ライフサイエンスコーパス: gene circuit

1 e to propose an integrated model for the fim gene circuit.

2 cture and biokinetic rates of the underlying gene circuit.

3 capture the full stochastic behavior of the gene circuit.

4 of noise arising from any source within the gene circuit.

5 ontrol transcription from a simple synthetic gene circuit.

6 iding new ways to engineer arbitrary complex gene circuits.

7 onents can be used for large-scale synthetic gene circuits.

8 eloped numerous parts for building synthetic gene circuits.

9 e library of components for use in synthetic gene circuits.

10 tokines, via multiple repressor-of-repressor gene circuits.

11 ofiles and facilitate mathematical models of gene circuits.

12 , and experimentally, using simple synthetic gene circuits.

13 cally modifying and reprogramming cells with gene circuits.

14 nce of regulatory interactions in endogenous gene circuits.

15 roposed as mechanisms for decision making in gene circuits.

16 gical networks and for engineering synthetic gene circuits.

17 therapeutic molecules via several synthetic gene circuits.

18 atural networks and designing noise-tolerant gene circuits.

19 tematic experimental or theoretical study of gene circuits.

20 rinsic noise within negatively autoregulated gene circuits.

21 r maintaining reliable function in synthetic gene circuits.

22 linear resource competition within synthetic gene circuits.

23 re the coupling of oscillatory and pulsatile gene circuits.

24 e their unique ability to prioritize SNP-ARE-gene circuits.

25 t growth patterns influence the operation of gene circuits.

26 stabilize the functionality of intracellular gene circuits.

27 oring genes each, creating highly integrated gene circuits.

28 achine learning to rapidly screen and design gene circuits.

29 endogenous signalling pathways and synthetic gene circuits.

30 ust modelling method for designing synthetic gene circuits.

31 ibe and predict the behaviours of engineered gene circuits.

32 'smart bioparticles' controlled by designed gene circuits.

33 y through the predictive design of synthetic gene circuits.

34 ting and expanding the function of synthetic gene circuits.

35 cell metabolism, cell biology and synthetic gene circuits.

36 xamine the sources of variability in dynamic gene circuits.

37 sion is well understood for individual model gene circuits(2,3).

38 thetic biologists have gone from single-cell gene circuits(8-11) to controlling whole populations usi

39 ntrol mediated by degronLOCKR on a synthetic gene circuit(9), to quantify the feedback capabilities a

40 Adaptability of synthetic gene circuits across different organisms could enable a

41 roving the predictability and performance of gene circuits across diverse applications.

42 However, the processes affecting gene circuit adaptability have not been systematically i

43 ble circuit performance such as insulating a gene circuit against unwanted interactions with its cont

44 uits as a control strategy for desensitizing gene circuits against growth fluctuations.

45 Synthetic gene circuits allow the behavior of living cells to be r

46 le that adds a layer of control to synthetic gene circuits, allowing dynamic regulation of circuit el

47 emonstrating the probative value of noise in gene circuit analysis.

48 oise transmission through this signaling and gene circuit, analyzing data obtained from 43,775 indivi

49 rgue that f(c) is an intrinsic property of a gene circuit and it varies with circuit parameters and a

50 nd show its utility using a ligand-inducible gene circuit and toehold switch-based sensors by demonst

51 urate predictive design of complex synthetic gene circuits and accompanying large sets of quality mod

52 ew how CRISPR can be used to build synthetic gene circuits and discuss recent advances in CRISPR-medi

53 ur study generates a detailed roadmap of TAM gene circuits and identifies ZEB2 as a master switch wit

54 regulation of regulator genes in repressible gene circuits and lead to testable predictions, which we

55 toolkit can be used for programming scalable gene circuits and perturbing endogenous networks for bio

56 t, facilitating the understanding of natural gene circuits and the design of cell-based therapeutic s

57 he mutual interactions between the synthetic gene circuits and the host growth could cause unexpected

58 perturbations, underscoring the intimacy of gene circuits and their hosts and elucidating the comple

59 tresses in development impact the underlying gene circuits and, if so, how?

60 tics may serve to 'fill in the gaps' between genes, circuits and behavior, in a manner that should he

61 f the architecture of the mutual suppression gene circuit, and thus is a design option readily availa

62 ermination by viruses, dynamics of synthetic gene circuits, and constraints on evolutionary adaptatio

63 e viral vector production, control synthetic gene circuits, and other purposes.

