A5019681901- Gene Regulatory Network Analysis
- Evolutionary Algorithms and Applications
- Single-cell and spatial transcriptomics
- Bacterial Genetics and Biotechnology
- CRISPR and Genetic Engineering
- Advanced Memory and Neural Computing
- Modular Robots and Swarm Intelligence
- Bacteriophages and microbial interactions
- Plant and Biological Electrophysiology Studies
- RNA and protein synthesis mechanisms
- Cellular Automata and Applications
- Microfluidic and Bio-sensing Technologies
- Genomics and Phylogenetic Studies
- DNA and Biological Computing
- Microbial Metabolic Engineering and Bioproduction
- Advanced biosensing and bioanalysis techniques
Centro Nacional de Biotecnología
2024
Universidad Politécnica de Madrid
2022-2024
Centre for Plant Biotechnology and Genomics
2022-2024
Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria
2022-2024
Newcastle University
2019-2022
The SEVA platform (https://seva-plasmids.com) was launched one decade ago, both as a database (DB) and physical repository of plasmid vectors for genetic analysis engineering Gram-negative bacteria with structure nomenclature that follows strict, fixed architecture functional DNA segments. While the current update keeps basic features earlier versions, has been upgraded not only many more ready-to-use plasmids but also expand range target species, harmonize assembly methods enable new...
Abstract The implementation of Boolean logic circuits in cells have become a very active field within synthetic biology. Although these are mostly focussed on the genetic components alone, context which circuit performs is crucial for its outcome. We characterise 20 NOT gates up to 7 bacterial-based contexts each, generate 135 different functions. we focus combinations four plasmid backbones and three hosts, two Escherichia coli one Pseudomonas putida strains. Each gate shows seven dynamic...
Boolean NOR gates have been widely implemented in Escherichia coli as transcriptional regulatory devices for building complex genetic circuits. Yet, their portability to other bacterial hosts/chassis is generally hampered by frequent changes the parameters of INPUT/OUTPUT response functions brought about new and biochemical contexts. Here, we used circuit design tool CELLO assembling a gate soil bacterium metabolic engineering platform Pseudomonas putida with components tailored E. coli. To...
Abstract Genetic circuits confer computing abilities to living cells, performing novel transformations of input stimuli into output responses. These genetic are routinely engineered for insertion bacterial plasmids and chromosomes, using a design paradigm whose only spatial consideration is linear ordering the individual components. However, chromosomal DNA has complex three dimensional conformation which alters mechanics gene expression, leading dynamics that specific location. Here we...
The Synthetic Biology Open Language (SBOL) is an emerging synthetic biology data exchange standard, designed primarily for unambiguous and efficient machine-to-machine communication. However, manual editing of SBOL generally difficult nontrivial designs. Here, we describe ShortBOL, a lightweight scripting language that bridges the gap between editing, visual design tools, direct programming. ShortBOL shorthand textual developed to enable users create designs quickly easily, without requiring...
Abstract Synthetic biology uses molecular to implement genetic circuits that perform computations. These can process inputs and deliver outputs according predefined rules are encoded, often entirely, into parts. However, the field has recently begun focus on using mechanisms beyond realm of parts for engineering biological circuits. We analyse use electrogenic processes circuit design present a model merged electrogenetic toggle switch operating in biofilm attached an electrode....
Abstract The programming of computations in living cells can be done by manipulating information flows within genetic networks. Typically, a single bit is encoded gene’s steady state expression. Expression discretized into high and low levels that correspond to 0 1 logic values, analogous the voltages electronic circuits. However, processes molecular signaling computation systems challenge this computational paradigm with their dynamic, stochastic continuous operation. Although there good...
The design and implementation of Boolean logic functions in living cells has become a very active field within synthetic biology. By controlling networks regulatory proteins, novel genetic circuits are engineered to generate predefined output responses. Although many current implementations focus solely on the components circuit, host context which circuit performs is crucial for its outcome. Here, we characterise 20 NOT gates (inverters) up 7 bacterial-based contexts each, finally 135...
Abstract Motivation Measuring fluorescence by flow cytometry is fundamental for characterising single-cell performance. While it known that and scattering values tend to positively correlate, the impact of cell volume on typically overlooked. This makes alone an inaccurate measurement high-precision characterisations. Results We developed FlowScatt, open-source software package removes volume-dependency in channel. Using flourescence are re-calculated based unified per arises from...
Abstract Synthetic biology uses molecular to implement genetic circuits that perform computations. These can process inputs and deliver outputs according predefined rules are encoded, often entirely, into parts. However, the field has recently begun focus on using mechanisms beyond realm of parts for engineering biological circuits. We analyse use electrogenic processes circuit design present a model merged electrogenetic toggle switch. Computational simulations explore conditions under...