Quiet Wing

EMSL’s Quiet Wing supports a wide range of research areas, including climate, biological, environmental and energy systems, of importance to the Department of Energy. It is among the most advanced quiet laboratories in the world for high-resolution imaging capabilities.

The Quiet Wing is a unique research environment housing a suite of ultrasensitive microscopy and scanning instruments. It was designed to help accelerate critical science by allowing state-of-the-art ultrasensitive microscopy equipment to operate at optimal resolution. A temperature-controlled facility, the wing’s design eliminates or reduces to a minimum the vibrations, acoustics and electromagnetic noise that can interfere with the resolution of ultrasensitive scientific instrumentation.

The 9,500-square-foot facility features eight quiet laboratory cells and a sample preparation area. The wing currently houses seven microscopy instruments and has room for one more. These microscopes are just a few of the extensive suite of microscopy instruments at EMSL available for scientific inquiry.

EMSL's microscopy capabilities, including those in the Quiet Wing, are available to the scientific community at typically no cost for openly published research. Scientists gain access to instruments and collaborate with onsite microscopy experts through a peer-reviewed proposal process. Learn more about becoming an EMSL user.

Learn more about each instrument and the science it advances on EMSL's YouTube channel and watch the video below on the Quiet Wing.

EMSL's ultra-high vacuum, low-temperature scanning probe microscope instrument, or UHV LT SPM, is the preeminent system dedicated to surface...
Custodian(s): Igor Lyubinetsky
Type of Instrument:
Microscope
EMSL's ultra-high vacuum, variable-temperature scanning probe microscope system, or UHV VT SPM, is a state-of-the-art surface science tool...
Custodian(s): Igor Lyubinetsky
EMSL's environmental transmission electron microscope (ETEM) is a state-of-the-art, Cs-corrected field emission gun (FEG) scanning transmission...
Custodian(s): Libor Kovarik
Helium ion microscope The Helium Ion Microscope promises to advance biological, geochemical, biogeochemical, and surface/interface studies using its...
The JEOL JEM-3000SFF was designed for high-resolution cryogenic transmission electron microscopy (cryo-EM) of biological samples and expands EMSL/...
Posted: August 03, 2014
The Science Nanocatalysts consisting of two metals can offer superior performance compared with those made up of only one metal, so they are widely...
Posted: April 15, 2014
Scientists at EMSL and Pacific Northwest National Laboratory are studying energy storage devices to make them last longer and be able to be...
Posted: March 12, 2014
The Science Lithium-sulfur batteries are promising options for electric vehicles and for storing renewable energy because they can store a lot of...
Posted: March 05, 2014
Lithium-ion batteries fade because the materials lose their structure in response to charging and discharging. This fading relates to electron-rich...
Posted: December 26, 2013
Researchers have developed a way to microscopically view battery electrodes while they are bathed in wet electrolytes, mimicking realistic...

EMSL’s Quiet Wing supports a wide range of research areas, including climate, biological, environmental and energy systems, of importance to the Department of Energy. It is among the most advanced quiet laboratories in the world for high-resolution imaging capabilities.

The Quiet Wing is a unique research environment housing a suite of ultrasensitive microscopy and scanning instruments. It was designed to help accelerate critical science by allowing state-of-the-art ultrasensitive microscopy equipment to operate at optimal resolution. A temperature-controlled facility, the wing’s design eliminates or reduces to a minimum the vibrations, acoustics and electromagnetic noise that can interfere with the resolution of ultrasensitive scientific instrumentation.

The 9,500-square-foot facility features eight quiet laboratory cells and a sample preparation area. The wing currently houses seven microscopy instruments and has room for one more. These microscopes are just a few of the extensive suite of microscopy instruments at EMSL available for scientific inquiry.

EMSL's microscopy capabilities, including those in the Quiet Wing, are available to the scientific community at typically no cost for openly published research. Scientists gain access to instruments and collaborate with onsite microscopy experts through a peer-reviewed proposal process. Learn more about becoming an EMSL user.

Learn more about each instrument and the science it advances on EMSL's YouTube channel and watch the video below on the Quiet Wing.

Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies .

Abstract: 

Characterization of geomicrobial protein expression provides information necessary to better understand the unique biological pathways that occur within soil microbial communities and the role they play in regulating atmospheric CO2 levels and the Earth’s climate. A significant challenge in studying soil microbial proteins is their initial dissociation from the complex mixture of particles found in natural soil. Due to bias of the most robust cells, the removal of intact bacterial cells limits the characterization of the complete representation of a microbial community. However, in-situ lysis of bacterial cells leads to the expulsion of proteins to the soil surface, which can lead to potentially high levels of adsorption due to the physicochemical properties of both the protein and the soil. We investigated various compounds for their ability to block protein adsorption soil sites prior to in-situ lysis of bacterial cells, as well as their compatibility with both tryptic digestion and mass spectrometric analysis. The treatments were tested by adding lysed Escherichia coli proteins to representative treated and untreated soil samples. The results show that it is possible to significantly increase protein identifications through blockage of binding sites on a variety of soil textures; use of an optimized desorption buffer further increases the number of identifications.

