Feedforward loops: evolutionary conserved network motifs redesigned for synthetic biology applications

T Weldemichael, MD Asemoloye, MA Marchisio - Applied Sciences, 2022 - mdpi.com
Feedforward loops (FFLs) are relatively simple network motifs, made of three interacting
genes, that have been found in a large number in E. coli and S. cerevisiae. More recently …

Evolution of cell size control is canalized towards adders or sizers by cell cycle structure and selective pressures

F Proulx-Giraldeau, JM Skotheim, P François - Elife, 2022 - elifesciences.org
Cell size is controlled to be within a specific range to support physiological function. To
control their size, cells use diverse mechanisms ranging from 'sizers', in which differences in …

Network motifs and hypermotifs in TGFβ-induced epithelial to mesenchymal transition and metastasis

G Sai Bhavani, A Palanisamy - Frontiers in Systems Biology, 2023 - frontiersin.org
Epithelial to mesenchymal transition (EMT) is a complex, non-linear, dynamic multistep
process that plays an integral role in the development of metastatic cancers. A diverse range …

Model-based investigation of the relationship between regulation level and pulse property of I1-FFL gene circuits

J Ryan, S Hong, M Foo, J Kim, X Tang - ACS synthetic biology, 2022 - ACS Publications
Mathematical models are powerful tools in guiding the construction of synthetic biological
circuits, given their capability of accurately capturing and predicting circuit dynamics. Recent …

Characterization of Arabidopsis eskimo1 reveals a metabolic link between xylan O‐acetylation and aliphatic glucosinolate metabolism

D Singh, H Zhao, SK Gupta, Y Kumar… - Physiologia …, 2024 - Wiley Online Library
Glucuronoxylan is present mainly in the dicot of the secondary cell walls, often O‐acetylated,
which stabilizes cell structure by maintaining interaction with cellulose and other cell wall …

Integrated analysis of smRNAome, transcriptome, and degradome data to decipher microRNAs regulating costunolide biosynthesis in Saussurea lappa

R Kaur, S Pathania, M Kajal, V Thakur, J Kaur, K Singh - Plant Science, 2023 - Elsevier
Saussurea lappa (S. lappa) has been known to synthesize medicinally important,
costunolide. Due to its immense therapeutic importance, understanding of regulatory …

Differences in evolutionary accessibility determine which equally effective regulatory motif evolves to generate pulses

K Xiong, M Gerstein, J Masel - Genetics, 2021 - academic.oup.com
Transcriptional regulatory networks (TRNs) are enriched for certain “motifs.” Motif usage is
commonly interpreted in adaptationist terms, ie, that the optimal motif evolves. But certain …

In enzymatic reactions, the reverse reaction reduces product noise

CC Hsieh, YC Lin, WB Lin, CC Shu - BioSystems, 2024 - Elsevier
Enzymatic reactions are essential for most cellular reactions and ubiquitous in living
organisms. In the present study, we explore the pivotal role of the reverse reaction in …

Extrinsic noise of the target gene governs abundance pattern of feed-forward loop motifs

MSA Momin, A Biswas - Physical Review E, 2020 - APS
Feed-forward loop (FFL) is found to be a recurrent structure in bacterial and yeast gene
transcription regulatory networks. In a generic FFL, transcription factor (TF) S regulates …

Association between gene expression plasticity and regulatory network topology

AJR Petit, A Genissel, A Le Rouzic - bioRxiv, 2024 - biorxiv.org
Over the past two decades, numerous studies have been conducted with the aim of
identifying the the structures within regulatory networks responsible for gene expression …