A partially self-regenerating synthetic cell

Self-regeneration is a fundamental function of all living systems. Here we demonstrate partial molecular self-regeneration in a synthetic cell. By implementing a minimal transcription-translation system within microfluidic reactors, the system is able to regenerate essential protein components from DNA templates and sustain synthesis activity for over a day. By quantitating genotype-phenotype relationships combined with computational modeling we find that minimizing resource competition and optimizing resource allocation are both critically important for achieving robust system function. With this understanding, we achieve simultaneous regeneration of multiple proteins by determining the required DNA ratios necessary for sustained self-regeneration. This work introduces a conceptual and experimental framework for the development of a self-replicating synthetic cell. A fundamental function of living systems is regenerating essential components. Here the authors design an artificial cell using a minimal transcription-translation system in microfluidic reactors for sustained regeneration of multiple essential proteins

Bottom-up construction of complex biomolecular systems with cell-free synthetic biology

Cell-free systems offer a promising approach to engineer biology since their open nature allows for well-controlled and characterized reaction conditions. In this review, we discuss the history and recent developments in engineering recombinant and crude extract systems, as well as breakthroughs in enabling technologies, that have facilitated increased throughput, compartmentalization, and spatial control of cell-free protein synthesis reactions. Combined with a deeper understanding of the cell-free systems themselves, these advances improve our ability to address a range of scientific questions. By mastering control of the cell-free platform, we will be in a position to construct increasingly complex biomolecular systems, and approach natural biological complexity in a bottom-up manner

Spin Density Matrix Elements in Exclusive ρ0\rho ^0 Meson Muoproduction

We report on a measurement of Spin Density Matrix Elements (SDMEs) in hard exclusive $\rho ^0$ meson muoproduction at COMPASS using 160~GeV/$c$ polarised $\mu ^{+}$ and $\mu ^{-}$ beams impinging on a liquid hydrogen target. The measurement covers the kinematic range 5.0~GeV/$c^2$ $< W <$ 17.0~GeV/$c^2$, 1.0 (GeV/$c$)$^2$ $< Q^2 <$ 10.0 (GeV/$c$)$^2$ and 0.01 (GeV/$c$)$^2$ $< p_{\rm{T}}^2 <$ 0.5 (GeV/$c$)$^2$. Here, $W$ denotes the mass of the final hadronic system, $Q^2$ the virtuality of the exchanged photon, and $p_{\rm{T}}$ the transverse momentum of the $\rho ^0$ meson with respect to the virtual-photon direction. The measured non-zero SDMEs for the transitions of transversely polarised virtual photons to longitudinally polarised vector mesons ($\gamma^*_T \to V^{ }_L$) indicate a violation of $s$-channel helicity conservation. Additionally, we observe a dominant contribution of natural-parity-exchange transitions and a very small contribution of unnatural-parity-exchange transitions, which is compatible with zero within experimental uncertainties. The results provide important input for modelling Generalised Parton Distributions (GPDs). In particular, they may allow one to evaluate in a model-dependent way the role of parton helicity-flip GPDs in exclusive $\rho ^0$ production

Collins and Sivers transverse-spin asymmetries in inclusive muoproduction of ρ0\rho^0 mesons

The production of vector mesons in deep inelastic scattering is an interesting yet scarsely explored channel to study the transverse spin structure of the nucleon and the related phenomena. The COMPASS collaboration has performed the first measurement of the Collins and Sivers asymmetries for inclusively produced $\rho^0$ mesons. The analysis is based on the data set collected in deep inelastic scattering in $2010$ using a $160\,\,\rm{GeV}/c$ $\mu^+$ beam impinging on a transversely polarized $\rm{NH}_3$ target. The $\rho^{0}$ mesons are selected from oppositely charged hadron pairs, and the asymmetries are extracted as a function of the Bjorken-$x$ variable, the transverse momentum of the pair and the fraction of the energy $z$ carried by the pair. Indications for positive Collins and Sivers asymmetries are observed

Triangle Singularity as the Origin of the a1(1420)

The COMPASS Collaboration experiment recently discovered a new isovector resonancelike signal with axial-vector quantum numbers, the a(1)(1420), decaying to f(0)(980)(pi). With a mass too close to and a width smaller than the axial-vector ground state a(1)(1260), it was immediately interpreted as a new light exotic meson, similar to the X, Y, Z states in the hidden-charm sector. We show that a resonancelike signal fully matching the experimental data is produced by the decay of the a(1) (1260) resonance into K* (-> K pi) (K) over bar and subsequent rescattering through a triangle singularity into the coupled f(0)(980)p channel. The amplitude for this process is calculated using a new approach based on dispersion relations. The triangle-singularity model is fitted to the partial-wave data of the COMPASS experiment. Despite having fewer parameters, this fit shows a slightly better quality than the one using a resonance hypothesis and thus eliminates the need for an additional resonance in order to describe the data. We thereby demonstrate for the first time in the lightmeson sector that a resonancelike structure in the experimental data can be described by rescattering through a triangle singularity, providing evidence for a genuine three-body effect

