Synthetic Biology Enabled Modification of Bone Cells and the Impact on Bone Mineral Formation.
Abstract not provided.
Hayes, Dulce↗
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Synthetic Biology Enabled Modification of Bone Cells and Impact on Bone Mineral Resorption
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Hayes, Dulce C.↗
SYNTHETIC BIOLOGY ENABLED MODIFICATION OF BONE CELLS AND IMPACT ON BONE MINERAL RESORPTION
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Hayes, Dulce C.↗
Virus-Like Particles (VLPs) as a Platform for Hierarchical Compartmentalization
Hierarchically self-assembled structures are common in biology, but it is often challenging to design and fabricate synthetic analogs. The archetypal cell is defined by hierarchically organized multicompartmentalized structures with boundaries that delineate the interior from exterior environments and is an inspiration for complex functional materials. Here, we have demonstrated an approach to the design and construction of a nested protein cage system that can additionally incorporate the packing of other functional macromolecules and exhibit some of the features of a minimal synthetic cell-like material. We have demonstrated a strategy for controlled co-packaging of subcompartments, ferritin (Fn) cages, together with active cellobiose-hydrolyzing β-glycosidase enzyme macromolecules, CelB, inside the sequestered volume of the bacteriophage P22 capsid. Using controlled in vitro assembly, we were able to modulate the stoichiometry of Fn cages and CelB encapsulated inside the P22 to control the degree of compartmentalization. The co-encapsulated enzyme CelB showed catalytic activity even when packaged at high total macromolecular concentrations comparable to an intracellular environment. Here, this approach could be used as a model to create synthetic protein-based protocells that can confine smaller functionalized proto-organelles and additional macromolecules to support a range of biochemical reactions.
59 BASIC BIOLOGICAL SCIENCES↗
Leakless end-to-end transport of small molecules through micron-length DNA nanochannels
Designed and engineered protein and DNA nanopores can be used to sense and characterize single molecules and control transmembrane transport of molecular species. However, designed biomolecular pores are less than 100 nm in length and are used primarily for transport across lipid membranes. Nanochannels that span longer distances could be used as conduits for molecules between nonadjacent compartments or cells. We design micrometer-long, 7-nm-diameter DNA nanochannels that small molecules can traverse according to the laws of continuum diffusion. Binding DNA origami caps to channel ends eliminates transport and demonstrates that molecules diffuse from one channel end to the other rather than permeating through channel walls. These micrometer-length nanochannels can also grow, form interconnects, and interface with living cells. This work thus shows how to construct multifunctional, dynamic agents that control molecular transport, opening ways of studying intercellular signaling and modulating molecular transport between synthetic and living cells.
59 BASIC BIOLOGICAL SCIENCES↗
FtsZ-mediated fission of a cuboid bacterial symbiont
Less than a handful of cuboid and squared cells have been described in nature, which makes them a rarity. Here, we show how Candidatus Thiosymbion cuboideus, a cube-like gammaproteobacterium, reproduces on the surface of marine free-living nematodes. Immunostaining of symbiont cells with an anti-fimbriae antibody revealed that they are host-polarized, as these appendages exclusively localized at the host-proximal (animal-attached) pole. Moreover, by applying a fluorescently labeled metabolic probe to track new cell wall insertion in vivo, we observed that the host-attached pole started septation before the distal one. Similarly, Ca. T. cuboideus cells immunostained with an anti-FtsZ antibody revealed a proximal-to-distal localization pattern of this tubulin homolog. Although FtsZ has been shown to arrange into squares in synthetically remodeled cuboid cells, here we show that FtsZ may also mediate the division of naturally occurring ones. This implies that, even in natural settings, membrane roundness is not required for FtsZ function.
59 BASIC BIOLOGICAL SCIENCES↗
Synthetic Biochemistry: The Bio-inspired Cell-Free Approach to Commodity Chemical Production
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Surface Ligand Management Aided by a Secondary Amine Enables Increased Synthesis Yield of CsPbI 3 Perovskite Quantum Dots and High Photovoltaic Performance
Lead-halide perovskite quantum dots (PQDs) or more broadly, nanocrystals possess advantageous features for solution-processed photovoltaic devices. The nanocrystal surface ligands play a crucial role in the transport of photogenerated carriers and ultimately affect the overall performance of PQD solar cells. Here, significantly improved CsPbI 3 PQD synthetic yield and solar-cell performance through surface ligand management are demonstrated. The treatment of a secondary amine, di- n -propylamine (DPA), provides a mild and efficient approach to control the surface ligand density of PQDs, which has an apparently different working mechanism compared to previously reported surface treatments. Using an optimal DPA concentration, the treatment can simultaneously remove both long-chain insulating surface ligands of oleic acid and oleylamine, even for unpurified PQDs with high ligand density. As a result, the electrical coupling between PQDs is enhanced, leading to improved charge transport, reduced carrier recombination, and a high power conversion efficiency approaching 15% for CsPbI 3 -PQD-based solar cells. In addition, the production yield of CsPbI 3 PQDs can be increased by a factor of 8. These results highlight the importance of developing new ligand-management strategies, specifically for emerging PQDs to achieve scalable and high-performance perovskite-based optoelectronic devices.
