Population-Level Coordination of Pigment Response in Individual Cyanobacterial Cells Under Altered Nitrogen Levels

Cyanobacterial phycobilisome (PBS) pigment-protein complexes harvest light and transfer the energy to reaction centers. Previous ensemble studies have shown that cyanobacteria respond to changes in nutrient availability by modifying the structure of PBS complexes, but this process has not been visualized for individual pigments at the single-cell level due to spectral overlap. We characterized the response of four key photosynthetic pigments to nitrogen depletion and repletion at the subcellular level in individual, live Synechocystis sp. PCC 6803 cells using hyperspectral confocal fluorescence microscopy and multivariate image analysis. Our results revealed that PBS degradation and re-synthesis comprise a rapid response to nitrogen fluctuations, with coordinated populations of cells undergoing pigment modifications. Chlorophyll fluorescence originating from photosystem I and II decreased during nitrogen starvation, but no alteration in subcellular chlorophyll localization was found. We observed differential rod and core pigment responses to nitrogen deprivation, suggesting that PBS complexes undergo a stepwise degradation process

Intelligent Front-End Sample Preparation Tool Using Acoustic Streaming

We have successfully developed a nucleic acid extraction system based on a microacoustic lysis array coupled to an integrated nucleic acid extraction system all on a single cartridge. The microacoustic lysing array is based on 36{sup o} Y cut lithium niobate, which couples bulk acoustic waves (BAW) into the microchannels. The microchannels were fabricated using Mylar laminates and fused silica to form acoustic-fluidic interface cartridges. The transducer array consists of four active elements directed for cell lysis and one optional BAW element for mixing on the cartridge. The lysis system was modeled using one dimensional (1D) transmission line and two dimensional (2D) FEM models. For input powers required to lyse cells, the flow rate dictated the temperature change across the lysing region. From the computational models, a flow rate of 10 {micro}L/min produced a temperature rise of 23.2 C and only 6.7 C when flowing at 60 {micro}L/min. The measured temperature changes were 5 C less than the model. The computational models also permitted optimization of the acoustic coupling to the microchannel region and revealed the potential impact of thermal effects if not controlled. Using E. coli, we achieved a lysing efficacy of 49.9 {+-} 29.92 % based on a cell viability assay with a 757.2 % increase in ATP release within 20 seconds of acoustic exposure. A bench-top lysing system required 15-20 minutes operating up to 58 Watts to achieve the same level of cell lysis. We demonstrate that active mixing on the cartridge was critical to maximize binding and release of nucleic acid to the magnetic beads. Using a sol-gel silica bead matrix filled microchannel the extraction efficacy was 40%. The cartridge based magnetic bead system had an extraction efficiency of 19.2%. For an electric field based method that used Nafion films, a nucleic acid extraction efficiency of 66.3 % was achieved at 6 volts DC. For the flow rates we tested (10-50 {micro}L/min), the nucleic acid extraction time was 5-10 minutes for a volume of 50 {micro}L. Moreover, a unique feature of this technology is the ability to replace the cartridges for subsequent nucleic acid extractions

First-principles flocculation as the key to low energy algal biofuels processing.

This document summarizes a three year Laboratory Directed Research and Development (LDRD) program effort to improve our understanding of algal flocculation with a key to overcoming harvesting as a techno-economic barrier to algal biofuels. Flocculation is limited by the concentrations of deprotonated functional groups on the algal cell surface. Favorable charged groups on the surfaces of precipitates that form in solution and the interaction of both with ions in the water can favor flocculation. Measurements of algae cell-surface functional groups are reported and related to the quantity of flocculant required. Deprotonation of surface groups and complexation of surface groups with ions from the growth media are predicted in the context of PHREEQC. The understanding of surface chemistry is linked to boundaries of effective flocculation. We show that the phase-space of effective flocculation can be expanded by more frequent alga-alga or floc-floc collisions. The collision frequency is dependent on the floc structure, described in the fractal sense. The fractal floc structure is shown to depend on the rate of shear mixing. We present both experimental measurements of the floc structure variation and simulations using LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). Both show a densification of the flocs with increasing shear. The LAMMPS results show a combined change in the fractal dimension and a change in the coordination number leading to stronger flocs

Efficient breakdown of lignocellulose using mixed-microbe populations for bioethanol production.

This report documents progress in discovering new catalytic technologies that will support the development of advanced biofuels. The global shift from petroleum-based fuels to advanced biofuels will require transformational breakthroughs in biomass deconstruction technologies, because current methods are neither cost effective nor sufficiently efficient or robust for scaleable production. Discovery and characterization of lignocellulolytic enzyme systems adapted to extreme environments will accelerate progress. Obvious extreme environments to mine for novel lignocellulolytic deconstruction technologies include aridland ecosystems (ALEs), such as those of the Sevilleta Long Term Ecological Research (LTER) site in central New Mexico (NM). ALEs represent at least 40% of the terrestrial biosphere and are classic extreme environments, with low nutrient availability, high ultraviolet radiation flux, limited and erratic precipitation, and extreme variation in temperatures. ALEs are functionally distinct from temperate environments in many respects; one salient distinction is that ALEs do not accumulate soil organic carbon (SOC), in marked contrast to temperate settings, which typically have large pools of SOC. Low productivity ALEs do not accumulate carbon (C) primarily because of extraordinarily efficient extracellular enzyme activities (EEAs) that are derived from underlying communities of diverse, largely uncharacterized microbes. Such efficient enzyme activities presumably reflect adaptation to this low productivity ecosystem, with the result that all available organic nutrients are assimilated rapidly. These communities are dominated by ascomycetous fungi, both in terms of abundance and contribution to ecosystem-scale metabolic processes, such as nitrogen and C cycling. To deliver novel, robust, efficient lignocellulolytic enzyme systems that will drive transformational advances in biomass deconstruction, we have: (1) secured an award through the Department of Energy (DoE) Joint Genome Institute (JGI) to perform metatranscriptomic functional profiling of eukaryotic microbial communities of blue grama grass (Bouteloua gracilis) rhizosphere (RHZ) soils and (2) isolated and provided initial genotypic and phenotypic characterization data for thermophilic fungi. Our preliminary results show that many strains in our collection of thermophilic fungi frequently outperform industry standards in key assays; we also demonstrated that this collection is taxonomically diverse and phenotypically compelling. The studies summarized here are being performed in collaboration with University of New Mexico and are based at the Sevilleta LTER research site

