About
35
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Introduction
Francesca Ceroni currently works at the Department of Chemical Engineering, Imperial College London. Francesca does research in Synthetic Biology, Molecular and Cell Biology and Bioengineering.
Additional affiliations
October 2016 - October 2016
January 2013 - present
January 2012 - September 2012
Education
January 2008 - April 2011
October 2004 - March 2007
September 2001 - October 2004
Publications
Publications (35)
Resource competition can be the cause of unintended coupling between co-expressed genetic constructs. Here we report the quantification of the resource load imposed by different mammalian genetic components and identify construct designs with increased performance and reduced resource footprint. We use these to generate improved synthetic circuits...
Automated and non-invasive mammalian cell analysis is currently lagging behind due to a lack of methods suitable for a variety of cell lines and applications. Here, we report the development of a high throughput non-invasive method for tracking mammalian cell growth and performance based on plate reader measurements. We show the method to be suitab...
Resource competition can be the cause of unintended coupling between co-expressed genetic constructs. Here we report quantification of the resource load imposed by different mammalian genetic components and identify construct designs with increased performance and reduced resource footprint. We use these to generate improved synthetic circuits and...
The use of cell-free protein synthesis (CFPS) has become increasingly widespread in synthetic biology over recent years, providing an effective platform for the study and engineering of cellular processes. The versatility and portability of CFPS systems have also boosted their potential for usage outside of the laboratory in a wide number of applic...
Cellular burden limits the applications of bacterial synthetic biology. Experimental approaches for burden minimisation have recently become available. Tools to identify construct design with low footprint on the host include capacity monitors that quantify cellular capacity, high-throughput approaches and cell-free systems for construct prototypin...
Transient transfections are routinely used in basic and synthetic biology studies to unravel pathway regulation and to probe and characterise circuit designs. As each experiment has a component of intrinsic variability, reporter gene expression is usually normalized with co-delivered genes that act as transfection controls. Recent reports in mammal...
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Individual cells exhibit specific proliferative responses to changes in microenvironmental conditions. Whether such potential is constrained by the cell density throughout the growth process is however unclear. Here, we identify a theoretical framework that captures how the information encoded in the initial density of cancer cell populations impac...
Construction of DNA-encoded programs is central to synthetic biology and the chosen method often determines the time required to design and build constructs for testing. Here, we describe and summarise key features of the available toolkits for DNA construction for mammalian cells. We compare the different cloning strategies based on their complexi...
RNA-seq enables the analysis of gene expression profiles across different conditions and organisms. Gene expression burden slows down growth, which results in poor predictability of gene constructs and product yields. Here, we describe how we applied RNA-seq to study the transcriptional profiles of Escherichia coli when burden is elicited during he...
Protein methylation is a key post-translational modification whose effects on gene expression have been intensively studied over the last two decades. Recently, renewed interest in non-histone protein methylation has gained momentum for its role in regulating important cellular processes and the activity of many proteins, including transcription fa...
As biological research and its applications rapidly evolve, new attempts at the governance of biology are emerging, challenging traditional assumptions about how science works and who is responsible for governing. However, these governance approaches often are not evaluated, analyzed, or compared. This hinders the building of a cumulative base of e...
Synthetic gene circuits perturb the physiology of their cellular host. The extra load on endogenous processes shifts the equilibrium of resource allocation in the host, leading to slow growth and reduced biosynthesis. Here we built integrated host-circuit models to quantify growth defects caused by synthetic gene circuits. Simulations reveal a comp...
Synthetic gene circuits perturb the physiology of their cellular host. The extra load on endogenous processes shifts the equilibrium of resource allocation in the host, leading to slow growth and reduced biosynthesis. Here we built integrated host-circuit models to quantify growth defects caused by synthetic gene circuits. Simulations reveal a comp...
Synthetic biology is maturing into a true engineering discipline for model microorganisms, but remains far from straightforward for most eukaryotes. Here, we outline the key challenges facing those trying to engineer biology across eukaryota and suggest areas of focus that will aid future progress.
Cells use feedback regulation to ensure robust growth despite fluctuating demands for resources and differing environmental conditions. However, the expression of foreign proteins from engineered constructs is an unnatural burden that cells are not adapted for. Here we combined RNA-seq with an in vivo assay to identify the major transcriptional cha...
Cells use feedback regulation to ensure robust growth despite fluctuating demands on resources and different environmental conditions. Yet the expression of foreign proteins from engineered constructs is an unnatural burden on resources that cells are not adapted for. Here we combined multiplex RNAseq with an in vivo assay to reveal the major trans...
