Glycosyl linkage analysis of fractionated cell walls from P.deltoides WT and PdGAUT4-KD lines.
Glycosyl linkage analysis of fractionated cell walls from P.deltoides WT and PdGAUT4-KD lines.
bio engineered↗
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Adenovirus infection induces HuR relocalization to facilitate virus replication
HuR is an RNA-binding protein of the embryonic lethal abnormal vision (ELAV) family, which binds to the AU-rich element (ARE) in the 3′-untranslated region (UTR) of certain mRNAs and is involved in the nucleo-cytoplasmic export and stabilization of ARE-mRNAs. The cytoplasmic relocalization of ARE-mRNAs with several proteins such as HuR and pp32 increases in cells transformed by the adenovirus oncogene product E4orf6. Additionally, these ARE-mRNAs were stabilized and acquired the potential to transform cells. Although, the relocalization of HuR and the stabilization of ARE-mRNAs are crucial for cell transformation, evidence regarding the relationship of HuR and ARE-mRNAs with adenovirus replication is lacking. In this report, we demonstrate that adenovirus infection induces the relocation of HuR to the cytoplasm of host cells. Analysis using the luciferase-ARE fusion gene and the tetracycline (tet)-off system revealed that the process of stabilizing ARE-mRNAs is activated in adenovirus-infected cells. Heat shock treatment or knockdown-mediated depletion of HuR reduced adenovirus production. Furthermore, expression of ARE-including viral IVa2 mRNA, decreased in HuR-depleted infected cells. These results indicate that HuR plays an important role in adenovirus replication, at least in part, by up-regulating IVa2 mRNA expression and that ARE-mRNA stabilization is required for both transformation and virus replication.
60 APPLIED LIFE SCIENCES↗
Comprehensive single-shot biophysical cytometry using simultaneous quantitative phase imaging and Brillouin spectroscopy
Abstract Single-cell analysis, or cytometry, is a ubiquitous tool in the biomedical sciences. Whereas most cytometers use fluorescent probes to ascertain the presence or absence of targeted molecules, biophysical parameters such as the cell density, refractive index, and viscosity are difficult to obtain. In this work, we combine two complementary techniques—quantitative phase imaging and Brillouin spectroscopy—into a label-free image cytometry platform capable of measuring more than a dozen biophysical properties of individual cells simultaneously. Using a geometric simplification linked to freshly plated cells, we can acquire the cellular diameter, volume, refractive index, mass density, non-aqueous mass, fluid volume, dry volume, the fractional water content of cells, both by mass and by volume, the Brillouin shift, Brillouin linewidth, longitudinal modulus, longitudinal viscosity, the loss modulus, and the loss tangent, all from a single acquisition, and with no assumptions of underlying parameters. Our methods are validated across three cell populations, including a control population of CHO-K1 cells, cells exposed to tubulin-disrupting nocodazole, and cells under hypoosmotic shock. Our system will unlock new avenues of research in biophysics, cell biology, and medicine.
Steelman, Zachary A.↗
Optimization methods and silicon solar cell numerical models
The goal of this project is the development of an optimization algorithm for use with a solar cell model. It is possible to simultaneously vary design variables such as impurity concentrations, front junction depth, back junctions depth, and cell thickness to maximize the predicted cell efficiency. An optimization algorithm has been developed and interfaced with the Solar Cell Analysis Program in 1 Dimension (SCAPID). SCAPID uses finite difference methods to solve the differential equations which, along with several relations from the physics of semiconductors, describe mathematically the operation of a solar cell. A major obstacle is that the numerical methods used in SCAPID require a significant amount of computer time, and during an optimization the model is called iteratively until the design variables converge to the value associated with the maximum efficiency. This problem has been alleviated by designing an optimization code specifically for use with numerically intensive simulations, to reduce the number of times the efficiency has to be calculated to achieve convergence to the optimal solution. Adapting SCAPID so that it could be called iteratively by the optimization code provided another means of reducing the cpu time required to complete an optimization. Instead of calculating the entire I-V curve, as is usually done in SCAPID, only the efficiency is calculated (maximum power voltage and current) and the solution from previous calculations is used to initiate the next solution.
