Symbolic recording of signalling and cis-regulatory element activity to DNA.

Measurements of gene expression or signal transduction activity are conventionally performed using methods that require either the destruction or live imaging of a biological sample within the timeframe of interest. Here we demonstrate an alternative paradigm in which such biological activities are stably recorded to the genome. Enhancer-driven genomic recording of transcriptional activity in multiplex (ENGRAM) is based on the signal-dependent production of prime editing guide RNAs that mediate the insertion of signal-specific barcodes (symbols) into a genomically encoded recording unit. We show how this strategy can be used for multiplex recording of the cell-type-specific activities of dozens to hundreds of cis-regulatory elements with high fidelity, sensitivity and reproducibility. Leveraging signal transduction pathway-responsive cis-regulatory elements, we also demonstrate time- and concentration-dependent genomic recording of WNT, NF-κB and Tet-On activities. By coupling ENGRAM to sequential genome editing via DNA Typewriter1, we stably record information about the temporal dynamics of two orthogonal signalling pathways to genomic DNA. Finally we apply ENGRAM to integratively record the transient activity of nearly 100 transcription factor consensus motifs across daily windows spanning the differentiation of mouse embryonic stem cells into gastruloids, an in vitro model of early mammalian development. Although these are proof-of-concept experiments and much work remains to fully realize the possibilities, the symbolic recording of biological signals or states within cells, to the genome and over time, has broad potential to complement contemporary paradigms for how we make measurements in biological systems.

A single-cell time-lapse of mouse prenatal development from gastrula to birth.

The house mouse (Mus musculus) is an exceptional model system, combining genetic tractability with close evolutionary affinity to humans1,2. Mouse gestation lasts only 3 weeks, during which the genome orchestrates the astonishing transformation of a single-cell zygote into a free-living pup composed of more than 500 million cells. Here, to establish a global framework for exploring mammalian development, we applied optimized single-cell combinatorial indexing3 to profile the transcriptional states of 12.4 million nuclei from 83 embryos, precisely staged at 2- to 6-hour intervals spanning late gastrulation (embryonic day 8) to birth (postnatal day 0). From these data, we annotate hundreds of cell types and explore the ontogenesis of the posterior embryo during somitogenesis and of kidney, mesenchyme, retina and early neurons. We leverage the temporal resolution and sampling depth of these whole-embryo snapshots, together with published data4-8 from earlier timepoints, to construct a rooted tree of cell-type relationships that spans the entirety of prenatal development, from zygote to birth. Throughout this tree, we systematically nominate genes encoding transcription factors and other proteins as candidate drivers of the in vivo differentiation of hundreds of cell types. Remarkably, the most marked temporal shifts in cell states are observed within one hour of birth and presumably underlie the massive physiological adaptations that must accompany the successful transition of a mammalian fetus to life outside the womb.

A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues.

Light-sheet microscopy has emerged as the preferred means for high-throughput volumetric imaging of cleared tissues. However, there is a need for a flexible system that can address imaging applications with varied requirements in terms of resolution, sample size, tissue-clearing protocol, and transparent sample-holder material. Here, we present a 'hybrid' system that combines a unique non-orthogonal dual-objective and conventional (orthogonal) open-top light-sheet (OTLS) architecture for versatile multi-scale volumetric imaging. We demonstrate efficient screening and targeted sub-micrometer imaging of sparse axons within an intact, cleared mouse brain. The same system enables high-throughput automated imaging of multiple specimens, as spotlighted by a quantitative multi-scale analysis of brain metastases. Compared with existing academic and commercial light-sheet microscopy systems, our hybrid OTLS system provides a unique combination of versatility and performance necessary to satisfy the diverse requirements of a growing number of cleared-tissue imaging applications.

Free Energies of Proton-Coupled Electron Transfer Reagents and Their Applications.

