Identification and profiling of volatile metabolites of the biocontrol fungus Trichoderma atroviride by HS-SPME-GC-MS

In the present study we describe a method, which is based on solid phase microextraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS) and which can be used for the profiling of microbial volatile organic compounds (MVOCs) in the headspace (HS) of cultures of filamentous fungi. The method comprises the following successive steps: 1. growth of the fungus on a solid culture medium directly in headspace vials, 2. measurement of volatiles by HS-SPME-GC-MS, 3. deconvolution of mass spectra, 4. identification of volatiles by comparison of measured, deconvoluted mass spectra and linear temperature programmed retention indices (LTPRI) on two stationary GC phases with database entries and LTPRI published in the literature, and 5. profiling of the identified MVOCs.The developed method was successfully applied to cultures of the biocontrol fungus Trichoderma atroviride. An in-house library consisting of mass spectra and LTPRI values of fungal VOCs was established and used to study the profiles of MVOCs of this fungus. In total, 25 different MVOCs were identified by applying strict criteria (spectral match factor at least 90% and a maximum relative deviation of LTPRI of ± 2% from literature values). The MVOCs were assigned to the compound classes of alcohols, ketones, alkanes, furanes, pyrones (mainly the bioactive 6-pentyl-alpha-pyrone), mono- and sesquiterpenes, 13 of which have never been reported to be produced by Trichoderma spp. before. Eleven of these volatiles have been additionally confirmed using authentic standards. Finally, time course experiments and cultivation of T. atroviride in the presence of the mycotoxin fusaric acid demonstrated the potential of the method to study the dynamics of MVOC profiles as well as the effect of different environmental/biological conditions on the expression of MVOCs of filamentous fungi.     

A new method for nonhomogeneous time course expression analysis

Time course expression analysis constitutes a large portion of applications of microarray experiments. One primary goal of such experiments is to detect genes with the temporal changes over a period of time or at some interested time points. Difficulties arising from data with small number of replicates over only a few unaligned time points in multiple groups pose challenges for efficient statistical analysis. Some known methods are limited by the unverifiable assumptions or by the scope of applications for only two groups. We present a new method for detecting differentially expressed genes under nonhomogeneous time course experiments in multiple groups. The new method first models the time course curve of one gene by a Gaussian process to align the nonhomogeneous time course data and to compute the gradient of the time course curve as well, the latter of which is used as directional information to enhance the sensitivity of detection for temporal changes. Second, we adopt a nonparametric method to test a surrogate hypothesis based on the augmented data from the Gaussian process model. The proposed method is robust in terms of model fitting and testing. It does not require any distributional assumption for the observations or the test statistic and the method works for the case with as few as triplicate samples over four or five time points under multiple groups. We show the effectiveness and superiority of the new method in comparison with some existing methods using simulated models and two real data sets.     

Sensitive determination of pheomelanin after 5-carboxyfluorescein succinimidyl ester precapillary derivatization and micellar electrokinetic capillary chromatography with laser-induced fluorescence detection

The suitability of micellar electrokinetic capillary chromatography (MEKC) with laser-induced fluorescence (LIF) detection for the determination of pheomelanin in biological materials has been investigated. 5-Carboxyfluorescein succinimidyl ester was chosen as the labeling reagent to precapillary derivatize the two marker aminohydroxyphenylalanine (AHP) isomers produced after reductive hydrolysis of pheomelanin with hydriodic acid (HI). Various parameters affecting derivatization and separation were systematically studied. Under optimal conditions, the analytes could be separated within 18 min, and the relative standard deviations (R.S.D.) of migration time and corrected peak areas were less than 5.5%. Compared with the conventional high-performance liquid chromatography (HPLC) method with electrochemical detection, the 100-fold improvements in sensitivity were achieved by applying LIF detection. As a preliminary application, this method has been successfully applied to the determination of pheomelanin in two human melanoma cell cultures, black hair, melanoma tissue and urine samples of human melanoma patients with the spiked recoveries in the range of 88-96%.     