Citation: 
Nicora CD, BJ Anderson, SJ Callister, AD Norbeck, SO Purvine, JK Jansson, OU Mason, M David, DD Jurelevicius, RD Smith, and MS Lipton.2013."Amino acid treatment enhances protein recovery from sediment and soils for metaproteomic studies ."Proteomics 13(18-19):2776-2785. doi:10.1002/pmic.201300003
Authors: 
CD Nicora
BJ Anderson
SJ Callister
AD Norbeck
SO Purvine
JK Jansson
OU Mason
M David
DD Jurelevicius
RD Smith
MS Lipton
Facility: 
Instruments: 
Volume: 
13
Pages: 
2776-2785
Publication year: 
2013

Proteome Analyses of Strains ATCC 51142 and PCC 7822 of the Diazotrophic Cyanobacterium Cyanothece sp under Culture Conditions

Abstract: 

Cultures of the cyanobacterial genus Cyanothece have been shown to produce high levels of biohydrogen. These strains are diazotrophic and undergo pronounced diurnal cycles when grown under N2-fixing conditions in light-dark cycles. We seek to better understand the way in which proteins respond to these diurnal changes and we performed quantitative proteome analysis of Cyanothece ATCC 51142 and PCC 7822 grown under 8 different nutritional conditions. Nitrogenase expression was limited to N2-fixing conditions, and in the absence of glycerol, nitrogenase gene expression was linked to the dark period. However, glycerol induced expression of nitrogenase during part of the light period, together with cytochrome c oxidase (Cox), glycogen phosphorylase (Glp), and glycolytic and pentose-phosphate pathway (PPP) enzymes. This indicated that nitrogenase expression in the light was facilitated via higher respiration and glycogen breakdown. Key enzymes of the Calvin cycle were inhibited in Cyanothece ATCC 51142 in the presence of glycerol under H2 producing conditions, suggesting a competition between these sources of carbon. However, in Cyanothece PCC 7822, the Calvin cycle still played a role in cofactor recycling during H2 production. Our data comprise the first comprehensive profiling of proteome changes in Cyanothece PCC 7822, and allows an in-depth comparative analysis of major physiological and biochemical processes that influence H2-production in both the strains. Our results revealed many previously uncharacterized proteins that may play a role in nitrogenase activity and in other metabolic pathways and may provide suitable targets for genetic manipulation that would lead to improvement of large scale H2 production.

Citation: 
Aryal UK, SJ Callister, S Mishra, X Zhang, JI Shutthanandan, TE Angel, AK Shukla, ME Monroe, RJ Moore, DW Koppenaal, RD Smith, and L Sherman.2013."Proteome Analyses of Strains ATCC 51142 and PCC 7822 of the Diazotrophic Cyanobacterium Cyanothece sp under Culture Conditions Resulting in Enhanced H-2 Production."Applied and Environmental Microbiology 79(4):1070-1077. doi:10.1128/AEM.02864-12
Authors: 
UK Aryal
SJ Callister
S Mishra
X Zhang
JI Shutthanan
TE Angel
AK Shukla
ME Monroe
RJ Moore
DW Koppenaal
RD Smith
L Sherman
Facility: 
Instruments: 
Volume: 
79
Issue: 
4
Pages: 
1070-1077
Publication year: 
2013

Aerosolized ZnO nanoparticles induce toxicity in alveolar type II epithelial cells at the air-liquid interface.

Abstract: 

The majority of in vitro studies characterizing the impact of engineered nanoparticles (NPs) on cells that line the respiratory tract were conducted in cells exposed to NPs in suspension. This approach introduces processes that are unlikely to occur during inhaled NP exposures in vivo, such as the shedding of toxic doses of dissolved ions. ZnO NPs are used extensively and pose significant sources for human exposure. Exposures to airborne ZnO NPs can induce adverse effects, but the relevance of the dissolved Zn2+ to the observed effects in vivo is still unclear. Our goal was to mimic in vivo exposures to airborne NPs and decipher the contribution of the intact NP from the contribution of the dissolved ions to airborne ZnO NP toxicity. We established the exposure of alveolar type II epithelial cells to aerosolized NPs at the air-liquid interface (ALI), and compared the impact of aerosolized ZnO NPs and NPs in suspension at the same cellular doses, measured as the number of particles per cell. By evaluating membrane integrity and cell viability 6 and 24 hours post exposure we found that aerosolized NPs induced toxicity at the ALI at doses that were in the same order of magnitude as doses required to induce toxicity in submersed cultures. In addition, distinct patterns of oxidative stress were observed in the two exposure systems. These observations unravel the ability of airborne ZnO NPs to induce toxicity without the contribution of dissolved Zn2+ and suggest distinct mechanisms at the ALI and in submersed cultures.

