Synthetic circuits that process multiple light and chemical signal inputs

Liu, Lizhong; Huang, Wei; Huang, Jiandong

doi:10.1186/s12918-016-0384-y

Cited by 5 publications

(3 citation statements)

References 34 publications

(39 reference statements)

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“…For instance, Chen et al engineered a set of chimeric promoters that simultaneously responded to tetracycline and blue light for the spatial control of toxin gene expression for gene therapy . Liu et al built a synthetic circuit that can respond simultaneously to multiple light and ligand outputs . Finally, our approach can be easily adapted to other commonly used ligand-inducible promoters with only minor refactoring and could be applied in prokaryotic hosts other than E. coli .…”

Section: Discussionmentioning

confidence: 99%

Programming the Dynamic Control of Bacterial Gene Expression with a Chimeric Ligand- and Light-Based Promoter System

et al. 2018

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To program cells in a dynamic manner, synthetic biologists require precise control over the threshold levels and timing of gene expression. However, in practice, modulating gene expression is widely carried out using prototypical ligand-inducible promoters, which have limited tunability and spatiotemporal resolution. Here, we built two dual-input hybrid promoters, each retaining the function of the ligand-inducible promoter while being enhanced with a blue-light-switchable tuning knob. Using the new promoters, we show that both ligand and light inputs can be synchronously modulated to achieve desired amplitude or independently regulated to generate desired frequency at a specific amplitude. We exploit the versatile programmability and orthogonality of the two promoters to build the first reprogrammable logic gene circuit capable of reconfiguring into logic OR and N-IMPLY logic on the fly in both space and time without the need to modify the circuit. Overall, we demonstrate concentration- and time-based combinatorial regulation in live bacterial cells with potential applications in biotechnology and synthetic biology.

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Section: Discussionmentioning

confidence: 99%

Programming the Dynamic Control of Bacterial Gene Expression with a Chimeric Ligand- and Light-Based Promoter System

et al. 2018

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“…Mutual information is the maximum likelihood information theoretic measure of statistical dependence. Since it is capable to capture non-linear relationships between features, it has been successfully used for gene co-expression network reconstruction (de Anda-Jáuregui et al, 2016 ; He et al, 2017 ). It has also been previously used for bipartite network reconstruction of multiomic data (de Anda-Jáuregui et al, 2018 , 2019 ).…”

Section: Methodsmentioning

confidence: 99%

Gene-Microbiome Co-expression Networks in Colon Cancer

2021

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It is known that cancer onset and development arise from complex, multi-factorial phenomena spanning from the molecular, functional, micro-environmental, and cellular up to the tissular and organismal levels. Important advances have been made in the systematic analysis of the molecular (mostly genomic and transcriptomic) within large studies of high throughput data such as The Cancer Genome Atlas collaboration. However, the role of the microbiome in the induction of biological changes needed to reach these pathological states remains to be explored, largely because of scarce experimental data. In recent work a non-standard bioinformatics strategy was used to indirectly quantify microbial abundance from TCGA RNA-seq data, allowing the evaluation of the microbiome in well-characterized cancer patients, thus opening the way to studies incorporating the molecular and microbiome dimensions altogether. In this work, we used such recently described approaches for the quantification of microbial species alongside with gene expression. With this, we will reconstruct bipartite networks linking microbial abundance and gene expression in the context of colon cancer, by resorting to network reconstruction based on measures from information theory. The rationale is that microbial communities may induce biological changes important for the cancerous state. We analyzed changes in microbiome-gene interactions in the context of early (stages I and II) and late (stages III and IV) colon cancer, studied changes in network descriptors, and identify key discriminating features for early and late stage colon cancer. We found that early stage bipartite network is associated with the establishment of structural features in the tumor cells, whereas late stage is related to more advance signaling and metabolic features. This functional divergence thus arise as a consequence of changes in the organization of the corresponding gene-microorganism co-expression networks.

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“…This can be achieved through genetic engineering and synthetic biology techniques, allowing the introduction, amplification, or knockdown of specific genes of interest [207]. Additionally, the ability to trigger transcriptomic or proteomic changes in vascular cells using lightor chemically induced constructs provides temporal control over cell behavior [208,209], which is particularly relevant for modeling transitions or the onset of pathophysiological states.…”

Section: Integration Of the Angiogenic Niche Physiology Within Smart ...mentioning

confidence: 99%

Mimicking Molecular Pathways in the Design of Smart Hydrogels for the Design of Vascularized Engineered Tissues

Nicosia,

Salamone,

Costa

et al. 2023

IJMS

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Biomaterials are pivotal in supporting and guiding vascularization for therapeutic applications. To design effective, bioactive biomaterials, understanding the cellular and molecular processes involved in angiogenesis and vasculogenesis is crucial. Biomaterial platforms can replicate the interactions between cells, the ECM, and the signaling molecules that trigger blood vessel formation. Hydrogels, with their soft and hydrated properties resembling natural tissues, are widely utilized; particularly synthetic hydrogels, known for their bio-inertness and precise control over cell–material interactions, are utilized. Naturally derived and synthetic hydrogel bases are tailored with specific mechanical properties, controlled for biodegradation, and enhanced for cell adhesion, appropriate biochemical signaling, and architectural features that facilitate the assembly and tubulogenesis of vascular cells. This comprehensive review showcases the latest advancements in hydrogel materials and innovative design modifications aimed at effectively guiding and supporting vascularization processes. Furthermore, by leveraging this knowledge, researchers can advance biomaterial design, which will enable precise support and guidance of vascularization processes and ultimately enhance tissue functionality and therapeutic outcomes.

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Synthetic circuits that process multiple light and chemical signal inputs

Cited by 5 publications

References 34 publications

Programming the Dynamic Control of Bacterial Gene Expression with a Chimeric Ligand- and Light-Based Promoter System

Programming the Dynamic Control of Bacterial Gene Expression with a Chimeric Ligand- and Light-Based Promoter System

Gene-Microbiome Co-expression Networks in Colon Cancer

Mimicking Molecular Pathways in the Design of Smart Hydrogels for the Design of Vascularized Engineered Tissues

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