We present an update and revision to our 2010 review on the topic of proton-coupled electron transfer (PCET) reagent thermochemistry. Over the past decade, the data and thermochemical formalisms presented in that review have been of value to multiple fields. Concurrently, there have been advances in the thermochemical cycles and experimental methods used to measure these values. This Review (i) summarizes those advancements, (ii) corrects systematic errors in our prior review that shifted many of the absolute values in the tabulated data, (iii) provides updated tables of thermochemical values, and (iv) discusses new conclusions and opportunities from the assembled data and associated techniques. We advocate for updated thermochemical cycles that provide greater clarity and reduce experimental barriers to the calculation and measurement of Gibbs free energies for the conversion of X to XHn in PCET reactions. In particular, we demonstrate the utility and generality of reporting potentials of hydrogenation, E°(V vs H2), in almost any solvent and how these values are connected to more widely reported bond dissociation free energies (BDFEs). The tabulated data demonstrate that E°(V vs H2) and BDFEs are generally insensitive to the nature of the solvent and, in some cases, even to the phase (gas versus solution). This Review also presents introductions to several emerging fields in PCET thermochemistry to give readers windows into the diversity of research being performed. Some of the next frontiers in this rapidly growing field are coordination-induced bond weakening, PCET in novel solvent environments, and reactions at material interfaces.

Linear Free Energy Relationships and Transition State Analysis of CO2 Reduction Catalysts Bearing Second Coordination Spheres with Tunable Acidity.

In molecular catalysts, protic functional groups in the secondary coordination sphere (SCS) work in conjunction with an exogenous acid to relay protons to the active site of electrochemical CO2 reduction; however, it is not well understood how the acidity of the SCS and exogenous acid together determine the kinetics of catalytic turnover. To evaluate the relative contributions of proton transfer driving forces, we synthesized a series of modular iron tetraphenylporphyrin electrocatalysts bearing SCS amides of tunable pKa (17.6 to 20.0 in dimethyl sulfoxide (DMSO)) and employed phenols of variable acidity (15.3 to 19.1) as exogenous acids. This system allowed us to (1) evaluate contributions from proton transfer driving forces associated with either the SCS or exogenous acid and (2) obtain mechanistic insights into CO2 reduction as a function of pKa. A series of linear free-energy relationships show that kinetics become increasingly sensitive to variations in SCS pKa when more acidic exogenous acids are used (0.82 ≥ Brønsted α ≥ 0.13), as well as to variations in exogenous acid pKa when SCS acidity is increased (0.62 ≥ Brønsted α ≥ 0.32). An Eyring analysis suggests that the rate-determining transition state becomes more ordered with decreasing SCS acidity, which is consistent with the proposal that SCS acidity modulates charge accumulation and solvation at the rate-limiting transition state. Together, these insights enable the optimization of activation barriers as a function of both SCS and exogenous acid pKa and can further guide the rational design of electrocatalytic systems wherein contributions from all participants in a proton relay are considered.

Templating Bicarbonate in the Second Coordination Sphere Enhances Electrochemical CO2 Reduction Catalyzed by Iron Porphyrins.

Bicarbonate-based electrolytes are ubiquitous in aqueous electrochemical CO2 reduction, particularly in heterogenous catalysis, where they demonstrate improved catalytic performance relative to other buffers. In contrast, the presence of bicarbonate in organic electrolytes and its roles in homogeneous electrocatalysis remain underexplored. Here, we investigate the influence of bicarbonate on iron porphyrin-catalyzed electrochemical CO2 reduction. We show that bicarbonate is a viable proton donor in organic electrolyte (pKa = 20.8 in dimethyl sulfoxide) and that urea pendants in the second coordination sphere can be used to template bicarbonate in the vicinity of a molecular iron porphyrin catalyst. The templated binding of bicarbonate increases its acidity, resulting in a 1500-fold enhancement in catalytic rates relative to unmodified parent iron porphyrin. This work emphasizes the importance of bicarbonate speciation in wet organic electrolytes and establishes second-sphere bicarbonate templating as a design strategy to harness this adventitious acid and enhance CO2 reduction catalysis.

Interfacial Acid-Base Equilibria and Electric Fields Concurrently Probed by In Situ Surface-Enhanced Infrared Spectroscopy.

