scholarly journals Robust Singing Transcription System Using Local Homogeneity in the Harmonic Structure

2017 ◽  
Vol E100.D (5) ◽  
pp. 1114-1123 ◽  
Author(s):  
Hoon HEO ◽  
Kyogu LEE
Keyword(s):  
Harmonic Structure ◽  
Local Homogeneity ◽  
Transcription System

Efficient 3D mesh salient region detection using local homogeneity measure

2018 ◽  
Vol 12 (9) ◽  
pp. 1663-1672 ◽  
Author(s):  
Abdul Rahman El Sayed ◽  
Abdallah El Chakik ◽  
Hassan Alabboud ◽  
Adnan Yassine
Keyword(s):  
Salient Region Detection ◽  
3D Mesh ◽  
Local Homogeneity ◽  
Salient Region ◽  
Region Detection

scholarly journals The dyskerin ribonucleoprotein complex as an OCT4/SOX2 coactivator in embryonic stem cells

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Yick W Fong ◽  
Jaclyn J Ho ◽  
Carla Inouye ◽  
Robert Tjian
Keyword(s):  
Stem Cell ◽  
Es Cells ◽  
Embryonic Stem ◽  
In Vitro Transcription ◽  
Specific Gene ◽  
Transcriptional Level ◽  
Ips Cell ◽  
Ribonucleoprotein Complex ◽  
Transcription System

Acquisition of pluripotency is driven largely at the transcriptional level by activators OCT4, SOX2, and NANOG that must in turn cooperate with diverse coactivators to execute stem cell-specific gene expression programs. Using a biochemically defined in vitro transcription system that mediates OCT4/SOX2 and coactivator-dependent transcription of the Nanog gene, we report the purification and identification of the dyskerin (DKC1) ribonucleoprotein complex as an OCT4/SOX2 coactivator whose activity appears to be modulated by a subset of associated small nucleolar RNAs (snoRNAs). The DKC1 complex occupies enhancers and regulates the expression of key pluripotency genes critical for self-renewal in embryonic stem (ES) cells. Depletion of DKC1 in fibroblasts significantly decreased the efficiency of induced pluripotent stem (iPS) cell generation. This study thus reveals an unanticipated transcriptional role of the DKC1 complex in stem cell maintenance and somatic cell reprogramming.

scholarly journals The dynamics of gene transcription with a periodic synthesis rate

2021 ◽  
Author(s):  
Qiwen Sun ◽  
Feng Jiao ◽  
Jianshe Yu
Keyword(s):  
Gene Activation ◽  
Transcript Level ◽  
Cyclic Behavior ◽  
Synthesis Rate ◽  
Activation Process ◽  
Transcription System ◽  
Constant Rate ◽  
Real Value ◽  
The Mean ◽  
Two State Model

AbstractThe periodic transcription output is ubiquitously observed in an isogenic cell population. To understand mechanisms of cyclic behavior in transcription, we extend the gene activation process in the two-state model by assuming that the synthesis rate is periodic. We derive the analytical forms of the mean transcript level and the noise. The limits of them indicate that the mean level and the noise display periodic behaviors. Numerical examples strongly suggest that the transcription system with a periodic synthesis rate generates more noise than that with a constant rate but maintains transcription homeostasis in each period. It is also suggested that if the periodicity is not considered, the calculated noise may be greater than the real value.

scholarly journals Cell-Free Transcription at 95°: Thermostability of Transcriptional Components and DNA Topology Requirements of Pyrococcus Transcription

Genetics ◽  
1999 ◽  
Vol 152 (4) ◽  
pp. 1325-1333
Author(s):  
Carina Hethke ◽  
Agnes Bergerat ◽  
Winfried Hausner ◽  
Patrick Forterre ◽  
Michael Thomm
Keyword(s):  
Transcription Factors ◽  
Half Life ◽  
Pyrococcus Furiosus ◽  
Polymerase Activity ◽  
Supercoiled Dna ◽  
Eukaryotic Transcription ◽  
Transcription System ◽  
Archaeal Transcription ◽  
Protein Components

