Mechanical culture conditions effect gene expression

2001 ◽  
Author(s):  
J. Love ◽  
T. Hammond ◽  
P. Allen ◽  
L. Cubano ◽  
T. Baker ◽  
...  
Keyword(s):  
Gene Expression ◽  
Culture Conditions ◽  
Effect Gene

Mechanical culture conditions effect gene expression: gravity-induced changes on the space shuttle

2000 ◽  
Vol 3 (3) ◽  
pp. 163-173 ◽  
Author(s):  
T. G. HAMMOND ◽  
E. BENES ◽  
K. C. O’REILLY ◽  
D. A. WOLF ◽  
R. M. LINNEHAN ◽  
...  
Keyword(s):  
Gene Expression ◽  
Shear Stress ◽  
Transcription Factors ◽  
Suspension Culture ◽  
Space Shuttle ◽  
Primary Cultures ◽  
Three Dimensional ◽  
Culture Conditions ◽  
Induced Changes ◽  
Effect Gene

Hammond, T. G., E. Benes, K. C. O’Reilly, D. A. Wolf, R. M. Linnehan, J. H. Kaysen, P. L. Allen, and T. J. Goodwin. Mechanical culture conditions effect gene expression: gravity-induced changes on the space shuttle. Physiol Genomics 3: 163–173, 2000.—Three-dimensional suspension culture is a gravity-limited phenomenon. The balancing forces necessary to keep the aggregates in suspension increase directly with aggregate size. This leads to a self-propagating cycle of cell damage by balancing forces. Cell culture in microgravity avoids this trade-off. We determined which genes mediate three-dimensional culture of cell and tissue aggregates in the low-shear stress, low-turbulent environment of actual microgravity. Primary cultures of human renal cortical cells were flown on the space shuttle. Cells grown in microgravity and ground-based controls were grown for 6 days and fixed. RNA was extracted, and automated gene array analysis of the expression of 10,000 genes was performed. A select group of genes were regulated in microgravity. These 1,632 genes were independent of known shear stress response element-dependent genes and heat shock proteins. Specific transcription factors underwent large changes in microgravity including the Wilms’ tumor zinc finger protein, and the vitamin D receptor. A specific group of genes, under the control of defined transcription factors, mediate three-dimensional suspension culture under microgravity conditions.

Establishing Standard Protocols for Bacterial Culture in Biological Research in Canisters (BRIC) Hardware

2020 ◽  
Vol 4 (2) ◽  
pp. 58-69 ◽  
Author(s):  
Patricia Fajardo-Cavazos ◽  
Wayne L. Nicholson
Keyword(s):  
Gene Expression ◽  
Bacterial Culture ◽  
Culture Conditions ◽  
Media Culture ◽  
Ground Control ◽  
Biological Research ◽  
Confounding Factors ◽  
Cross Experiment ◽  
Spaceflight Experiments ◽  
Control Samples

AbstractThe NASA GeneLab Data System (GLDS) was recently developed to facilitate cross-experiment comparisons in order to understand the response of microorganisms to the human spaceflight environment. However, prior spaceflight experiments have been conducted using a wide variety of different hardware, media, culture conditions, and procedures. Such confounding factors could potentially mask true differences in gene expression between spaceflight and ground control samples. In an attempt to mitigate such confounding factors, we describe here the development of a standardized set of hardware, media, and protocols for liquid cultivation of microbes in Biological Research in Canisters (BRIC) spaceflight hardware, using the model bacteria Bacillus subtilis strain 168 and Staphylococcus aureus strain UAMS-1 as examples.

scholarly journals Transcriptome comparisons of in vitro intestinal epithelia grown under static and microfluidic gut-on-chip conditions with in vivo human epithelia

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kornphimol Kulthong ◽  
Guido J. E. J. Hooiveld ◽  
Loes Duivenvoorde ◽  
Ignacio Miro Estruch ◽  
Victor Marin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Culture Conditions ◽  
Gene Set Enrichment Analysis ◽  
Shear Stresses ◽  
Static Culture ◽  
Dynamic Culture ◽  
Intestinal Segments ◽  
On Chip