Girardini, K.↗
Optimization methods and silicon solar cell numerical models
An optimization algorithm for use with numerical silicon solar cell models was developed. By coupling an optimization algorithm with a solar cell model, it is possible to simultaneously vary design variables such as impurity concentrations, front junction depth, back junction depth, and cell thickness to maximize the predicted cell efficiency. An optimization algorithm was developed and interfaced with the Solar Cell Analysis Program in 1 Dimension (SCAP1D). SCAP1D uses finite difference methods to solve the differential equations which, along with several relations from the physics of semiconductors, describe mathematically the performance of a solar cell. A major obstacle is that the numerical methods used in SCAP1D require a significant amount of computer time, and during an optimization the model is called iteratively until the design variables converge to the values associated with the maximum efficiency. This problem was alleviated by designing an optimization code specifically for use with numerically intensive simulations, to reduce the number of times the efficiency has to be calculated to achieve convergence to the optimal solution.
Girardini, K.↗
Sensitivity analysis for III–V/Si tandem solar cells: A theoretical study
Material and structural parameters may affect the efficiency of a tandem solar cell differently from the way they do in a single-junction solar cell. Here, we fabricated a III–V/Si four-terminal tandem solar cell and developed an opto-electronic model simulating this device. The optical properties were simulated with the transfer matrix method, while the electrical properties were simulated using the numerical device simulator PC1D. For this simulated tandem structure, we determined the parameters which have the largest potential impact on the device efficiency. A sensitivity analysis of the impact of these parameters on the device efficiency was also performed. Furthermore, to reduce the cost of the tandem solar cells, we identified the parameters that do not require tight control during the manufacturing process. The Si cell was simulated both as a single-junction cell and as the bottom cell of a tandem device. Lastly, we determined those device parameters that are more critical in a tandem configuration than in a single-junction configuration.
14 SOLAR ENERGY↗
Separation of cells from the rat anterior pituitary gland
Various techniques for separating the hormone-producing cell types from the rat anterior pituitary gland are examined. The purity, viability, and responsiveness of the separated cells depend on the physiological state of the donor, the tissue dissociation procedures, the staining technique used for identification of cell type, and the cell separation technique. The chamber-gradient setup and operation, the characteristics of the gradient materials, and the separated cell analysis of velocity sedimentation techniques (in particular Staput and Celsep) are described. Consideration is given to the various types of materials used in density gradient centrifugation and the operation of a gradient generating device. The use of electrophoresis to separate rat pituitary cells is discussed.
Hymer, Wesley C.↗
Development of Large-Format Lithium-Ion Cells with Silicon Anode and Low Flammable Electrolyte
NASA is developing safe, high energy and high capacity lithium-ion cell designs and batteries for future missions under NASAs Advanced Space Power System (ASPS) project. Advanced cell components, such as high specific capacity silicon anodes and low-flammable electrolytes have been developed for improving the cell specific energy and enhancing safety. To advance the technology readiness level, we have developed large-format flight-type hermetically sealed battery cells by incorporating high capacity silicon anodes, commercially available lithium nickel, cobalt, aluminum oxide (NCA) cathodes, and low-flammable electrolytes. In this report, we will present the performance results of these various battery cells. In addition, we will also discuss the post-test cell analysis results as well.
lithium-ion cell↗
Design and Demonstration of Three-Electrode Pouch Cells for Lithium-Ion Batteries
Simple three-electrode pouch cells which can be used in distinguishing the voltage and resistance in individual electrodes of lithium ion batteries have been designed. Baseline (1 mm-staggered alignment, cathode away from a reference electrode) and aligned electrodes to a reference electrode located outside of the anode and cathode were studied to see alignment effects on resistance analysis. Cells composed of A12 graphite anodes, LiNi 0.5 Mn 0.3 Co 0.2 O 2 (NMC 532 or NCM 523) cathodes, lithium foil references, microporous tri-layer membranes, and electrolytes, were cycled with cathode cutoff voltages between 3.0 V and 4.3 V for formation cycles or 4.6 V for C-rate performance testing. By applying a hybrid pulse power characterization (HPPC) technique to the cells, resistances of the baseline cells contributed by the anode and cathode were found to be different from those of the aligned cells, although overall resistances were close to ones from aligned cells. As a result, resistances obtained via electrochemical impedance spectroscopy (EIS) and 2D simulation were also compared with those obtained from HPPC.
