Advances in the Application of Single-Cell Transcriptomics in Plant Systems and Synthetic Biology
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59 BASIC BIOLOGICAL SCIENCES↗
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Results for “single cell”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Material Science-Based Predictions of Single-Cell Thermal Failures.
Abstract not provided.
Shurtz, Randy↗
Concurrent evaluation of autophagy induction and Burkholderia infection at the single cell level.
Abstract not provided.
Maes, Danae Maria↗
Concurrent evaluation of autophagy induction and Burkholderia infection at the single cell level.
Abstract not provided.
Maes, Danae Maria↗
Algae: A Single Cell for Multiple Solutions
An overview of the BETO support of public and private partners that work to improve and increase the use of algae for production of biofuels and bioproducts.
algae, biofuels, bioproducts↗
Single molecule-based fliFISH validates radial and heterogeneous gene expression patterns in pancreatic islet ß cells
Single cell RNA sequencing (scRNA-Seq) technologies have greatly enhanced our understanding of islet cell transcriptomes and have revealed the existence of ß cell heterogeneity. However, comparison of scRNA-Seq datasets from different groups have highlighted inconsistencies in gene expression patterns, primarily due to variable detection of lower abundance transcripts. Furthermore, such analyses are unable to uncover the spatial organization of heterogeneous gene expression. Here we used fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) to quantify transcripts in single cells in mouse pancreatic islet sections. We compared the expression patterns of Insulin 2 (Ins2) with Mafa and Ucn3 – two genes expressed in ß cells as they mature, as well as Rgs4 – a factor with variably reported expression in the islet. This approach accurately quantified transcripts across a wide range of expression levels - from single copies to over hundred copies per cell in one islet. Importantly, fliFISH allowed evaluation of transcript heterogeneity in the spatial context of an intact islet. These studies confirm the existence of a high degree of heterogeneous gene expression levels within the islet and highlight relative and radial expression patterns that likely reflect distinct ß cell maturation states along the radial axis of the islet.
Li, Fangjia↗
scMicrobe PTA: near complete genomes from single bacterial cells
Microbial genomes produced by standard single-cell amplification methods are largely incomplete. Here, we show that primary template-directed amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard multiple displacement amplification-based approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.
59 BASIC BIOLOGICAL SCIENCES↗
Effects of Trigger Method on Fire Propagation during the Thermal Runaway Process in Li-ion Batteries
Lithium-ion batteries are prone to fire hazards due to the possibility of thermal runaway propagation. During battery product development and subsequent safety tests for design validation and safety certification, the thermal runaway onset is triggered by various test methods such as nail penetration, thermal ramp, or external short circuit. This failure initiation method affects the amount of heat contributions and the composition of gas generations. This study compares two such trigger methods, external heating and using a thermally-activated internal short circuit device (ISCD). The effects of the trigger method on total heat generation are experimentally investigated within 18650 cylindrical cells at single cell level as well as at multiple cell configuration level. The severity of failure was observed to be worse for cells with ISCDs at single cell level, whereas quite the opposite results were observed at multiple cell configuration level. A preliminary numerical analysis was performed to better understand the battery safety performance with respect to thermal runaway trigger methods and heat transfer conditions.
25 ENERGY STORAGE↗
Data for "Enhancing Lipid Production in Plant Cells through Automated High-Throughput Genome Engineering and Phenotyping"
Plant bioengineering is a time-consuming and labor-intensive process with no guarantee of achieving desired traits. Here, we present a fast, automated, scalable, high-throughput pipeline for plant bioengineering (FAST-PB) in maize (Zea mays) and Nicotiana benthamiana. FAST-PB enables genome editing and product characterization by integrating automated biofoundry engineering of callus and protoplast cells with single-cell matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). We first demonstrated that FAST-PB could streamline Golden Gate cloning, with the capacity to construct 96 vectors in parallel. Using FAST-PB in protoplasts, we found that PEG2050 increased transfection efficiency by over 45%. For proof-of-concept, we established a reporter-gene-free method for CRISPR editing and phenotyping via mutation of high chlorophyll fluorescence 136. We show that diverse lipids were enhanced up to 6-fold using CRISPR activation of lipid controlling genes. In callus cells, an automated transformation platform was employed to regenerate plants with enhanced lipid traits through introducing multigene cassettes. Lastly, FAST-PB enabled high-throughput single-cell lipid profiling by integrating MALDI-MS with the biofoundry, protoplast, and callus cells, differentiating engineered and unengineered cells using single-cell lipidomics. These innovations massively increase the throughput of synthetic biology, genome editing, and metabolic engineering and change what is possible using single-cell metabolomics in plants.
