Stability and lability of circadian period of gene expression in the cyanobacterium Synechococcus elongatus

Molecular aspects of the circadian clock in the cyanobacterium Synechococcus elongatus have been described in great detail. Three-dimensional structures have been determined for the three proteins, KaiA, KaiB and KaiC, that constitute a central oscillator of the clock. Moreover, a temperature-compensated circadian rhythm of KaiC phosphorylation can be reconstituted in vitro with the addition of KaiA, KaiB and ATP. These data suggest a relatively simple circadian system in which a single oscillator provides temporal information for all downstream processes. However, in vivo the situation is more complex, and additional components contribute to the maintenance of a normal period, the resetting of relative phases of circadian oscillations, and the control of rhythms of gene expression. We show here that two well-studied promoters in the S. elongatus genome report different circadian periods of expression under a given set of conditions in wild-type as well as mutant genetic backgrounds. Moreover, the period differs between these promoters with respect to modulation by light intensity, growth phase, and the presence or absence of a promoter-recognition subunit of RNA polymerase. These data contrast sharply with the current clock model in which a single Kai-based oscillator governs circadian period. Overall, these findings suggest that complex interactions among the circadian oscillator, perhaps other oscillators, and other cellular machinery result in a clock that is plastic and sensitive to the environment and to the physiological state of the cell.

Download Full-text

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

Bioscience Biotechnology and Biochemistry ◽

10.1093/bbb/zbab136 ◽

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.

Download Full-text

Campylobacter jejuni Gene Expression in the Chick Cecum: Evidence for Adaptation to a Low-Oxygen Environment

Infection and Immunity ◽

10.1128/iai.73.8.5278-5285.2005 ◽

2005 ◽

Vol 73 (8) ◽

pp. 5278-5285 ◽

Cited By ~ 77

Author(s):

C. A. Woodall ◽

M. A. Jones ◽

P. A. Barrow ◽

J. Hinds ◽

G. L. Marsden ◽

...

Keyword(s):

Gene Expression ◽

Electron Transport ◽

Campylobacter Jejuni ◽

Metabolic Pathways ◽

Transcriptional Profiling ◽

Physiological State ◽

Low Oxygen ◽

Oxygen Environment

ABSTRACT Transcriptional profiling of Campylobacter jejuni during colonization of the chick cecum identified 59 genes that were differentially expressed in vivo compared with the genes in vitro. The data suggest that C. jejuni regulates electron transport and central metabolic pathways to alter its physiological state during establishment in the chick cecum.

Download Full-text

Three-dimensional imaging of nucleosomes from transcriptionally active genes using electron spectroscopic imaging

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100162739 ◽

1996 ◽

Vol 54 ◽

pp. 54-55

Author(s):

G. J. Czarnota ◽

D. P. Bazett-Jones ◽

F. P. Ottensmeyer

Keyword(s):

Gene Expression ◽

Three Dimensional ◽

Spectroscopic Imaging ◽

Dimensional Structure ◽

Crystallographic Structure ◽

Electron Spectroscopic Imaging ◽

Nucleosome Structure ◽

Active Genes

The three-dimensional structure of the nucleosome was determined using particles purified from transcriptionally active genes in conjunction with electron spectroscopic imaging, and quaternion-assisted angular reconstitution procedures. The results reveal a configuration which is very different from the canonical compact crystallographic structure for this fundamental chromosome subunit, implying a structural disruption of the nucleosome with the activation of gene expression in accord with numerous physico-chemical observations.Previous analyses of nucleosomes purified from transcriptionally quiescent genes have indicated numerous structural states dependent on factors in vitro which modify charge based interactions in nucleoprotein complexes. Nucleosomes from transcriptionally active genes undergo chemical alterations in vivo which similarly modify charge based interactions. In order to investigate the effects of the gene expression associated chemical alterations on nucleosome structure, particles were purified from transcriptionally active genes using mercury affinity chromatography. These nucleosome particles are hyperacetylated with respect to particles from transcriptionally quiescent genes. Here additionally, sulphydryls normally buried within the protein core of the transcriptionally inactive particle are exposed to chemical modifying agents thus facilitating purification as described.

