Exhaled breath analysis: a review of ‘breath-taking’ methods for off-line analysis

Background

The potential of exhaled breath sampling and analysis has long attracted interest in the areas of medical diagnosis and disease monitoring. This interest is attributed to its non-invasive nature, access to an unlimited sample supply (i.e., breath), and the potential to facilitate a rapid at patient diagnosis. However, progress from laboratory setting to routine clinical practice has been slow. Different methodologies of breath sampling, and the consequent difficulty in comparing and combining data, are considered to be a major contributor to this. To fulfil the potential of breath analysis within clinical and pre-clinical medicine, standardisation of some approaches to breath sampling and analysis will be beneficial.

Objectives

The aim of this review is to investigate the heterogeneity of breath sampling methods by performing an in depth bibliometric search to identify the current state of art in the area. In addition, the review will discuss and critique various breath sampling methods for off-line breath analysis.

Methods

Literature search was carried out in databases MEDLINE, BIOSIS, EMBASE, INSPEC, COMPENDEX, PQSCITECH, and SCISEARCH using the STN platform which delivers peer-reviewed articles. Keywords searched for include breath, sampling, collection, pre-concentration, volatile. Forward and reverse search was then performed on initially included articles. The breath collection methodologies of all included articles was subsequently reviewed.

Results

Sampling methods differs between research groups, for example regarding the portion of breath being targeted. Definition of late expiratory breath varies between studies.

Conclusions

Breath analysis is an interdisciplinary field of study using clinical, analytical chemistry, data processing, and metabolomics expertise. A move towards standardisation in breath sampling is currently being promoted within the breath research community with a view to harmonising analysis and thereby increasing robustness and inter-laboratory comparisons.

     

Response analysis of the lumbar spine during regular daily activities—A finite element analysis

A non-linear poroelastic finite element model of the lumbar spine was developed to investigate spinal response during daily dynamic physiological activities. Swelling was simulated by imposing a boundary pore pressure of 0.25 MPa at all external surfaces. Partial saturation of the disc was introduced to circumvent the negative pressures otherwise computed upon unloading. The loading conditions represented a pre-conditioning full day followed by another day of loading: 8 h rest under a constant compressive load of 350 N, followed by 16 h loading phase under constant or cyclic compressive load varying in between 1000 and 1600 N. In addition, the effect of one or two short resting periods in the latter loading phase was studied.The model yielded fairly good agreement with in-vivo and in-vitro measurements. Taking the partial saturation of the disc into account, no negative pore pressures were generated during unloading and recovery phase. Recovery phase was faster than the loading period with equilibrium reached in only ～3 h. With time and during the day, the axial displacement, fluid loss, axial stress and disc radial strain increased whereas the pore pressure and disc collagen fiber strains decreased. The fluid pressurization and collagen fiber stiffening were noticeable early in the morning, which gave way to greater compression stresses and radial strains in the annulus bulk as time went by. The rest periods dampened foregoing differences between the early morning and late in the afternoon periods. The forgoing diurnal variations have profound effects on lumbar spine biomechanics and risk of injury.     

染色体分析法（chromosome analysis）

人们已经知道染色体的变化与癌症等疾病相关。作为一种视觉检测方法，FISH法受到人们的关注。将正常细胞和痛细胞的染色体进行比较的CGH法也在开发当中。本讲由东京医科齿科大学的稻泽让治教授进行讲解。[编者按]     

Quo vadis plant hormone analysis?

Plant hormones act as chemical messengers in the regulation of myriads of physiological processes that occur in plants. To date, nine groups of plant hormones have been identified and more will probably be discovered. Furthermore, members of each group may participate in the regulation of physiological responses in planta both alone and in concert with members of either the same group or other groups. The ideal way to study biochemical processes involving these signalling molecules is ‘hormone profiling’, i.e. quantification of not only the hormones themselves, but also their biosynthetic precursors and metabolites in plant tissues. However, this is highly challenging since trace amounts of all of these substances are present in highly complex plant matrices. Here, we review advances, current trends and future perspectives in the analysis of all currently known plant hormones and the associated problems of extracting them from plant tissues and separating them from the numerous potentially interfering compounds.     

Segregation analysis of α-L-fucosidase activity

Summary Complex segregation analysis of plasma -L-fucosidase in 45 British families provides evidence for an additive major gene causing low activities of fucosidase. There was no significant evidence of polygenic heritability or common family environment.     