AI/ML↗
Enhancing lipid production in plant cells through automated high-throughput genome engineering and phenotyping
Plant bioengineering is a time-consuming and labor-intensive process with no guarantee of achieving desired traits. Here, we present a fast, automated, scalable, high-throughput pipeline for plant bioengineering (FAST-PB) in maize (Zea mays) and Nicotiana benthamiana. FAST-PB enables genome editing and product characterization by integrating automated biofoundry engineering of callus and protoplast cells with single-cell matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). We first demonstrated that FAST-PB could streamline Golden Gate cloning, with the capacity to construct 96 vectors in parallel. Using FAST-PB in protoplasts, we found that PEG2050 increased transfection efficiency by over 45%. For proof-of-concept, we established a reporter-gene-free method for CRISPR editing and phenotyping via mutation of high chlorophyll fluorescence 136. We show that diverse lipids were enhanced up to 6-fold using CRISPR activation of lipid controlling genes. In callus cells, an automated transformation platform was employed to regenerate plants with enhanced lipid traits through introducing multigene cassettes. Lastly, FAST-PB enabled high-throughput single-cell lipid profiling by integrating MALDI-MS with the biofoundry, protoplast, and callus cells, differentiating engineered and unengineered cells using single-cell lipidomics. Furthermore, these innovations massively increase the throughput of synthetic biology, genome editing, and metabolic engineering and change what is possible using single-cell metabolomics in plants.
59 BASIC BIOLOGICAL SCIENCES↗
A multi-material platform for imaging of single cell-cell junctions under tensile load fabricated with two-photon polymerization
We previously reported a single-cell adhesion micro tensile tester (SCAμTT) fabricated from IP-S photoresin with two-photon polymerization (TPP) for investigating the mechanics of a single cell-cell junction under defined tensile loading. A major limitation of the platform is the autofluorescence of IP-S, the photoresin for TPP fabrication, which significantly increases background signal and makes fluorescent imaging of stretched cells difficult. In this study, we report the design and fabrication of a new SCAμTT platform that mitigates autofluorescence and demonstrate its capability in imaging a single cell pair as its mutual junction is stretched. By employing a two-material design using IP-S and IP-Visio, a photoresin with reduced autofluorescence, we show a significant reduction in autofluorescence of the platform. Further, by integrating apertures onto the substrate with a gold coating, the influence of autofluorescence on imaging is almost completely mitigated. With this new platform, we demonstrate the ability to image a pair of epithelial cells as they are stretched up to 250% strain, allowing us to observe junction rupture and F-actin retraction while simultaneously recording the accumulation of over 800 kPa of stress in the junction. In conclusion, the platform and methodology presented here can potentially enable detailed investigation of the mechanics of and mechanotransduction in cell-cell junctions and improve the design of other TPP platforms in mechanobiology applications.
