Rapid and multiplexed transcript analysis of microbial cultures using capillary electophoresis-detectable oligonucleotide probe pools

Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains

“…This indicates that the adjustment of the glycolytic flux to fermentative conditions is to a large extent determined by changes in the levels of metabolic intermediates and effectors; that is, flux control is primarily at the metabolic level. This finding is consistent with earlier more detailed studies on glycolysis [18][19][20][21][22] . The metabolome data, however, do not provide any insight into the differences in fluxes between the two strains, as there are very small differences in metabolite levels between the different strains, and most differences indicate slightly higher metabolite concentrations in the YSBN2 strain, which has lower fluxes.…”

“…Thus, one could speculate whether the ability of CEN.PK to grow faster when resources are abundant has come at the expense of efficiency in carbon and energy utilization under nutrient limitation. Our analysis involved sampling for determination of mRNA levels, using DNA arrays (Affymetrix and Agilent), quantitative PCR (qPCR) and TRAC (TRanscript analysis with Affinity Capture) 18 ; enzyme activities, using optimized and in vivo-like assays; and endometabolome, using several analytical platforms including liquid chromatography-mass spectrometry (LC-MS), gas chromatography time-of-flight mass spectrometry (GC-TOF), two dimensional gas chromatography coupled to time-of-flight mass spectrometry (GCxGC-TOF), nuclear magnetic resonance (NMR), high-performance liquid chromatography-diode array detection (HPLC-DAD) and enzymatic analysis. Table 2 gives an overview of the sampling procedure, which was designed taking into account the large number of samples needed and the fast turnover of some molecules to be analysed (for example, intracellular metabolites).…”

“…r-project.org). A subset of about 40 genes (selected on the basis of results from microarray analysis) were measured using quantitative reverse transcription PCR (qRT-PCR) at Vrije Universiteit Amsterdam (VUA) and Bogazici University (BU), as well as by TRanscript analysis with the aid of the Affinity Capture (TRAC) method 18 at VTT Technical Research Centre of Finland (VTT). Five housekeeping genes (TOA2, IPP1, PDA1, PDI1 and SHE10) were carefully chosen and pooled as the reference in the qPCR analysis.…”

10 Genomics Analysis of Biocontrol Species and Industrial Enzyme Producers from the Genus Trichoderma

“…Although these analyses only yielded a small number of regulated genes compared to microarrays, they nevertheless revealed involvement of novel genes (Mukherjee et al 2007;Schmoll et al 2004;Schuster et al 2011). A medium-scale approach for transcript analysis in multiple samples was provided by the TRAC (transcript analysis with the aid of affinity capture) system, which allows for simultaneous analysis of 96 samples for around 30 genes (Kataja et al 2006;Rautio et al 2006Rautio et al , 2007. After publication of the fully sequenced genome of T. reesei (Martinez et al 2008) and later also of other Trichoderma spp., construction of full-genome microarrays became possible (Arvas et al 2011;Häkkinen et al 2012;Tisch et al 2011b), followed by large-scale sequencing and transcriptome analysis, which is a standard technique today.…”

Combined capillary electrophoresis and DNA‐fluorescence in situ hybridization for rapid molecular identification of Salmonella Typhimurium in mixed culture

“…Recently, CE-based analyses have been used for genetic detection and/or characterization of pathogenic bacteria or other microorganisms. These approaches include detection of "signature" single strand conformational polymorphisms (SSCPs) generated via PCR from bacterial 16S or 16S-23S spacer region rRNA [5], use of a combined PCR-ligase detection reaction-CE approach targeting bacterial 16S rRNA genes [6], in-solution hybridization to mRNA with fluorescently labeled riboprobes, followed by detection of probe-target hybrids via CE-LIF [7] and multiplex mRNA transcript analysis of microbial cultures using CE-detectable oligonucleotide probe pools [8].…”