Phosphorus in sediments — speciation and analysis

Characterization of sediment phosphorus is commonly based on sequential chemical extractions, in which phosphorus is supposed to be selectively removed from different compounds in the sediments. The first extraction schemes were designed to quantify discrete chemical or mineralogical compounds. As extraction schemes have been tested on different sediments, several systematic errors have been detected and the schemes have been modified and simplified accordingly. Other chemical extractions or treatments have attempted to determine phosphorus bound to particles with a certain strength or binding energy, the purpose being to determine the labile, loosely bound, exchangeable, mobile or algal-available fraction of sediment phosphorus. All extraction procedures yield operationally defined fractions and cannot be used for identification of discrete phosphorus compounds. The many methodological modifications make it necessary to be cautious when comparing results from the literature in this field.     

Non-covalent interactions – QTAIM and NBO analysis

MP2(full)/6-311++G(3df,3pd) calculations were carried out on complexes linked through various non-covalent Lewis acid – Lewis base interactions. These are: hydrogen bond, dihydrogen bond, hydride bond and halogen bond. The quantum theory of ´atoms in molecules´ (QTAIM) as well as the natural bond orbitals (NBO) method were applied to analyze properties of these interactions. It was found that for the A-H…B hydrogen bond as well as for the A-X…B halogen bond (X designates halogen) the complex formation leads to the increase of s-character in the A-atom hybrid orbital aimed toward the H or X atom. In opposite, for the A…H-B hydride bond, where the H-atom possesses negative charge, the decrease of s-character in the B-atom orbital is observed. All these changes connected with the redistribution of the electron charge being the effect of the complex formation are in line with Bent´s rule. The numerous correlations between energetic, geometrical, NBO and QTAIM parameters were also found.

Two approaches for metabolic pathway analysis?

Metabolic pathway analysis is becoming increasingly important for assessing inherent network properties in (reconstructed) biochemical reaction networks. Of the two most promising concepts for pathway analysis, one relies on elementary flux modes and the other on extreme pathways. These concepts are closely related because extreme pathways are a subset of elementary modes. Here, the common features, differences and applicability of these concepts are discussed. Assessing metabolic systems by the set of extreme pathways can, in general, give misleading results owing to the exclusion of possibly important routes. However, in certain network topologies, the sets of elementary modes and extreme pathways coincide. This is quite often the case in realistic applications. In our opinion, the unification of both approaches into one common framework for metabolic pathway analysis is necessary and achievable.     

Computational analysis of storage synthesis in developing Brassica napus L. (oilseed rape) embryos: flux variability analysis in relation to ¹³C metabolic flux analysis

Plant oils are an important renewable resource, and seed oil content is a key agronomical trait that is in part controlled by the metabolic processes within developing seeds. A large‐scale model of cellular metabolism in developing embryos of Brassica napus (bna572) was used to predict biomass formation and to analyze metabolic steady states by flux variability analysis under different physiological conditions. Predicted flux patterns are highly correlated with results from prior ¹³C metabolic flux analysis of B. napus developing embryos. Minor differences from the experimental results arose because bna572 always selected only one sugar and one nitrogen source from the available alternatives, and failed to predict the use of the oxidative pentose phosphate pathway. Flux variability, indicative of alternative optimal solutions, revealed alternative pathways that can provide pyruvate and NADPH to plastidic fatty acid synthesis. The nutritional values of different medium substrates were compared based on the overall carbon conversion efficiency (CCE) for the biosynthesis of biomass. Although bna572 has a functional nitrogen assimilation pathway via glutamate synthase, the simulations predict an unexpected role of glycine decarboxylase operating in the direction of NH₄⁺ assimilation. Analysis of the light‐dependent improvement of carbon economy predicted two metabolic phases. At very low light levels small reductions in CO₂ efflux can be attributed to enzymes of the tricarboxylic acid cycle (oxoglutarate dehydrogenase, isocitrate dehydrogenase) and glycine decarboxylase. At higher light levels relevant to the ¹³C flux studies, ribulose‐1,5‐bisphosphate carboxylase activity is predicted to account fully for the light‐dependent changes in carbon balance.     