36 MATERIALS SCIENCE↗
Three-dimensional traction microscopy accounting for cell-induced matrix degradation
Tractions exerted by cells on the extracellular matrix (ECM) are critical in many important physiological and pathological processes such as embryonic morphogenesis, wound healing, and cancer metastasis. Three-dimensional Traction Microscopy (3DTM) is a tool to quantify cellular tractions by first measuring the displacement field in the ECM in response to these tractions, and then using this measurement to infer tractions. Most applications of 3DTM have assumed that the ECM has spatially-uniform mechanical properties, but cells secrete enzymes that can locally degrade the ECM. In this work, a novel computational method is developed to quantify both cellular tractions and ECM degradation. In particular, the ECM is modeled as a hyperelastic, Neo-Hookean solid, whose material parameters are corrupted by a single degradation parameter. The feasibility of determining both the traction and the degradation parameter is first demonstrated by showing the existence and uniqueness of the solution. An inverse problem is then formulated to determine the nodal values of the traction vector and the degradation parameter, with the objective of minimizing the difference between a predicted and measured displacement field, under the constraint that the predicted displacement field satisfies the equation of equilibrium. The inverse problem is solved by means of a gradient-based optimization approach, and the gradient is computed efficiently using appropriately derived adjoint fields. The computational method is validated in-silico using a geometrically realistic neuronal cell model and synthetic traction and degradation fields. It is found that the method accurately recovers both the traction and degradation fields. Moreover, it is found that neglecting ECM degradation can yield significant errors in traction measurements. Finally, our method can extend the range of context where tractions can be appropriately measured.
42 ENGINEERING↗
Biomimetic Rebuilding of Multifunctional Red Blood Cells: Modular Design Using Functional Components
The design and synthesis of artificial materials that mimic the structures, mechanical properties, and ultimately functionalities of biological cells remains a current holy grail of materials science. Here based on a silica cell bio-replication approach, we report the design and construction of synthetic rebuilt red blood cells (RRBCs) that fully mimic the broad properties of native RBCs: size, biconcave shape, deformability, oxygen carrying capacity, long circulation time. Four successive nano-scale processing steps: RBC bioreplication, layer-by-layer polymer deposition, and precision silica etching, followed by RBC ghost membrane vesicles fusion are employed for RRBC construction. A panel of physicochemical analyses including zeta potential measurement, fluorescence microscopy, and antibody-mediated agglutination assay proved the recapitulation of RBC shape, size, and membrane structure. Flow-based deformation studies carried out in a microfluidic blood capillary model confirrned the ability of RRBCs to deform and pass through small slits and reconstitute themselves in a manner comparable to native RBCs. Circulation studies of RRBCs conducted ex-ovo in a chick embryo and in vivo in a mouse model demonstrated the requirement of both deformability and native cell membrane surface to achieve long-term circulation. To confer additional non-native functionalities to RRBCs, we developed modular procedures in which to load functional cargos such as hemoglobin, drugs, magnetic nanoparticles, and ATP biosensors within the RRBC interior to enable various functions, including oxygen delivery, therapeutic drug delivery, magnetic manipulation, and toxin biosensing and detection. Taken together, RRBCs represent a class of long circulating RBC-inspired artificial hybrid materials with a broad range of potential applications.
59 BASIC BIOLOGICAL SCIENCES↗
Particle interspacing effects on the mechanical behavior of a Fe–TiB 2 metal matrix composite using FFT-based mesoscopic field dislocation mechanics
This paper presents an application to metal matrix composites (MMCs) of an enhanced elasto-viscoplastic Fast Fourier Transform (EVP-FFT) formulation coupled with a phenomenological continuum Mesoscale Field Dislocation Mechanics (MFDM) theory. Contrary to conventional crystal plasticity, which only accounts for plastic flow and hardening induced by statistically stored dislocations (SSDs), MFDM-EVP-FFT also describes the evolution of polarized geometrically necessary dislocation (GND) density and its effect on both plastic flow and hardening. Numerical results for a Fe–TiB 2 MMC made of a ferrite matrix (α-Fe) and elastic ceramic particles (TiB 2 ) are presented. Full-field simulations are performed using synthetic periodic unit cells representative of the MMC, with single-crystalline and polycrystalline matrix, for different particle interspacing distances. A strong dependence of the predicted equivalent stress, cumulated plastic strain and GND density fields with particle interspacing distance is observed, in contrast with conventional crystal plasticity. Correlations between these mechanical fields and microstructural features, and their influence on local and global mechanical behavior are examined for the different MMC microstructures.
