College of Chemistry

In vivo genetic diversifiers have previously enabled efficient searches of genetic variant fitness landscapes for continuous directed evolution. However, existing genomic diversification modalities for mammalian genomic loci exclusively rely on deaminases to generate transition mutations within target loci, forfeiting access to most missense mutations. Here, we engineer CRISPR-guided error-prone DNA polymerases (EvolvR) to diversify all four nucleotides within genomic loci in mammalian cells. We demonstrate that EvolvR generates both transition and transversion mutations throughout a mutation window of at least 40 bp and implement EvolvR to evolve previously unreported drug-resistant MAP2K1 variants via substitutions not achievable with deaminases. Moreover, we discover that the nickases mismatch tolerance limits EvolvRs mutation window and substitution biases in a gRNA-specific fashion. To compensate for gRNA-to-gRNA variability in mutagenesis, we maximize the number of gRNA target sequences by incorporating a PAM-flexible nickase into EvolvR. Finally, we find a strong correlation between predicted free energy changes underlying R-loop formation and EvolvRs performance using a given gRNA. The EvolvR system diversifies all four nucleotides to enable the evolution of mammalian cells, while nuclease and gRNA-specific properties underlying nickase fidelity can be engineered to further enhance EvolvRs mutation rates.

Although synthetic biology can produce valuable chemicals in a renewable manner, its progress is still hindered by a lack of predictive capabilities. Media optimization is a critical, and often overlooked, process which is essential to obtain the titers, rates and yields needed for commercial viability. Here, we present a molecule- and host-agnostic active learning process for media optimization that is enabled by a fast and highly repeatable semi-automated pipeline. Its application yielded 60% and 70% increases in titer, and 350% increase in process yield in three different campaigns for flaviolin production in Pseudomonas putida KT2440. Explainable Artificial Intelligence techniques pinpointed that, surprisingly, common salt (NaCl) is the most important component influencing production. The optimal salt concentration is very high, comparable to seawater and close to the limits that P. putida can tolerate. The availability of fast Design-Build-Test-Learn (DBTL) cycles allowed us to show that performance improvements for active learning are rarely monotonous. This work illustrates how machine learning and automation can change the paradigm of current synthetic biology research to make it more effective and informative, and suggests a cost-effective and underexploited strategy to facilitate the high titers, rates and yields essential for commercial viability.

Biotechnology offers a sustainable route to manufacturing, but closing the loop towards safeguarding biodiversity remains challenging. Here, we explore how partnerships with Indigenous Peoples and Local Communities (IP&LC) can promote an ethical and circular bioeconomy.

The efficient removal of CO₂ from exhaust streams and even directly from air is necessary to forestall climate change, lending urgency to the search for new materials that can rapidly capture CO₂ at high capacity. The recent discovery that diamine-appended metal-organic frameworks can exhibit cooperative CO₂ uptake via the formation of ammonium carbamate chains begs the question of whether simple organic polyamine molecules could be designed to achieve a similar switch-like behavior with even higher separation capacities. Here, we present a solid molecular triamine, 1,3,5-tris(aminomethyl)benzene (TriH), that rapidly captures large quantities of CO₂ upon exposure to humid air to form the porous, crystalline, ammonium carbamate network solid TriH(CO₂)_1.5·xH₂O (TriHCO₂). The phase transition behavior of TriH converting to TriHCO₂ was studied through powder and single-crystal X-ray diffraction analysis, and additional spectroscopic techniques further verified the formation of ammonium carbamate species upon exposing TriH to humid air. Detailed breakthrough analyses conducted under varying temperatures, relative humidities, and flow rates reveal record CO₂ absorption capacities as high as 8.9 mmol/g. Computational analyses reveal an activation barrier associated with TriH absorbing CO₂ under dry conditions that is lowered under humid conditions through hydrogen bonding with a water molecule in the transition state associated with N-C bond formation. These results highlight the prospect of tunable molecular polyamines as a new class of candidate absorbents for high-capacity CO₂ capture.

Lithium (Li)-excess transition metal oxide materials which crystallize in the cation-disordered rock salt (DRX) structure are promising cathodes for realizing low-cost, high-energy-density Li batteries. However, the state-of-the-art electrolytes for Li-ion batteries cannot meet the high-voltage stability requirement for high-voltage DRX cathodes, thus new electrolytes are urgently demanded. It has been reported that the solvation structures and properties of the electrolytes critically influence the performance and stability of the batteries. In this study, the structure-property relationships of various electrolytes with different solvent-to-diluent ratios are systematically investigated through a combination of theoretical calculations and experimental tests and analyses. This approach guides the development of electrolytes with unique solvation structures and characteristics, exhibiting high voltage stability, and enhancing the formation of stable electrode/electrolyte interphases. These electrolytes enable the realization of Li||Li_1.094Mn_0.676Ti_0.228O₂ (LMTO) DRX cells with improved performance compared to the conventional electrolyte. Specifically, Li||LMTO cells with the optimized advanced controlled-solvation electrolyte deliver higher specific capacity and longer cycle life compared to cells with the conventional electrolyte. Additionally, the investigation into the structure-property relationship provides a foundational basis for designing advanced electrolytes, which are crucial for the stable cycling of emerging high-voltage cathodes.