Understanding how applied potentials and electrolyte solution conditions affect interfacial proton (charge) transfers at electrode surfaces is critical for electrochemical technologies. Herein, we examine mixed self-assembled monolayers (SAMs) of 4-mercaptobenzoic acid (4-MBA) and 4-mercaptobenzonitrile (4-MBN) on gold using in situ surface-enhanced infrared absorption spectroscopy (SEIRAS). Measurements as a function of the applied potential, the electrolyte pD, and the electrolyte concentration determined both the relative surface populations of acidic and basic forms of 4-MBA, as well as the local electric fields at the SAM-solution interface by following the Stark shifts of 4-MBN. The effective acidity of the SAM varied with the applied potential, requiring a 600 mV change to move the pKa by one unit. Since this is ca. 10× the Nernstian value of 59 mV/pKa, ∼90% of the applied potential dropped across the SAM layer. This emphasizes the importance of distinguishing applied potentials from the potential experienced at the interface. We use the measured interfacial electric fields to estimate the experienced potential at the SAM edge. The SAM pKa showed a roughly Nernstian dependence on this estimated experienced potential. An analysis of the combined acid-base equilibria and Stark shifts reveals that the interfacial charge density has significant contributions from both SAM carboxylate headgroups and electrolyte components. Ion pairing and ion penetration into the SAM also influence the observed surface acidity. To our knowledge, this study is the first concurrent examination of both effective acidity and electric fields, and highlights the relevance of experienced potentials and specific ion effects at functionalized electrode surfaces.

Hybrid Catalysts for Artificial Photosynthesis: Merging Approaches from Molecular, Materials, and Biological Catalysis.

Increasing demand for sustainable energy sources continues to motivate the development of new catalytic processes that store intermittent energy in the form of chemical bonds. In this context, photosynthetic organisms harvest light to drive dark reactions reducing carbon dioxide, an abundant and accessible carbon source, to store solar energy in the form of glucose and other biomass feedstocks. Inspired by this biological process, the field of artificial photosynthesis aims to store renewable energy in chemical bonds spanning fuels, foods, medicines, and materials using light, water, and CO2 as the primary chemical feedstocks, with the added benefit of mitigating the accumulation of CO2 as a greenhouse gas in the atmosphere. As such, devising new catalyst platforms for transforming CO2 into value-added chemical products is of importance. Historically, catalyst design for artificial photosynthesis has been approached from the three traditional fields of catalysis: molecular, materials, and biological. In this Account, we show progress from our laboratory in constructing new hybrid catalysts for artificial photosynthesis that draw upon design concepts from all three of these traditional fields of catalysis and blur the boundaries between them. Starting with molecular catalysis, we incorporated biological design elements that are prevalent in enzymes into synthetic systems. Specifically, we demonstrated that proper positioning of intramolecular hydrogen bond donors or addition of intermolecular multipoint hydrogen bond donors with classic iron porphyrin and nickel cyclam platforms can substantially increase rates of CO2 reduction and break electronic scaling relationships. In parallel, we incorporated a key materials design element, namely, high surface area and porosity for maximizing active site exposure, into molecular systems. A supramolecular porous organic cage molecule was synthesized with iron porphyrin building blocks, and the porosity was observed to facilitate substrate and charge transport through the catalyst film. In turn, molecular design elements can be incorporated into materials catalysts for CO2 reduction. First, we utilized molecular synthons in a bottom-up reticular approach to drive polymerization/assembly into a bulk framework material. Second, we established an organometallic approach in which molecular ligands, including chelating ones, are adsorbed onto a bulk inorganic solid to create and tune new active sites on surfaces. Finally, we describe two examples in which molecular, materials, and biological design elements are all integrated to catalyze the reduction of CO2 into CH4 using a hybrid biological-materials interface with sustainably generated H2 as the reductant or to reduce CO into value-added C2 products acetate and ethanol using a hybrid molecular-materials interface to construct a biomimetic, bimetallic active site. Taken together, our program in catalysis for energy and sustainability has revealed that combining more conventional design strategies in synergistic ways can lead to advances in artificial photosynthesis.