MARD: a new method to detect differential gene expression in treatment-control time courses

MOTIVATION: Characterizing the dynamic regulation of gene expression by time course experiments is becoming more and more important. A common problem is to identify differentially expressed genes between the treatment and control time course. It is often difficult to compare expression patterns of a gene between two time courses for the following reasons: (1) the number of sampling time points may be different or hard to be aligned between the treatment and the control time courses; (2) estimation of the function that describes the expression of a gene in a time course is difficult and error-prone due to the limited number of time points. We propose a novel method to identify the differentially expressed genes between two time courses, which avoids direct comparison of gene expression patterns between the two time courses. RESULTS: Instead of attempting to 'align' and compare the two time courses directly, we first convert the treatment and control time courses into neighborhood systems that reflect the underlying relationships between genes. We then identify the differentially expressed genes by comparing the two gene relationship networks. To verify our method, we apply it to two treatment-control time course datasets. The results are consistent with the previous results and also give some new biologically meaningful findings. AVAILABILITY: The algorithm in this paper is coded in C++ and is available from http://leili-lab.cmb.usc.edu/yeastaging/projects/MARD/     

Sensitivity of biochemical test in comparison with other methods for the detection of mycoplasma contamination in human and animal cell lines stored in the National Cell Bank of Iran

Mycoplasma contamination in cell culture is considered as serious problem in the manufacturing of biological products. Our goal in this research is to find the best standard and rapid method with high sensitivity, specificity, accuracy and predictive values of positive and negative results for detection of mycoplasma contamination in cell cultures of the National Cell Bank of Iran. In this study, 40 cell lines suspected to mycoplasma contamination were evaluated by three different methods: microbial culture, enzymatic mycoalert^® and molecular. Enzymatic evaluation was performed using the mycoalert^® kit while in the molecular technique, a universal primer pair was designed based on the common and fixed 16SrRNA ribosomal sequences used. Mycoplasma contaminations in cell cultures with molecular, enzymatic and microbial culture methods were determined as 57.5, 52.5 and 40 %, respectively. These results confirmed the higher rate of sensitivity, specificity and accuracy for the molecular method in comparison with enzymatic and microbial methods. Polymerase chain reaction (PCR) assay based on fixed and common sequences in the 16SrRNA, is a useful valuable and reliable technique with high sensitivity, specificity and accuracy for detection of mycoplasma contamination in cell cultures and other biological products. The enzymatic mycoalert^® method can be considered as a substitution for conventional microbial culture and DNA staining fluorochrome methods due to its higher sensitivity, specificity and speed of detection (<20 min).     

Increased enzymatic activities and levels of superoxide anion and phenolic compounds in cultures of basidiomycetes after temperature stress

Selected strains of basidiomycetes (Abortiporus biennis, Trametes versicolor and Cerrena unicolor) were shown to produce enhanced extracellular peroxidase (EP), superoxide dismutase (SOD) and laccase activities following the exposure of 10-day-old fungal cultures to separate high and low temperature stress. The stressful conditions also caused an increase in the concentrations of phenol compounds and superoxide anion radicals in these cultures. At first, peroxidase activity was observed at 12 hours from the moment of temperature stress application. Laccase activity appeared at 96 hours after the maximum levels of superoxide anion radicals (48 h) and SOD activity (36–72 h). The concentration of phenolic substances grew steadily during the period of cultivation. These relations between laccase, SOD and EP as well as superoxide radicals and phenol levels in the environment of ligninolytic fungi seems to be important in the course of the biosynthesis or biodegradation of lignin, as the consequence of adaptation of these basidiomycetes to environmental temperature conditions.     

