Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles.

RNA profiling has emerged as a powerful tool to investigate the biomarker potential of human biofluids. However, despite enormous interest in extracellular nucleic acids, RNA sequencing methods to quantify the total RNA content outside cells are rare. Here, we evaluate the performance of the SMARTer Stranded Total RNA-Seq method in human platelet-rich plasma, platelet-free plasma, urine, conditioned medium, and extracellular vesicles (EVs) from these biofluids. We found the method to be accurate, precise, compatible with low-input volumes and able to quantify a few thousand genes. We picked up distinct classes of RNA molecules, including mRNA, lncRNA, circRNA, miscRNA and pseudogenes. Notably, the read distribution and gene content drastically differ among biofluids. In conclusion, we are the first to show that the SMARTer method can be used for unbiased unraveling of the complete transcriptome of a wide range of biofluids and their extracellular vesicles.

In vitro assessment of the growth and plasma membrane H+ -ATPase inhibitory activity of ebselen and structurally related selenium- and sulfur-containing compounds in Candida albicans.

Ebselen (EB, compound 1) is an investigational organoselenium compound that reduces fungal growth, in part, through inhibition of the fungal plasma membrane H+ -ATPase (Pma1p). In the present study, the growth inhibitory activity of EB and of five structural analogs was assessed in a fluconazole (FLU)-resistant strain of Candida albicans (S2). While none of the compounds were more effective than EB at inhibiting fungal growth (IC50  âˆ¼ 18 µM), two compounds, compounds 5 and 6, were similar in potency. Medium acidification assays performed with S2 yeast cells revealed that compounds 4 and 6, but not compounds 2, 3, or 5, exerted an inhibitory activity comparable to EB (IC50  âˆ¼ 14 µM). Using a partially purified Pma1p preparation obtained from S2 yeast cells, EB and all the analogs demonstrated a similar inhibitory activity. Taken together, these results indicate that EB analogs are worth exploring further for use as growth inhibitors of FLU-resistant fungi.

Assessment of Antigen-Specific Cellular Immunogenicity Using Intracellular Cytokine Staining, ELISpot, and Culture Supernatants.

Quantification of cytokine production by CD4 and CD8 T cells after in vitro recall stimulation with the immunizing antigen is a powerful approach to characterize the cellular immune responses to immunization. Here we describe three complementary methods for such quantification including flow cytometric analysis of cytokine production by intracellular staining, ELISpot determination of the numbers of cytokine-producing cells, and generation of secreted cytokines and chemokines in culture supernatants for analysis by ELISA and/or cytometric bead arrays.

Assessment of the effect of a Salmonella enterica ser. Typhimurium culture supernatant on the single-cell lag time of foodborne pathogens.

The objective of this study was the in vitro evaluation of the effect of a cell-free microbial supernatant, produced by a luxS-positive Salmonella enterica ser. Typhimurium strain, on the single-cell growth kinetic behavior of two strains of S. enterica (serotypes Enteritidis and Typhimurium) and a methicillin-resistant Staphylococcus aureus strain. The single-cell lag time (λ) of the pathogens was estimated in the absence and presence (20% v/v) of microbial supernatant based on optical density measurements. As demonstrated by the obtained results, the tested microbial supernatant had a strain-specific effect on the single-cell λ and its variability. Although the mean λ values were similar in the absence and presence of microbial supernatant in the case of Salmonella Enteritidis, a significant (P ≤ 0.05) reduction and increase in the mean value of this parameter in the presence of microbial supernatant were observed for Salmonella Typhimurium and St. aureus, respectively. With regard to the effect of the tested microbial supernatant on the single-cell variability of λ, similar λ distributions were obtained in its absence and presence for S. Enteritidis, while considerable differences were noted for the other two tested organisms; the coefficient of variation of λ in the absence and presence of microbial supernatant was 41.6 and 69.8% for S. Typhimurium, respectively, with the corresponding values for St. aureus being 74.0 and 56.9%. As demonstrated by the results of bioassays, the tested microbial supernatant exhibited autoinducer-2 activity, indicating a potential association of such quorum sensing compounds with the observed effects. Although preliminary in nature, the collected data provide a good basis for future research on the role of quorum sensing in the single-cell growth behavior of foodborne pathogens.

Comparison of five different C18 HPLC analytical columns for the analysis of ochratoxin A in different matrices.