Autofluorescence↗
Identification and characterization of distinct cell cycle stages in cardiomyocytes using the FUCCI transgenic system
Understanding the regulatory mechanism by which cardiomyocyte proliferation transitions to endoreplication and cell cycle arrest during the neonatal period is crucial for identifying proproliferative factors and developing regenerative therapies. }We used a transgenic mouse model based on the fluorescent ubiquitination-based cell cycle indicator (FUCCI) system to isolate and characterize cycling cardiomyocytes at different cell cycle stages at a single-cell resolution. Single-cell transcriptome analysis of cycling and noncycling cardiomyocytes was performed at postnatal days 0 (P0) and 7 (P7). }The FUCCI system proved to be efficient for the identification of cycling cardiomyocytes with the highest mitotic activity at birth, followed by a gradual decline in the number of cycling and mitotic cardiomyocytes during the neonatal period. Cardiomyocytes showed premature cell cycle exit at G1/S shortly after birth and delayed G1/S progression during endoreplication at P7. Single-cell RNA-seq confirmed previously described signaling pathways involved in cardiomyocyte proliferation (Erbb2 and Hippo/YAP), and maturation-related transcriptional changes during postnatal development, including the metabolic switch from glycolysis to fatty acid oxidation in cardiomyocytes. Importantly, we generated transcriptional profiles specific to cell division and endoreplication in cardiomyocytes at different developmental stages that may facilitate the identification of genes important for adult cardiomyocyte proliferation and heart regeneration. }In conclusion, the FUCCI mouse provides a valuable system to study cardiomyocyte cell cycle activity at single cell resolution that can help to decipher the switch from cardiomyocyte proliferation to endoreplication, and to revert this process to facilitate endogenous repair.
60 APPLIED LIFE SCIENCES↗
Enabling reactive microscopy with MicroMator
Microscopy image analysis has recently made enormous progress both in terms of accuracy and speed thanks to machine learning methods and improved computational resources. This greatly facilitates the online adaptation of microscopy experimental plans using real-time information of the observed systems and their environments. Applications in which reactiveness is needed are multifarious. Here we report MicroMator, an open and flexible software for defining and driving reactive microscopy experiments. It provides a Python software environment and an extensible set of modules that greatly facilitate the definition of events with triggers and effects interacting with the experiment. We provide a pedagogic example performing dynamic adaptation of fluorescence illumination on bacteria, and demonstrate MicroMator’s potential via two challenging case studies in yeast to single-cell control and single-cell recombination, both requiring real-time tracking and light targeting at the single-cell level.
47 OTHER INSTRUMENTATION↗
A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics
Effective phosphoproteome of nanoscale sample analysis remains a daunting task, primarily due to significant sample loss associated with non-specific surface adsorption during enrichment of low stoichiometric phosphopeptide. We develop a tandem tip phosphoproteomics sample preparation method that is capable of sample cleanup and enrichment without additional sample transfer, and its integration with our recently developed SOP (Surfactant-assisted One-Pot sample preparation) and iBASIL (improved Boosting to Amplify Signal with Isobaric Labeling) approaches provides a streamlined workflow enabling sensitive, high-throughput nanoscale phosphoproteome measurements. This approach significantly reduces both sample loss and processing time, allowing the identification of >3000 (>9500) phosphopeptides from 1 (10) µg of cell lysate using the label-free method without a spectral library. It also enables precise quantification of ~600 phosphopeptides from 100 sorted cells (single-cell level input for the enriched phosphopeptides) and ~700 phosphopeptides from human spleen tissue voxels with a spatial resolution of 200 µm (equivalent to ~100 cells) in a high-throughput manner. The new workflow opens avenues for phosphoproteome profiling of mass-limited samples at the low nanogram level.