Antigenic affinity of meningococci and human A- and B-group erythrocytes

The use of the modified method of isohemagglutinin adsorption by microbial antigens in experiments with the causative agent of meningococcal infection has led, for the first time, to the detection of meningococcal antigens affined to the antigens of human erythrocytes, groups A and B. The antigenic affinity of group A erythrocytes and meningococci has proved to be more pronounced in meningococcal strains isolated from the spinal fluid of patients than in cultures obtained from the nasopharynx of healthy persons. The detection of the affinity of these antigens makes it possible to explain the mechanism of differences in the susceptibility of persons with different blood groups to meningococcal infection by "antigenic mimicry".     

Comparison of different carbon ink based screen-printed electrodes towards amperometric immunosensing

The aim of the present work was to make amperometric immunosensors based on the principle of enzyme-linked immunosorbent assay (ELISA). For this purpose, screen-printed electrodes (SPEs) were fabricated using various carbon inks (commercially available inks Gwent, Acheson, Eltecks and two homemade inks PSG & PVCG) to determine the best ink in realizing immunosensors. Amperometric immunosensors made by different carbon inks were compared with standard ELISA in terms of total assay time, amount of biological materials used and sensitivity of detection. A model system containing rabbit anti-mouse immunoglobulin G (RαMIgG) as the capturing antibody, mouse IgG (MIgG) as antigen and alkaline phosphatase conjugated RαMIgG as revealing antibody was used. In these studies, 1-naphthyl phosphate was used as substrate. The experiments done include electrochemical characterization of electrodes, optimization of dilutions of antibodies, immobilization of antibody on the electrode were carried out. The minimum detection limit for the best results of MIgG determination were obtained on screen-printed electrode made by Gwent carbon ink and PSG carbon ink, with a detection limit of 1.0 and 2.0 ng/ml respectively. The time required for detection of mouse IgG was 40 min for SPEs. By using the conventional spectrophotometric method (ELISA method), the minimum detection limit for the MIgG (antigen) detection was 50 ng/ml and the time required for analysis was found to be 140 min.     

Real-time PCR assay is superior to other methods for the detection of mycoplasma contamination in the cell lines of the National Cell Bank of Iran

Mycoplasmas are the most important contaminants of cell cultures throughout the world. They are considered as a major problem in biological studies and biopharmaceutical economic issues. In this study, our aim was to find the best standard technique as a rapid method with high sensitivity, specificity and accuracy for the detection of mycoplasma contamination in the cell lines of the National Cell Bank of Iran. Thirty cell lines suspected to mycoplasma contamination were evaluated by five different techniques including microbial culture, indirect DNA DAPI staining, enzymatic mycoalert^® assay, conventional PCR and real-time PCR. Five mycoplasma-contaminated cell lines were assigned as positive controls and five mycoplasma-free cell lines as negative controls. The enzymatic method was performed using the mycoalert^® mycoplasma detection kit. Real-time PCR technique was conducted by PromoKine diagnostic kits. In the conventional PCR method, mycoplasma genus-specific primers were designed to analyze the sequences based on a fixed and common region on 16S ribosomal RNA with PCR product size of 425 bp. Mycoplasma contamination was observed in 60, 56.66, 53.33, 46.66 and 33.33 % of 30 different cell cultures by real-time PCR, PCR, enzymatic mycoalert^®, indirect DNA DAPI staining and microbial culture methods, respectively. The analysis of the results of the different methods showed that the real-time PCR assay was superior the other methods with the sensitivity, specificity, accuracy, predictive value of positive and negative results of 100 %. These values were 94.44, 100, 96.77, 100 and 92.85 % for the conventional PCR method, respectively. Therefore, this study showed that real-time PCR and PCR assays based on the common sequences in the 16S ribosomal RNA are reliable methods with high sensitivity, specificity and accuracy for detection of mycoplasma contamination in cell cultures and other biological products.     