AbstractGut-on-chip devices enable exposure of cells to a continuous flow of culture medium, inducing shear stresses and could thus better recapitulate the in vivo human intestinal environment in an in vitro epithelial model compared to static culture methods. We aimed to study if dynamic culture conditions affect the gene expression of Caco-2 cells cultured statically or dynamically in a gut-on-chip device and how these gene expression patterns compared to that of intestinal segments in vivo. For this we applied whole genome transcriptomics. Dynamic culture conditions led to a total of 5927 differentially expressed genes (3280 upregulated and 2647 downregulated genes) compared to static culture conditions. Gene set enrichment analysis revealed upregulated pathways associated with the immune system, signal transduction and cell growth and death, and downregulated pathways associated with drug metabolism, compound digestion and absorption under dynamic culture conditions. Comparison of the in vitro gene expression data with transcriptome profiles of human in vivo duodenum, jejunum, ileum and colon tissue samples showed similarities in gene expression profiles with intestinal segments. It is concluded that both the static and the dynamic gut-on-chip model are suitable to study human intestinal epithelial responses as an alternative for animal models.

scholarly journals Hypoxic culture conditions induce increased metabolic rate and collagen gene expression in ACL-derived cells

2015 ◽  
Vol 34 (6) ◽  
pp. 985-994 ◽  
Author(s):  
Tomasz J. Kowalski ◽  
Natalie L. Leong ◽  
Ayelet Dar ◽  
Ling Wu ◽  
Nima Kabir ◽  
...  
Keyword(s):  
Gene Expression ◽  
Metabolic Rate ◽  
Culture Conditions ◽  
Collagen Gene ◽  
Collagen Gene Expression

scholarly journals Genetic determinants of growth phase-dependent and adenovirus 5-responsive expression of the Chinese hamster thymidine kinase gene are contained within thymidine kinase mRNA sequences.

1986 ◽  
Vol 6 (6) ◽  
pp. 2262-2266 ◽  
Author(s):  
J A Lewis ◽  
D A Matkovich
Keyword(s):  
Gene Expression ◽  
Cell Culture ◽  
Thymidine Kinase ◽  
Growth Phase ◽  
Chinese Hamster ◽  
Culture Conditions ◽  
Kinase Gene ◽  
Simplex Virus ◽  
Adenovirus 5

We have constructed a chimeric thymidine kinase (TK) minigene, pHe delta 6Ha, which combines the complete coding and 3' noncoding regions of a Chinese hamster TK cDNA with the promoter region and 5' untranslated region of the TK gene of herpes simplex virus type 1. We have transformed rat 4 cells to Tk+ with this gene and analyzed the pattern of TK gene expression in these transformants under various conditions of in vitro cell culture. We find that TK gene expression in these Tk+ transformants is growth phase dependent, responsive to adenovirus 5 infection, and indistinguishable in character under a variety of cell culture conditions from the pattern of TK gene expression in rat 4 cells transformed to Tk+ with the genomic Chinese hamster TK gene clone lambda HaTK.5. We are led to the conclusion that the genetic elements which mediate growth phase-dependent TK gene expression are contained entirely within the sequences of the mature cytoplasmic hamster TK mRNA.

scholarly journals Hands-free control of heterologous gene expression in batch cultures

2017 ◽  
Author(s):  
Olivier Borkowski ◽  
Drew Endy ◽  
Pakpoom Subsoontorn
Keyword(s):  
Gene Expression ◽  
Batch Culture ◽  
Communication Systems ◽  
Heterologous Gene Expression ◽  
Cell Communication ◽  
Culture Conditions ◽  
Heterologous Gene ◽  
Synthetic Cell ◽  
Genetic Systems ◽  
Application Specific