25 ENERGY STORAGE↗
Characterization of viable bacteria from Siberian permafrost by 16S rDNA sequencing
Viable bacteria were found in permafrost core samples from the Kolyma-Indigirka lowland of northeast Siberia. The samples were obtained at different depths; the deepest was about 3 million years old. The average temperature of the permafrost is -10 degrees C. Twenty-nine bacterial isolates were characterized by 16S rDNA sequencing and phylogenetic analysis, cell morphology, Gram staining, endospore formation, and growth at 30 degrees C. The majority of the bacterial isolates were rod shaped and grew well at 30 degrees C; but two of them did not grow at or above 28 degrees C, and had optimum growth temperatures around 20 degrees C. Thirty percent of the isolates could form endospores. Phylogenetic analysis revealed that the isolates fell into four categories: high-GC Gram-positive bacteria, beta-proteobacteria, gamma-proteobacteria, and low-GC Gram-positive bacteria. Most high-GC Gram-positive bacteria and beta-proteobacteria, and all gamma-proteobacteria, came from samples with an estimated age of 1.8-3.0 million years (Olyor suite). Most low-GC Gram-positive bacteria came from samples with an estimated age of 5,000-8,000 years (Alas suite).
Non-NASA Center↗
Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs
We recently reported the presence of nicotinamide adenine dinucleotide (NAD)-capped RNAs in mammalian cells and a role for DXO and the Nudix hydrolase Nudt12 in decapping NAD-capped RNAs (deNADding) in cells. Analysis of 5'caps has revealed that in addition to NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). In the present study we systematically screened all mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity. We demonstrate that Nudt16 is a novel deNADding enzyme in mammalian cells. Additionally, we identified seven Nudix proteins—Nudt2, Nudt7, Nudt8, Nudt12, Nudt15, Nudt16 and Nudt19, to possess deCoAping activity in vitro. Moreover, our screening revealed that both mammalian Nudt2 and Nudt16 hydrolyze FAD-capped RNAs in vitro with Nudt16 regulating levels of FAD-capped RNAs in cells. All decapping activities identified hydrolyze the metabolite cap substrate within the diphosphate linkage. Crystal structure of human Nudt16 in complex with FAD at 2.7 Å resolution provide molecular insights into the binding and metal-coordinated hydrolysis of FAD by Nudt16. In summary, our study identifies novel cellular deNADding and deFADding enzymes and establishes a foundation for the selective functionality of the Nudix decapping enzymes on non-canonical metabolite caps.
