Publications by authors named "Giansimone Perrino"
Article Synopsis
- Synthetic and native genes in cells compete for expression machinery, affecting how cellular processes work together due to shared resources.
- A coarse-grained E. coli cell model is proposed to balance the complexity of metabolic regulation with the need for simplicity in biocircuit design, helping to understand the connection between resource availability and bacterial growth rates.
- The model allows for effective prototyping of biocircuits and provides analytical insights that help in designing robust systems for managing ribosome availability in cells.
Article Synopsis
- Competition for cellular resources can impact the interaction of co-expressed genes, making gene circuits less predictable in mammalian cells.
- Researchers found that downregulation of certain genes by microRNAs can lead to the upregulation of other co-expressed genes, suggesting a change in how resources are allocated within the cell.
- By creating a synthetic genetic system and a mathematical model called MIRELLA, the study reveals that this gene interplay is influenced by ribosome movement and RNA degradation processes, providing new insights for designing genetic circuits that can adapt based on resource availability.
Article Synopsis
- Low-cost sustainable feedstocks from plant or food waste are vital for biotechnologies but require multiple enzymes for breakdown, often leading to limitations in standard monoculture systems.
- A two-strain consortium model was tested, where each strain specializes in different stages of substrate degradation, showing improved performance compared to traditional single-cell cultures once a certain expression threshold is exceeded.
- Resource-aware whole-cell models can predict when using division of labor (DOL) is advantageous, helping inform design choices for efficient degradation of complex substrates like starch.
Article Synopsis
- The development of new functions in living cells is essential in the field of synthetic biology, which has seen significant advancements in the past decade.
- Control engineering has played a crucial role by providing concepts and tools that help analyze and design biological systems.
- This review emphasizes recent research that applies control theory to enhance the analysis and design of synthetic biology systems specifically in microbial cells.
The cell cycle is the process by which eukaryotic cells replicate. Yeast cells cycle asynchronously with each cell in the population budding at a different time. Although there are several experimental approaches to synchronise cells, these usually work only in the short-term.
View Article and Find Full Text PDFExtracting quantitative measurements from time-lapse images is necessary in external feedback control applications, where segmentation results are used to inform control algorithms. We describe ChipSeg, a computational tool that segments bacterial and mammalian cells cultured in microfluidic devices and imaged by time-lapse microscopy, which can be used also in the context of external feedback control. The method is based on thresholding and uses the same core functions for both cell types.
View Article and Find Full Text PDFAggregation of α-synuclein and formation of inclusions are hallmarks of Parkinson's disease (PD). Aggregate formation is affected by cellular environment, but it has been studied almost exclusively in cell-free systems. We quantitatively analyzed α-synuclein inclusion formation and clearance in a yeast cell model of PD expressing either wild-type (WT) α-synuclein or the disease-associated A53T mutant from the galactose (Gal)-inducible promoter.
View Article and Find Full Text PDFReal-time automatic regulation of gene expression is a key technology for synthetic biology enabling, for example, synthetic circuit's components to operate in an optimal range. Computer-guided control of gene expression from a variety of inducible promoters has been only recently successfully demonstrated. Here we compared, in silico and in vivo, three different control algorithms: the Proportional-Integral (PI) and Model Predictive Control (MPC) controllers, which have already been used to control gene expression, and the Zero Average Dynamics (ZAD), a control technique used to regulate electrical power systems.
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