistance phenotypes. Specifically, we observed a two fold increase of m73 (unidentified C4 compound) within 10h after the addition of ciprofloxacin and a threefold increase of m45 (acetaldehyde) within 4h after the addition of gentamicin as compared to values before the addition. Monitoring the emission of specific volatiles into the culture headspace thus has the potential for rapid drug susceptibility testing. Moreover, these and other differences in the measured responses to the two tested compounds provide evidence that monitoring multiple compounds may also give an indication of the mechanism of action of the compound added.

An off-line breath sampling and analysis method suitable for large screening studies.

We present a new, off-line breath collection and analysis method, suitable for large screening studies. The breath collection system is based on the guidelines of the American Thoracic Society for the sampling of exhaled NO. Breath containing volatile gases is collected in custom-made black-layered Tedlar bags and analyzed by proton-transfer reaction mass spectrometry (PTR-MS). The collection method and data analysis is validated for its accuracy, precision, selectivity, limits of detection, sensitivity and reproducibility. Consecutive fillings of five bags by the same person gave reproducible results to within 12% relative standard deviation (RSD) for methanol, acetaldehyde, acetone and water content from breath, whereas isoprene was constant to within 30% RSD. In an exploratory small-scale case-control study, we monitor the exhaled breath of 11 lung cancer patients on the day before surgery. The control group consisted of 57 age-matched subjects, the so-called 'healthy smokers'. This study is used as an example of the use of the system presented here.

Real-time trace gas sensing of ethylene, propanal and acetaldehyde from human skin in vivo.

Trace gases emitted by human skin in vivo are monitored non-invasively and in real time using laser-based photoacoustic detection and proton-transfer reaction mass spectrometry. A small quartz cuvette is placed on the skin to create a headspace from which a carrier gas transports the skin emissions to the detection systems. The transparency of quartz to ultraviolet radiation (UVR) allows investigation of UVR-related trace gas emissions. As a demonstration of this measurement system, the effect of supplemental intake of systemic antioxidants on UVR-induced lipid peroxidation is investigated. The production by the skin of three biomarkers of UVR-induced lipid peroxidation (ethylene, acetaldehyde and propanal) is monitored. Although no significant effect of antioxidant intake was observed, the method presented here is a novel and promising technique for investigation of human skin in vivo.

Sub-part-per-billion monitoring of nitric oxide by use of wavelength modulation spectroscopy in combination with a thermoelectrically cooled, continuous-wave quantum cascade laser.

We used a thermoelectrically cooled, continuous-wave, quantum cascade laser operating between 1847 and 1854 cm(-1) in combination with wavelength modulation spectroscopy for the detection of nitric oxide (NO) at the sub-part-per-billion by volume (ppbv) level. The laser emission overlaps the P7.5 doublet of NO centered around 1850.18 cm(-1). Using an astigmatic multiple-pass absorption cell with an optical path length of 76 m, we achieved a detection limit of 0.2 ppbv at 10 kPa, with a total acquisition time of 30 s. The corresponding minimal detectable absorption is 8.8 x 10(-9) cm(-1) Hz(-1/2).

trans-Resveratrol and grape disease resistance. A dynamical study by high-resolution laser-based techniques.

Two modern laser-based techniques were synchronously applied to study the dynamics of the trans-resveratrol activity in Botrytis cinerea-infected grapes. Direct analysis of trans-resveratrol in both infected and noninfected grapes (Vitis vinifera, Aledo variety) was performed by using an analytical technique incorporating laser desorption coupled with laser resonant ionization and time-of-flight mass spectrometry. On the other hand, one of the most sensitive on-line methods for trace gas detection, laser photoacoustic spectroscopy, was used to investigate the involvement of the plant hormone ethylene (C(2)H(4)) in the B. cinerea grapes interaction and its temporal relationship with the trans-resveratrol content upon infection. The trans-resveratrol content and the ethylene released by noninfected grapes showed an opposite behavior. In this case, a high trans-resveratrol content corresponds to a low ethylene emission. For the B. cinerea-infected grapes, ethylene emission rises up after 48 h when the analogous content of trans-resveratrol started to decrease irreversibly. Moreover, the activity of trans-resveratrol as natural pesticide has been investigated by exogenous application on grapes. A short submerge (5 s) of the grapes in 1.6 x 10(-4) M solution of trans-resveratrol delays the increase of C(2)H(4) emission with about 48 h and produces a decrease of the C(2)H(4) concentration and its emission rate. The treatment has positive effects on fruit conservation during storage; it doubled the normal shelf-life of grapes at room temperature, maintaining their post-harvest quality within 10 d.

Molecular cloning and characterization of a transcription factor for the copia retrotransposon with homology to the BTB-containing lola neurogenic factor.

By transfection experiments, we previously identified a 72-bp enhancer sequence within the Drosophila copia retrotransposon which is involved in the control of the transcription level of this mobile element in cells in culture. Gel shift assays with nuclear extracts from Drosophila hydei-derived DH-33 cells further demonstrated specific interactions of at least two nuclear factors with this enhancer sequence. Using this sequence as a probe for the screening of an expression cDNA library that we constructed from DH-33 cells RNA, we have isolated a cDNA clone encoding a 110-kDa protein with features common to those of known transcription factors; these include a two-zinc-finger motif at the C terminus, three glutamine-rich domains in the presumptive activation domain of the protein, and an N-terminal domain which shares homology with the Bric-à-brac, Tramtrack, and Broad-Complex BTB boxes. The precise DNA recognition sequence for this transcription factor has been determined by both gel shift assays and footprinting experiments with a recombinant protein made in bacteria. The functionality of the cloned element was demonstrated upon transcriptional activation of copia reporter genes, as well as of a minimal promoter coupled with the identified target DNA sequence, in cotransfection assays in cells in culture with an expression vector for the cloned factor. Southern blot and nucleotide sequence analyses revealed a related gene in Drosophila melanogaster (the lola gene) previously identified by a genetic approach as involved in axon growth and guidance. Transfection assays in cells in culture with lola gene expression vectors and in situ hybridization experiments with lola gene mutants finally provided evidence that the copia retrotransposon is regulated by this neurogenic gene in D.melanogaster, with a repressor effect in the central nervous systems of the embryos.