Lipid analysis of bronchoalveolar lavage fluid (BAL) by MALDI-TOF mass spectrometry and 31P NMR spectroscopy

Despite the high clinical relevance, only the cellular moiety of bronchoalveolar lavage (BAL) has been intensively investigated and is used for diagnosis purposes. On the other hand, the cell-free fluid is, by far, less characterized. Although this fluid represents a relatively simple mixture of only a few different phospholipids (mainly phosphatidylcholine, phosphatidylglycerol and cholesterol), methods for the routine analysis of these fluids are still lacking. In the present investigation we have applied, for the first time, MALDI-TOF mass spectrometry, as well as 31P NMR spectroscopy to the analysis of organic extracts of bronchoalveolar lavage fluids. BAL from different mammals (rat, minipig, rabbit and man) were investigated and, for means of comparison, organic extracts of lung tissue were also examined. Both applied methods provide fast and reliable information on the lipid composition of the bronchoalveolar lavage. However, despite of its comparably low sensitivity, 31P NMR spectroscopy detects all phospholipid species in a single experiment and with the same sensitivity, whereas MALDI-TOF fails in the detection of phosphatidylethanolamine in the presence of higher quantities of phosphatidylcholine. In contrast, MALDI-TOF mass spectrometry is more suitable for the detection of cholesterol and the determination of the fatty acid composition of the individual phospholipids, especially lysolipids. It will be shown that all BALs exhibit significant, species-dependent differences that mainly concern the content of phosphatidylglycerol and lyso-phosphatidylcholine. It is concluded that both methods are suitable tools in lipid research due to the (in comparison to alternative methods) simplicity of performance.     

Measurement of lipoxygenase activity in crude and partially purified potato extracts

Two assay systems, one a spectrophotometric assay at 234 nm, the other based on the oxygen electrode, were compared as methods for the routine analysis of lipoxygonase activity in crude and partially purified potato extracts. The spectrophotometric assay was unsuitable for the analysis of crude extracts and only gave meaningful results under very restricted reaction conditions. The oxygen electrode provided a reliable method for routine analysis of lipoxygenase activity.     

A note on interobserver error in multivariate analyses of populations

The effect of interobserver error on a principal components analysis of a small sample of human crania is examined. A comparison of individual specimen scores for components is made to find rotated principal components which identify interobserver error. The individual variables which load highly on such components are then tested for interobserver error univariately. Multivariate components which must identify interobserver error contain no high loadings for variables which demonstrate interobserver error in the univariate case. Principal component analysis, in defining new component variables, extracts such error in an easily identified way which makes comparison of samples measured by more than one anthropometrist more reliable.     

The use of immunological methods to detect and identify bacteria in the environment

Immunological detection methods have become increasingly important in microbial ecology for the tracking of specific microorganisms and for community analysis. For a reliable application of these techniques, the monoclonal antibodies or polyclonal antisera used have to fulfill several quality criteria. Cross reactivity, cellular localization of the antigenic determinant, affinity characteristics and the expression of the antigenic determinant at environmental conditions have to be determined. Immunological methods can be used for the identification, quantification and enrichment of specific bacteria in extracts as well as for the visualization of cells in situ. The sensitivity of advanced immunological methods can be compared to PCR techniques. Using image processing of epifluorescence micrographs or confocal laser scanning microscopy, the immunofluorescence approach can now be applied to study complex environmental samples.     

Quantitative analysis and molecular species fingerprinting of triacylglyceride molecular species directly from lipid extracts of biological samples by electrospray ionization tandem mass spectrometry

Herein we describe a rapid, simple, and reliable method for the quantitative analysis and molecular species fingerprinting of triacylglycerides (TAG) directly from chloroform extracts of biological samples. Previous attempts at direct TAG quantitation by positive-ion electrospray ionization mass spectrometry (ESI/MS) were confounded by the presence of overlapping peaks from choline glycerophospholipids requiring chromatographic separation of lipid extracts prior to ESI/MS analyses. By exploiting the rapid loss of phosphocholine from choline glycerophospholipids, in conjunction with neutral-loss scanning for individual fatty acids, overlapping peaks in the ESI mass spectrum were deconvoluted generating a detailed molecular species fingerprint of individual TAG molecular species directly from chloroform extracts of biological samples. This method readily detects as little as 0.1 pmol of each TAG molecular species from chloroform extracts and is linear over a 1000-fold dynamic range. The sensitivity of individual TAG molecular species to ESI/MS/MS analyses correlated with the unsaturation index and inversely correlated with total aliphatic chain length of TAG. An algorithm was developed which identifies sensitivity factors, thereby allowing the rapid quantitation and molecular species fingerprinting of TAG molecular species directly from chloroform extracts of biological samples.     