Download Full-text

In Vitro Follicle Growth, Maturation, and Gene Expression: Three-Dimensional (3D) Matrigel Culture versus Two-Dimensional Culture (2D)

Journal of Biomaterials and Tissue Engineering ◽

10.1166/jbt.2021.2831 ◽

2021 ◽

Vol 11 (12) ◽

pp. 2512-2515

Author(s):

Byoung-San Moon ◽

Seungki Lee ◽

Jung Kyu Choi

Keyword(s):

Gene Expression ◽

Three Dimensional ◽

Ovarian Follicles ◽

Dimensional System ◽

Two Dimensional ◽

Follicle Growth ◽

Adult Mice ◽

Three Dimensional Culture

This research aimed to compare the In Vitro growth, maturation, and gene expression in ovarian follicles collected from adult mice (6–8-week-old) between two-dimensional and three-dimensional cultures. First, we confirmed In Vitro follicle growth and maturation using adult mice with outbred characteristics and analyzed the expression of genes related to follicular development. We found that the three-dimensional culture system utilizing a Matrigel drop to create an in vivo-like ovarian microenvironment was more efficient in terms of In Vitro follicle growth, maturation, and gene expression than the two-dimensional system (non-physical environment). The in vivo-like three-dimensional culture of ovarian follicles provides new insights into the physiology and development of ovarian follicle in vivo, thereby contributing to new strategies to improve female fertility.

Download Full-text

Perfusion Flow Enhances Osteogenic Gene Expression and the Infiltration of Osteoblasts and Endothelial Cells into Three-Dimensional Calcium Phosphate Scaffolds

International Journal of Biomaterials ◽

10.1155/2012/915620 ◽

2012 ◽

Vol 2012 ◽

pp. 1-10 ◽

Cited By ~ 21

Author(s):

Matthew J. Barron ◽

Jeremy Goldman ◽

Chung-Jui Tsai ◽

Seth W. Donahue

Keyword(s):

Gene Expression ◽

Endothelial Cells ◽

Endothelial Cell ◽

Three Dimensional ◽

Mrna Levels ◽

Cellular Viability ◽

Vegf Mrna ◽

Perfusion Flow

Maintaining cellular viabilityin vivoandin vitrois a critical issue in three-dimensional bone tissue engineering. While the use of osteoblast/endothelial cell cocultures on three-dimensional constructs has shown promise for increasingin vivovascularization,in vitromaintenance of cellular viability remains problematic. This study used perfusion flow to increase osteogenic and angiogenic gene expression, decrease hypoxic gene expression, and increase cell and matrix coverage in osteoblast/endothelial cell co-cultures. Mouse osteoblast-like cells (MC3T3-E1) were cultured alone and in co-culture with mouse microvascular endothelial cells (EOMA) on three-dimensional scaffolds for 1, 2, 7, and 14 days with or without perfusion flow. mRNA levels were determined for several osteogenic, angiogenic, and hypoxia-related genes, and histological analysis was performed. Perfusion flow downregulated hypoxia-related genes (HIF-1α, VEGF, and OPN) at early timepoints, upregulated osteogenic genes (ALP and OCN) at 7 days, and downregulated RUNX-2 and VEGF mRNA at 14 days in osteoblast monocultures. Perfusion flow increased cell number, coverage of the scaffold perimeter, and matrix area in the center of scaffolds at 14 days. Additionally, perfusion flow increased the length of endothelial cell aggregations within co-cultures. These suggest perfusion stimulated co-cultures provide a means of increasing osteogenic and angiogenic activity.

Download Full-text

In vitro and in vivo polysaccharides assembly: ultrastructural and cytochemical study of growing plant cell wall components.

