Functional interactions between bottom-up synthetic cells and living matter for biomedical applications

Bottom-up synthetic cells, where diverse non-living materials are combined in creative ways in order to construct increasingly life-like and adaptive systems, are fast approaching a level of function that will enable significant advances in solving specific biomedical challenges. Over the last 10 years, we have seen a wide variety of synthetic cell based approaches to challenges in regulating antimicrobial activity, delivering cargo to mammalian cells, and “growth support”. Despite this progress, there has not been a widespread uptake of synthetic cell technologies in biomedical engineering. In this Review, we highlight both the strengths and limitations of these existing synthetic cell applications, as well as give an overview of the state-of-the-art of synthetic cell technology that has yet been applied to cellular contexts. In doing so we aim to identify opportunities for the advancement of this unique intersection of research fields

Confined Motion: Motility of Active Microparticles in Cell-Sized Lipid Vesicles

[EN] Active materials can transduce external energy into kinetic energy at the nano and micron length scales. This unique feature has sparked much research, which ranges from achieving fundamental understanding of their motility to the assessment of potential applications. Traditionally, motility is studied as a function of internal features such as particle topology, while external parameters such as energy source are assessed mainly in bulk. However, in real-life applications, confinement plays a crucial role in determining the type of motion active particles can adapt. This feature has been however surprisingly underexplored experimentally. Here, we showcase a tunable experimental platform to gain an insight into the dynamics of active particles in environments with restricted 3D topology. Particularly, we examined the autonomous motion of coacervate micromotors confined in giant unilamellar vesicles (GUVs) spanning 10¿50 ¿m in diameter and varied parameters including fuel and micromotor concentration. We observed anomalous diffusion upon confinement, leading to decreased motility, which was more pronounced in smaller compartments. The results indicate that the theoretically predicted hydrodynamic effect dominates the motion mechanism within this platform. Our study provides a versatile approach to understand the behavior of active matter under controlled, compartmentalized conditions.The authors would like to acknowledge the support from the Dutch Ministry of Education, Culture and Science (Gravitation program 024.001.035 and Spinoza premium) and the ERC Advanced Grant (Artisym 694120) . A.L.-L. acknowledges the support from the MSCA Cofund Project of Life, which has received funding from the European Union's Horizon 2020 research and innovation program under the grant agreement 847675, and the Maria Zambrano Program from the Spanish Government funded by NextGenerationEU from the European Union. Dr. Bastiaan Buddingh is thanked for useful discussions regarding GUV preparation and handling. Dr. Shoupeng Cao is thanked for providing the azido-functionalized block polymer. We specially thank Prof. Samuel Sanchez for the tailor-made particle-tracking software based on Python.Song, S.; Llopis-Lorente, A.; Mason, AF.; Abdelmohsen, LK.; Van Hest, JCM. (2022). Confined Motion: Motility of Active Microparticles in Cell-Sized Lipid Vesicles. Journal of the American Chemical Society. 144:13831-13838. https://doi.org/10.1021/jacs.2c05232138311383814

Regulating Chemokine-Receptor Interactions through the Site-Specific Bioorthogonal Conjugation of Photoresponsive DNA Strands

Oligonucleotide conjugation has emerged as a versatile molecular tool for regulating protein activity. A state-of-the-art labeling strategy includes the site-specific conjugation of DNA, by employing bioorthogonal groups genetically incorporated in proteins through unnatural amino acids (UAAs). The incorporation of UAAs in chemokines has to date, however, remained underexplored, probably due to their sometimes poor stability following recombinant expression. In this work, we designed a fluorescent stromal-derived factor-1β (SDF-1β) chemokine fusion protein with a bioorthogonal functionality amenable for click reactions. Using amber stop codon suppression, p-azido-L-phenylalanine was site-specifically incorporated in the fluorescent N-terminal fusion partner, superfolder green fluorescent protein (sfGFP). Conjugation to single-stranded DNAs (ssDNA), modified with a photocleavable spacer and a reactive bicyclononyne moiety, was performed to create a DNA-caged species that blocked the receptor binding ability. This inhibition was completely reversible by means of photocleavage of the ssDNA strands. The results described herein provide a versatile new direction for spatiotemporally regulating chemokine-receptor interactions, which is promising for tissue engineering purposes.</p

Regulating Chemokine-Receptor Interactions through the Site-Specific Bioorthogonal Conjugation of Photoresponsive DNA Strands