59 BASIC BIOLOGICAL SCIENCES↗
Optimization of LIBS Acquisition Parameters for Chemical Analysis on HLW Liquid Solution - 18291
Research programs are currently underway in the Joint CEA-AREVA Vitrification Laboratory (LCV) to develop and optimize Laser Induced Breakdown Spectroscopy (LIBS) for nuclear waste streams analyses. The laboratory has full scale prototypes with the advantage of working on simulated inactive solutions of fission products. LIBS is an elemental chemical analysis technology that uses a short laser pulse to create a micro-plasma on the sample surface. This analytical technique offers many advantages compared to other techniques. It includes a sample preparation-free measurement and an extremely fast measurement time, from a few seconds to a few minutes. This paper presents the LIBS technique available in the laboratory. The first LIBS analyzes results of liquid samples from the off-gas treatment unit integrated on the full scale vitrification process are also presented and discussed. These complex solutions contain suspended particles and up to 30 chemical elements. A vision of an online LIBS analysis cell is also proposed with the development and associated research steps. (authors)
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Long cycle life rechargeable lithium batteries
Cycle life and safety of delta-LiAl/TiS2 cells were evaluated using laboratory and AA-size cells. Analysis of the alloys (which contained 60, 70, 80, or 85 wt-pct. lithium and are designated 60 LiAl etc.) showed them to contain a mixture of elemental Li and Al4Li9. Cycling efficiencies correlated with the amount of free lithium in the anode. Using an electrolyte with the composition 48 v/o THF:48 v/o 2-MeTHF:4 v/o 2-MeF/LiAsF6(1.5M), a 70 LiAl/TiS2 laboratory cell yielded a cycling efficiency of 96.4 pct. when cycled at a 100 pct. discharge depth which compares well with Li anode cycling efficiencies of 96 to 97.5 pct. obtained previously in this electrolyte. The highest cycling efficiency of any delta-LiAl/TiS2 laboratory cell was 96.7 pct. when the 60 LiAl alloy was used with the 35 v/o PC:35 v/o EC:30 v/o triglyme/LiAsF6(1.0M) electrolyte. The 70 LiAl alloy was selected for further testing in AA cells since it was malleable for the fabrication of spirally wound electrodes, and its overall cycling performance was sufficiently good. AA-size 70 LiAl/TiS2 cells appear to have capacity/rate properties similar to those for identical Li/TiS2 cells. The use of the delta-LiAl alloy anodes does not appear to offer any safety advantage when cycled cells are shorted or heated.
Pasquariello, D. M.↗
LIBS Measurement in Vitrification of HLW Process: Towards a Development of Online Chemical Analyses - 18290
Research programs are currently underway in the Joint CEA-AREVA Vitrification Laboratory (LCV) to develop and optimize Laser Induced Breakdown Spectroscopy (LIBS) for nuclear waste streams analyses. The laboratory has full scale prototypes with the advantage of working on simulated inactive solutions of fission products. LIBS is an elemental chemical analysis technology that uses a short laser pulse to create a micro-plasma on the sample surface. This analytical technique offers many advantages compared to other techniques. It includes a sample preparation-free measurement and an extremely fast measurement time, from a few seconds to a few minutes. This paper presents the LIBS technique available in the laboratory. The first LIBS analyzes results of liquid samples from the off-gas treatment unit integrated on the full scale vitrification process are also presented and discussed. These complex solutions contain suspended particles and up to 30 chemical elements. A vision of an online LIBS analysis cell is also proposed with the development and associated research steps. (authors)
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Using flow cytometry and multistage machine learning to discover label-free signatures of algal lipid accumulation
Most applications of flow cytometry or cell sorting rely on the conjugation of fluorescent dyes to specific biomarkers. However, labeled biomarkers are not always available, they can be costly, and they may disrupt natural cell behavior. Label-free quantification based upon machine learning approaches could help correct these issues, but label replacement strategies can be very difficult to discover when applied labels or other modifications in measurements inadvertently modify intrinsic cell properties. Here we demonstrate a new, but simple approach based upon feature selection and linear regression analyses to integrate statistical information collected from both labeled and unlabeled cell populations and to identify models for accurate label-free single-cell quantification. We verify the method’s accuracy to predict lipid content in algal cells (Picochlorum soloecismus) during a nitrogen starvation and lipid accumulation time course. Our general approach is expected to improve label-free single-cell analysis for other organisms or pathways, where biomarkers are inconvenient, expensive, or disruptive to downstream cellular processes.