42 ENGINEERING↗
Advanced Algal Biofoundries for the Production of Polyurethane Precursors
The primary goal of the BEEPs project was to develop a process that could accelerate the development of algae as bioproduction platforms, from initial chemical product concept to an economically viable market supply. Under this program we elected to develop strains of algae that could generate polyurethane precursors, while simultaneously developing basic genetic tools to enable improved algal production systems. This program was specifically designed to incorporate National Laboratories as a means to utilize the expertise and facilities for new bio-production platforms. To that end, we designed a program to collaborate with the Agile BioFoundry at Lawrence Berkeley National Laboratory (LBNL) and computational platforms at Pacific Northwest National Laboratory (PNNL). In addition to these National Laboratory partners, we also had academic partners from UC Davis and Georgia Tech, as well as commercial partners Algenesis Materials and BASF. To achieve these goals, we initially focused on developing the genetic tools and high throughput screening technologies necessary to generate and assess production of polymer precursors (succinic acid) in algae and cyanobacteria, including advanced promoters and biosensors. In parallel, we computationally identified potential production bottlenecks and then used the developed genetic tools to increase production rates and yields. Constant feedback of data was used in conjunction with machine learning, high-throughput cell sorting, and synthetic biology, for additional targeted metabolic engineering. Multiple rounds of tool design, building, testing, and learning were supplied to partners at PNNL and LBNL to develop new models and tools that could expedite bioproduction platform development and increase yield performance. We targeted, and achieved, the FOA requirement yield metric of 20 g/L, as a milestone and deliverable from at least one of our engineered strains for the production of succinic acid.
09 BIOMASS FUELS↗
Bifunctional Janus Particles as Multivalent Synthetic Nanoparticle Antibodies (SNAbs) for Selective Depletion of Target Cells
Monoclonal antibodies (mAb) have had a transformative impact on treating cancers and immune disorders. SNAbs However, their use is limited by high development time and monetary cost, manufacturing complexities, suboptimal pharmacokinetics, and availability of disease-specific targets. To address some of these challenges, we developed an entirely synthetic, multivalent, Janus nanotherapeutic platform, called Synthetic Nanoparticle Antibodies (SNAbs). SNAbs, with phage-display-identified cell-targeting ligands on one "face" and Fc-mimicking ligands on the opposite "face", were synthesized using a custom, multistep, solid-phase chemistry method. SNAbs efficiently targeted and depleted myeloid-derived immune-suppressor cells (MDSCs) from mouse-tumor and rat-trauma models, ex vivo. Systemic injection of MDSC-targeting SNAbs efficiently depleted circulating MDSCs in a mouse triple-negative breast cancer model, enabling enhanced T cell and Natural Killer cell infiltration into tumors. Finally, our results demonstrate that SNAbs are a versatile and effective functional alternative to mAbs, with advantages of a plug- and-play, cell-free manufacturing process, and high-throughput screening (HTS)-enabled library of potential targeting ligands.
60 APPLIED LIFE SCIENCES↗
An Anthradithiophene Donor Polymer for Organic Solar Cells with a Good Balance between Efficiency and Synthetic Accessibility
Over the past few years, the organic photovoltaics technology (OPV) has reached remarkable power conversion efficiencies (PCEs), mostly thanks to the advent of nonfullerene acceptors as well as to a high level of materials engineering. Yet, the complex materials syntheses behind these results ultimately limit technological readiness. The quest for scalable organic compounds offering high PCE and reasonably low synthetic complexity is a must to close the gap between laboratory R&D and commercial products. The synthesis and full characterization of a new conjugated polymer called PATTD is reported herein, based on a novel anthradithiophene as an electron–rich building block coupled with a commercially available dithienylbenzodithiophenedione as an electron–withdrawing comonomer. Its photovoltaic properties are studied in blends with IT–4F and IDIC as acceptors. PATTD:IT–4F–based photovoltaic devices exhibit a PCE approaching 10% and over 2300 h shelf–life stability. Finally, the PATTD scalability factor (SF), together with the PATTD–based photovoltaic performances, lead to a PCE/SF value equal to 0.297, placing such devices into the innermost circle of OPV materials, achieving one of the best compromises between efficiency and synthetic complexity and at the same time offering promising industrial perspectives.