Engineered E. coli can be made to autonomously switch from growth to production by a modular two-gate system that reduces the burden of biosynthesis.
Synthetic Biology is now in its second decade and many goals have been achieved toward the rational design of biological systems. This Research Topic features and reviews some of the latest progress in Synthetic Biology with a focus on research at the intersection between rational design and natural complexity with a potential outcome to concrete b...
Heterologous gene expression can be a significant burden for cells. Here we describe an in vivo monitor that tracks changes in the capacity of Escherichia coli in real time and can be used to assay the burden imposed by synthetic constructs and their parts. We identify construct designs with reduced burden that predictably outperformed less efficie...
Heterologous gene expression can be a significant burden to cells, consuming resources and causing decreased growth and stability. We describe here an in vivo monitor that tracks E. coli capacity changes in real-time and can be used to assay the burden synthetic constructs and their parts impose. By measuring capacity, construct designs with reduce...
Characterisation of genetic control elements is essential for the predictable engineering of synthetic biology systems. The current standard for in vivo characterisation of control elements is through the use of fluorescent reporter proteins such as green fluorescent protein (GFP). Gene expression, however, involves not only protein production but...
The assembly from modular parts is an efficient approach for creating new devices in Synthetic Biology. In the "bottom-up" designing strategy, modular parts are characterized in advance, and then mathematical modeling is used to predict the outcome of the final device. A prerequisite for bottom-up design is that the biological parts behave in a mod...
RNA interference is a natural gene expression silencing system that appears throughout the tree of life. As the list of cellular processes linked to RNAi grows, so does the demand for tools to accurately measure RNAi dynamics in living cells. We engineered a synthetic RNAi sensor that converts this negative regulatory signal into a positive output...
Fluorescent signals are widely used in life sciences to investigate cellular behavior. Using a fluorometer is a reliable approach to measure the amount of a specific fluorescent radiation emitted by a cellular population. On the other hand, measuring fluorescent signals at the single-cell level requires the use of properly equipped microscopes to a...
Preliminary dynamical measurements. Time-course measurements of normalized fluorescence and optical density in cells transformed with different gene-circuits.
Mathematical model without induced LacI residual affinity. Equations of the mathematical model without residual affinity between induced lactose repressor molecules and operator sites
Most of synthetic circuits developed so far have been designed by an ad hoc approach, using a small number of components (i.e. LacI, TetR) and a trial and error strategy. We are at the point where an increasing number of modular, inter-changeable and well-characterized components is needed to expand the construction of synthetic devices and to allo...
Synthetic biology aims to the rational design of gene circuits with predictable behaviours. Great efforts have been done so far to introduce in the field mathematical models that could facilitate the design of synthetic networks. Here we present a mathematical model of a synthetic gene-circuit with a negative feedback. The closed loop configuration...
Questions
Questions (9)
Hi all,
I am looking for an equivalent of the M9 cuture medium in bacteria but for mammalian cells.
I would need to grow my cells in very controlled conditions [sugars, aa, vitamins...etc].
Does anybody have experience?
Best,
Francesca
I have run my DS cDNA libraries on the Bioanalyzer [see the traces attached].
There is a weird small peak near the lower marker peak and I do not know if these libraries are good or not. Can anyone provide feedback?
I did a two step ds cDNA synthesis starting from 50 ng and 150 ng enriched mRNA.
How can I check my cDNA? I do not see peaks at Bioanalyzer, and I am wondering if the material is too low or if it means I do not have any cDNA.
I have to use it for a library preparation...
Thanks for any suggestion.
Can someone tell me if Qubit is really better than Nanodrop in nucleic acids quantification, even for small concentrations?
Does anybody have or know a protocol to understand how to optimize RNA/random hexames/temperature in ds cDNA synthesis reaction to get a precise fragment size?
Which is the advantage of performing a paired end sequencing instead of a single read one? I know it gives information for eukaryotic samples about the splicing variants... but for prokaryotes?
Is there any way to control it?
I am about to perform RNAseq on E. coli total transcriptome.
I am planning to use the Nextera kit so I need to prepare my own cDNA from total RNA.
Since the kits for ds cDNA synthesis are crazily expensive, I am planning to use a Tetro cDNA synthesis kit for first strand synthesis with random examers and then use a second stran buffer + polI+ all the components to synthesize the second strand.
Do you have experience on this?
Could this work fine?
I am trying to express Beta hCG in Escherichia coli but I can`t see any 23 KDa band on my SDS page. I know it forms inclusion bodies, but what I am using is codon optimized. I am wondering if this changes what I should expect on my gel and if there is a way to express it in an efficient way. I do not need it to be active, that is why I am not refolding it.