59 BASIC BIOLOGICAL SCIENCES↗
Evaluating the effect of ionomer chemical composition in silver-ionomer catalyst inks toward the oxygen evolution reaction by half-cell measurements and water electrolysis
The effect of anion exchange ionomer (AEI) chemistry on the kinetics of the oxygen evolution reaction (OER) was systematically studied in both half-cell and single-cell electrolysis experiments. OER was studied in 1 M K 2 CO 3 at 50°C using an array of ionomer-silver catalyst inks deposited on Ni foam. Different ionomer modifications were investigated to optimize the OER performance. The AEI used in this work features a block copolymer backbone of polychloromethylstyrene-b-polycyclooctene-b-polychloromethylstyrene which was functionalized with either benzyltrimethylammonium (TMA) or benzylmethylpiperidinium (MPRD) quaternary ammonium cations. Here, using an MPRD quaternary ammonium cation shifted the rate determining step at high overpotentials, ultimately providing enhanced performance. Increasing the catalyst ink dilution was also found to substantially improve mass activity and catalyst utilization (increase from 35 to 88 A g –1 Ag), likely by reducing the ionomer thickness and decreasing transport resistances. In the final ionomer modification, the Ni foam substrate was leveraged to partially hydrogenate the polycyclooctene midblock to be polyethylene-like at the Ni interface. A significant increase in the electrochemical surface area (Cdl increased from 8.8 to 20.8 mF cm –2 ) and performance (by 47 mA cm –2 or 29 A g –1 Ag) was observed with the incorporation of polyethylene. Kinetic results from half-cell experiments were validated via single-cell anion exchange membrane electrolysis experiments, where the optimized electrode displayed enhanced performance in both 1 M K 2 CO 3 and DI H 2 O.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Lithium-Ion Battery Design for Grid-Scale Energy Storage App
A software that delivers parameters from energy storage system (ESS) to container, rack, module and single cell design, as well as data analysis on arbitrage energy and frequency regulation of ESS in different regions, has been developed. The Lithium-ion Battery Design for Grid-scale Energy Storage App V1.0 has the capability to output the system, module and cell design with the energy, power, capacity, group method, cost of single cell, and single cell test protocol which break down from input energy storage system data in different regions. The default chemistry of the battery is LiFePO4 and graphite. The energy density of the graphite/LiFePO 4 pouch cell ranges from 100 Wh/kg to 200 Wh/Kg in the software. Graphite/LiFePO 4 pouch cell (up to 1Ah in lab) manufacturing line is also built and can be used to evaluate the test protocol, moreover, for electrolyte evaluation in other ESMI seedling projects. The software enables rapid prototyping to accelerate energy storage research, development, and manufacturing.
Liu, Dianying↗
In-Situ Characterization of Dynamic Morphological and Phase Changes of Selenium-doped Germanium Using a Single Particle Cell and Synchrotron Transmission X-ray Microscopy
The dynamic information of lithium-ion battery active materials obtained from coin cell-based in-situ characterizations might not represent the properties of the active material itself because many other factors in the cell could have impacts on the cell performance. To address this problem, a single particle cell was developed to perform the in-situ characterization without the interference of inactive materials in the battery electrode as well as the X-ray-induced damage. In this study, the dynamic morphological and phase changes of selenium-doped germanium (Ge 0.9 Se 0.1 ) at the single particle level were investigated via synchrotron-based in-situ transmission X-ray microscopy. The results demonstrate the good reversibility of Ge 0.9 Se 0.1 at high cycling rate that helps understand its good cycling performance and rate capability. This in-situ and operando technique based on a single particle battery cell provides an approach to understanding the dynamic electrochemical processes of battery materials during charging and discharging at the particle level.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Quantitative multiplexed analysis of gene and protein expression patterns in Yarrowia lipolytica
In this report, we present coordinated observations of protein and mRNA transcript counts at the single-cell level in the oleaginous yeast model Yarrowia lipolytica. The transcription factor Xbp1p regulates entry into a quiescent state, representing a shift of resources to sequestration of nutrients rather than cell division. We observed the responses of wild-type and Δxbp1 cells to protein (by fluorescence) and transcript quantification and localization at both single-cell and population-averaged levels. Data were collected via single-molecule fluorescence in situ hybridization (smFISH) and qPCR under nitrogen depletion, a condition that drives lipid accumulation. These techniques reveal a complex and heterogeneous population of Xbp1p dynamics and downstream regulation. Our findings highlight the need for single-cell resolution analyses to describe cellular dynamics and regulatory processes.
Yarrowia lipolytica↗