AbstractBackgroundAutonomous cell-based control of heterologous gene expression can simplify batch-culture bioprocessing by eliminating external monitoring and extrinsic control of culture conditions. Existing approaches use auto-induction media, synthetic cell-cell communication systems, or application-specific biosensors. A simpler, resource-efficient, and general-purpose expression control system responsive to common changes during batch culture would be useful.ResultsWe used nativeE.colipromoters and recombinase-based switches to repurpose endogenous transcription signals for control of heterologous gene expression. Specifically, natural changes in transcription from endogenous promoters result in recombinase expression at different phases of batch culture. So-expressed recombinases invert a constitutive promoter regulating expression of arbitrary heterologous genes. We realized reversible and single-use switching, reduced static and dynamic cell-to-cell variation, and overall expression amplification. We used “off-the-shelf” genetic parts and abstraction-based composition frameworks to realize reliable forward engineering of our synthetic genetic systems.ConclusionWe engineered autonomous control systems for regulating heterologous gene expression. Our system uses generic endogenous promoters to sense and control heterologous expression during growth-phase transitions. Our system does not require specialized auto-induction media, production or activation of quorum sensing, or the development of application-specific biosensors. Cells programmed to control themselves could simplify existing bioprocess operations and enable the development of more powerful synthetic genetic systems.

scholarly journals Comparison of the Biological Characteristics of Mesenchymal Stem Cells Derived from Bone Marrow and Skin

2016 ◽  
Vol 2016 ◽  
pp. 1-12 ◽  
Author(s):  
Ruifeng Liu ◽  
Wenjuan Chang ◽  
Hong Wei ◽  
Kaiming Zhang
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Bone Marrow ◽  
Mesenchymal Stem Cells ◽  
Cell Types ◽  
Culture Conditions ◽  
Biological Characteristics ◽  
Cytokine Secretion ◽  
Surface Markers ◽  
Tissue Repair And Regeneration

Mesenchymal stem cells (MSCs) exhibit high proliferation and self-renewal capabilities and are critical for tissue repair and regeneration during ontogenesis. They also play a role in immunomodulation. MSCs can be isolated from a variety of tissues and have many potential applications in the clinical setting. However, MSCs of different origins may possess different biological characteristics. In this study, we performed a comprehensive comparison of MSCs isolated from bone marrow and skin (BMMSCs and SMSCs, resp.), including analysis of the skin sampling area, separation method, culture conditions, primary and passage culture times, cell surface markers, multipotency, cytokine secretion, gene expression, and fibroblast-like features. The results showed that the MSCs from both sources had similar cell morphologies, surface markers, and differentiation capacities. However, the two cell types exhibited major differences in growth characteristics; the primary culture time of BMMSCs was significantly shorter than that of SMSCs, whereas the growth rate of BMMSCs was lower than that of SMSCs after passaging. Moreover, differences in gene expression and cytokine secretion profiles were observed. For example, secretion of proliferative cytokines was significantly higher for SMSCs than for BMMSCs. Our findings provide insights into the different biological functions of both cell types.

Photobiomodulation of inflamed dental pulp stem cells under different nutritional conditions

2021 ◽  
Author(s):  
Seyedeh Sareh Hendi ◽  
Leila Gholami ◽  
Massoud Saidijam ◽  
Roghayeh Mahmoudi ◽  
Ali Asghar Arkian ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Cell Proliferation ◽  
Laser Irradiation ◽  
Dental Pulp ◽  
Culture Conditions ◽  
Dental Pulp Stem Cells ◽  
Reverse Transcription Pcr ◽  
Nutritional Conditions ◽  
Proliferation And Differentiation

Aim: The present study aimed to investigate photobiomodulation's (PBM) effect on inflamed dental pulp stem cells (IDPSCs) under different nutritional conditions. Methods: Cell proliferation and odontogenic differentiation were evaluated using the MTT assay and real-time quantitative reverse transcription PCR, respectively after laser PBM of cells in 5 or 10% fetal bovine serum (FBS) culture conditions. Results: A significant positive effect of laser irradiation on cell proliferation under both nutritional conditions after 24 and 48 h was observed. DMP-1 gene expression increased in the groups with laser irradiation and 5% FBS. Comparison of gene expression levels in the four groups revealed no statistically significant stimulatory effect. The highest gene expression was observed in the non-laser group with 5% FBS. Conclusion: Further studies are required to obtain an irradiation setup to ideally improve inflamed dental pulp stem cells' proliferation and differentiation.