Double J/ψJ/\psi production in pion-nucleon scattering at COMPASS

We present the study of the production of double $J/\psi$ mesons using COMPASS data collected with a 190 GeV/$c$ $\pi^-$ beam scattering off NH$_{3}$, Al and W targets. Kinematic distributions of the collected double $J/\psi$ events are analysed, and the double $J/\psi$ production cross section is estimated for each of the COMPASS targets. The results are compared to predictions from single- and double-parton scattering models as well as the pion intrinsic charm and the tetraquark exotic resonance hypotheses. It is demonstrated that the single parton scattering production mechanism gives the dominant contribution that is sufficient to describe the data. An upper limit on the double intrinsic charm content of pion is evaluated. No significant signatures that could be associated with exotic tetraquarks are found in the double $J/\psi$ mass spectrum.Comment: 12 pages, 4 figure

Towards an artificial cell: Development of a system which self-regenerates the protein components of the PURE system in microfluidic reactors

Thanks to recent advancements in synthetic biology, the dream of creating a synthetic cell has become feasible. However, due to its inherent complexity, one of the fundamental functions of all living systems, i.e., self-replication, remains to be introduced. The development of a system capable of self-regeneration faces several challenges, as the system needs to be able to functionally synthesize all of its components at sufficient capacity in an environment that allows continuous and sustained regeneration. In this work, we have developed a system coupling a microfluidic platform with cell-free systems, which provides a viable approach for developing and optimizing self-regeneration at non-equilibrium conditions. Reconstituted transcription-translation systems are a viable starting point for achieving a self-regeneration system. Therefore, in this work, we begin by presenting a simple, robust, and low-cost production method for the cell-free system called protein synthesis using recombinant elements (PURE). Our approach relies on streamlining protein purification by coculturing and co-purification. We show that our "OnePot" method allows for minimizing time and labor requirements while preserving the versatility and purity of the system. Moreover, we demonstrate that the OnePot PURE system can achieve a similar protein synthesis yield to a commercial PURE system, which leads to a 14-fold improvement in cost-normalized protein synthesis yield over existing PURE systems with similar composition. Living organisms continuously exchange energy and matter with their environment. Similarly, one of the requirements of continuous and sustained regeneration is a life-like non-equilibrium environment. Therefore, we developed an improved microfluidic chemostat with fluidically hard-coded dilution fractions defined by the reactor geometry, which enable long-term steady-state reactions. We employed the introduced microfluidic platform in combination with the PURE systems to study self-regeneration. We demonstrated that the system can regenerate proteins essential for transcription and translation from DNA templates and that simultaneous self-regeneration of multiple proteins is sustainable in the system. Moreover, in combination with computational modeling, we showed that minimizing resource competition and optimizing resource allocation is critically important for achieving robust system functions. Lastly, we developed a microfluidic platform with an integrated hydrogel membrane with adjustable permeability. The integrated membranes separate transcription-translation machinery from the feeding solution of small molecular components, which can diffuse into the reactor through the membranes without diluting the machinery. Utilizing the dialysis-based continuous-exchange reaction, we extended the protein synthesis beyond traditional batch conditions

A Simple, Robust, and Low-Cost Method To Produce the PURE Cell Free System

We demonstrate a simple, robust, and low-cost method for producing the PURE cell-free transcription translation system. Our OnePot PURE system achieved a protein synthesis yield of 156 peg/mL at a cost of 0.09 USD/ktL, leading to a 14-fold improvement in cost normalized protein synthesis yield over existing PURE systems. The one pot method makes the PURE system easy to generate and allows it to be readily optimized and modified

OnePot PURE Cell-Free System

The defined PURE (protein synthesis using recombinant elements) transcription-translation system provides an appealing chassis for cell-free synthetic biology. Unfortunately, commercially available systems are costly, and their tunability is limited. In comparison, a home-made approach can be customized based on user needs. However, the preparation of home-made systems is time-consuming and arduous due to the need for ribosomes as well as 36 medium scale protein purifications. Streamlining protein purification by coculturing and co-purification allows for minimizing time and labor requirements. Here, we present an easy, adjustable, time- and cost-effective method to produce all PURE system components within 1 week, using standard laboratory equipment. Moreover, the performance of the OnePot PURE is comparable to commercially available systems. The OnePot PURE preparation method expands the accessibility of the PURE system to more laboratories due to its simplicity and cost-effectiveness