Biology subjects

Tas, H.

Publications and source records attributed to Tas, H..

6 recordsLinked to original sources

bioRxiv2026

Histone neutralization protects the ischemic brain against stroke-associated pneumonia

Bacterial pneumonia aggravates ischemic stroke via mechanisms that still remain to be determined. In ischemic stroke patients and mice exposed to middle cerebral artery occlusion, we show that stroke-associated pneumonia markedly worsens clinical stroke outcome. In mice, pneumonia induced 3 days after stroke impaired neurological recovery and increased brain neutrophil infiltrates, blood-brain barrier breakdown, cerebral microvascular thrombosis, and progressive brain atrophy. The antibiotic amoxicillin only partially ameliorated pneumonia-associated neurological deficits and neutrophil infiltrates. Neutrophils were critical mediators of pneumonia-induced blood-brain barrier breakdown and microvascular thrombosis. Notably, administration of a neutralizing anti-histone antibody during pneumonia--unlike degradation or blockade of neutrophil extracellular trap formation or myeloperoxidase inhibition--restored long-term neurological recovery and prevented brain atrophy in stroke-associated pneumonia mice. This study identifies extracellular histones as key drivers of secondary inflammatory brain injury and establishes histone neutralization as a therapeutic strategy with an extended treatment window in the post-acute stroke phase. One Sentence SummaryNeutralizing extracellular histones reverses pneumonia-driven secondary brain injury and restores long-term recovery after ischemic stroke.

neuroscience↗

bioRxiv2024

Preventing escape and malfunction of recoded cells due to tRNA base changes

Engineering the genetic code restricts DNA transfer (cellular bioisolation) and enables new chemistries via non-standard amino acid incorporation. These distinct properties make recoded cells state-of-the-art safe technologies. However, evolutionary pressures may endanger the longevity of the recoding. Here, we reveal that recoded Escherichia coli lacking 18,214 serine codons and two tRNASer can express wild-type antibiotic resistance genes and escape up to seven orders of magnitude faster than expected. We show a two-step escape process whereby recoded cells mistranslate antibiotic resistance genes to survive until modified or mutated tRNAs reintroduce serine into unassigned codons. We developed genetic-code-sensitive kill switches that sense serine incorporation and prevent cellular escape while preserving encoding of three distinct non-standard amino acids. This work lays the foundation for the long-term controlled function of cells that incorporate new chemistries, with implications for the design, use, and biosafety of synthetic genomes in clinical and environmental applications where physical containment is insufficient.

synthetic biology↗

bioRxiv2024

Reprogramming genetic circuits using space

Genetic circuits confer computing abilities to living cells, performing novel transformations of input stimuli into output responses. Circuit editing often focuses on substituting DNA components, such as RBSs, regulators, or promoters, from part libraries to achieve desired performance. However, this approach is inherently limited by the availability of DNA components. Here, we show that circuit performance can be reprogrammed without altering its DNA sequence by using a library of positions: a set of physical locations within the cells volume. Using bacteria as the living chassis, we engineer 219 spatially unique genetic circuits of four different types--three regulatory cascades and a toggle switch--by either inserting the entire circuit in a specific chromosomal position or separating and distributing circuit modules. Their analysis, together with a mathematical model, reveals that spatial positioning can be used not only to optimize circuits but also to switch circuits between modes of operation, giving rise to new functions as circuit complexity increases. We provide foundational insights into leveraging intracellular space for circuit design.

synthetic biology↗

bioRxiv2020

FlowScatt: enabling volume-independent flow cytometry data by decoupling fluorescence from scattering

MotivationMeasuring fluorescence by flow cytometry is fundamental for characterising single-cell performance. While it is known that fluorescence and scattering values tend to positively correlate, the impact of cell volume on fluorescence is typically overlooked. This makes of fluorescence values alone an inaccurate measurement for high-precision characterisations. ResultsWe developed FlowScatt, an open-source software package that removes volume-dependency in the fluorescence channel. Using FlowScatt, flourescence values are re-calculated based on the unified volume per cell that arises from scattering decomposition. AvailabilityFlowScatt is openly available as a Python package on https://github.com/rstoof/FlowScatt. Experimental data for validation is available online. Contactangel.goni-moreno@newcastle.ac.uk

bioinformatics↗

bioRxiv2020

A standardized broad host range inverter package for genetic circuitry design in Gram-negative bacteria

Genetically encoded logic gates, especially inverters--NOT gates--are the building blocks for designing circuits, engineering biosensors or decision-making devices in synthetic biology. However, the repertoire of inverters readily available for different species is rather limited. In this work, a large whole of NOT gates that was shown to function previously in a specific strain of Escherichia coli, was recreated as broad host range (BHR) collection of constructs assembled in low, medium and high copy number plasmid backbones of the SEVA (Standard European Vector Architecture) collection. The input/output function of each of the gates was characterized and parameterized in the environmental bacterium and metabolic engineering chassis Pseudomonas putida. Comparisons of the resulting fluorescence cytometry data with those published for the same gates in Escherichia coli provided useful hints on the portability of the corresponding gates. The hereby described BHR inverter package (20 different versions of 12 distinct gates) thus becomes a toolbox of choice for designing genetic circuitries in a variety of Gram-negative species other than E. coli.

synthetic biology↗

bioRxiv2020

Contextual dependencies expand the re-usability of genetic inverters

The design and implementation of Boolean logic functions in living cells has become a very active field within synthetic biology. By controlling networks of regulatory proteins, novel genetic circuits are engineered to generate predefined output responses. Although many current implementations focus solely on the genetic components of the circuit, the host context in which the circuit performs is crucial for its outcome. Here, we characterise 20 genetic NOT logic gates (inverters) in up to 7 bacterial-based contexts each, to finally generate 135 different functions. The contexts we focus on are particular combinations of four plasmid backbones and three hosts, two Escherichia coli and one Pseudomonas putida strains. Each NOT logic gate shows seven different logic behaviours, depending on the context. That is, gates can be reconfigured to fit response requirements by changing only contextual parameters. Computational analysis shows that this range of behaviours improves the compatibility between gates, because there are considerably more possibilities for combination than when considering a unique function per genetic construct. Finally, we address the issue of interoperability and portability by measuring, scoring, and comparing gate performance across contexts. Rather than being a limitation, we argue that the effect of the genetic background on synthetic constructs expand the scope of the functions that can be engineered in complex cellular environments, and advocate for considering context as a fundamental design parameter for synthetic biology.

synthetic biology↗