Radioimmunoassay for the determination of loganin and the biotransformation of loganin to secologanin by plant cell cultures

A radioimmunoassay technique has been developed for the quantitative measurement of loganin in crude extracts from both fresh and dried material of whole plants and cultivated plant cells. The assay makes use of 6′-carboxyloganin which is rendered immunogenic through linkage to bovine serum albumin. The tracer molecule was synthesized via periodate opening of the glucose moiety of loganin and subsequent reduction with sodium borotritide of high specific activity. The rabbit antibodies had a high affinity (K_a = 1.6 × 10⁹1/mol) for loganin and permitted the detection of as little as 0.1 ng per 0.05 ml of sample. The antiserum was highly specific for loganin and its aglycone, with only 10-hydroxyloganin and 7-epi-loganin showing a substantial cross reactivity. A number of cell cultures of the Caprifoliaceae were tested for their ability to transform added loganin to secologanin. By labelled precursor feeding experiments members of the genera Weigelia, Lonicera, Hydrangea and Symphoricarpus were found to open the cyclopentane ring of loganin. The time course of the biotransformation of loganin was monitored using radioimmunoassays for both loganin and secologanin and cell cultures of Lonicera tatarica as biological material.     

High‐throughput screening of optimal solution conditions for structural biological studies by fluorescence correlation spectroscopy

Protein aggregation is an essential molecular event in a wide variety of biological situations, and is a causal factor in several degenerative diseases. The aggregation of proteins also frequently hampers structural biological analyses, such as solution NMR studies. Therefore, precise detection and characterization of protein aggregation are of crucial importance for various research fields. In this study, we demonstrate that fluorescence correlation spectroscopy (FCS) using a single‐molecule fluorescence detection system enables the detection of otherwise invisible aggregation of proteins at higher protein concentrations, which are suitable for structural biological experiments, and consumes relatively small amounts of protein over a short measurement time. Furthermore, utilizing FCS, we established a method for high‐throughput screening of protein aggregation and optimal solution conditions for structural biological experiments.     

Polyamines-an improved automated ion-exchange method

An accurate, precise, and improved automated cation-exchange chromatographic method with ninhydrin detection for the analysis of di- and polyamines (putrescine, cadaverine, spermidine, and spermine) has been developed. We have shown that different types of biological fluids such as urine, blood plasma, blood sera, tissue extracts, and cancer cell culture media can be analyzed under identical chromatographic conditions. The simplicity and precision of the method was achieved by eliminating the sample pre-separation and using an internal standard technique. Thus, not only has the sample preparation been simplified, but the accuracy and precision and sensitivity of the method have been greatly improved. Twenty-four unattended analyses were performed each day. With minor modifications of the instrument a two-fold analytical output can be achieved with analysis time cut to 30 min. The ruggedness and applicability of the method has been demonstrated in our laboratory during the past six months. More than two thousand urine and hundreds of other physiological samples have been analyzed by this method with a relative standard deviation from 3.3 to 7.8%, and recoveries of 94 to 97%.This automated ion-exchange chromatographic method for the polyamines will be useful to researchers in biological markers programs for monitoring the course of cancer and effectiveness of chemotherapy.     

Rapid diagnosis of phenylketonuria and other aminoacidemias by quantitative analysis of amino acids in neonatal blood spots by gas chromatography-mass spectrometry

A reversed-phase HPLC method compatible with evaporative light scattering (ELS) and electrospray mass spectrometric (ES-MS) detection was developed for separation of phosphatidylserine (PS) molecular species. The method was optimised for separation of three disaturated synthetic species: dipalmitoyl glycerophosphoserine, palmitoyl-stearoyl glycerophosphoserine and distearoyl glycerophosphoserine using isocratic elution with a mixture of 2-propanol, tetrahydrofuran and ammonium formate. Baseline separation was obtained on three different columns: one polystyrene/divinylbenzene (PS/DVB) column and two silica based C(18) and C(30) columns. The best chromatographic resolution was achieved with the C(30) column. The limit of detection for DPPS was 5 microg/ml (S/N=3) with ELS detection and 0.1 microg/ml (S/N=3) with negative ion ES-MS in the single ion monitoring mode. Baseline separation of the five main species in a biological PS sample, bovine brain PS, was obtained with the PS/DVB column. Species identification was done by using the retention times of the intact PS species and their corresponding carboxylate anion fragments obtained by in-source fragmentation. Data have shown that individual PS species can be identified by their retention times using direct ELS detection in a mixture of disaturated PS species. However, for the bovine brain PS electrospray-MS detection was necessary for species identification due to the many possible fatty acid combinations in biological PS.     

