Effects of cell culture conditions on primary rat hepatocytes—Cell morphology and differential gene expression

Toxicology ◽  
2006 ◽  
Vol 218 (2-3) ◽  
pp. 205-215 ◽  
Author(s):  
G TUSCHL ◽  
S MUELLER
Keyword(s):  
Gene Expression ◽  
Cell Culture ◽  
Differential Gene Expression ◽  
Cell Morphology ◽  
Rat Hepatocytes ◽  
Culture Conditions ◽  
Primary Rat Hepatocytes ◽  
Differential Gene ◽  
Cell Culture Conditions

scholarly journals Select Gene Expression Across Variable PrPSc Permissive Ovine Microglia

2019 ◽  
Author(s):  
Valerie McElliott ◽  
Kelcey Dinkel ◽  
Zachary Nesbit ◽  
James B. Stanton
Keyword(s):  
Gene Expression ◽  
Cell Culture ◽  
Prion Protein ◽  
Differential Gene Expression ◽  
Cellular Prion Protein ◽  
Transmissible Spongiform Encephalopathies ◽  
Specific Cell ◽  
Culture Models ◽  
Differential Gene ◽  
Cell Culture Models

Abstract Abstract Abstract Background: Transmissible spongiform encephalopathies (TSEs) are a group of fatal, neurodegenerative diseases that affect multiple species, including sheep, cattle, and humans. A misfolded, pathogenic isoform (PrPD) of the normal, host-encoded, cellular prion protein (PrPC) is the causative agent for TSEs. While there have been advances in understanding TSEs, antemortem diagnostic tests are limited in many species, and there are no effective treatment protocols. Filling these reagent gaps will require knowledge of the molecular pathophysiology of PrPD accumulation. Previous work has suggested that the extracellular matrix (i.e., fibronectin 1) and physiological functions (i.e., cell division) maybe key factors for cellular prion permissibility, at least in specific cell culture models. Using a natural scrapie isolate, six immortalized, ovine microglial clones, of varying permissiveness to classical scrapie were evaluated for differential gene expression in seven genes based on previous RNASeq studies (fibronectin 1 [FN1], follistatin-like 1 [FSTL1], osteonectin [SPARC], survivin [BIRC5], syndecan 4 [SDC4], AXL receptor tyrosine kinase [AXL], and prion protein [PRNP]), and to determine correlations with prion permissibility. Results: Significant differential gene expression was frequently observed for survivin, follistatin-like 1 and osteonectin between clones, and when evaluated relative to PRNP expression. However, only fibronectin 1 and survivin were significantly correlated with prion permissibility, and only when evaluated relative to PRNP expression. Inoculation had a significant effect on follistatin-like 1, syndecan 4, and osteonectin. Conclusions: Similar to previous studies in other systems, fibronectin and mitotic rate show promise as potential determinants of prion permissibility in ovine microglia. As determinants of prion permissibility, the expression of fibronectin 1 and survivin coupled with PRNP could be utilized as biomarkers for detection of prion permissibility phenotype in ovine microglia, and perhaps other cell culture models of prion disease.

scholarly journals Cell culture-based profiling across mammals reveals DNA repair and metabolism as determinants of species longevity

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Siming Ma ◽  
Akhil Upneja ◽  
Andrzej Galecki ◽  
Yi-Miau Tsai ◽  
Charles F Burant ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Culture ◽  
Dna Repair ◽  
Protein Transport ◽  
Global Gene Expression ◽  
Culture Conditions ◽  
Identical Cell ◽  
Species Specific ◽  
Cell Culture Conditions ◽  
Species Longevity

Mammalian lifespan differs by >100 fold, but the mechanisms associated with such longevity differences are not understood. Here, we conducted a study on primary skin fibroblasts isolated from 16 species of mammals and maintained under identical cell culture conditions. We developed a pipeline for obtaining species-specific ortholog sequences, profiled gene expression by RNA-seq and small molecules by metabolite profiling, and identified genes and metabolites correlating with species longevity. Cells from longer lived species up-regulated genes involved in DNA repair and glucose metabolism, down-regulated proteolysis and protein transport, and showed high levels of amino acids but low levels of lysophosphatidylcholine and lysophosphatidylethanolamine. The amino acid patterns were recapitulated by further analyses of primate and bird fibroblasts. The study suggests that fibroblast profiling captures differences in longevity across mammals at the level of global gene expression and metabolite levels and reveals pathways that define these differences.

scholarly journals Inhibition of JAK-STAT ERK/MAPK and Glycogen Synthase Kinase-3 Induces a Change in Gene Expression Profile of Bovine Induced Pluripotent Stem Cells

2016 ◽  
Vol 2016 ◽  
pp. 1-11 ◽  
Author(s):  
Luis F. Malaver-Ortega ◽  
Huseyin Sumer ◽  
Jun Liu ◽  
Paul J. Verma
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Cell Culture ◽  
Induced Pluripotent Stem Cells ◽  
Gene Expression Profile ◽  
Pluripotent Stem Cells ◽  
Culture Conditions ◽  
Nuclear Reprogramming ◽  
Induced Pluripotent ◽  
Cell Culture Conditions

Pluripotent stem cells (PSCs) fall in two states, one highly undifferentiated, the naïve state, and the primed state, characterized by the inability to contribute to germinal lineage. Several reports have demonstrated that these states can be modified by changes to the cell culture conditions. With the advent of nuclear reprogramming, bovine induced pluripotent stem cells (biPSCs) have been generated. These cells represent examples of a transient-intermediate state of pluripotency with remarkable characteristics and biotechnological potential. Herein, we generated and characterized biPSC. Next, we evaluated different culture conditions for the ability to affect the expression of the set of core pluripotent transcription factors in biPSC. It was found that the use of 6-bromoindirubin-3-oxime and Sc1 inhibitors alone or in combination with 5-AzaC induced significantly higher levels of expression of endogenousREX1,OCT4,NANOG, andSOX2. Furthermore, LIF increased the levels of expression ofOCT4andREX1, compared with those cultured with LIF + bFGF. By contrast, bFGF decreased the levels of expression for bothREX1andOCT4. These results demonstrate that the biPSC gene expression profile is malleable by modification of the cell culture conditions well after nuclear reprogramming, and the culture conditions may determine their differentiation potential.

GENETIC LEARNING FOR BIOLOGICALLY INSPIRED AESTHETIC PROCESSES

2006 ◽  
Vol 15 (04) ◽  
pp. 577-598 ◽  
Author(s):  
GARY GREENFIELD
Keyword(s):  
Gene Expression ◽  
Genetic Algorithm ◽  
Differential Gene Expression ◽  
Cell Morphology ◽  
Biologically Inspired ◽  
Interactive Genetic Algorithm ◽  
Fitness Functions ◽  
Aesthetic Results ◽  
Differential Gene ◽  
Evolutionary Art

We investigate the use of the non-interactive genetic algorithm as a tool in evolutionary art for evolving aesthetic images. We consider two problem domains. Our first uses a modification of a model for differential gene expression in order to simulate cell morphology and evolve images consisting of matrices of cells meeting our subjective aesthetic criteria. Our second uses a modification of a model for simulating ants that can deposit and follow scent (in the guise of color trails) in order to evolve ant paintings meeting out subjective aesthetic criteria. In both cases, we focus upon the design of fitness functions that are particularly well suited for ensuring that genetic learning can effectively guide the evolution of cellular or behavioral processes to yield aesthetic results.

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