Novel genetic analysis in Beh?et's disease

Behçet''s disease (BD) is characterized by oral and genital ulceration and is complicated by eye, skin, joint and central nervous system lesions. It has long been understood that BD has a strong genetic component, but to date the identified genes account for only around 30% of the risk for developing the disease, and the work has mostly been based on candidate gene analysis. In a recent report, Fei and coworkers presented the results of the first genome-wide analysis of patients with BD. These findings suggest new pathways for investigation in this complex disease.Error, like straws, upon the surface flowHe who would search for pearls must dive belowJohn Dryden, 1678Fei and coworkers [1] identified novel single nucleotide polymorphisms (SNPs) in five genes (KIAA1529, CPVL, LOC100129342, UBASH3B and UBAC2) that encode proteins with both known and unknown functions. Moreover, subset analysis showed links between some of the SNPs and particular manifestations of Behçet''s disease (BD).KIAA1529 and LOC100129342 have no known function, but the latter SNP on chromosome 1p34 confirms a locus previously identified in a multiplex family study [2]. UBASH3B and UBAC2 encode ubiquitin-associated proteins. The ubiquitin system is best described in targeting misfolded or damaged proteins for proteosomal degradation, but it is also involved in several other cellular processes, including regulation of nuclear factor-κB function and autophagy. Such processes are involved in cells of both innate and adaptive immune responses, which is of interest with respect to the ongoing debate on whether BD is an autoinflammatory or an autoimmune disorder [3]. Dysfunction of the ubiquitin pathway has been implicated in cancer, neurodegenerative diseases and type 2 diabetes [4,5].Carboxypeptidase vitellogenic-like protein is upregulated in monocytes on conversion to macrophages, in which it co-localizes to the secreted proteins tumour necrosis factor and the chemokine CCL3 (C-C chemokine ligand 3). It has been implicated in the processing/transport of peptides for loading onto major histocompatibility complex (MHC) class I molecules [6]. The strongest genetic association with BD is human leucocyte antigen (HLA)-B*5101 and HLA-B*5108, an MHC class I molecule. Microsatellite analysis confirms HLA-{"type":"entrez-nucleotide","attrs":{"text":"B85101","term_id":"2926233","term_text":"B85101"}}B85101/5108 as the most likely causative gene in BD, but SNPs in other genes in close proximity on chromosome 6 – MICA, MICB and TNF – have also been reported [7]. Moreover, the mechanism of action of HLA-B*5101/5108 in BD has not been elucidated. Alteration in the process of peptide production by the CVLP SNP could have important implications in the expression or maintenance of MHC class I molecules on the cell surface and be linked to the pathogenesis of the disease.In subset analysis the UBASH3B SNP was more common in patients with ocular and vascular manifestations, whereas the KIAA1529 SNP was more common in patients without such involvement. The authors correctly stated that the numbers with each manifestation make such an analysis very preliminary, but several other SNPs have been linked to ocular disease specifically, so these findings are not unexpected [8]. It should be noted, however, that eye and vascular disease can take many forms in BD, and more detailed analysis will be required when greater numbers are tested for these SNPs.There are certain caveats to the findings. Genome-wide analysis (GWAS) is normally performed on a large number of samples, which is not easy for a rare condition such as BD. The authors addressed this point by performing the initial analysis on pooled samples and then, having identified potential SNPs, validating the findings in each sample individually. However, it is important for these results to be validated in other cohorts of BD patients. There are extensive data describing ethnic differences in SNPs studied by candidate analysis, and the association of these newly identified SNPs in BD patients from different geographical areas will be important. Similarly, in several studies males have been shown to have a worse prognosis, and the association of these SNPs with sex should be examined. Other GWAS are ongoing or planned in Japanese, European and Turkish patients with BD, and comparison with the current study will be of great interest. Finally, and most importantly, the functional relevance of these SNPs will need to be investigated and – if found – tested in different cell types such as lymphoid, myeloid, epithelial and endothelial cells that are involved in BD.BD is a complex disease. Different patients will experience different symptoms, and there is a clear geographical distribution of the disease. The candidate gene approach has been useful in identifying susceptibility and severity genes in BD, but the ability to undertake GWAS has led to the identification of several new SNPs in many human diseases, increasing our understanding of the pathogenic mechanisms involved. Fei and coworkers [1] are to be commended for such a study in BD.     