A novel rich source of human mesenchymal stem cells from the debris of bone marrow samples

The debris from human bone marrow (BM) samples is generally filtered out and discarded prior to isolation of mesenchymal stem cells (MSCs). The purpose of this study is to develop a method to harvest MSCs from the debris and investigate their biological characteristics compared with the marrow counterparts. The BM tissue fragments were digested with collagenase and this treatment yielded mononuclear cells half to those from the corresponding filtered BM. The frequencies of colony-forming unit-fibroblast in these two cell populations were not significantly different. MSCs of two origins exhibited similar morphological and phenotypic features. Fluorescent dye-dilution assay showed that they grew at comparable rates both in the primary and passaging cultures. Further, they could be induced into osteoblasts, chondroblasts and adipocytes, as revealed by histological and molecular examinations. Thus, BM tissue fragments may serve as a new source of MSCs in the settings of bench experiments and clinical trials.     

Evaluation of killing, superoxide anion and nitric oxide production by Leishmania infantum-infected dog monocytes

Protozoa of the genus Leishmania infect reticuloendothelial cells of several mammalian species, including dogs, in which they often give rise to a chronic, not self-healing visceral disease. The parasitocidal mechanism of peripheral blood monocytes towards Leishmania in the dog has not been investigated in detail. Consequently, Leishmania infantum-infected monocyte cultures of healthy dogs were evaluated using the following parameters: (1) phagocytosis and killing capacities; (2) oxidative burst, in terms of superoxide anion (O2-) release, and (3) nitric oxide (NO) activity, in terms of nitrite (NO2-) production in the presence or absence of the NO synthase inhibitor NG-monomethyl-L-arginine (NGMMLA). Parallel experiments were performed on monocytes stimulated with supernatants of concanavalin A-activated PBMC and on unstimulated monocytes. The amount of IFN-gamma in PBMC supernatants used for monocyte activation was determined by a biological assay on a canine Madin Darby cell line. Results demonstrated that phagocytosis, killing capacity and O2- production significantly increased in monocytes stimulated with supernatants, in comparison with unstimulated cells. A positive correlation was observed between the killing capacity, the O2- production and the amount of IFN-gamma in PBMC supernatants employed for monocyte activation. No significant differences were observed in NO production between unstimulated and stimulated cultures, or between the same cultures with and without NGMMLA. Finally, the killing percentage was similar in the presence or absence of NGMMLA, suggesting that in this experimental model peripheral blood dog monocytes lack NO-mediated killing.     

Analysis of 3-nitrotyrosine in biological fluids and protein hydrolyzates by high-performance liquid chromatography using a postseparation, on-line reduction column and electrochemical detection: results with various nitrating agents.

Nitric oxide reacts rapidly with superoxide to form the strong nitrating agent peroxynitrite, which is responsible for much of the tissue damage associated with diverse pathophysiological conditions such as inflammation. The occurrence of free or protein-bound nitrotyrosine (NTYR) has been considered as evidence for in vivo formation of peroxynitrite. However, various agents can nitrate tyrosine, and their relative significance in vivo has not been determined due to lack of a sensitive method to analyze NTYR in tissue proteins and biological fluids. We have developed a new HPLC-electrochemical detection method to analyze NTYR in protein hydrolyzates or biological fluids. The sample is injected directly into a reversed-phase HPLC column and NTYR is subsequently reduced by a platinum column to 3-aminotyrosine, which is quantified with an electrochemical detector. The method is simple, selective, and sensitive (detection limit, 0.1 pmol per 20-microl injection). We have applied this method to compare in vitro the ability of various nitrating agents to form NTYR in bovine serum albumin and human plasma. Yields of NTYR formed in human plasma proteins incubated with 1 or 10 mM nitrating agent decreased in the following order: synthetic peroxynitrite > 3-morpholinosydonimine, a generator of both NO and superoxide > Angeli's salt, which forms nitroxyl anion (NO-) > spermine-NONOate, which releases NO > sodium nitrite plus hypochlorite, which forms the nitrating agent nitryl chloride (NO2Cl). A simple purification method using a C18 Sep-Pak cartridge is also described for analysis of free NTYR in human plasma.     