Comparison of gene expression and activation of transcription factors in organoid-derived monolayer intestinal epithelial cells and organoids

2021 ◽  
Author(s):  
Yu Takahashi ◽  
Yu Inoue ◽  
Keitaro Kuze ◽  
Shintaro Sato ◽  
Makoto Shimizu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Epithelial Cells ◽  
Gene Expression Regulation ◽  
Intestinal Epithelial Cells ◽  
Three Dimensional ◽  
Culture Conditions ◽  
Dependent Manner ◽  
Intestinal Epithelial

Abstract Intestinal organoids better represent in vivo intestinal properties than conventionally used established cell lines in vitro. However, they are maintained in three-dimensional culture conditions that may be accompanied by handling complexities. We characterized the properties of human organoid-derived two-dimensionally cultured intestinal epithelial cells (IECs) compared with those of their parental organoids. We found that the expression of several intestinal markers and functional genes were indistinguishable between monolayer IECs and organoids. We further confirmed that their specific ligands equally activate intestinal ligand-activated transcriptional regulators in a dose-dependent manner. The results suggest that culture conditions do not significantly influence the fundamental properties of monolayer IECs originating from organoids, at least from the perspective of gene expression regulation. This will enable their use as novel biological tools to investigate the physiological functions of the human intestine.

scholarly journals The immunomodulatory effect of cathelicidin-B1 on chicken macrophages

2020 ◽  
Vol 51 (1) ◽  
Author(s):  
Lianci Peng ◽  
Maaike R. Scheenstra ◽  
Roel M. van Harten ◽  
Henk P. Haagsman ◽  
Edwin J. A. Veldhuizen
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Inflammatory Cytokines ◽  
Culture Conditions ◽  
Titration Calorimetry ◽  
Macrophage Response ◽  
Microbial Infections ◽  
Chicken Macrophage ◽  
Inflammatory Profile ◽  
Pro Inflammatory Cytokines

Abstract Cathelicidins (CATHs) play an important role in the innate immune response against microbial infections. Among the four chicken cathelicidins, CATH-B1 is studied the least. In this study, the effect of CATH-B1 on the macrophage response towards avian pathogenic E. coli (APEC) and bacterial ligands was investigated. Our results show that APEC induced CATH-B1 gene expression in both a chicken macrophage cell line (HD11 cells) and primary macrophages, while expression of the other three CATHs was virtually unaffected. While the antimicrobial activity of CATH-B1 is very low under cell culture conditions, it enhanced bacterial phagocytosis by macrophages. Interestingly, CATH-B1 downregulated APEC-induced gene expression of pro-inflammatory cytokines (IFN-β, IL-1β, IL-6 and IL-8) in primary macrophages. In addition, CATH-B1 pre-incubated macrophages showed a significantly higher gene expression of IL-10 after APEC challenge, indicating an overall anti-inflammatory profile for CATH-B1. Using isothermal titration calorimetry (ITC), CATH-B1 was shown to bind LPS. This suggests that CATH-B1 reduces toll like receptor (TLR) 4 dependent activation by APEC which may partly explain the decreased production of pro-inflammatory cytokines by macrophages. On the contrary, direct binding of CATH-B1 to ODN-2006 enhanced the TLR21 dependent activation of macrophages as measured by nitric oxide production. In conclusion, our results show for the first time that CATH-B1 has several immunomodulatory activities and thereby could be an important factor in the chicken immune response.

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