Proteases in malaria-infected red blood cells

The discrimination between erythrocyte and Plasmodium proteases is now made easier by using synthetic fluorogenic substrates, high-pressure liquid chromatography, reliable methods of cell preparation, as well as radiolabeled extracts from in vitro cultures of P. falciparum. The reinvasion process of an erythrocyte by a merozoite involves specific proteinases, which were recently identified using fluorogenic peptidyl-AEC substrates and by analysis of schizont and merozoite extracts with the gelatin-SDS-PAGE method. The biological targets of both host and parasite proteinases are not yet well characterized because Plasmodium-infected red blood cells contain at least four compartments with different pH values, which could modulate the proteinase activities according to their pH range activity. The processing of the precursor for the major merozoite surface antigens involves cleavage of very specific peptidic bonds by, so far unknown, proteinases. The depletion of the erythrocyte cytoskeleton could depend on a 37 kD proteinase, which cleaves spectrin and the 4.1 component, as shown in P. berghei and P. falciparum species. In contrast to leupeptin, which inhibits the merozoite release from schizont-infected erythrocytes, the structural inhibitor analogous to the Val-Leu-Gly-Lys (or Arg) P. falciparum neutral proteinase substrates appears to block the invasion step of erythrocytes by merozoites and may open new trends in chemotherapeutical strategies.     

Preparative scale expression of membrane proteins in Escherichia coli-based continuous exchange cell-free systems

Cell-free expression is emerging as a prime method for the rapid production of preparative quantities of high-quality membrane protein samples. The technology facilitates easy access to large numbers of proteins that have been extremely difficult to obtain. Most frequently used are cell-free systems based on extracts of Escherichia coli cells, and the reaction procedures are reliable and efficient. This protocol describes the preparation of all essential reaction components such as the E. coli cell extract, T7 RNA polymerase, DNA templates as well as the individual stock solutions. The setups of expression reactions in analytical and preparative scales, including a variety of reaction designs, are illustrated. We provide detailed reaction schemes that allow the preparation of milligram amounts of functionally folded membrane proteins of prokaryotic and eukaryotic origin in less than 24 h.     

Comparison of sample preparation methods for the high-performance liquid chromatographic analysis of cell culture extracts for triphosphate ribonucleosides and deoxyribonucleosides

We compared four different procedures for the purification and concentration of nucleoside triphosphates in cell extracts prior to HPLC analysis. Two methods involved precipitation, with either acetonitrile or calcium fluoride. The acetonitrile procedure yielded reasonable recovery and sufficient purity for the subsequent HPLC analysis. The calcium fluoride coprecipitation procedure gave both good recovery and purity; but the recovery was shown to be dependent on the concentration of the nucleoside triphosphates. The other two methods involved small Sep-Pak cartridges. The silica cartridge procedure yielded unfavorable recoveries in periodate-treated cell extracts, apparently due to poor solubility of nucleoside triphosphates in the requisite solvents. The strong anion exchange cartridge procedure yielded both good recovery and purity. This procedure was found to be fast, efficient, and reliable for purifying and concentrating nucleotides in cell extracts.     

Acid-labile sulfide and zero-valence sulfur in plant extracts containing chlorophyll and ionic detergents

Two methods for analysis of acid-labile sulfide and zero-valence sulfur in plant extracts containing chlorophyll as well as ionic and/or nonionic detergents are presented. Both methods are based on the conversion of sulfide into methylene blue. In the first method an ethyl acetate extraction step is used to remove chlorophyll and its degradation products which otherwise prevent spectrophotometric quantitation of methylene blue. The second assay method employs 35S-labeled plant extracts. This method, which involves thin-layer chromatography and autoradiography, is potentially more sensitive than the spectrophotometric assay in detecting acid-labile sulfide and zero-valence sulfur.     

