Computational modeling of the PKA-RN was performed by extending the well-established "discrete dynamics modeling framework" [ 1, 38, 71, 90] in order to take into account the fact that gene expression measurements of batch cultures average out individual expression patterns.
Thus, the gene expression profile of batch 4 overlapped significantly (p<10−7) with both induced and repressed synovial sarcoma gene signatures, whereas that of batch 3 overlapped significantly with the list of repressed (p<10−16) but not with that of induced SS genes.
The sRNAs with significant expression changes during the fermentation are mainly a result of differential expression between batch exponential and stationary phases (Table 2), where seventy-six oft of 462 sRNAs (16.5 %) show differential expression between these two growth phases.
Redox difference spectroscopy was used to analyze the expression of cytochromes in batch cultures that were incubated under various initial oxygen concentrations ranging from 3 to 21 vol%.
Effectively, while Murphy et al. [ 14] limited their analysis of Gadd153 expression to 6 h after feeding, Lengwehasatit and Dickson [ 13] did a more thorough analysis of Gadd153 expression over several days of batch culture, but performed repeated nutrient supplementations during the culture period.
At 36 h post transduction, transduced cells were treated with 1 μg/ml of puromycin for stable expression in batch cultures.
To determine if tub var alleles on average substantially reduce gene expression, we assayed tube expression in batches of embryos from tub var/tub null females by both quantitative RT-PCR (qRT-PCR) of first-strand cDNA and immunoblotting of protein in embryo extract.
We began issuing survey packs to participants identified from the expression-of-interest database in weekly batches from the beginning of May 2009 and continued until the end of October.
The nine sRNAs with differential expression in fed-batch versus batch exponential phases are novel except for SroA and SroC and may have potential utility in the regulation of metabolism in the fed-batch phase.
We monitored at high frequency the expression of 34 marker genes in batch, fed-batch and continuous cultures of the filamentous fungus Trichoderma reesei by the transcriptional analysis method TRAC (TRanscript analysis with the aid of Affinity Capture).
Based on the expression of these genes during the batch, fed-batch and continuous processes, 30% dissolved oxygen (DO) concentration even at relatively high cell density (DW ~ 20 g l-1) is apparently sufficient to maintain aerobic culture conditions, although at lower density (4 g l-1) and higher DO (80%) the expression of these genes was more than 2-fold lower.