The performance of five different C18 chromatography analytical columns with different lengths, particle sizes and porosities were compared for analysis of ochratoxin A (OTA) in fungal cultures and raisin samples. Chromatographic parameters including retention time, limit of detection, limit of quantification, number of theoretical plates and reduced plate height were obtained and compared. This showed that, compared with traditional columns, shorter ones (100 and 75mm×4.6mm) with 2.7µm solid core particles are suitable for analysis of OTA in different matrices and allows a reduction of the total analysis time by approximately 50% without any detrimental effect on performance. This leads to significant reduction in analysis costs by savings in use of organic solvents and increasing the total number of analyses per day. The capability of these columns for analyzing samples, from different matrices, was assessed by analyzing OTA-contaminated samples from cultures of Aspergillus westerdijkiae and Aspergillus niger grown on a defined nutritional media (yeast extract sucrose agar) and from natural and OTA spiked raisins.

Co-assessment of cell cycle and micronucleus frequencies demonstrates the influence of serum on the in vitro genotoxic response to amorphous monodisperse silica nanoparticles of varying sizes.

Serum proteins have been shown to modulate the cytotoxic and genotoxic responses to nanomaterials. The aim was to investigate the influence of serum on the induction of micronuclei (MN) by nanoparticles (NPs) of different sizes. Therefore, A549 human lung carcinoma cells and amorphous monodisperse silica nanoparticles (SNPs) were used as models. Assessment of the cell viability, cell cycle changes and induction of MN by SNPs ranging from 12 to 174 nm was performed in presence or absence of serum, applying the in vitro flow cytometry-based MN assay. Here, it has been demonstrated that serum has an influence on these end points, with a lower cell viability in absence of serum compared with the presence of serum. Further, cell cycle changes, specifically, G1 and S-phase arrest, were observed in absence of serum for four out of six SNPs tested. A size-dependent MN induction was observed: larger SNPs being more active in absence of serum. In addition, the serum influence was characterised by a size-dependency for cytotoxic and genotoxic effects, with a higher influence of serum for smaller particles. The data indicate that the in vitro micronucleus assay in presence and absence of serum could be advised for hazard assessment because it demonstrates a higher sensitivity in serum-free conditions than in conditions with serum. However, this recommendation applies only if the cell line used is able to proliferate under serum-free conditions because cell division is a prerequisite for MN expression.

DNA spike studies for demonstrating improved clearance on chromatographic media.

DNA spike clearance methods were used to demonstrate improved clearance factors on anion exchange and hydrophobic interaction columns used in the production of human therapeutic proteins. DNA clearance at large-scale was first measured for a monoclonal antibody expressed in Chinese Hamster Ovary (CHO) cells and an antibody fragment expressed in Escherichia coli. Small-scale spike experiments were then performed on individual chromatographic steps using host-specific DNA paired with TaqMan PCR assay methods. This approach has advantages of improved specificity, sensitivity, cost and throughput compared to other types of spike clearance methods. The anion exchange column used in the monoclonal antibody process was shown to have very high capacity for CHO DNA, resulting in greater than 7.1 log reduction. The anion exchange and hydrophobic interaction columns used in the antibody fragment process were shown to have high E. coli DNA clearance capability, with greater than 5.1 and 5.3 logs clearance, respectively. Compared to the large-scale process, higher log reduction values were achieved in small-scale spike clearance studies by challenging the chromatographic steps with load DNA levels 2-5 logs higher than the large-scale process levels. Using highly specific and sensitive spike clearance methods, we demonstrated consistently high DNA clearance factors for each of the production processes that meet industry and regulatory standards for human therapeutics. The method is applicable to a broad range of industrial scale processes where demonstration of the robustness of DNA clearance is necessary to support development or licensure of biopharmaceutical products.

Differential analysis of secondary metabolites by LC-MS following strain improvement of Streptomyces lydicus AS 4.2501.

