Giansimone Perrino

• Doctor of Philosophy
• Postdoctoral Research Associate at Imperial College London

Real-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,...

Aggregation 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 (...

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. Here, we build a cyber-genetic system to achieve long-term synchronisati...

The implementation of novel functionalities in living cells is a key aspect of synthetic biology. In the last decade, the field of synthetic biology has made progress working in synergy with control engineering, whose solid framework has provided concepts and tools to analyse biological systems and guide their design. In this review, we briefly hig...

Competition for intracellular resources, also known as gene expression burden, induces coupling between independently co-expressed genes, a detrimental effect on predictability and reliability of gene circuits in mammalian cells. We recently showed that microRNA (miRNA)-mediated target downregulation correlates with the upregulation of a co-express...

Within a cell, synthetic and native genes compete for expression machinery, influencing cellular process dynamics through resource couplings. Models that simplify competitive resource binding kinetics can guide the design of strategies for countering these couplings. However, in bacteria resource availability and cell growth rate are interlinked, w...

Synthetic genes compete among themselves and with the host cell’s genes for expression machinery, exhibiting resource couplings that affect the dynamics of cellular processes. The modeling of such couplings can be facilitated by simplifying the kinetics of resource-substrate binding. Model-guided design allows to counter unwanted indirect interacti...

Background Low-cost sustainable feedstocks are essential for commercially viable biotechnologies. These feedstocks, often derived from plant or food waste, contain a multitude of different complex biomolecules which require multiple enzymes to hydrolyse and metabolise. Current standard biotechnology uses monocultures in which a single host expresse...

Extracting 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...

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 work only in the short-term. Here, we built a cyber-genetic system to achieve long-term synchronisation of...

Extracting quantitative measurements from time-lapse images is necessary in external feedback control applications, where segmentation results are used to inform control algorithms. While such image segmentation applications have been previously reported, there is in the literature a lack of open-source and documented code for the community. We des...

The cell cycle is present in all cells of all species and it is of fundamental importance in coordinating all the steps required for cell replication, including growth, DNA replication and cell division. Budding yeast is an unicellular organism characterised by a mother cell that buds to generate a daughter cell at each cell cycle. Each cell in a p...

The cell cycle is present in all cells of all species and it is of fundamental importance in coordinating all the steps required for cell replication, including growth, DNA replication and cell division. Budding yeast is an unicellular organism characterised by a mother cell that buds to generate a daughter cell at each cell cycle. Each cell in a p...

The periodic process of cell replication by division , known as cell-cycle, is a natural phenomenon occurring asynchronously in any cell population. Here, we consider the problem of synchronising cell-cycles across a population of yeast cells grown in a microfluidics device. Cells were engineered to reset their cell-cycle in response to low methion...

The transcription factor EB (TFEB) is a key component of the transcriptional regulation of lysosomal biogenesis and autophagy in response to starvation. Autophagy is a self-degradative process activated by cells to survive during nutrient deficiency. In normal conditions, TFEB is sequestered in the cytoplasm through phosphorylation. Following starv...

Cells are defined by their unique ability to self-replicate through cell division. This periodic process is known as the cell-cycle and it happens with a defined period in each cell. The budding yeast divides asymmetrically with a mother cell generating multiple daughter cells. Within the cell population each cell divides with the same period but a...

When information and measures obtained from sequences of microscopic images are subject to time constraints, suitable fast algorithms must be implemented to process the whole data set. In this work, we deal with sequences of images obtained from time-lapse microscopy in order to detect single yeast cells in a microfluidics chip over time. The under...

Neurodegenerative disorders are characterised by the progressive disruption of specific neuronal population partly due to the formation of abnormal protein aggregates that interfere with normal cell functions. In Parkinson's disease, the role of abnormal α-synuclein protein aggregates in causing the disease is well established. Mutations in α-synuc...

Real-time automatic regulation of gene expression in living cells is a key technology for synthetic biology. Unlike traditional control engineering applications, cells grow and divide over time, and the natural variability arising in individual cell gene expression makes the population time-varying and heterogeneous. Therefore, the application of t...

Real‐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,...

Automatic control is an engineering approach to regulate the behaviour of a system in an automated and precise manner. Controllers are used in everyday appliances from thermostats to microwaves, as well as, in complex and large systems such as airplanes and power-plants. The design principle is based on negative feedback, where the quantity to be m...