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BioPKS Pipeline is a computational pipeline for retrosynthetic design of small molecule biosynthesis pathways (e.g. retrobiosynthesis). It combines capabilities by interfacing with existing retrobiosynthesis tools- RetroTide (developed at LBNL) and DORAnet to create pathways that combine multiple biosynthesis approaches- both megasynthase assembly line enzymes and single step enzymes.
Multiplexed CRISPR technologies have great potential for pathway engineering and genome editing. However, their applications are constrained by complex, laborious and time-consuming cloning steps. In this research, we developed a novel method, PARA, which allows for the one-step assembly of multiple guide RNAs (gRNAs) into a CRISPR vector with up to 18 gRNAs. Here, we demonstrate that PARA is capable of the efficient assembly of transfer RNA/Csy4/ribozyme-based gRNA arrays. To aid in this process and to streamline vector construction, we developed a user-friendly PARAweb tool for designing PCR primers and component DNA parts and simulating assembled gRNA arrays and vector sequences.
Regenerative fuel cells provide a pathway to energy storage system development that are game changers for NASA missions. The fuel cell/ electrolysis MEA performance requirements 0.92 V/ 1.44 V at 200 mA/cm2 can be met. Fuel Cell MEAs have been incorporated into advanced NFT stacks. Electrolyzer stack development in progress. Fuel Cell MEA performance is a strong function of membrane selection, membrane selection will be driven by durability requirements. Electrolyzer MEA performance is catalysts driven, catalyst selection will be driven by durability requirements. Round Trip Efficiency, based on a cell performance, is approximately 65%.
MaizeMine is the data mining resource of the Maize Genetics and Genome Database (MaizeGDB; http://maizemine.maizegdb.org). It enables researchers to create and export customized annotation datasets that can be merged with their own research data for use in downstream analyses. MaizeMine uses the InterMine data warehousing system to integrate genomic sequences and gene annotations from the Zea mays B73 RefGen_v3 and B73 RefGen_v4 genome assemblies, Gene Ontology annotations, single nucleotide polymorphisms, protein annotations, homologs, pathways, and precomputed gene expression levels based on RNA-seq data from the Z. mays B73 Gene Expression Atlas. MaizeMine also provides database cross references between genes of alternative gene sets from Gramene and NCBI RefSeq. MaizeMine includes several search tools, including a keyword search, built-in template queries with intuitive search menus, and a QueryBuilder tool for creating custom queries. The Genomic Regions search tool executes queries based on lists of genome coordinates, and supports both the B73 RefGen_v3 and B73 RefGen_v4 assemblies. The List tool allows you to upload identifiers to create custom lists, perform set operations such as unions and intersections, and execute template queries with lists. When used with gene identifiers, the List tool automatically provides gene set enrichment for Gene Ontology (GO) and pathways, with a choice of statistical parameters and background gene sets. With the ability to save query outputs as lists that can be input to new queries, MaizeMine provides limitless possibilities for data integration and meta-analysis.
Transporting and assembling large, complex structures poses significant challenges due to their size, geometry, and cost. Additionally, the installation sites are often inaccessible or hazardous for humans, necessitating self-assembling capabilities in these structures. To mitigate these challenges, we propose using 3D printing materials with shape memory effect (SME) for both transport and construction. This approach involves developing 3D modular components into flat sheets for easier transportation, and then self-assembling into 3D structures on-site using solar energy. To gain a deeper understanding of the factors influencing material memory performance, we have chosen a composite PLA/WF, which is polylactic acid (PLA) with 20 wt% wood flour (WF) for this purpose, leveraging its high tensile modulus at 0.966 GPa, low cost, and sustainability. Printed shapes with this material can maintain a recovery ratio over 90% after 3 cycles. While traditional composites fillers (e.g. glass or carbon fiber) are added to enhance mechanical and thermal properties, the addition of bio-based fillers like WF accomplish similar goals without compromising sustainability. We conducted multiple experiments to demonstrate how environmental conditions (i.e. temperature) maximize the material’s SME. Although still at an early stage, this study provides initial insights into bridging the gap between the small-scale nature of shape memory polymers (SMPs) and their potential for large-scale additive manufacturing, addressing a critical need for efficient and sustainable construction. In the long term, we hope our study contributes to the design vision of utilizing SMPs for transportation, assembly, and deployment of complex structures, providing a new pathway for sustainable construction and transportation of large-scale structures to hard-to-access locations such as disaster-affected areas and remote deserts, etc.