Metabolite variations in a high-yielding mutant and its parent strain were studied by comparative LC-MS analysis after strain improvement. Streptomyces lydicus AS 4.2501-P28, a propionate-resistant mutant isolated by the high-frequency screening method using the principle of eliminating precursor inhibition effects, showed an increase of 267% in streptolydigin titre over the starting strain. Culture extracts of this mutant and its parent strain were analysed in parallel by an LC-MS technique, including full scan and extracted-ion scan, ESI-MS (electrospray-ionization MS) detection, DAD (diode-array detection) and MS2 (tandem MS) measurement. The main metabolic variations were obviously found in intermediates, metabolites and biosynthetic pathways: two unknown metabolites with the molecular [M-H]- ions at m/z 423.3 and 687.2, corresponding to two branch pathways, were blocked in the mutant, and the accumulation of a significant intermediate at m/z 363.1 [M-H]- decreased dramatically in the mutant cultures, resulting in the overproduction of streptolydigin (an antibiotic that inhibits prokaryotic RNA polymerase) in the mutant. Ion fragmentations of the tandem-MS spectra provided experimental evidence for the structural characterization of the three compounds obtained. In comparison with the traditional methods, comparative LC-MS analysis was rapid, sensitive and suitable for characterizing intermediates, metabolites and pathways for elucidation of the metabolic alterations after the isolation of improved strains.

Exposure of bronchial epithelial cells to whole cigarette smoke: assessment of cellular responses.

Cigarette smoke is composed of approximately 5% particulate phase and 95% vapour phase by weight. However, routine in vitro toxicological testing of smoke normally only measures the activity of the particulate phase. This study describes a new system for exposing cells at an air-liquid interface to serial dilutions of gaseous smoke. Confluent monolayers of NCI-H292 human lung epithelial cells on semipermeable membranes were placed in a purpose-designed Perspex chamber at an air-liquid interface. The cells were exposed to dilute whole mainstream cigarette smoke for 30 minutes, followed by a 20-hour recovery period. Firstly, high and low delivery cigarettes were compared, and cytotoxicity was determined by using the neutral red uptake assay. Clear differential cytotoxic responses were observed with the two cigarette types, which correlated positively with the concentrations of components in smoke, and particularly compounds in the vapour phase, such as aldehydes. Secondly, low doses of smoke were found to up-regulate mRNA levels of the secreted mucin, MUC5AC, and to stimulate the production of interleukin (IL)-6, IL-8 and matrix-metalloprotease-1, but had no effect on growth-related oncogene alpha. This system will facilitate further investigations into the toxicological mechanisms of cigarette smoke components, and may be useful for studying other gaseous mixtures or aerosols.

Characterization of limonin glucoside metabolites from human prostate cell culture medium using high-performance liquid chromatography/electrospray ionization mass spectrometry and tandem mass spectrometry.

The metabolism of limonin 17-beta-D-glucopyranoside (LG) by non-cancerous (RWPE-1) and cancerous (PC-3) human prostate epithelial cells was investigated using high-performance liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS) with in-source fragmentation and tandem mass spectrometry (MS/MS). During positive ion LC/ESI-MS, LG formed an abundant sodiated species ([M+Na]+) while the protonated molecule was barely observable. [M+Na]+ further fragmented into the less abundant [LARL+H]+ and a predominantly protonated aglycone molecule (limonin) due to in-source fragmentation. The major metabolite, limonin A-ring lactone (LARL), formed an abundant protonated molecule that was fragmented into a protonated molecule of limonin by loss of one molecule of water. In MS/MS by collisionally activated dissociation (CAD), LG produced the sodiated aglycone, [aglycone+Na]+, while LARL fragmented into [M+H]+ of limonin and fragment ions resulted by further loss of water, carbon monoxide and carbon dioxide, indicating the presence of oxygenated-ring structures. The limits of detection of LG were 0.4 and 20 fmol in selected-ion monitoring (SIM) and selected-reaction monitoring (SRM) detection, respectively.

Assessment of cell viability in primary neuronal cultures.

Four commonly used methods for the assessment of neuronal (or glial) cell viability are described in this unit. The MTT assay is sensitive to the function of labile mitochondrial enzymes, which typically lose activity early in the progression towards death. The lactate dehydrogenase (LDH) assay measures the appearance of this cytosolic enzyme in the bathing medium, providing a measure of plasma membrane integrity. Loss of plasma membrane integrity is also the basis of the trypan blue dye assay and the propidium iodide assay. Trypan blue staining is assessed by cell counts; propidium iodide labeling can be assessed either by cell counts, typically in conjunction with fluorescein diacetate counterstaining to identify intact cells containing adequate levels of functional esterases, or with a fluorescence plate reader.