Nanosilica formation at lipid membranes induced by the parent sequence of a silaffin peptide

Diatoms are unicellular eukaryotic algae found in fresh and marine water. Each cell is surrounded by an outer shell called a frustule that is composed of highly structured amorphous silica. Diatoms are able to transform silicic acid into these sturdy intricate structures at ambient temperatures and pressures, whereas the chemical synthesis of silicabased materials typically requires extremes of temperature and pH. Cationic polypeptides, termed silica affinity proteins (or silaffins), recently identified from dissolved frustules of specific species of diatoms, are clearly involved and have been shown to initiate the formation of silica in solution. The relationship between the local environment of catalytic sites on these peptides, which can be influenced by the amino acid sequence and the extent of aggregation, and the structure of the silica is not understood. Moreover, the activity of these peptides in promoting silicification at lipid membranes has not yet been clarified. In this work, we developed a model system to address some of these questions. We studied peptide adsorption to Langmuir monolayers and subsequent silicification using X-ray reflectivity and grazing incidence X-ray diffraction. The results demonstrate the lipid affinity of the parent sequence of a silaffin peptide and show that the membrane-bound peptide promotes the formation of an interfacial nanoscale layer of amorphous silica at the lipid-water interface

Rapid Nucleic Acid Extraction and Purification Using a Miniature Ultrasonic Technique

Miniature ultrasonic lysis for biological sample preparation is a promising technique for efficient and rapid extraction of nucleic acids and proteins from a wide variety of biological sources. Acoustic methods achieve rapid, unbiased, and efficacious disruption of cellular membranes while avoiding the use of harsh chemicals and enzymes, which interfere with detection assays. In this work, a miniature acoustic nucleic acid extraction system is presented. Using a miniature bulk acoustic wave (BAW) transducer array based on 36° Y-cut lithium niobate, acoustic waves were coupled into disposable laminate-based microfluidic cartridges. To verify the lysing effectiveness, the amount of liberated ATP and the cell viability were measured and compared to untreated samples. The relationship between input power, energy dose, flow-rate, and lysing efficiency were determined. DNA was purified on-chip using three approaches implemented in the cartridges: a silica-based sol-gel silica-bead filled microchannel, nucleic acid binding magnetic beads, and Nafion-coated electrodes. Using E. coli, the lysing dose defined as ATP released per joule was 2.2× greater, releasing 6.1× more ATP for the miniature BAW array compared to a bench-top acoustic lysis system. An electric field-based nucleic acid purification approach using Nafion films yielded an extraction efficiency of 69.2% in 10 min for 50 µL samples

Thermally Stable Nanoporous Palladium Alloy Powders by Hydrogen Reduction in Surfactant Templates

Nanometer-scale pores in metals used for hydrogen storage are expected to facilitate mass transport in the materials – in particular, the release of helium decay products when tritium is stored. Scalable methods for production of bulk powders of nanoporous metals typically use chemical reducing agents that can leave impurities in the product. Hydrogen gas can be used as the reducing agent in such procedures. This not only improves purity, but also expands the range of accessible pore and particle sizes and particle compositions. Powders of nanoporous palladium and its alloys with rhodium are synthesized by chemical reduction of chloride complexes by hydrogen in a concentrated nonionic aqueous surfactant at room temperature. Particle diameters are typically several micrometers and each particle is perforated by 2–3 nm pores, as determined by electron microscopy and nitrogen porosimetry. Alloys show major improvement in thermal stability and pore regularity compared to pure palladium. In addition to facilitating heavier isotope storage, the high surface areas of these materials may allow development of metal hydride batteries with high power density

Neutron reflectometry and QCM-D study of the interaction of cellulases with films of amorphous cellulose

Improving the efficiency of enzymatic hydrolysis of cellulose is one of the key technological hurdles to reduce the cost of producing ethanol and other transportation fuels from lignocellulosic material. A better understanding of how soluble enzymes interact with insoluble cellulose will aid in the design of more efficient enzyme systems. We report a study involving neutron reflectometry (NR) and quartz crystal microbalance with dissipation monitoring (QCM-D) of the interaction of a fungal enzyme extract (T. viride) and an endoglucanse from A. niger with amorphous cellulose films. The use of amorphous cellulose is motivated by that the fact that several biomass pretreatments currently under investigation disrupt the native crystalline structure of cellulose and increase the amorphous content. NR reveals the profile of water through the film at nanometer resolution and is highly sensitive to interfacial roughness, whereas QCM-D provides changes in mass and film stiffness. NR can be performed using either HO- or DO-based aqueous reservoirs. NR measurement of swelling of a cellulose film in DO and in H O revealed that D/H exchange on the cellulose chains must be taken into account when a DO-based reservoir is used. The results also show that cellulose films swell slightly more in DO than in H O. Regarding enzymatic digestion, at 20 °C in HO buffer the T. viride cocktail rapidly digested the entire film, initially roughening the surface, followed by penetration and activity throughout the bulk of the film. In contrast, over the same time period, the endoglucanase was active mainly at the surface of the film and did not increase the surface roughness