The precise synthesis of high-purity materials is crucial in accelerating materials discovery. However, the lack of theoretical understanding and practical guidance poses challenges, particularly for materials with compositional and structural complexity. Here, we propose a feasible principle toward synthesizing complex inorganic solids. This principle involves the introduction of an inducer that induces crucial intermediates, which in turn guide the synthesis pathway toward the target materials through structural templating, named inducer-facilitated assembly through structural templating (i-FAST). We validate this principle with three distinct oxides: garnet Li6.5La3Zr1.5Ta0.5O12, perovskite BaCo0.8Sn0.2O3, and pyrochlore Gd1.5La0.5Zr2O7. This structural templating approach enables synthesis along predesigned pathways, forming intermediates that are thermodynamically favored for prior formation and kinetically preferred for the final product, resulting in precisely synthesizing high-purity target materials. This study not only represents a substantial advancement in comprehending the interplay between thermodynamics/kinetics and phase evolution in complex solid synthesis but also provides an effective strategy for guiding exploratory solid-state synthesis.
Heterogeneous integration of microelectronic components provides a pathway to improve circuit/component performance; however, this comes with assembly challenges, in particular due to complex interfaces via subsurface bump bonds. The ability of these bonds to transmit electrical signals and conduct heat to the carrier substrate limits component performance. In this work, hyperspectral frequency‐domain thermoreflectance (FDTR) imaging is demonstrated as a robust technique for evaluating the quality of subsurface indium bump bonds in a surrogate microelectronic sample. By performing microscale FDTR imaging with coarse motion image stitching, thermal phase maps that cover a 4 mm by 4 mm field‐of‐view with subsurface feature sensitivity at depths greater than 50 µm are obtained. The resulting FDTR hyperspectral data contains more than three million pixels and reveal the quality of subsurface microbump arrays. Wide‐field analysis of bonded versus gap regions is enabled by deep neural network feature reconstruction, that after training, rapidly provides an interpretable representation of bond quality. Utility of noisy higher frequency FDTR phase maps, i.e., near the computationally predicted sensing depth limit, results in an average prediction error of 11%. Taken together, FDTR with neural network‐based analysis demonstrates subsurface bond monitoring at length scales relevant for heterogeneously integrated microelectronics.
Prussian blue analogs (PBAs) exhibit potential as low-cost and eco-friendly nanocatalysts that can be fabricated with ease. However, the PBA framework structure suffers from poor electronic conductivity, which limits the catalytic efficiency for this class of materials. Noble metals represent an alternative class of materials that display inherent catalytic activity but suffer from aggregation, ultimately reducing the amount of accessible catalytic sites. Herein, we demonstrate a combinatory approach that circumvents the known disadvantages with these classes of catalytic materials in which PBA-supported nanocatalysts were synthesized. These composite materials exhibit excellent catalytic activity for the reduction of nitroaromatics to aminoaromatics while displaying long-term cycling stability, which is attributed to the availability of multiple electron transfer pathways. Overall, this work opens the study on the assembly of PBA-supported heterogeneous nanocatalysts and potentially paves the way toward future applications.
In this work, we explore how the chemical reactivity toward an aprotic battery electrolyte changes as a function of lithium salt and silicon surface termination chemistry. The reactions are highly correlated, where one decomposition reaction leads to a subsequent decomposition reaction. We report the data show that the presence of silicon hydrides (SiH$_x$) promotes the formation of CO gas, while surface oxides SiO$_x$ drive the formation of CO 2 . The extent and rate of oxidation depend on the surface basicity of the SiO 2 surface species. The most acidic surfaces seem to hinder CO 2 generation but not the decomposition of the salt. Indeed, the presence of F-containing salts (LiPF 6 and LiTFSI) promotes the reactions between carbonate electrolyte and silicon surfaces. Surfaces with high Li content seem to be the most passivating to gassing reactions, pointing to a pathway to stabilize the interfaces during cell formation and assembly.