Oligonucleotide conjugation has emerged as a versatile molecular tool for regulating protein activity. A state-of-the-art labeling strategy includes the site-specific conjugation of DNA, by employing bioorthogonal groups genetically incorporated in proteins through unnatural amino acids (UAAs). The incorporation of UAAs in chemokines has to date, however, remained underexplored, probably due to their sometimes poor stability following recombinant expression. In this work, we designed a fluorescent stromal-derived factor-1β (SDF-1β) chemokine fusion protein with a bioorthogonal functionality amenable for click reactions. Using amber stop codon suppression, p-azido-L-phenylalanine was site-specifically incorporated in the fluorescent N-terminal fusion partner, superfolder green fluorescent protein (sfGFP). Conjugation to single-stranded DNAs (ssDNA), modified with a photocleavable spacer and a reactive bicyclononyne moiety, was performed to create a DNA-caged species that blocked the receptor binding ability. This inhibition was completely reversible by means of photocleavage of the ssDNA strands. The results described herein provide a versatile new direction for spatiotemporally regulating chemokine-receptor interactions, which is promising for tissue engineering purposes.</p

Dynamic Network Centrality Summarizes Learning in the Human Brain

We study functional activity in the human brain using functional Magnetic Resonance Imaging and recently developed tools from network science. The data arise from the performance of a simple behavioural motor learning task. Unsupervised clustering of subjects with respect to similarity of network activity measured over three days of practice produces significant evidence of `learning', in the sense that subjects typically move between clusters (of subjects whose dynamics are similar) as time progresses. However, the high dimensionality and time-dependent nature of the data makes it difficult to explain which brain regions are driving this distinction. Using network centrality measures that respect the arrow of time, we express the data in an extremely compact form that characterizes the aggregate activity of each brain region in each experiment using a single coefficient, while reproducing information about learning that was discovered using the full data set. This compact summary allows key brain regions contributing to centrality to be visualized and interpreted. We thereby provide a proof of principle for the use of recently proposed dynamic centrality measures on temporal network data in neuroscience

Enzymatic Regulation of Protein-Protein Interactions in Artificial Cells

Membraneless organelles are important for spatial organization of proteins and regulation of intracellular processes. Proteins can be recruited to these condensates by specific protein–protein or protein–nucleic acid interactions, which are often regulated by post-translational modifications. However, the mechanisms behind these dynamic, affinity-based protein recruitment events are not well understood. Here, a coacervate system that incorporates the 14-3-3 scaffold protein to study enzymatically regulated recruitment of 14-3-3-binding proteins is presented, which mostly bind in a phosphorylation-dependent manner. Synthetic coacervates are efficiently loaded with 14-3-3, and phosphorylated binding partners, such as the c-Raf pS233/pS259 peptide (c-Raf), show 14-3-3-dependent sequestration with up to 161-fold increase in local concentration. The c-Raf domain is fused to green fluorescent protein (GFP-c-Raf) to demonstrate recruitment of proteins. In situ phosphorylation of GFP-c-Raf by a kinase leads to enzymatically regulated uptake. The introduction of a phosphatase into coacervates preloaded with the phosphorylated 14-3-3-GFP-c-Raf complex results in a significant cargo efflux mediated by dephosphorylation. Finally, the general applicability of this platform to study protein–protein interactions is demonstrated by the phosphorylation-dependent and 14-3-3-mediated active reconstitution of a split-luciferase inside artificial cells. This work presents an approach to study dynamically regulated protein recruitment in condensates, using native interaction domains.</p

XMM-Newton 13H Deep field - I. X-ray sources

We present the results of a deep X-ray survey conducted with XMM-Newton, centred on the UK ROSAT 13H deep field area. This region covers 0.18 deg^2 and is the first of two areas covered with XMM-Newton as part of an extensive multi-wavelength survey designed to study the nature and evolution of the faint X-ray source population. We have produced detailed Monte-Carlo simulations to obtain a quantitative characterisation of the source detection procedure and to assess the reliability of the resultant sourcelist. We use the simulations to establish a likelihood threshold above which we expect less than 7 (3%) of our sources to be spurious. We present the final catalogue of 225 sources. Within the central 9 arcmin, 68 per cent of source positions are accurate to 2 arcsec, making optical follow-up relatively straightforward. We construct the N(>S) relation in four energy bands: 0.2-0.5 keV, 0.5-2 keV, 2-5 keV and 5-10 keV. In all but our highest energy band we find that the source counts can be represented by a double powerlaw with a bright end slope consistent with the Euclidean case and a break around 10^-14 cgs. Below this flux the counts exhibit a flattening. Our source counts reach densities of 700, 1300, 900 and 300 deg^-2 at fluxes of 4.1x10^-16, 4.5x10^-16, 1.1x10^-15 and 5.3x10^-15 cgs in the 0.2-0.5, 0.5-2, 2-5 and 5-10 keV energy bands respectively. We have compared our source counts with those in the two Chandra deep fields and Lockman hole and find our source counts to be amongst the highest of these fields in all energy bands. We resolve >51% (>50%) of the X-ray background emission in the 1-2 keV (2-5 keV) energy bands.Comment: 27 pages, 18 figures, MNRAS accepte

Examining the safety of menstrual cups among rural primary school girls in western Kenya: observational studies nested in a randomised controlled feasibility study.