14 SOLAR ENERGY↗
Leveraging a synthetic biology approach to enhance BCG-mediated expansion of Vγ9Vδ2 T cells
There is an urgent need to develop a more efficacious anti-tuberculosis vaccine as the current live-attenuated vaccine strain BCG fails to prevent pulmonary infection in adults. In this study, we leverage a synthetic biology approach to engineer BCG to produce more (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMBPP), an intermediate of bacterial—but not host—isoprenoid biosynthesis via the methylerythritol phosphate (MEP) pathway. HMBPP strongly activates and expands Vγ9Vδ2 T cells, which are unique to higher-order primates and protect against Mycobacterium tuberculosis infection. BCG has been engineered to produce specific ligands and antigens to some success; in contrast, our strategy exploits a self-nonself recognition mechanism in the host via HMBPP sensing, which has not been attempted before. To inform the design of our recombinant strains, we performed synteny analyses of >63 mycobacterial species and found that isoprenoid biosynthetic genes are not operonic across all the 356 surveyed genomes, but some genes are frequently found in pairs. Thus, we generated synthetic loci with the goal of specifically overproducing HMBPP and tested the ability of these engineered strains to induce human Vγ9Vδ2 expansion in an in vitro stimulation assay. We found that BCG expressing a synthetic MEP locus significantly enhanced Vγ9Vδ2 T cell expansion over the wild-type vaccine strain, and overexpression of the HMBPP synthase GcpE alone potently induced Vγ9Vδ2 T cell expansion with no downregulation of other pathway genes. Together these engineered strains present two successful strategies to accumulate HMBPP and overcome feedback inhibition of the MEP pathway.
59 BASIC BIOLOGICAL SCIENCES↗
Simultaneous inhibition of ATM, ATR, and DNA-PK causes synergistic lethality
Here, in this paper, we report that simultaneous inhibition of the three primary DNA damage recognition PI3 kinase-like kinases (PIKKs) —ATM, ATR, and DNA-PK— induces severe combinatorial synthetic lethality in mammalian cells. Utilizing Chinese hamster cell lines CHO and V79 and their respective PIKK mutants, we evaluated effects of inhibiting these three kinases on cell viability, DNA damage response, and chromosomal integrity. Our results demonstrate that while single or dual kinase inhibition increased cytotoxicity, inhibition of all three PIKKs results in significantly higher synergistic lethality, chromosomal aberrations, and DNA double-strand break (DSB) induction as calculated by their synergy scores. These findings suggest that the overlapping redundancy of ATM, ATR, and DNA-PK functions is critical for cell survival, and their combined inhibition greatly disrupts DNA damage signaling and repair processes, leading to cell death. This study provides insights into the potential of multi-targeted DDR kinase inhibition as an effective anticancer strategy, necessitating further research to elucidate underlying mechanisms and therapeutic applications.
59 BASIC BIOLOGICAL SCIENCES↗
Bioactive scaffolds with enhanced supramolecular motion promote recovery from spinal cord injury
The signaling of cells by scaffolds of synthetic molecules that mimic proteins is known to be effective in the regeneration of tissues. Here, we describe peptide amphiphile supramolecular polymers containing two distinct signals and test them in a mouse model of severe spinal cord injury. One signal activates the transmembrane receptor β1-integrin and a second one activates the basic fibroblast growth factor 2 receptor. By mutating the peptide sequence of the amphiphilic monomers in nonbioactive domains, we intensified the motions of molecules within scaffold fibrils. This resulted in notable differences in vascular growth, axonal regeneration, myelination, survival of motor neurons, reduced gliosis, and functional recovery. Here, we hypothesize that the signaling of cells by ensembles of molecules could be optimized by tuning their internal motions.
36 MATERIALS SCIENCE↗
Cecropin P1 antimicrobial peptide modulates differential expression of immune relevant genes in rainbow trout ( Oncorhynchus mykiss ) gill cell line, RTgill-W1
Accumulated evidence indicates that antimicrobial peptides modulate immune activities in fish. In this study, we profiled the differential expression patterns of representative immune relevant genes in an epithelial-like cell line of rainbow trout gill, RTgill-W1, in response to exposure of cecropin P1 antimicrobial peptide. RTgill-W1 cells were treated with synthetic cecropin P1 over time (0, 2, 4 and 24 h) with or without the present of lipopolysaccharide (LPS) or polyinosinic polycytidylic acid (PolyI:C). The relative abundances of each mRNA were measured by real-time quantitative PCR. The dose-response study revealed significant perturbations of mRNA levels of genes related to pro-inflammation, acute phase, surface proteins and transcription factors at 30 μM of cecropin P1. In addition, cecropin P1 altered the differential expression patterns that were induced by LPS or PolyI:C, at different time points in RTgill-W1. Overall, our results indicate that cecropin P1 exhibits pro-inflammation activity, modulate cell-cell interaction and cytokine signal transduction in rainbow trout gill cell, and may suggest a potential application of this peptide as an immune adjuvant for disease control in aquaculture.
59 BASIC BIOLOGICAL SCIENCES↗