Mathematical Modelling of Alternative Pathway of Complement System.

The complement system (CS) is an integral part of innate immunity and can be activated via three different pathways. The alternative pathway (AP) has a central role in the function of the CS. The AP of complement system is implicated in several human disease pathologies. In the absence of triggers, the AP exists in a time-invariant resting state (physiological steady state). It is capable of rapid, potent and transient activation response upon challenge with a trigger. Previous models of AP have focused on the activation response. In order to understand the molecular machinery necessary for AP activation and regulation of a physiological steady state, we built parsimonious AP models using experimentally supported kinetic parameters. The models further allowed us to test quantitative roles played by negative and positive regulators of the pathway in order to test hypotheses regarding their mechanisms of action, thus providing more insight into the complex regulation of AP.

Reticular Electronic Tuning of Porphyrin Active Sites in Covalent Organic Frameworks for Electrocatalytic Carbon Dioxide Reduction.

The electronic character of porphyrin active sites for electrocatalytic reduction of CO2 to CO in a two-dimensional covalent organic framework (COF) was tuned by modification of the reticular structure. Efficient charge transport along the COF backbone promotes electronic connectivity between remote functional groups and the active sites and enables the modulation of the catalytic properties of the system. A series of oriented thin films of these COFs was found to reduce CO2 to CO at low overpotential (550 mV) with high selectivity (faradaic efficiency of 87%) and at high current densities (65 mA/mg), a performance well beyond related molecular catalysts in regard to selectivity and efficiency. The catalysts are stable for more than 12 h without any loss in reactivity. X-ray absorption measurements on the cobalt L-edge for the modified COFs enable correlations between the inductive effects of the appended functionality and the electronic character of the reticulated molecular active sites.

Hybrid bioinorganic approach to solar-to-chemical conversion.

Natural photosynthesis harnesses solar energy to convert CO2 and water to value-added chemical products for sustaining life. We present a hybrid bioinorganic approach to solar-to-chemical conversion in which sustainable electrical and/or solar input drives production of hydrogen from water splitting using biocompatible inorganic catalysts. The hydrogen is then used by living cells as a source of reducing equivalents for conversion of CO2 to the value-added chemical product methane. Using platinum or an earth-abundant substitute, α-NiS, as biocompatible hydrogen evolution reaction (HER) electrocatalysts and Methanosarcina barkeri as a biocatalyst for CO2 fixation, we demonstrate robust and efficient electrochemical CO2 to CH4 conversion at up to 86% overall Faradaic efficiency for ≥ 7 d. Introduction of indium phosphide photocathodes and titanium dioxide photoanodes affords a fully solar-driven system for methane generation from water and CO2, establishing that compatible inorganic and biological components can synergistically couple light-harvesting and catalytic functions for solar-to-chemical conversion.

Iron Porphyrins Embedded into a Supramolecular Porous Organic Cage for Electrochemical CO2 Reduction in Water.

A porous organic cage composed of six iron tetraphenylporphyrins was used as a supramolecular catalyst for electrochemical CO2 -to-CO conversion. This strategy enhances active site exposure and substrate diffusion relative to the monomeric catalyst, resulting in CO generation with near-quantitative Faradaic efficiency in pH 7.3 water, with activities reaching 55 250 turnovers. These results provide a starting point for the design of supramolecular catalysts that can exploit the properties of the surrounding matrix yet retain the tunability of the original molecular unit.

Chelating N-Heterocyclic Carbene Ligands Enable Tuning of Electrocatalytic CO2 Reduction to Formate and Carbon Monoxide: Surface Organometallic Chemistry.