Solid-state batteries (SSBs) offer a safer, higher-energy-density alternative to lithium-ion batteries, yet commercialization is hindered by incompatibility with lithium metal. Here, to overcome these challenges, we developed a cost-effective, commercially available prelithiated micro carbon fiber framework (Li-Cf) anode featuring a high-pressure-tolerance, for use with argyrodite solid-state electrolytes (SSEs). This 3D structure accommodates uniform lithium deposition, simplifies cell assembly under elevated pressure, inhibits dendrite growth toward SSEs, reduces heat generation, and enhances overall compatibility. Notably, our architecture enables the cell to tolerate pressures up to 400 MPa without short-circuiting during assembly. Meanwhile, the 3D framework serves as a preferential pathway for lithium deposition, thereby reducing lithium growth toward the SSEs and mitigating the risk of dendrite formation in SSEs. Operando calorimetry and distribution of relaxation times analysis reveal that lithium morphology degradation at the interface with the SSEs is a key failure mechanism in lithium metal argyrodite SSBs, leading to increased diffusion resistance and heat generation. In contrast, the Li-Cf anode mitigates these issues by reducing both heat flux and charge transfer resistance. Full cells with LiNi 0.8 Co 0.1 Mn 0.1 O 2 /Li 6 PS 5 Cl/Li-Cf retain ~79% capacity after 600 cycles, demonstrating significantly improved cycling stability and strong potential for practical energy storage applications.
The main goal of this project was to follow up on prior discovery of the communal nature of methane utilization by the aerobic methanotrophic bacteria, resulting in carbon transfer along a food chain. This goal was approached via manipulation of specially designed, synthetic bacterial communities, fed exclusively by methane, under a variety of simulated environmental conditions. Using (meta)genomics, metatranscriptomics, stable isotope probing and mutant generation, we obtained solid evidence for the nature of the core microbiota involved in collaborative methane consumption, the major players (true methanotrophs) being the members of the family Methylococcaceae, their major partners (non-methanotrophic methylotrophs) being members of the family Methylophilaceae, and minor but persistent partners in the communities being members of the orders Burkholderiales and Bacteroidetes. Metabolic reconstruction from single genomes and metagenome-assembled genomes (MAGs), along with metatranscriptomics results delineated major pathways for carbon metabolism, suggesting that the methanotrophs share different organic compounds with different functional guilds: methanol with Methylophilaceae, acetate with Burkholderiales, and polymeric substances with Bacteroidetes. Overall, the results of this project expand our understanding of microbial metabolism of methane and, thus, provide basis for strategies for microbial methane mitigation, with obvious benefits to the society of the United States and worldwide.
Colibactin is a genotoxic natural product produced by select commensal bacteria in the human gut microbiota. The compound is a bis-electrophile that is predicted to form interstrand DNA cross-links in target cells, leading to double-strand DNA breaks. The biosynthesis of colibactin is carried out by a mixed NRPS–PKS assembly line with several noncanonical features. An amidase, ClbL, plays a key role in the pathway, catalyzing the final step in the formation of the pseudodimeric scaffold. ClbL couples α-aminoketone and β-ketothioester intermediates attached to separate carrier domains on the NRPS–PKS assembly. Here, the 1.9 Å resolution structure of ClbL is reported, providing a structural basis for this key step in the colibactin biosynthetic pathway. The structure reveals an open hydrophobic active site surrounded by flexible loops, and comparison with homologous amidases supports its unusual function and predicts macromolecular interactions with pathway carrier-protein substrates. Modeling protein–protein interactions supports a predicted molecular basis for enzyme–carrier domain interactions. Overall, the work provides structural insight into this unique enzyme that is central to the biosynthesis of colibactin.