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100083035 ◽

1978 ◽

Vol 36 (2) ◽

pp. 434-435

Author(s):

D. Reis ◽

B. Vian ◽

J. C. Roland

Keyword(s):

Cell Wall ◽

Self Assembly ◽

Plant Cell Wall ◽

Higher Plants ◽

Three Dimensional ◽

Cytochemical Study ◽

Wall Components

Wall morphogenesis in higher plants is a problem still open to controversy. Until now the possibility of a transmembrane control and the involvement of microtubules were mostly envisaged. Self-assembly processes have been observed in the case of walls of Chlamydomonas and bacteria. Spontaneous gelling interactions between xanthan and galactomannan from Ceratonia have been analyzed very recently. The present work provides indications that some processes of spontaneous aggregation could occur in higher plants during the formation and expansion of cell wall.Observations were performed on hypocotyl of mung bean (Phaseolus aureus) for which growth characteristics and wall composition have been previously defined.In situ, the walls of actively growing cells (primary walls) show an ordered three-dimensional organization (fig. 1). The wall is typically polylamellate with multifibrillar layers alternately transverse and longitudinal. Between these layers intermediate strata exist in which the orientation of microfibrils progressively rotates. Thus a progressive change in the morphogenetic activity occurs.

Download Full-text

Identification of genes early responsive to gamma-irradiation in isolated rat hepatocytes in vitro and rat liver in vivo by cDNA array gene expression analysis

Zeitschrift für Gastroenterologie ◽

10.1055/s-2005-920060 ◽

2005 ◽

Vol 43 (05) ◽

Author(s):

DS Batusic ◽

H Christiansen ◽

B Saile ◽

RM Hermann ◽

J Dudas ◽

...

Keyword(s):

Gene Expression ◽

Gamma Irradiation ◽

Rat Liver ◽

Gene Expression Analysis ◽

Cdna Array ◽

Rat Hepatocytes ◽

Isolated Rat Hepatocytes ◽

Isolated Rat

Download Full-text

Effect of X-irradiation on gene expression of rat liver chemokines: in vivo and in vitro studies

Zeitschrift für Gastroenterologie ◽

10.1055/s-2008-1037499 ◽

2008 ◽

Vol 46 (01) ◽

Cited By ~ 1

Author(s):

F Moriconi ◽

H Christiansen ◽

N Sheikh ◽

J Dudas ◽

...

Keyword(s):

Gene Expression ◽

Rat Liver ◽

In Vitro Studies ◽

X Irradiation

Download Full-text

Vibrio harveyi virulence gene expression in vitro and in vivo during infection in black tiger shrimp Penaeus monodon

Diseases of Aquatic Organisms ◽

10.3354/dao03475 ◽

2020 ◽

Vol 139 ◽

pp. 153-160

Author(s):

S Peeralil ◽

TC Joseph ◽

V Murugadas ◽

PG Akhilnath ◽

VN Sreejith ◽

...

Keyword(s):

Gene Expression ◽

Virulence Genes ◽

Vibrio Harveyi ◽

Penaeus Monodon ◽

Challenge Test ◽

Virulence Gene ◽

Economic Losses ◽

Virulence Gene Expression

Luminescent Vibrio harveyi is common in sea and estuarine waters. It produces several virulence factors and negatively affects larval penaeid shrimp in hatcheries, resulting in severe economic losses to shrimp aquaculture. Although V. harveyi is an important pathogen of shrimp, its pathogenicity mechanisms have yet to be completely elucidated. In the present study, isolates of V. harveyi were isolated and characterized from diseased Penaeus monodon postlarvae from hatcheries in Kerala, India, from September to December 2016. All 23 tested isolates were positive for lipase, phospholipase, caseinase, gelatinase and chitinase activity, and 3 of the isolates (MFB32, MFB71 and MFB68) showed potential for significant biofilm formation. Based on the presence of virulence genes, the isolates of V. harveyi were grouped into 6 genotypes, predominated by vhpA+ flaB+ ser+ vhh1- luxR+ vopD- vcrD+ vscN-. One isolate from each genotype was randomly selected for in vivo virulence experiments, and the LD50 ranged from 1.7 ± 0.5 × 103 to 4.1 ± 0.1 × 105 CFU ml-1. The expression of genes during the infection in postlarvae was high in 2 of the isolates (MFB12 and MFB32), consistent with the result of the challenge test. However, in MFB19, even though all genes tested were present, their expression level was very low and likely contributed to its lack of virulence. Because of the significant variation in gene expression, the presence of virulence genes alone cannot be used as a marker for pathogenicity of V. harveyi.

Download Full-text