64 netic switches, rapid prototyping of complex gene circuits, and programmable in vitro diagnostics, in

65 mics and the noise behavior of autoregulated gene circuits, and this T-based technique provides a sim

66 tegrated logic and memory by using synthetic gene circuits, and we demonstrated the implementation of

67 investigations into the interactions between genes, circuits, and computation.

68 ereby shedding light on a promising path for gene circuit applications in complex contexts.

69 Moreover, we use the LITer gene circuit architecture to control gene expression of

70 ere, we describe a modular recombinase-based gene circuit architecture, comprising tandem gene pertur

71 se intrinsic to a prototypical two-component gene-circuit architecture composed of interacting positi

72 er, there are few scalable and generalizable gene circuit architectures for the programming of sequen

73 biological role for noise that is encoded in gene circuit architectures.

74 L and IPTG signals with a synthetic AND gate gene circuit are shown to respond only in the presence o

75 the steady states and the stabilities of the gene circuits are affected by host cell growth is not fu

76 Synthetic gene circuits are designed to program new biological beh

77 Gene circuits are dynamical systems that regulate cellul

78 Synthetic gene circuits are emerging as a versatile means to targe

79 Gene circuits are important in many aspects of biology,

80 However, synthetic gene circuits are often unreliable, as changes to enviro

81 ur of an inducible, negatively autoregulated gene circuit arranged in different transcriptional confi

82 erturbations that interact directly with the gene circuit as well as for a variety of generic perturb

83 ose the incorporation of repressive links in gene circuits as a control strategy for desensitizing ge

84 ed to the investigation of specific bacteria gene circuits as functioning modules.

85 genetic regulatory elements, genes and multi-gene circuits as well as facile development of libraries

86 ling two dynamical mechanisms by which small gene circuits attenuate the effect of noise in order to

87 e design the CASwitch, a mammalian synthetic gene circuit based on combining two well-known network m

88 t can convert the activation of conventional gene circuit-based sensors into a glucose output that ca

89 ll-free synthetic biology have given rise to gene circuit-based sensors with the potential to provide

90 To date, gene-circuit-based sensors have primarily used optical p

91 expanded multiplexed reporting for cell-free gene-circuit-based sensors.

92 However, as synthetic gene circuits become larger and more complicated, we are

93 cooperative assemblies can program nonlinear gene circuit behavior in yeast.

94 k advances our quantitative understanding of gene circuit behaviours and also benefits the rational d

95 medium for the safe deployment of engineered gene circuits beyond the lab.

96 e the dynamics and improve the robustness of gene circuits, biological engineers have proposed variou

97 ynthetic biology devices, such as engineered gene circuits, bring new capabilities to molecular diagn

98 an regulatory networks including the largest gene circuit built and chromosomally integrated to date

99 Sophisticated gene circuits built by synthetic biology can enable bact

100 ntial parameter in the dynamics of synthetic gene circuits but typically is not explicitly considered

101 n the design and implementation of synthetic gene circuits, but real-world applications of such circu

102 Executing gene circuits by cell-free transcription-translation int

103 This work demonstrates that synthetic gene circuits can be engineered to be robust to extracel

104 Here we demonstrate that synthetic analog gene circuits can be engineered to execute sophisticated

105 Autoregulatory gene circuits can be physically encoded within the genom

106 These results show that simple gene circuits can be used within multicellular synthetic

107 Cells endowed with synthetic gene circuits can control the localization, timing and d

108 This coupling of elementary gene circuits can lead to three patterns of regulator an

109 n of engineered cells that harbour synthetic gene circuits capable of biological sensing and computat

110 st platform for building mammalian synthetic gene circuits capable of precisely modulating cellular b

111 rder to construct progressively more complex gene circuits capable of processing information in livin

112 Here, we engineered an autoregulatory gene circuit (cisCXp-shRunx2) that negatively controls R

113 Here, using synthetic gene circuits constructed in yeast, we find that high re

114 Robust gene circuit construction requires use of promoters exhi

115 mics of a binary fate decision governed by a gene-circuit containing auto-stimulation and cross-inhib

116 aracterized an inducible, bistable synthetic gene circuit controlling the expression of a bifunctiona

117 This gene circuit defines segments sequentially in double seg

118 , making them especially useful as synthetic gene circuit design equations.

119 euro-inspired models can transform synthetic gene circuit design in a manner that is reliable, effici

120 ts in vitro and demonstrate their utility in gene circuit design in Escherichia coli.