42 ENGINEERING↗
Evaluating Linear Ion Trap for MS3-Based Multiplexed Single-Cell Proteomics
There is a growing demand to develop high-throughput and high-sensitivity mass spectrometry methods for single-cell proteomics. The commonly used isobaric labeling-based multiplexed single-cell proteomics approach suffers from distorted protein quantification due to co-isolated interfering ions during MS/MS fragmentation, also known as ratio compression. We reasoned that the use of MS3-based quantification could mitigate ratio compression and provide better quantification. However, previous studies indicated reduced proteome coverages in the MS3 method, likely due to long duty cycle time and ion losses during multilevel ion selection and fragmentation. Here, in this paper, we described an improved MS acquisition method for MS3-based single-cell proteomics by employing a linear ion trap to measure reporter ions. We demonstrated that linear ion trap can increase the proteome coverages for single-cell-level peptides with even higher gain obtained via the MS3 method. The optimized real-time search MS3 method was further applied to study the immune activation of single macrophages. Among a total of 126 single cells studied, over 1200 and 1000 proteins were quantifiable when at least 50 and 75% nonmissing data were required, respectively. Our evaluation also revealed several limitations of the low-resolution ion trap detector for multiplexed single-cell proteomics and suggested experimental solutions to minimize their impacts on single-cell analysis.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Enabling Single Cell Research in Hollow Hydrogel Microparticles
Studying biology at the single cell level enables novel discoveries through ultra-high throughput identification and isolation of rare cells and interesting subpopulations. Encapsulation of single cells in hollow hydrogel microparticles, or PicoShells, enables easy visualization, manipulation, and assaying of single cells. The PicoShell’s porous hydrogel shell allows diffusion of nutrients and wastes into and out of the hollow liquid core, allowing uninhibited cell growth. The porous shell also allows diffusion of assay reagents, enabling solution changes, and multi-step assays. Finally, single cells and their progeny can be tracked through time, for example to measure single cell growth rates. However, PicoShells are fabricated using microfluidic techniques, which require specialized expertise, equipment, and facilities. This limits PicoShell’s widespread utility for single cell biology. For Saccharomyces cerevisiae and other desiccation-tolerant microbes, desiccating PicoShells containing cells of interest offers a solution, enabling those without microfluidic capabilities to obtain dried, shelf-stable PicoShells containing their cells of interest from a specialized microfluidics facility. Researchers could then rehydrate the PicoShells and perform their single cell assays, bypassing the microfluidic steps. Desiccated PicoShells could also be flown in space, where desiccation is already a common practice for microbes (i.e. BioSentinel and BioNutrients), bringing single cell analysis capabilities to space. In this work, we develop a method to desiccate PicoShells containing S. cerevisiae while maintaining characteristics similar to fresh, non-desiccated PicoShells. We show good microparticle morphology and hydrogel pore size as well as high yeast viability in line with previous studies. We also demonstrate sorting of a fast-growing yeast population using size-based filtration, as S. cerevisiae in PicoShells are able to physically stretch the microparticle as they grow, increasing the PicoShell diameter. These efforts contribute to the feasibility of leveraging microparticle PicoShells for single cell space biology research on Earth and in space.
Simon Ng↗
Developmentally regulated GTP-binding protein 2 depletion leads to mitochondrial dysfunction through downregulation of dynamin-related protein 1
Mitochondrial dynamics, including constant fusion and fission, play critical roles in maintaining mitochondrial morphology and function. Here, we report that developmentally regulated GTP-binding protein 2 (DRG2) regulates mitochondrial morphology by modulating the expression of the mitochondrial fission gene dynamin-related protein 1 (Drp1). shRNA-mediated silencing of DRG2 induced mitochondrial swelling, whereas expression of an shRNA-resistant version of DRG2 decreased mitochondrial swelling in DRG2-depleted cells. Analysis of the expression levels of genes involved in mitochondrial fusion and fission revealed that DRG2 depletion significantly decreased the level of Drp1. Overexpression of Drp1 rescued the defect in mitochondrial morphology induced by DRG2 depletion. DRG2 depletion reduced the mitochondrial membrane potential, oxygen consumption rate (OCR), and amount of mitochondrial DNA (mtDNA), whereas it increased reactive oxygen species (ROS) production and apoptosis. Taken together, our data demonstrate that DRG2 acts as a regulator of mitochondrial fission by controlling the expression of Drp1. - Highlights: • DRG2 depletion increased mitochondrial swelling. • DRG2 depletion inhibited the expression of Drp1. • Overexpression of DRG2 or Drp1 rescued mitochondrial shape in DRG2 depleted cells. • DRG2 depletion induced mitochondrial dysfunction.
60 APPLIED LIFE SCIENCES↗