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Slow Adaptive Response of Budding Yeast Cells to Stable Conditions of Continuous Culture Can Occur Without Genome Modifications

ABSTRACT: Slow Adaptive Response of Budding Yeast Cells to Stable Conditions of Continuous Culture Can Occur Without Genome Modifications

PROVIDER: PRJNA681181 | ENA |

REPOSITORIES: ENA

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Slow Adaptive Response of Budding Yeast Cells to Stable Conditions of Continuous Culture Can Occur Without Genome Modifications

Project description:Continuous cultures assure the invariability of environmental conditions and the metabolic state of cultured microorganisms, whereas batch-cultured cells undergo constant changes in nutrients availability. For that reason, continuous culture is sometimes employed in the whole transcriptome, whole proteome, or whole metabolome studies. However, the typical method for establishing uniform growth of a cell population, i.e., by limited chemostat, results in the enrichment of the cell population gene pool with mutations adaptive for starvation conditions. These adaptive changes can skew the results of large-scale studies. It is commonly assumed that these adaptations reflect changes in the genome, and this assumption has been confirmed experimentally in rare cases. Here we show that in a population of budding yeast cells grown for over 200 generations in continuous culture in non-limiting minimal medium and therefore not subject to selection pressure, remodeling of transcriptome occurs, but not as a result of the accumulation of adaptive mutations. The observed changes indicate a shift in the metabolic balance towards catabolism, a decrease in ribosome biogenesis, a decrease in general stress alertness, reorganization of the cell wall, and transactions occurring at the cell periphery. These adaptive changes signify the acquisition of a new lifestyle in a stable nonstressful environment. The absence of underlying adaptive mutations suggests these changes may be regulated by another mechanism.

2020-12-02 | GSE162203 | GEO

Slow Adaptive Response of Budding Yeast Cells to Stable Conditions of Continuous Culture Can Occur without Genome Modifications.

| S-EPMC7759791 | biostudies-literature

Tumor Budding in Patients With Colorectal Cancer Under Different MMR Status

Project description:This study investigates the ability of tumor budding to identify prognosis in different MMR states and different levels of tumor lymphocyte infiltration. Tumor budding is usually defined as an isolated single cancer cell or a cluster of up to four cancer cells located at the front of an infiltrating tumor.

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Differences in gene expression between fast and slow muscle or between normal and denervated slow muscles

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Post-transcriptional splicing can occur in a slow-moving zone around the gene

Project description:Splicing is the stepwise molecular process by which introns are removed from pre-mRNA and exons are joined together to form mature mRNA sequences. The ordering and spatial distribution of these steps remain controversial, with opposing models suggesting splicing occurs either during or after transcription. We used single molecule RNA FISH, expansion microscopy, and live cell imaging to reveal the spatiotemporal distribution of nascent transcripts in mammalian cells. At super-resolution levels, we found that pre-mRNA formed clouds around the transcription site. These clouds indicate the existence of a transcription site proximal zone through which RNA move more slowly than in the nucleoplasm. Full length pre-mRNA undergo continuous splicing as they move through this zone following transcription, suggesting a model in which splicing can occur post-transcriptionally but still within the proximity of the transcription site, thus seeming co-transcriptional by most assays. These results may unify conflicting reports of co-transcriptional versus post-transcriptional splicing.

2024-02-02 | GSE254859 | GEO

Differences in gene expression between fast and slow muscle or between normal and denervated slow muscles

Project description:Fast and slow skeletal muscles show different characteristics and phenotypes. This data obtained from microarray includes the comparison of normal fast plantaris and slow soleus muscles of adult rats. Characters of slow muscle are strongly dependent on the level of muscular activity. Denervation silences the muscular activity. Therefore, we determined the effects of denervation on gene expression in slow soleus muscle of adult rats. Denervation was performed by transection (~5 mm) of left sciatic nerve at the gluteal level. No treatments were made in the normal control rats. Sampling of soleus and/or plantaris was performed in both normal and experimental groups 28 days after the surgery.

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DBP1 in budding yeast

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Transcription profiling of human diaphragm Chronic Obstructive Pulmonary Disease (COPD) patients vs. controls to study diaphragm muscle fast to slow adaptive transformation.

Project description:Diaphragm muscles in Chronic Obstructive Pulmonary Disease (COPD) patients undergo an adaptive fast to slow transformation that includes cellular adaptations. This project studies the signaling mechanisms responsible for this transformation.

2007-10-25 | E-GEOD-475 | biostudies-arrayexpress

Small RNAs in budding yeast

Project description:RNAi, a gene-silencing pathway triggered by double-stranded RNA, is conserved in diverse eukaryotic species but has been lost in the model budding yeast, Saccharomyces cerevisiae. We report that RNAi is present in other budding-yeast species, including Saccharomyces castellii and Candida albicans. These species use noncanonical Dicer proteins to generate siRNAs, which mostly correspond to transposable elements and Y´ subtelomeric repeats. In S. castellii, RNAi mutants are viable but have excess Y´ mRNA levels. In S. cerevisiae, introducing Dicer and Argonaute of S. castellii restores RNAi, and the reconstituted pathway silences endogenous retrotransposons. These results identify a novel class of Dicer proteins, bring the tool of RNAi to the study of budding yeasts, and bring the tools of budding yeast to the study of RNAi.

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