121 A limiting factor in synthetic gene circuit design is the number of independent control

122 Robust gene circuit design requires an understanding of how the

123 In the lower part of the three gene circuit diagrams in panel b, the flat-headed arrow

124 velopments have signalled the emergence of a gene circuit discipline, which provides a framework for

125 rning algorithms to significantly accelerate gene circuit discovery.

126 We show that, for prokaryotic gene circuits dominated by local promoter control, dynam

127 We trained gene circuits, dynamical models that learn genetic archi

128 in messenger RNAs and noncoding RNAs to tune gene circuit dynamics and enhance CRISPR interference in

129 icroscopy is a powerful method for analyzing gene circuit dynamics and heterogeneous cell behavior.

130 alysis that remains valid for many important gene circuit elements even as molecular populations appr

131 l accelerates the design and optimization of gene circuits, enables efficient probing of metabolic bu

132 on of RUNX2 activity with our autoregulatory gene circuit enhanced matrix synthesis and resisted ECM

133 ion, we apply this strategy to two synthetic gene circuits exhibiting anomalous behaviors.

134 ically engineer the performance of synthetic gene circuits, expanding the current toolkit for gene re

135 Such synthetic analog gene circuits exploit feedback to implement logarithmica

136 esults suggest that the self-repressing Hes1 gene circuit exploits this phenomenon to generate robust

137 Frequently, theoretical studies of gene circuits focus on steady-state behaviors and do not

138 transgenic human cells carrying an inducible gene circuit for the on-demand secretion of erythropoiet

139 nd analysis of several large scale synthetic gene circuits for artificial tissue homeostasis.

140 ells derived from E. coli strains containing gene circuits for biosensing were able to transduce the

141 his framework enables development of complex gene circuits for engineering mammalian cells with unpre

142 r quick and reliable construction of complex gene circuits for genetically engineering mammalian cell

143 ust and sophisticated computation-and-memory gene circuits for numerous biotechnological and biomedic

144 In this work, synthetic gene circuits for organofluorine biosynthesis are implem

145 e emerging field of synthetic biology builds gene circuits for scientific, industrial and therapeutic

146 has implications in the design of synthetic gene circuits for this purpose.

147 ning the structure and biokinetic rates of a gene circuit from its noise autocorrelation function.

148 d be generally relevant for transferring any gene circuit from yeast into mammalian cells.

149 in the capability of engineering artificial gene circuits from transcription factors (TFs), particul

150 (TFs) but is capable of evolving any gene-or gene circuit function-that can be linked to conditional

151 and leads to an increase in the stability of gene circuit functionality in cell culture.

152 eneous conditions, the mutual interaction of gene circuits, growth phenotype and the environment rema

153 n on the deterministic behavior of synthetic gene circuits has been studied, its effects on gene expr

154 Recently, synthetic gene circuits have become promising tools to achieve the

155 Although a variety of relatively small gene circuits have been constructed and characterized, t

156 Several fundamental gene circuits have been developed using this approach, i

157 cytoskeletal force dipoles, and the lamin A gene circuit illustrate the wide range of testable predi

158 ely address these questions, we engineered a gene circuit in Escherichia coli to control the synthesi

159 hetic integral feedback motif in a synthetic gene circuit in mammalian cells.

160 The clock gene circuit in plants comprises interlocking transcript

161 ay be either faster or slower than that of a gene circuit in which there is only one TF.

162 approach enables the construction of tunable gene circuits in complex eukaryotic organisms.

163 opment and clinical translation of synthetic gene circuits in diverse human cell types and contexts.

164 ing reactive oxygen species (ROS)-responsive gene circuits in Escherichia coli that exhibit concentra

165 ling using mathematical models and synthetic gene circuits in Escherichia coli.

166 mponents and tools available for engineering gene circuits in microbes, including recently developed

167 ate large gene cassettes that encode complex gene circuits in order to avoid simultaneous delivery of

168 pression patterns of nearly 17 million three-gene circuits in order to systematically explore the rel

169 asingly complex, programmable, and efficient gene circuits in the future.

170 that connect noise, the architecture of the gene circuits in which it is present, and the biological

171 up the possibility of designing bespoke mRNA gene circuits in which the amount of protein synthesised

172 CPR is based on gene circuits in which the selection of a 'partner' func

173 De novo engineering of gene circuits inside cells is extremely difficult, and e

174 by single-cell data analysis of a synthetic gene circuit integrated in human kidney cells.