Reported here is the chelate effect as a design principle for tuning heterogeneous catalysts for electrochemical CO2 reduction. Palladium functionalized with a chelating tris-N-heterocyclic carbene (NHC) ligand (Pd-timtmbMe ) exhibits a 32-fold increase in activity for electrochemical reduction of CO2 to C1 products with high Faradaic efficiency (FEC1 =86 %) compared to the parent unfunctionalized Pd foil (FE=23 %), and with sustained activity relative to a monodentate NHC-ligated Pd electrode (Pd-mimtmbMe ). The results highlight the contributions of the chelate effect for tailoring and maintaining reactivity at molecular-materials interfaces enabled by surface organometallic chemistry.

A Molecular Surface Functionalization Approach to Tuning Nanoparticle Electrocatalysts for Carbon Dioxide Reduction.

Conversion of the greenhouse gas carbon dioxide (CO2) to value-added products is an important challenge for sustainable energy research, and nanomaterials offer a broad class of heterogeneous catalysts for such transformations. Here we report a molecular surface functionalization approach to tuning gold nanoparticle (Au NP) electrocatalysts for reduction of CO2 to CO. The N-heterocyclic (NHC) carbene-functionalized Au NP catalyst exhibits improved faradaic efficiency (FE = 83%) for reduction of CO2 to CO in water at neutral pH at an overpotential of 0.46 V with a 7.6-fold increase in current density compared to that of the parent Au NP (FE = 53%). Tafel plots of the NHC carbene-functionalized Au NP (72 mV/decade) vs parent Au NP (138 mV/decade) systems further show that the molecular ligand influences mechanistic pathways for CO2 reduction. The results establish molecular surface functionalization as a complementary approach to size, shape, composition, and defect control for nanoparticle catalyst design.

Nanowire-bacteria hybrids for unassisted solar carbon dioxide fixation to value-added chemicals.

Direct solar-powered production of value-added chemicals from CO2 and H2O, a process that mimics natural photosynthesis, is of fundamental and practical interest. In natural photosynthesis, CO2 is first reduced to common biochemical building blocks using solar energy, which are subsequently used for the synthesis of the complex mixture of molecular products that form biomass. Here we report an artificial photosynthetic scheme that functions via a similar two-step process by developing a biocompatible light-capturing nanowire array that enables a direct interface with microbial systems. As a proof of principle, we demonstrate that a hybrid semiconductor nanowire-bacteria system can reduce CO2 at neutral pH to a wide array of chemical targets, such as fuels, polymers, and complex pharmaceutical precursors, using only solar energy input. The high-surface-area silicon nanowire array harvests light energy to provide reducing equivalents to the anaerobic bacterium, Sporomusa ovata, for the photoelectrochemical production of acetic acid under aerobic conditions (21% O2) with low overpotential (η < 200 mV), high Faradaic efficiency (up to 90%), and long-term stability (up to 200 h). The resulting acetate (∼6 g/L) can be activated to acetyl coenzyme A (acetyl-CoA) by genetically engineered Escherichia coli and used as a building block for a variety of value-added chemicals, such as n-butanol, polyhydroxybutyrate (PHB) polymer, and three different isoprenoid natural products. As such, interfacing biocompatible solid-state nanodevices with living systems provides a starting point for developing a programmable system of chemical synthesis entirely powered by sunlight.

Supramolecular Ga4L6(12-) Cage Photosensitizes 1,3-Rearrangement of Encapsulated Guest via Photoinduced Electron Transfer.

The K12Ga4L6 supramolecular cage is photoactive and enables an unprecedented photoreaction not observed in bulk solution. Ga4L6(12-) cages photosensitize the 1,3-rearrangement of encapsulated cinnamylammonium cation guests from the linear isomer to the higher energy branched isomer when irradiated with UVA light. The rearrangement requires light and guest encapsulation to occur. The Ga4L6(12-) cage-mediated reaction mechanism was investigated by UV/vis absorption, fluorescence, ultrafast transient absorption, and electrochemical experiments. The results support a photoinduced electron transfer mechanism for the 1,3-rearrangement, in which the Ga4L6(12-) cage absorbs photons and transfers an electron to the encapsulated cinnamylammonium ion, which undergoes C-N bond cleavage, followed by back electron transfer to the cage and recombination of the guest fragments to form the higher energy isomer.