Simplified Extraction Procedure for Serological Grouping of Beta-Hemolytic Streptococci

An adaptation of the nitrous acid extraction of streptococci proved to be a reliable and practical method for the preparation of extracts for routine serological group identification. The extracts of all groups tested gave strong capillary precipitin reactions as well as reactions of double diffusion in gel. For routine grouping, extracts were prepared from the first one-half-plate subculture of the initial throat culture. The technique is simple and reliable, and it requires a minimum of technical skill, reagents, and equipment. Its use would facilitate epidemiological surveillance of group A streptococci and rapid diagnosis of streptococcal infections at a low cost.     

A sensitive method for determination of 5-fluorouracil and 5-fluoro-2'-deoxyuridine in human plasma by high-pressure liquid chromatography

Polymerization-competent extracts of suspension-cultured HeLa cells and porcine brain tissue were assayed for tubulin content. Five different methods were used to assay identically prepared extracts: two types of sodium dodecyl sulfate-containing acrylamide gels, a DEAE retention assay, a colchicine-binding assay, and a radioimmunoassay. The colchicine-binding and radioimmunoassay results were in close agreement and are therefore considered reliable assays for tubulin content in cell extracts. The DEAE retention assay gave slight overestimates, but the gel methods seriously overestimated tubulin content. Based on data from colchicine binding and radioimmunoassay, the proportion of soluble cell protein which is tubulin is 4.3% for HeLa cell extracts and 12.1% for brain tissue extracts.     

The lipid composition of the unicellular green alga Chlamydomonas reinhardtii and the diatom Cyclotella meneghiniana investigated by MALDI-TOF MS and TLC

The lipid composition of algae is crucial for numerous structural and physiological aspects, e.g. the integrity of the photosynthetic complexes and the functionality of membrane-embedded processes as the photosynthetic electron transport in thylakoids or the mitochondrial respiration. In this paper the lipid composition of the organic extracts of the green alga Chlamydomonas reinhardtii and the diatom Cyclotella meneghiniana are compared by using matrix-assisted laser desorption and ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) in combination with thin-layer chromatography (TLC). The combined methods enable quantitative evaluation of the individual lipid classes as well as the determination of the relative acyl compositions. It will be shown that both algae differ in (a) the lipid classes, (b) the relative contribution of the individual lipid classes and (c) the acyl compositions. Differences in the acyl composition concern particularly the mono- and digalactosyl diacylglycerols. Glycerol-trimethylhomoserine and phosphatidylethanolamine are exclusively detected in the C. reinhardtii extracts, whereas phosphatidylcholine is a characteristic lipid of C. meneghiniana. Furthermore, the proportion of the acidic lipids sulfoquinovosyl-diacylglycerol and phosphatidylglycerol is significantly higher in the diatom than in C. reinhardtii.     

A small-scale method for the preparation of plant N-linked glycans from soluble proteins for analysis by MALDI-TOF mass spectrometry

The use of plants as production hosts for recombinant glycoproteins, which is rapidly developing, requires methods for fast and reliable analysis of plant N-linked glycans. This study describes a simple small-scale method for the preparation of N-linked glycans from soluble plant protein and analysis thereof by matrix assisted laser desorption ionisation time of flight mass spectrometry (MALDI-TOF MS). Concentration and protease digestion of plant protein as well as deglycosylation is carried out in a single concentrator unit without the need for intermittent purification to minimize adsorptive loss and to facilitate handling. Plant protein is concentrated in a unit with a 5 kDa cutoff, and after buffer exchange, pepsin (EC 3.4.23.1) digestion is carried out in the concentrator overnight to obtain peptides as substrates for deglycosylation. Deglycosylation is carried out with peptide-N-glycosidase A (PNGase A; EC 3.5.1.52) for 24 h. Released N-glycans are purified using reverse-phase and cation exchange chromatography micro-columns for removal of peptides and desalting. N-Glycans are directly analyzed by MALDI-TOF MS without derivatization. The method for isolation of N-glycans is compatible with secreted proteins from cell culture supernatant as well as with soluble protein extracts from leaf tissue. As little as 5 μg of plant glycoprotein is sufficient for N-glycan preparation for MALDI-TOF MS analysis using this method.     