Abstract Cell-free transcription of archaeal promoters is mediated by two archaeal transcription factors, aTBP and TFB, which are orthologues of the eukaryotic transcription factors TBP and TFIIB. Using the cell-free transcription system described for the hyperthermophilic Archaeon Pyrococcus furiosus by Hethke et al., the temperature limits and template topology requirements of archaeal transcription were investigated. aTBP activity was not affected after incubation for 1 hr at 100°. In contrast, the half-life of RNA polymerase activity was 23 min and that of TFB activity was 3 min. The half-life of a 328-nt RNA product was 10 min at 100°. Best stability of RNA was observed at pH 6, at 400 mm K-glutamate in the absence of Mg2+ ions. Physiological concentrations of K-glutamate were found to stabilize protein components in addition, indicating that salt is an important extrinsic factor contributing to thermostability. Both RNA and proteins were stabilized by the osmolyte betaine at a concentration of 1 m. The highest activity for RNA synthesis at 95° was obtained in the presence of 1 m betaine and 400 mm K-glutamate. Positively supercoiled DNA, which was found to exist in Pyrococcus cells, can be transcribed in vitro both at 70° and 90°. However, negatively supercoiled DNA was the preferred template at all temperatures tested. Analyses of transcripts from plasmid topoisomers harboring the glutamate dehydrogenase promoter and of transcription reactions conducted in the presence of reverse gyrase indicate that positive supercoiling of DNA inhibits transcription from this promoter.

scholarly journals Concentration dependence of transcriptional transactivation in inducible E1A-containing human cells.

1988 ◽  
Vol 8 (11) ◽  
pp. 4799-4807 ◽  
Author(s):  
L J Brunet ◽  
A J Berk
Keyword(s):  
Adenovirus Type ◽  
In Vitro Transcription ◽  
Mrna Levels ◽  
Adenovirus E1a ◽  
Transcription System ◽  
Nuclear Extracts ◽  
Tumor Virus ◽  
E1a Gene ◽  
High Level

The adenovirus E1A proteins are essential for the normal temporal activation of transcription from every other adenoviral early promoter. High-level E1A expression in the absence of viral infection would facilitate biochemical studies of E1A-mediated transactivation. Toward this end, we introduced the adenovirus type 2 E1A gene under the control of the murine mammary tumor virus promoter into HeLa cells. Uninduced cells expressed little or no detectable E1A mRNA. Upon induction, mRNA levels accumulated to about 50% of the level observed in 293 cells. The level of E1A expression in these cells could be controlled by varying the concentration of the inducing glucocorticoid. Under these conditions of varying E1A concentrations, it was observed that activation of the E2, E3, and E4 promoters of H5dl312 initiated at the same E1A concentration and that transcription from each promoter increased as the E1A concentration increased. These results indicate that E1A-mediated transactivation is proportional to the concentration of E1A protein. E1A-dependent transcriptional stimulation of the E4 promoter was reproduced in an in vitro transcription system, demonstrating that expression of only the E1A proteins was sufficient to increase the transcriptional activity of nuclear extracts.

Fluorescent primer-based in vitro transcription system of viral RNA-dependent RNA polymerases

2013 ◽  
Vol 433 (2) ◽  
pp. 92-94
Author(s):  
Qiang Wang ◽  
Leiyun Weng ◽  
Hongbing Jiang ◽  
Shijian Zhang ◽  
Tetsuya Toyoda
Keyword(s):  
In Vitro Transcription ◽  
Rna Polymerases ◽  
Viral Rna ◽  
Transcription System

scholarly journals Activation of yeast polymerase II transcription by herpesvirus VP16 and GAL4 derivatives in vitro.

1989 ◽  
Vol 9 (11) ◽  
pp. 4746-4749 ◽  
Author(s):  
D I Chasman ◽  
J Leatherwood ◽  
M Carey ◽  
M Ptashne ◽  
R D Kornberg
Keyword(s):  
Rna Polymerase Ii ◽  
Fusion Proteins ◽  
In Vitro System ◽  
Transcription System ◽  
Natural Mechanism ◽  
Transcription In Vitro ◽  
Rna Polymerase Ii Transcription ◽  
Fold Stimulation

Fusion proteins known to activate transcription in vivo were tested for the ability to stimulate transcription in vitro in a recently developed Saccharomyces cerevisiae RNA polymerase II transcription system. One fusion protein, whose activation domain was derived from the herpesvirus transcriptional activator VP16, gave more than 100-fold stimulation in the in vitro system. The order of effects of the various proteins was the same for transcription in vitro and in vivo, suggesting that the natural mechanism of activation is preserved in vitro.

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