Bayesian hierarchical modeling for time course microarray experiments

Time course microarray experiments designed to characterize the dynamic regulation of gene expression in biological systems are becoming increasingly important. One critical issue that arises when examining time course microarray data is the identification of genes that show different temporal expression patterns among biological conditions. Here we propose a Bayesian hierarchical model to incorporate important experimental factors and to account for correlated gene expression measurements over time and over different genes. A new gene selection algorithm is also presented with the model to simultaneously identify genes that show changes in expression among biological conditions, in response to time and other experimental factors of interest. The algorithm performs well in terms of the false positive and false negative rates in simulation studies. The methodology is applied to a mouse model time course experiment to correlate temporal changes in azoxymethane-induced gene expression profiles with colorectal cancer susceptibility.     

Microtiter Method for the Evaluation of Viable Cells in Bacterial Cultures

A microtiter technique was investigated as a means of evaluating viable cells in bacterial cultures. Parallel experiments were performed employing the conventional agar plate method along with the microtiter procedure. Statistical analyses showed that the correlation between the two methods was highly significant. With this new method, many samples were analyzed simultaneously, and readable results were obtained in 12 to 15 hr. Other advantages of this method were substantial savings of time, space, and materials. Also, the applicability of this method to estimates of mixed bacterial populations was demonstrated by studying the associative growth of two bacterial cultures.     

Analytical ultracentrifugation and the characterization of chromatin structure

This mini review consists of two parts. The first part will provide a brief overview of the theoretical aspects involved in the two kinds of experiments that can be conducted with the analytical ultracentrifuge (sedimentation velocity and sedimentation equilibrium) as they pertain to the study of chromatin. In the following sections, I describe the analytical ultracentrifuge experiments which, in my opinion, have contributed the most to our understanding of chromatin. Few other biophysical techniques, with the exception of X-ray scattering and diffraction, have contributed as extensively as the analytical ultracentrifuge to the characterization of so many different aspects of chromatin structure. In the course of his scientific career, Professor Henryk Eisenberg has made many important contributions to the theoretical aspects underlying ultracentrifuge analysis, especially in the analysis of solutions of polyelectrolytes and biological macromolecules [H. Eisenberg, Biological macromolecules and polyelectrolytes in solution, Clarendon Press, Oxford, 1976]. As an example he has devoted some of his research effort to the characterization of chromatin in solution. This review includes these important contributions.     

Metabolic profiling reveals that time related physiological changes in mammalian cell perfusion cultures are bioreactor scale independent

Metabolic profiling was used to characterize the time course of cell physiology both in laboratory- and manufacturing-scale mammalian cell perfusion cultures. Two independent experiments were performed involving three vials from the same BHK cell bank, used to inoculate three laboratory-scale bioreactors, from which four manufacturing-scale cultures were initiated. It was shown that metabolomic analysis can indeed enhance the prime variable dataset for the monitoring of perfusion cultures by providing a higher resolution view of the metabolic state. Metabolic profiles could capture physiological state shifts over the course of the perfusion cultures and indicated a metabolic “signature” of the phase transitions, which was not observable from prime variable data. Specifically, the vast majority of metabolites had lower concentrations in the middle compared to the other two phases. Notably, metabolomics provided orthogonal (to prime variables) evidence that all cultures followed this same metabolic state shift with cell age, independently of bioreactor scale.