Nonradioactive technique to measure protein phosphatase 2A-like activity and its inhibition by drugs in cell extracts

A nonradioactive assay has been developed that can be used to measure serine/threonine protein phosphatase (PP) activity, especially PP2A, in crude extracts from different cell lines. For this technique commercially available casein is used as an already phosphorylated substrate. The prerequisite for reliable measurements is the removal of free phosphate from cell extracts and substrate preparations with desalting columns. The use of different nonspecific or specific inhibitors as well as inhibition characteristics observed after extract dilution suggests that in the absence of magnesium, PP2A-like activity in the extracts is measured by this technique. Inclusion of magnesium allowed the detection of a protein phosphatase activity that is activated by magnesium, which is presumably PP2C. The use of structurally different as well as structurally related inhibitors of PP2A gave results comparable to those of reports from the literature that were obtained with radioactive assays. Thus, our data supported our hypothesis that this nonradioactive assay can be used for the identification of newly synthesized PP inhibitors as well as for performing structure-activity analysis within groups of such new agents.     

Comparative study of the population structure and population assignment of sockeye salmon Oncorhynchus nerka from West Kamchatka based on RAPD-PCR and microsatellite polymorphism

Using two types of molecular markers, a comparative analysis of the population structure of sockeye salmon from West Kamchatka as well as population assignment of each individual fish were carried out. The values of a RAPD-PCR-based population assignment test (94-100%) were somewhat higher than those based on microsatellite data (74-84%). However, these results seem quite satisfactory because of high polymorphism of the microsatellite loci examined. The UPGMA dendrograms of genetic similarity of three largest spawning populations, constructed using each of the methods, were highly reliable, which was demonstrated by high bootstrap indices (100% in the case of RAPD-PCR; 84 and 100%, in the case of microsatellite analysis), though the resultant trees differed from one another. The different topology of the trees, in our view, is explained by the fact that the employed methods explored different parts of the genome; hence, the obtained results, albeit valid, may not correlate. Thus, to enhance reliability of the results, several methods of analysis should be used concurrently.     

Comparative study of the population structure and population assignment of sockeye salmon Oncorhynchus nerka from West Kamchatka based on RAPD-PCR and microsatellite polymorphism

Using two types of molecular markers, a comparative analysis of the population structure of sockeye salmon from West Kamchatka as well as population assignment of each individual fish were carried out. The values of a RAPD-PCR-based population assignment test (94–100%) were somewhat higher than those based on microsatellite data (74–84%). However, these results seem quite satisfactory because of high polymorphism of the microsatellite loci examined. The UPGMA dendrograms of genetic similarity of three largest spawning populations, constructed using each of the methods, were highly reliable, which was demonstrated by high bootstrap indices (100% in the case of RAPD-PCR; 84 and 100%, in the case of microsatellite analysis), though the resultant trees differed from one another. The different topology of the trees, in our view, is explained by the fact that the employed methods explored different parts of the genome; hence, the obtained results, albeit valid, may not correlate. Thus, to enhance reliability of the results, several methods of analysis should be used concurrently.     

Smooth individual level covariates adjustment in disease mapping

Spatial models for disease mapping should ideally account for covariates measured both at individual and area levels. The newly available “indiCAR” model fits the popular conditional autoregresssive (CAR) model by accommodating both individual and group level covariates while adjusting for spatial correlation in the disease rates. This algorithm has been shown to be effective but assumes log‐linear associations between individual level covariates and outcome. In many studies, the relationship between individual level covariates and the outcome may be non‐log‐linear, and methods to track such nonlinearity between individual level covariate and outcome in spatial regression modeling are not well developed. In this paper, we propose a new algorithm, smooth‐indiCAR, to fit an extension to the popular conditional autoregresssive model that can accommodate both linear and nonlinear individual level covariate effects while adjusting for group level covariates and spatial correlation in the disease rates. In this formulation, the effect of a continuous individual level covariate is accommodated via penalized splines. We describe a two‐step estimation procedure to obtain reliable estimates of individual and group level covariate effects where both individual and group level covariate effects are estimated separately. This distributed computing framework enhances its application in the Big Data domain with a large number of individual/group level covariates. We evaluate the performance of smooth‐indiCAR through simulation. Our results indicate that the smooth‐indiCAR method provides reliable estimates of all regression and random effect parameters. We illustrate our proposed methodology with an analysis of data on neutropenia admissions in New South Wales (NSW), Australia.     