The temperature for complete disintegration of spent lithium-ion battery (LIB) cathode materials is typically in a range of 750-1400 °C, resulting in intensive energy consumption and high carbon emissions. Here, we promote the bond activation of oxygen in LiNi0.5Co0.2Mn0.3O2 and carbon in graphite electrodes, achieving rapid gasification and thermal decomposition of active crystals at lower temperatures in the absence of other activating agents. The activation of C and O bond leads to the storage of internal energy and the transition of the crystalline phase (single crystal to polycrystal) of the active crystals. Density functional theory modeling confirms that the CO adsorption energy is significantly higher with Ca-Oa (-3.35 eV, C and O activation) than with no activation (-1.66 eV). The differential charge results show that the bond activation model has the highest charge accumulation and consumption, improving the electron transfer. The Bader charge transfer between Ca-Oa and CO is also the largest, with a value of 0.433 |e|. Therefore, synchronous activation of C and O bonds can reduce the decomposition temperature of active crystals by 200 °C and allows a low-temperature pyrolysis recycling of retired LIB cathode materials. Our research provides a potential strategy for low-carbon recycling of retired LIBs worldwide.

The delivery of biomolecules to target cells has been a longstanding challenge in biotechnology. DNA viruses naturally evolved the ability to deliver genetic material to cells and modulate cellular processes. As such, they inherently possess requisite characteristics that have led to their extensive study, engineering, and development as biotechnological tools. Here, we overview the application of DNA viruses to biotechnology, with specific implications in basic research, health, biomanufacturing, and agriculture. For each application, we review how an increasing understanding of virology and technological methods to genetically manipulate DNA viruses has enabled advances in these fields. Additionally, we highlight the remaining challenges to unlocking the full biotechnological potential of DNA viral technologies. Finally, we discuss the importance of balancing continued technological progress with ethical and biosafety considerations.

Prenol and isoprenol are promising advanced biofuels and serve as biosynthetic precursors for pharmaceuticals, fragrances, and other industrially relevant compounds. Despite engineering improvements that circumvent intermediate cytotoxicity and lower energy barriers, achieving high titer 'mevalonate (MVA)-derived' prenol has remained elusive. Difficulty in selective prenol production stems from the necessary isomerization of isopentenyl diphosphate (IPP) to dimethylallyl diphosphate (DMAPP) as well as the intrinsic toxicity of these diphosphate precursors. Here, the expression of specific isopentenyl monophosphate kinases with model-guided enzyme substitution of diphosphate isomerases and phosphatases enabled selective cycling of monophosphates and diphosphates, dramatically improving prenol titers and selectivity in Escherichia coli. Pairing this approach with the canonical MVA pathway resulted in 300 mg/L prenol at a 30:1 ratio with isoprenol. Further pairing with the "IPP-Bypass" pathway resulted in 526 mg/L prenol at a 72:1 ratio with isoprenol, the highest and purest MVA-derived prenol titer to date. Additionally, modifying this "IPP-Repass" for DMAPP production and coexpressing the prenyltransferase acPT1 yielded 48.3 mg/L of the potential therapeutic precursor drupanin from p-coumarate. These novel repass pathways establish a unique strategy for tuning diphosphate precursors to drive isoprenoid biosynthesis and prenylation reactions.

A soft lithographic method is developed for making bipolar membranes (BPMs) with catalytic junctions formed from arrays of vertically oriented microscale cylinders. The membranes are cast from reusable polydimethylsiloxane (PDMS) molds made from silicon masters, which are fabricated on 2″ to 4″ wafer scales by nanosphere lithography. High-aspect-ratio junctions are made on a length scale similar to the thickness of optimized catalyst layers for water dissociation, creating a platform for probing the dual effects of catalysis and local electric field at the microscale BPM junction. Optimized polymer materials and nanoscale metal oxide catalysts are used in this study. 3D BPMs are tested under reverse and forward bias conditions, exhibiting superior performance relative to their 2D counterparts. Under forward bias in H2-O2 fuel cells, 3D BPMs achieve a current density of 1500 mA cm−2, ≈7 times higher than 2D membranes made from the same materials.

How early sensory experience during "critical periods" of postnatal life affects the organization of the mammalian neocortex at the resolution of neuronal cell types is poorly understood. We previously reported that the functional and molecular profiles of layer 2/3 (L2/3) cell types in the primary visual cortex (V1) are vision-dependent [S. Cheng et al., Cell 185, 311-327.e24 (2022)]. Here, we characterize the spatial organization of L2/3 cell types with and without visual experience. Spatial transcriptomic profiling based on 500 genes recapitulates the zonation of L2/3 cell types along the pial-ventricular axis in V1. By applying multitasking theory, we suggest that the spatial zonation of L2/3 cell types is linked to the continuous nature of their gene expression profiles, which can be represented as a 2D manifold bounded by three archetypal cell types. By comparing normally reared and dark reared L2/3 cells, we show that visual deprivation-induced transcriptomic changes comprise two independent gene programs. The first, induced specifically in the visual cortex, includes immediate-early genes and genes associated with metabolic processes. It manifests as a change in cell state that is orthogonal to cell-type-specific gene expression programs. By contrast, the second program impacts L2/3 cell-type identity, regulating a subset of cell-type-specific genes and shifting the distribution of cells within the L2/3 cell-type manifold. Through an integrated analysis of spatial transcriptomics with single-nucleus RNA-seq data, we describe how vision patterns cortical L2/3 cell types during the critical period.