175 e, we use a synthetic positive-feedback (PF) gene circuit integrated into haploid Saccharomyces cerev

176 protein-level tuning, noise-aware synthetic gene circuits into a well-defined human genomic safe har

177 Here, we engineer optogenetic gene circuits into mammalian cells to achieve noise-redu

178 ure efforts to convert functional multi-copy gene circuits into optimized single-copy circuits for pr

179 r a GATA2/3- and TFAP2A/C-driven trophoblast gene circuit irrespective of karyotype, differential exp

180 The cisCXp-shRunx2 gene circuit is designed based on the observation that i

181 Our results suggest that dynamics of a gene circuit is mainly determined by its topology, not b

182 X2 activity in turn negatively regulates the gene circuit itself.

183 on, costimulation, and addition of synthetic genes, circuits, knockouts and base edits to finely tune

184 ency content is determined by the underlying gene circuits, leading to a mapping between gene circuit

185 designed to reshape the response profiles of gene circuits, lending multifaceted tuning capacities in

186 We show that noise-induced oscillations in a gene circuit model display stochastic coherence, that is

187 Here we present a gene circuit modelling framework that explicitly integra

188 ging from a computational perspective, since gene circuit models are complex systems with many parame

189 Three separate gene-circuit models differing in the location of the pos

190 How gene circuits modulate this noise in gene expression to

191 red predictably using exchangeable synthetic gene circuit modules to sense and integrate multiple-inp

192 Regulatory gene circuit motifs play crucial roles in performing and

193 species, therapeutic payloads, and synthetic gene circuits of engineered bacteria within multicellula

194 rk, we demonstrate construction of synthetic gene circuits of up to 64 kb in size comprising 11 trans

195 Engineered gene circuits often degrade due to mutation and selectio

196 c models of transcription, which assume that gene circuits operate at equilibrium, have previously be

197 an extent that is infeasible for engineered gene circuits or other cell-based technologies.

198 n reveal the mechanisms behind non-intuitive gene circuit output dynamics.

199 ts into gene regulation, as perturbations of gene circuit parameters are discernible in the measured

200 widely applicable for engineering artificial gene circuit parts.

201 present a proof-of-concept immunomodulatory gene circuit platform that enables tumor-specific expres

202 on of a negative feedback-based 'linearizer' gene circuit previously developed in yeast.

203 ease in constructing robust and predictable gene circuits promises myriad applications in gene and c

204 Regulatory interactions found in gap gene circuits provide consistent and sufficient mechanis

205 This pair-rule gene circuit provides insight into short-germ segmentati

206 dynamical analyses of synthetic and natural gene circuits, providing an essential step toward the pr

207 The construction of synthetic gene circuits relies on our ability to engineer regulato

208 erformed across conditions to define dynamic gene circuits required to establish resting and activate

209 Engineering of cell fate through synthetic gene circuits requires methods to precisely implement co

210 The construction of synthetic gene circuits requires the rational combination of multi

211 or future engineering of synthetic mammalian gene circuits requiring nonlinear responses to HGF signa

212 size of the crowding molecules can fine-tune gene circuit response to molecular crowding.

213 x, model is proposed for the dynamics of the gene circuit responsible for regulating nitrogen catabol

214 These synthetic gene circuits reveal a unique approach to support daily

215 ay be insufficient to capture how eukaryotic gene circuits sense and respond to input transcription f

216 oretical analyses and simulations of various gene circuits show that the noise regulatory vector is c

217 ures of E. coli, and verify the link between gene circuit structure and noise spectra by demonstratin

218 gene circuits, leading to a mapping between gene circuit structure and the noise frequency range.

219 The analysis elucidates important aspects of gene circuit structure that control functionality, and m

220 oscillations, have been found in specialized gene circuits such as the bacteriophage lambda switch an

221 in qualitatively similar findings in natural gene circuits, such as the yeast GAL network.

222 By constructing simple gene circuits, such studies have generated new insights

223 Like other gene circuits, synthetic gene oscillators are noisy and

224 ue engineering, we developed circadian-based gene circuits, termed "chronogenetics", that express a p

225 ectors for directed evolution, combinatorial gene circuit tests, and for CRISPR multiplexing.

226 consider the design of a type of repressible gene circuit that is common in bacteria.