Calcium regulates diverse cellular activities in plants through the action of calmodulin (CaM). By using (35)S-labeled CaM to screen an Arabidopsis seedling cDNA expression library, a cDNA designated as AtCh-CPN10 (Arabidopsis thaliana chloroplast chaperonin 10) was cloned. Chloroplast CPN10, a nuclear-encoded protein, is a functional homolog of E. coli GroES. It is believed that CPN60 and CPN10 are involved in the assembly of Rubisco, a key enzyme involved in the photosynthetic pathway. Northern analysis revealed that AtCh-CPN10 is highly expressed in green tissues. The recombinant AtCh-CPN10 binds to CaM in a calcium-dependent manner. Deletion mutants revealed that there is only one CaM-binding site in the last 31 amino acids of the AtCh-CPN10 at the C-terminal end. The CaM-binding region in AtCh-CPN10 has higher homology to other chloroplast CPN10s in comparison to GroES and mitochondrial CPN10s, suggesting that CaM may only bind to chloroplast CPN10s. Furthermore, the results also suggest that the calcium/CaM messenger system is involved in regulating Rubisco assembly in the chloroplast, thereby influencing photosynthesis. Copyright 2000 Academic Press.
Each flashlamp is supported coaxially within a pyrex water-jacket tube by two identical connector assemblies, one at each end. These connector assemblies not only support the flashlamp mechanically, but also provide source and return pathways for flashlamp DI cooling water and for electrical current. At each end of the flashlamp, the (presumably) tungsten feed-through rod that supports the electrode is attached to a connector assembly through a Multilam fitting. O rings seated on the outside of each connector assembly form a water-tight seal between the connector assembly and the inside of the pyrex water-jacket tube. During operation, DI cooling water enters the tube located at the end of one of the connectors, flows over that connector’s Multilam fitting, flows through a ring of holes in the connector assembly and then flows into the 1-mm gap between the flashlamp and the pyrex water-jacket tube. After passing over the length of the flashlamp, the water flows through the connector assembly at the opposite end of the flashlamp and exits through that connector assembly’s end tube. Electrical pulses are delivered to the flashlamp through the tubes coming out of the connector assemblies.
Plasmonic interactions between metal nanostructures and fluorophores have been increasingly employed to alter photoexcitation pathways in multichromophore photosynthetic proteins like photosystem I (PSI). Our recent experimental studies demonstrated a sixfold plasmon-enhanced photocurrent from PSI assembled on Fischer patterns of Ag nanopyramids. However, lack of control over the specific resonance modes limited the magnitude and selectivity of the plasmonic enhancement. To this end, the present study investigates the excitation wavelength-dependent plasmon-enhanced photocurrents from PSI immobilized around highly ordered Au (AuND) and Ag (AgND) nanodisks with dipolar plasmon resonances that are tuned to ~680 and 560 nm, respectively. Specifically, we report plasmon-induced photocurrent enhancements of ~6.8 and 17.5 for excitation wavelengths of ~680 and 565 nm, respectively, as compared to PSI assembled on planar ITO substrates. We also report the action spectra for photocurrent enhancements recorded over wavelengths of 395–810 nm with nine discrete LED light sources. The results indicate the following: (1) concurrence between the photocurrent-enhancement spectra from PSI assemblies and the plasmonic resonances for the respective nanopatterned substrates, and (2) broadband photocurrent enhancements due to plasmon-coupled photoactivation in the otherwise blind chlorophyll regions of the native PSI absorption spectra. Lastly, these intriguing findings pave the path for rational assembly of future biohybrid structures composed of natural light-harvesting antennae and plasmonic metal nanostructures.
A study of the formation of microstructures in the reaction of oleic acid with arginine elucidates dynamical self-assembly processes at the molecular level. Terahertz spectroscopy combined with density functional calculations reveals the initial hydrogen-bonding motifs in the assembly process, leading to the formation of micelles and vesicles. Small-angle X-ray scattering measurements allow for kinetic analysis of the growth processes of these nanostructures, revealing a prenucleation pathway of vesicles and micelles which lead to spongelike structures. This final stage of the assembly into spongelike aggregates is investigated with optical microscopy. The formed structures only occur at pH > 8 and are resistant to extreme acidic and basic conditions. Here, a mechanistic pathway to the formation of the spongelike aggregates is described.