Rapid and efficient genetic engineering of both wild type and axenic strains of Dictyostelium discoideum DOI Creative Commons
Peggy Paschke, David A. Knecht, Augustinas Silale

et al.

PLoS ONE, Journal Year: 2018, Volume and Issue: 13(5), P. e0196809 - e0196809

Published: May 30, 2018

Dictyostelium has a mature technology for molecular-genetic manipulation based around transfection using several different selectable markers, marker re-cycling, homologous recombination and insertional mutagenesis, all supported by well-annotated genome. However this is optimized mutant, axenic cells that, unlike non-axenic wild type, can grow in liquid medium. There pressing need methods to manipulate type ones with defects macropinocytosis, neither of which media. Here we present panel molecular genetic techniques on the selection transfectants growth bacteria rather than As well as extending range strains that be manipulated, these are faster conventional methods, often giving usable numbers transfected within few days. The plasmids described here allow efficient extrachromosomal vectors, chromosomal integration at ‘safe haven’ relatively uniform cell-to-cell expression, gene knock-in knock-out an inducible expression system. We have thus created complete new system no longer requires cell feeding

Language: Английский

Transcription Factor Dynamics DOI Open Access

Feiyue Lu,

Timothée Lionnet

Cold Spring Harbor Perspectives in Biology, Journal Year: 2021, Volume and Issue: 13(11), P. a040949 - a040949

Published: May 17, 2021

Feiyue Lu and Timothée Lionnet Institute for Systems Genetics Cell Biology Department, NYU School of Medicine, New York, York 10016, USA Correspondence: Timothee.lionnet{at}nyulangone.org

Language: Английский

Citations

58
Analytical Time-Dependent Distributions for Gene Expression Models With Complex Promoter Switching Mechanisms DOI
Jia Chen, Youming Li

SIAM Journal on Applied Mathematics, Journal Year: 2023, Volume and Issue: 83(4), P. 1572 - 1602

Published: Aug. 3, 2023

.Classical gene expression models assume exponential switching time distributions between the active and inactive promoter states. However, recent experiments have shown that many genes in mammalian cells may produce nonexponential distributions, implying existence of multiple states molecular memory dynamics. Here we analytically solve a model with random bursting complex switching, derive time-dependent mRNA protein copy numbers, generalizing steady-state solution obtained [T. Zhou J. Zhang, SIAM Appl. Math., 72 (2012), pp. 789–818] [U. Herbach, 79 (2019), 1007–1029]. Using multiscale simplification techniques, find has no influence on distribution when is very fast or slow, while it significantly affects neither too nor slow. By analyzing dynamical phase diagram system, also state weakens transient stationary bimodality number distribution, enhances such bimodality.Keywordstransient distributionburstingmolecular memorymultiscale simplificationMSC codes60J2760J2892C4078A7092B05

Language: Английский

Citations

23
Rapid Rates of Pol II Elongation in the Drosophila Embryo DOI Creative Commons
Takashi Fukaya, Bomyi Lim, Michael Levine

et al.

Current Biology, Journal Year: 2017, Volume and Issue: 27(9), P. 1387 - 1391

Published: April 27, 2017

Language: Английский

Citations

87
Cell-Size-Dependent Transcription of FLC and Its Antisense Long Non-coding RNA COOLAIR Explain Cell-to-Cell Expression Variation DOI Creative Commons
Robert Ietswaart, Stefanie Rosa, Zhe Wu

et al.

Cell Systems, Journal Year: 2017, Volume and Issue: 4(6), P. 622 - 635.e9

Published: June 1, 2017

Single-cell quantification of transcription kinetics and variability promotes a mechanistic understanding gene regulation. Here, using single-molecule RNA fluorescence in situ hybridization mathematical modeling, we dissect cellular dynamics for Arabidopsis FLOWERING LOCUS C (FLC). FLC expression quantitatively determines flowering time is regulated by antisense (COOLAIR) transcription. In cells without observable COOLAIR expression, quantify initiation, elongation, intron processing, lariat degradation, as well mRNA release from the locus degradation. these heterogeneously sized cells, number increases linearly with cell size, resulting large cell-to-cell transcript level. This variation accounted cell-size-dependent, Poissonian production, but not transcriptional bursts. COOLAIR-expressing however, size contributes to decreasing size. Our analysis therefore reveals an unexpected role modulating scaling

Language: Английский

Citations

81
Rapid and efficient genetic engineering of both wild type and axenic strains of Dictyostelium discoideum DOI Creative Commons
Peggy Paschke, David A. Knecht, Augustinas Silale

et al.

PLoS ONE, Journal Year: 2018, Volume and Issue: 13(5), P. e0196809 - e0196809

Published: May 30, 2018

Dictyostelium has a mature technology for molecular-genetic manipulation based around transfection using several different selectable markers, marker re-cycling, homologous recombination and insertional mutagenesis, all supported by well-annotated genome. However this is optimized mutant, axenic cells that, unlike non-axenic wild type, can grow in liquid medium. There pressing need methods to manipulate type ones with defects macropinocytosis, neither of which media. Here we present panel molecular genetic techniques on the selection transfectants growth bacteria rather than As well as extending range strains that be manipulated, these are faster conventional methods, often giving usable numbers transfected within few days. The plasmids described here allow efficient extrachromosomal vectors, chromosomal integration at ‘safe haven’ relatively uniform cell-to-cell expression, gene knock-in knock-out an inducible expression system. We have thus created complete new system no longer requires cell feeding

Language: Английский

Citations

74