Toward predictive engineering of gene circuits

E Şimşek, Y Yao, D Lee, L You - Trends in Biotechnology, 2023 - cell.com
Many synthetic biology applications rely on programming living cells using gene circuits–the
assembly and wiring of genetic elements to control cellular behaviors. Extensive progress …

[HTML][HTML] Stochastic models coupling gene expression and partitioning in cell division in Escherichia coli

ISC Baptista, AS Ribeiro - BioSystems, 2020 - Elsevier
Regulation of future RNA and protein numbers is a key process by which cells continuously
best fit the environment. In bacteria, RNA and proteins exist in small numbers and their …

Optimum threshold minimizes noise in timing of intracellular events

S Kannoly, T Gao, S Dey, N Wang, A Singh… - Iscience, 2020 - cell.com
How the noisy expression of regulatory proteins affects timing of intracellular events is an
intriguing fundamental problem that influences diverse cellular processes. Here we use the …

[HTML][HTML] Gene copy number and negative feedback differentially regulate transcriptional variability of segmentation clock genes

OQH Zinani, K Keseroğlu, S Dey, A Ay, A Singh… - Iscience, 2022 - cell.com
Timely progression of a genetic program is critical for embryonic development. However,
gene expression involves inevitable fluctuations in biochemical reactions leading to …

Noise reduction as an emergent property of single-cell aging

P Liu, R Song, GL Elison, W Peng, M Acar - Nature communications, 2017 - nature.com
Noise-induced heterogeneity in gene expression is an inherent reality for cells. However, it
is not well understood how noise strength changes for a single gene while the host cell is …

Multi-scale model suggests the trade-off between protein and ATP demand as a driver of metabolic changes during yeast replicative ageing

B Schnitzer, L Österberg, I Skopa… - PLOS Computational …, 2022 - journals.plos.org
The accumulation of protein damage is one of the major drivers of replicative ageing,
describing a cell's reduced ability to reproduce over time even under optimal conditions …

Time-resolved microfluidics unravels individual cellular fates during double-strand break repair

N Vertti-Quintero, E Levien, L Poggi, A Amir… - BMC biology, 2022 - Springer
Background Double-strand break repair (DSBR) is a highly regulated process involving
dozens of proteins acting in a defined order to repair a DNA lesion that is fatal for any living …

Modeling aging and its impact on cellular function and organismal behavior

E Santiago, DF Moreno, M Acar - Experimental Gerontology, 2021 - Elsevier
Aging is a complex phenomenon of functional decay in a biological organism. Although the
effects of aging are readily recognizable in a wide range of organisms, the cause (s) of aging …

Altered expression response upon repeated gene repression in single yeast cells

L Schuh, I Kukhtevich, P Bheda, M Schulz… - PLOS Computational …, 2022 - journals.plos.org
Cells must continuously adjust to changing environments and, thus, have evolved
mechanisms allowing them to respond to repeated stimuli. While faster gene induction upon …

The switch of DNA states filtering the extrinsic noise in the system of frequency modulation

SC Lo, CX You, BR Chen, CC Hsieh, CE Li, CC Shu - Scientific Reports, 2021 - nature.com
There is a special node, which the large noise of the upstream element may not always lead
to a broad distribution of downstream elements. This node is DNA, with upstream element …