Ontology highlight
ABSTRACT:
PROVIDER: PRJNA866088 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21118737_1.fastq.gz | Fastqsanger.gz | |||
| SRR21118737_2.fastq.gz | Fastqsanger.gz |
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Project description:Over the past three decades, due to the universal application of Pichia yeast in the fermentation industry as well as the establishment of Pichia pastoris fermentation process for more than 30 years, the technology of the whole process has become very mature and has now reached a stagnated period of growth. However, studies and research conducted on the genomics of the classic fermentation process and the uncovering of the biological phenomena in the fermentation process from the point of view of high-throughput gene or protein is still in its early stages, and there is still insufficient data within this field. First, in collaboration with Agilent Company, we designed and prepared an expression microarray that could be used for the detection of Pichia pastoris transcriptomics. The transcriptomic changes in the five key technology steps (time points), during the fermentation process of Pichia pastoris would then be detected with the aid of an expression microarray. The five key steps of technology described above formed two important biological processes, namely, the limiting carbon source replacement and secondly, the fermentative production of exogenous proteins. The biological phenomena involved in these two processes were displayed and analyzed at the transcriptional level. In addition to this, with regard to the most important function in the fermentation process of Pichia pastoris, oxid-reduction, the metabolic drift process was analyzed and the important genes that might dominate the changes in the metabolic flux were discovered creatively by using the function tree method in this paper. This study was undertaken from the point of view of the transcriptome and the biological phenomena in the fermemntation process of Pichia pastoris. Both of which, were thoroughly explained during this study. The hope is for many more researchers to optimize the strain fermentation process, to produce proteins at the genetic level, as well as providing and obtaining new perspectives and detailed scientific data for the continued development within this field.
2014-04-18 | GSE56873 | GEO
Project description:To understand the complex mechanism of estrogen action, multiple assays based on different biological principles is important. Here, multiple assays based on cell, protein and transcription assays were used to evaluate estrogenic activity of soymilk extracts before and after fermentation, and four soy compounds, genistein and daidzein, and their glycosides, genistin and daidzin, respectively. The data obtained by a transcription assay, RNA-sequencing (RNA-seq), was further examined by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis to understand cell functions, i.e. biological processes and metabolic pathways. Among the cell functions identified, the sets of genes for cell division/cell cycle and DNA replication/DNA repair are significantly up-regulated, whereas those for autophagy are significantly down-regulated, which explains well the enhanced activity of cell proliferation by these materials. The applications of estrogenic activity of soymilk extracts and soy flavonoids, and the contribution of fermentation, include pharmacological benefits, such as bone protection/bone regeneration, cancer chemoprevention, neuroprotection and the treatment of menopausal syndromes.
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Project description:Lactococcus lactis is the main bacterium used for food fermentation and is a candidate for probiotic development. In addition to fermentation growth, supplementation with heme in aerobic conditions activates a cytochrome oxidase, which promotes respiration metabolism. In contrast to fermentation in which cells consume energy to produce mainly lactic acid, respiration metabolism dramatically changes energy metabolism, such that massive amounts of acetic acid and acetoin are produced at the expense of lactic acid. Our goal was to investigate the metabolic changes that correlate with significantly improved growth and survival during respiration growth. Using transcriptional time course analyses, mutational analyses, and promoter reporter fusions, we uncover two main pathways that can explain the robust growth and stability of respiration cultures: The acetate pathway contributes to biomass yield in respiration, without affecting medium pH. The acetoin pathway allows cells to cope with internal acidification, which directly affects cell density and survival in stationary phase. Our results suggest that manipulation of these pathways could lead to fine tuning respiration growth, with improved yield and stability.
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Project description:Ambient temperature potentially affects all biological systems. However, the period length of circadian clocks is close to 24 h over a broad range of physiological temperatures, known as temperature compensation. The mechanism underpinning the temperature compensation remains largely unknown. Here, we show that inhibitors of time progression, TIMING OF CAB EXPRESSION 1 (TOC1) and PSEUDO-RESPONSE REGULATOR 5 (PRR5) proteins, are required for the temperature compensation in Arabidopsis thaliana (Arabidopsis). Compared to the wild-type, the prr5 toc1 double mutant shows a short period at high temperatures. TOC1 and PRR5 proteins are ubiquitinated and degraded at low temperatures, by a ubiquitin E3 ligase LOV KELCH PROTEIN 2 (LKP2) that was sought as a minor player in the clock. The lkp2 mutants show long periods only at lower temperatures. Collectively, the clock keeps its periodicity against ambient temperature by the temperature-dependent quantity control of inhibitors of time progression.
DOI:10.1126/sciadv.adq0187
2024-10-04 | PXD044813 | JPOST Repository