BlotBase: a northern blot database

With the availability of high-throughput gene expression analysis, multiple public expression databases emerged, mostly based on microarray expression data. Although these databases are of significant biomedical value, they do hold significant drawbacks, especially concerning the reliability of single gene expression profiles obtained by microarray data. Simultaneously, reliable data on an individual gene's expression are often published as single northern blots in individual publications. These data were not yet available for high-throughput screening. To reduce the gap between high-throughput expression data and individual highly reliable expression data, we designed a novel database "BlotBase", a freely and easily accessible database, currently containing approximately 700 published northern blots of human or mouse origin (http://www.medicalgenomics.org/Databases/BlotBase). As the database is open for public data submission, we expect this database to quickly become a large expression profiling resource, eventually providing higher reliability in high-throughput gene expression analysis. Realizing BlotBase, Pubmed was searched manually and by computer based text mining methods to obtain publications containing northern blot results. Subsequently, northern blots were extracted and expression values of different tissues calculated utilizing Image J. All data were made available through a user friendly web front end. The data may be searched by either full text search or list of available northern blots of a specific tissue. Northern blot expression profiles were displayed by three expression states as well as a bar chart, allowing for automated evaluation. Furthermore, we integrated additional features, e.g. instant access to the corresponding RNA sequence or primer design tools making further expression analysis more convenient. Finally, through a semiautomatic submission system this database was opened to the bioinformatics community.     

Quantification and genetic profiling of DNA isolated from free-floating feces of the North Atlantic right whale (Eubalaena glacialis)

Fecal analysis from the highly endangered North Atlantic right whale provides valuable information about health and reproductive parameters of individual animals. Genetically profiling the feces facilitates this connection when the sample originator is unknown. Although genetic analysis of feces collected in terrestrial systems has become well established, genetic studies of cetacean DNA are rare. Here, the use of free‐floating feces as a source of right whale DNA and the reliability of the genotypes produced are examined. On average, fecal extracts yielded 25 ng of DNA/mg dry weight, but less than 1% was right whale DNA. Although all samples were amplified using genus‐specific mitochondrial control region primers, the quantity of right whale DNA present was over estimated when compared to amplifications using nuclear primers. No correlation was found between the quantity of right whale DNA recovered and the duration the sample sat in the water. Composite microsatellite profiles from multiple amplifications of 28 fecal samples of known origin were consistent with profiles of the same individuals obtained from skin biopsies, however, the rate of allelic dropout varied depending on the amount of right whale DNA added. A screening and genotyping protocol for reliable genetic profiling based on fecal DNA quantification is presented.     

Minimum sampling effort for reliable non-invasive estimations of excretion abundance of Elaphostrongylus cervi L1 in red deer (Cervus elaphus) populations

Faecal surveys are commonly used as non-invasive means to evaluate population abundance of animals as well as comparable indexes of prevalence and intensity of diseases between populations, especially macroparasites. While faecal surveys are among one of the simplest means to perform these evaluations, they are time consuming and labour intensive. The present study evaluated 80 red deer (Cervus elaphus) faecal samples collected in two study sites for the presence and abundance of first-stage larvae of the nematode Elaphostrongylus cervi and established pools of samples for epidemiological analysis. The analysis of 20-30 individual samples would produce a reliable estimate of the 'true' prevalence, and the error of the smaller sample size only doubled that of the 80 reference samples. The analysis of 5 pools of 5 pellet groups each, or of 4 pools of 10 pellet groups each, provided a reliable estimation of the 'true' excretion abundance estimated by the analysis of all 80 samples. These pools comprise a cost-effective and dependable alternative for measuring and obtaining comparable abundances of parasitic faecal excretion stages in red deer populations, which is very valuable for epidemiological and ecological research as well as for management purposes.