227 k control, we designed a synthetic mammalian gene circuit that maintains thyroid hormone homeostasis

228 olved from an adaptive temperature sensor: a gene circuit that responds only to temperature changes.

229 Here we develop a two-strain gene circuit that senses and responds to which strain is

230 enome editing of iPSCs to create a synthetic gene circuit that senses changing levels of endogenous i

231 We build an all-in-one gene circuit that sequentially edits genomic loci, synch

232 uilding high-fidelity, evolutionarily robust gene circuits that can be scaled to a wide range of host

233 Synthetic gene circuits that combine DNA, protein, and RNA compone

234 odes has afforded new insights into opposing gene circuits that define canonical and neural NC fates

235 We developed inducible synthetic gene circuits that generate varying degrees of expressio

236 mework supporting the forward engineering of gene circuits that incorporate RNAi-based regulatory com

237 This review explores the gene circuits that influence longevity and highlights th

238 ively map the degree of crosstalk and design gene circuits that introduce compensatory crosstalk at t

239 signing and implementing intricate synthetic gene circuits that perform complex sensing and actuation

240 nal genetic circuits and describe artificial gene circuits that perform digital and analog computatio

241 Synthetic gene circuits that precisely control human cell function

242 study, we developed autonomous chronogenetic gene circuits that produce the biologic drug interleukin

243 pathways, we constructed inducible synthetic gene circuits that regulate bacterial encapsulation in E

244 Therapeutic plug and play gene circuits that restore physiological feedback contro

245 Here, we design gene circuits that sense and control phenotypic structur

246 evity that could lead to rationally designed gene circuits that slow aging.

247 est axial identity and directly controls the gene circuits that support skeletal differentiation.

248 Here we explore the potential for gene circuits that use each of these six mechanisms to e

249 these insulators are used to join synthetic gene circuits, the behavior of layered circuits can be p

250 ogress article, we review recently developed gene circuit therapies for cancer using immune cells, nu

251 es and future directions for realizing these gene circuit therapies in the clinic.

252 in response interplay trackable by synthetic gene circuits, thereby offering instructions for enginee

253 that Tc-eve, Tc-run, and Tc-odd form a three-gene circuit to regulate one another as well as their do

254 n in sister cells, and by re-engineering the gene circuit to specifically block exit.

255 We found these synthetic gene circuits to be stable and robust in the long-term,

256 Our approach enabled the largest, eukaryotic gene circuits to date and will form the basis for large,

257 sitive and negative feedback-based synthetic gene circuits to decouple noise from the mean for Puromy

258 present a framework for building comparator gene circuits to digitize analogue inputs based on diffe

259 logue-to-digital circuits with other digital gene circuits to enable concentration-dependent logic.

260 hat can be harnessed by native and synthetic gene circuits to provide greater control over sRNA activ

261 MBL Symposium 'Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture' was held in Heidel

262 MBL Symposium 'Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture' was held virtually

263 Here we use synthetic 'signal-recording' gene circuits to trace the evolution of signalling patte

264 Although there are thousands of three-gene circuit topologies that can robustly develop a stri

265 yses of biochemical activities or to trigger gene circuits using measured signaling events.

266 noise-reducing Light-Inducible Tuner (LITer) gene circuits using the TetR repressor fused with a Tet-

267 In modeling the system as a parsimonious gene circuit, we show that tension-dependent stabilizati

268 By modeling simple gene circuits, we analyze the impact of cellular noise o

269 y combining directed evolution and synthetic gene circuits, we developed a unique self-modulatory pla

270 ingle-cell protein dynamics of a minimal HIV gene circuit were monitored with time-lapse fluorescence

271 Gene circuits were activated in materials with IPTG embe

272 Gene circuits were transduced into induced pluripotent s

273 Our critical motif is built from a two-gene circuit, where SOC can be successfully implemented.

274 involved in gap gene regulation based on gap gene circuits, which are mathematical gene network model

275 ifferent topologies and verified a synthetic gene circuit with mutual inhibition and auto-activations

276 natural promoters and engineering synthetic gene circuits with desired expression properties.

277 Regulatory gene circuits with positive-feedback loops control stem

278 Gene circuits with predefined behaviours have been succe

279 gnificant challenge for assembling synthetic gene circuits with tested modules as they often do not f

280 vide one example of how the arrangement of a gene circuit within the genome can affect its behaviour.

281 le effect on the noise behavior of following gene circuits within a cascade.