An extended mini-complement factor H molecule ameliorates experimental C3 glomerulopathy.

Abnormal regulation of the complement alternative pathway is associated with C3 glomerulopathy. Complement factor H is the main plasma regulator of the alternative pathway and consists of 20 short consensus repeat (SCR) domains. Although recombinant full-length factor H represents a logical treatment for C3 glomerulopathy, its production has proved challenging. We and others have designed recombinant mini-factor H proteins in which 'non-essential' SCR domains have been removed. Here, we report the in vitro and in vivo effects of a mini-complement factor H protein, FH1-5^18-20, using the unique factor H-deficient (Cfh-/-) mouse model of C3 glomerulopathy. FH1-5^18-20 is comprised of the key complement regulatory domains (SCRs 1-5) linked to the surface recognition domains (SCRs 18-20). Intraperitoneal injection of FH1-5^18-20 in Cfh-/- mice reduced abnormal glomerular C3 deposition, similar to full-length factor H. Systemic effects on plasma alternative pathway control were comparatively modest, in association with a short half-life. Thus, FH1-5^18-20 is a potential therapeutic agent for C3 glomerulopathy and other renal conditions with alternative pathway-mediated tissue injury.

Porphyrin Aggregation under Homogeneous Conditions Inhibits Electrocatalysis: A Case Study on CO2 Reduction.

Metalloporphyrins are widely used as homogeneous electrocatalysts for transformations relevant to clean energy and sustainable organic synthesis. Metalloporphyrins are well-known to aggregate due to π-π stacking, but surprisingly, the influence of aggregation on homogeneous electrocatalytic performance has not been investigated previously. Herein, we present three structurally related iron meso-phenylporphyrins whose aggregation properties are different in commonly used N,N-dimethylformamide (DMF) electrolyte. Both spectroscopy and light scattering provide evidence of extensive porphyrin aggregation under conventional electrocatalytic conditions. Using the electrocatalytic reduction of CO2 to CO as a test reaction, cyclic voltammetry reveals an inverse dependence of the kinetics on the catalyst concentration. The inhibition extends to bulk performance, where up to 75% of the catalyst at 1 mM is inactive compared to at 0.25 mM. We additionally report how aggregation is perturbed by organic additives, axial ligands, and redox state. Periodic boundary calculations provide additional insights into aggregate stability as a function of metalloporphyrin structure. Finally, we generalize the aggregation phenomenon by surveying metalloporphyrins with different metals and substituents. This study demonstrates that homogeneous metalloporphyrins can aggregate severely in well-solubilizing organic electrolytes, that aggregation can be easily modulated through experimental conditions, and that the extent of aggregation must be considered for accurate catalytic benchmarking.

Predicting cell cycle stage from 3D single-cell nuclear-stained images.

The cell cycle governs the proliferation, differentiation, and regeneration of all eukaryotic cells. Profiling cell cycle dynamics is therefore central to basic and biomedical research spanning development, health, aging, and disease. However, current approaches to cell cycle profiling involve complex interventions that may confound experimental interpretation. To facilitate more efficient cell cycle annotation of microscopy data, we developed CellCycleNet, a machine learning (ML) workflow designed to simplify cell cycle staging with minimal experimenter intervention and cost. CellCycleNet accurately predicts cell cycle phase using only a fluorescent nuclear stain (DAPI) in fixed interphase cells. Using the Fucci2a cell cycle reporter system as ground truth, we collected two benchmarking image datasets and trained two ML models-a support vector machine (SVM) and a deep neural network-to classify nuclei as being in either the G1 or S/G2 phases of the cell cycle. Our results suggest that CellCycleNet outperforms state-of-the-art SVM models on each dataset individually. When trained on two image datasets simultaneously, CellCycleNet achieves the highest classification accuracy, with an improvement in AUROC of 0.08-0.09. The model also demonstrates excellent generalization across different microscopes, achieving an AUROC of 0.95. Overall, using features derived from 3D images, rather than 2D projections of those same images, significantly improves classification performance. We have released our image data, trained models, and software as a community resource.