Mutational analysis of human tumor necrosis factor-α

To understand the structure-function relationship of human tumor necrosis factor- (TNF-), mutational analysis was carried out on the lower regions (regions 1–6) of the molecule. The muteins were prepared as a soluble form by using a chaperonin co-expression system and the cytotoxic activities of the purified muteins were evaluated on TNF-sensitive murine fibrosarcoma L929 cells. Three regions (regions 1, 2 & 4) were found where mutations significantly influenced the bioactivity. In region 1 (residues 1–10), the number of deleted residues and the positioning of positive charges are important to achieve a maximum activity and in region 4 (residues 84–88), introduction of charged residues in one of the positions 86–88 significantly increased the cytotoxic activity. On the other hand, any mutation introduced in region 2 (residues 37–41) had a deleterious effect. The present study provides a structural basis for the design of highly potent TNF- as a therapeutic agent.Revisions requested 18 October 2004; Revisions received 22 November 2004     

Morphological analysis of the filamentous fungus Penicillium chrysogenum using flow cytometry—the fast alternative to microscopic image analysis

Applied Microbiology and Biotechnology - An important parameter in filamentous bioreactor cultivations is the morphology of the fungi, due to its interlink to productivity and its dependency on...     

Greenhouse tomato nutrition — A growth analysis study

Summary Chemical determination of the mineral content of a mature, healthy, high-yielding greenhouse tomato plant has shown that the total nutrient absorption is equivalent to 345 pounds per acre of nitrogen, 74 pounds per acre of phosphorus, 716 pounds per acre of potassium, 295 pounds per acre of calcium and 43 pounds per acre of magnesium. These figures form the basis for a more intelligent estimate of the fertilizer requirements of this crop than can be obtained from the more common empirical methods. The analysis of individual tissues of a whole plant harvested at mid-growth gives a clear picture of the distribution of nutrients throughout the plant.     

Functional analysis of guinea pig β1-adrenoceptor

Although similarity of pharmacological responses to certain stimuli between guinea pigs and humans has been reported, this has been poorly defined by a molecular biological approach. In this study, we cloned the gene of guinea pig ?1-adrenoceptor (ADRB1). The deduced amino acid sequence of guinea pig ADRB1 (467-aa) showed 91% and 92% identity with the human and rat ADRB1 sequences, respectively. Using HEK293T cells expressing guinea pig, human and rat ADRB1s independently, we elucidated the functional characteristics of each ADRB1. The ligand-binding profiles and the concentration-response relationships for isoprenaline-induced cyclic adenosine monophosphate (cAMP) production were similar among the three ADRB1s. Isoprenaline also induced phosphorylation of extracellular-signal related kinases (ERK) through ADRB1s in a concentration-dependent manner. The minimum effective concentration of isoprenaline for phosphorylation of ERK, through guinea pig ADRB1 was the same as through human ADRB1, but markedly lower than that of through rat ADRB1. ERK phosphorylation through guinea pig ADRB1 was sensitive to pertussis toxin, a dominant-negative ras and PD98059, indicating that a G(i)-mediated pathway is involved in the ADRB1/ERK signaling loop. These results suggest that the G(i)-coupling efficacy of guinea pig and human ADRB1s may be higher than that of rat ADRB1.     

Omiga™: A PC-based sequence analysis tool

Computer-based sequence analysis, notation, and manipulation are a necessity for all molecular biologists working with any but the most simple DNA sequences. As sequence data become increasingly available, tools that can be used to manipulate and annotate individual sequences and sequence elements will become an even more vital implement in the molecular biologist's arsenal. The Omiga DNA and Protein Sequence Analysis Software tool, version 2.0 provides an effective and comprehensive tool for the analysis of both nucleic acid and protein sequences that runs on a standard PC available in every molecular biology laboratory. Omiga allows the import of sequences in several common formats. Upon importing sequences and assigning them to various projects, Omiga allows the user to produce, analyze, and edit sequence alignments. Sequences may also be queried for the presence of restriction sites, sequence motifs, and other sequence features, all of which can be added into the notations accompanying each sequence. This newest version of Omiga also allows for sequencing and polymerase chain reaction (PCR) primer prediction, a functionality missing in earlier versions. Finally, Omiga allows rapid searches for putative coding regions, and Basic Local Alignment Search Tool (BLAST) queries against public databases at the National Center for Biotechnology Information (NCBI).