Examine the safety of menstrual cups against sanitary pads and usual practice in Kenyan schoolgirls. Observational studies nested in a cluster randomised controlled feasibility study. 30 primary schools in a health and demographic surveillance system in rural western Kenya. Menstruating primary schoolgirls aged 14-16 years participating in a menstrual feasibility study. Insertable menstrual cup, monthly sanitary pads or 'usual practice' (controls). Staphylococcus aureus vaginal colonization, Escherichia coli growth on sampled used cups, toxic shock syndrome or other adverse health outcomes. Among 604 eligible girls tested, no adverse event or TSS was detected over a median 10.9 months follow-up. S. aureusprevalence was 10.8%, with no significant difference over intervention time or between groups. Of 65 S.aureus positives at first test, 49 girls were retested and 10 (20.4%) remained positive. Of these, two (20%) sample isolates tested positive for toxic shock syndrome toxin-1; both girls were provided pads and were clinically healthy. Seven per cent of cups required replacements for loss, damage, dropping in a latrine or a poor fit. Of 30 used cups processed for E. coli growth, 13 (37.1%, 95% CI 21.1% to 53.1%) had growth. E. coli growth was greatest in newer compared with established users (53%vs22.2%, p=0.12). Among this feasibility sample, no evidence emerged to indicate menstrual cups are hazardous or cause health harms among rural Kenyan schoolgirls, but large-scale trials and post-marketing surveillance should continue to evaluate cup safety

Relaxation volumes of microscopic and mesoscopic irradiation-induced defects in tungsten

The low-energy structures of irradiation-induced defects in materials have been studied extensively over several decades, as these determine the available modes by which a defect can diffuse or relax, and how the microstructure of an irradiated material evolves as a function of temperature and time. Consequently, many studies concern the relative energies of possible defect structures, and empirical potentials are commonly fitted to or evaluated with respect to these. But recently [S. L. Dudarev et al., Nucl. Fusion 58, 126002 (2018)], we have shown that other parameters of defects not directly related to defect energies, namely, their elastic dipole tensors and relaxation volumes, determine the stresses, strains, and swelling of reactor components under irradiation. These elastic properties of defects have received comparatively little attention. In this study, we compute relaxation volumes of irradiation-induced defects in tungsten using empirical potentials and compare to density functional theory results. Different empirical potentials give different results, but some clear potential-independent trends can be identified. We show that the relaxation volume of a small defect cluster can be predicted to within 10% from its point-defect count. For larger defect clusters, we provide empirical fits as a function of defect cluster size. We demonstrate that the relaxation volume associated with a single primary-damage cascade can be estimated from the primary knock-on atom energy. We conclude that while annihilation of defects invariably reduces the total relaxation volume of the cascade debris, there is still no conclusive verdict about whether coalescence of defects reduces or increases the total relaxation volume. Published under license by AIP Publishing.Peer reviewe

Stress Propagation through Frictionless Granular Material

We examine the network of forces to be expected in a static assembly of hard, frictionless spherical beads of random sizes, such as a colloidal glass. Such an assembly is minimally connected: the ratio of constraint equations to contact forces approaches unity for a large assembly. However, the bead positions in a finite subregion of the assembly are underdetermined. Thus to maintain equilibrium, half of the exterior contact forces are determined by the other half. We argue that the transmission of force may be regarded as unidirectional, in contrast to the transmission of force in an elastic material. Specializing to sequentially deposited beads, we show that forces on a given buried bead can be uniquely specified in terms of forces involving more recently added beads. We derive equations for the transmission of stress averaged over scales much larger than a single bead. This derivation requires the Ansatz that statistical fluctuations of the forces are independent of fluctuations of the contact geometry. Under this Ansatz, the $d(d+1)/2$-component stress field can be expressed in terms of a d-component vector field. The procedure may be generalized to non-sequential packings. In two dimensions, the stress propagates according to a wave equation, as postulated in recent work elsewhere. We demonstrate similar wave-like propagation in higher dimensions, assuming that the packing geometry has uniaxial symmetry. In macroscopic granular materials we argue that our approach may be useful even though grains have friction and are not packed sequentially.=17Comment: 15 pages, 4 figures, revised vertion for Phys. Rev.