Citation: 
Xie Y, NG Williams, A Tolic, WB Chrisler, JG Teeguarden, BL Maddux, JG Pounds, A Laskin, and G Orr.2012."Aerosolized ZnO nanoparticles induce toxicity in alveolar type II epithelial cells at the air-liquid interface."Toxicological Sciences 125(2):450-461. doi:10.1093/toxsci/kfr251
Authors: 
Y Xie
NG Williams
A Tolic
WB Chrisler
JG Teeguarden
BL Maddux
JG Pounds
A Laskin
G Orr
Facility: 
Volume: 
125
Issue: 
2
Pages: 
450-461
Publication year: 
2012

ISDD: A Computational Model of Particle Sedimentation, Diffusion and Target Cell Dosimetry for In Vitro Toxicity Studies.

Abstract: 

Background: The difficulty of directly measuring cellular dose is a significant obstacle to application of target tissue dosimetry for nanoparticle and microparticle toxicity assessment. As a consequence, the target tissue paradigm for dosimetry and hazard assessment of nanoparticles has largely been ignored in favor of using metrics of exposure (e.g. μg particle/mL culture medium, particle surface area/mL, particle number/mL). We have developed a computational model of solution particokinetics (sedimentation, diffusion) and dosimetry for non-interacting spherical particles and their agglomerates in monolayer cell culture systems. Particle transport to cells is calculated by simultaneous solution of Stokes Law (sedimentation) and the Stokes-Einstein equation (diffusion). Results: The In vitro Sedimentation, Diffusion and Dosimetry model (ISDD) was tested against measured transport rates or cellular doses for multiple sizes of polystyrene spheres (20-1100 nm), 35 nm amorphous silica, and large agglomerates of 30 nm iron oxide particles. Overall, without adjusting any parameters, model predicted doses were in close agreement with the experimental data, differing from as little as 5% to as much as three-fold, but in most cases approximately two-fold, within the limits of the accuracy of the measurement systems. Applying the model, we generalize the effects of particle size, particle density, agglomeration state and agglomerate characteristics on target cell dosimetry in vitro. Conclusions: Our results confirm our hypothesis that the dose-rates for all particles are not equal, but can vary significantly, in direct contrast to the assumption of dose-equivalency implicit in the use of mass-based media concentrations as metrics of exposure for dose-response assessment. The difference between equivalent nominal media concentration exposures on a μg/mL basis and target cell doses on a particle surface area or number basis can be as high as three to six orders of magnitude. As a consequence, in vitro hazard assessments utilizing mass-based exposure metrics have inherently high errors where particle number or surface areas target cells doses are believed to drive response. The gold standard for particle dosimetry for in vitro nanotoxicology studies should be direct experimental measurement of the cellular content of the studied particle. However, where such measurements are impractical, unfeasible, and before such measurements become common, particle dosimetry models such as ISDD provide a valuable, immediately useful alternative, and eventually an adjunct to such measurements.

Citation: 
Hinderliter PM, KR Minard, G Orr, WB Chrisler, BD Thrall, JG Pounds, and JG Teeguarden.2010."ISDD: A Computational Model of Particle Sedimentation, Diffusion and Target Cell Dosimetry for In Vitro Toxicity Studies."Particle and Fibre Toxicology 7(November):Article No. 36. doi:10.1186/1743-8977-7-36
Authors: 
PM Hinderliter
KR Minard
G Orr
WB Chrisler
BD Thrall
JG Pounds
JG Teeguarden
Facility: 
Publication year: 
2010

Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size

Abstract: 

In biofluids (e.g., blood plasma) nanoparticles are readily embedded in layers of proteins that can affect their biological activity and biocompatibility. Herein, we report a study on the interactions between human plasma proteins and nanoparticles with a controlled systematic variation of properties using stable isotope labeling and liquid chromatography-mass spectrometry (LC-MS) based quantitative proteomics. Novel protocol has been developed to simplify the isolation of nanoparticle bound proteins and improve the reproducibility. Plasma proteins associated with polystyrene nanoparticles with three different surface chemistries and two sizes as well as for four different exposure times (for a total of 24 different samples) were identified and quantified by LC-MS analysis. Quantitative comparison of relative protein abundances were achieved by spiking an 18 O-labeled "universal reference" into each individually processed unlabeled sample as an internal standard, enabling simultaneous application of both label-free and isotopic labeling quantitation across the sample set. Clustering analysis of the quantitative proteomics data resulted in distinctive pattern that classifies the nanoparticles based on their surface properties and size. In addition, data on the temporal study indicated that the stable protein "corona" that was isolated for the quantitative analysis appeared to be formed in less than 5 minutes. The comprehensive results obtained herein using quantitative proteomics have potential implications towards predicting nanoparticle biocompatibility.

Citation: 
Zhang H, KE Burnum, ML Luna, BO Petritis, JS Kim, W Qian, RJ Moore, A Heredia-Langner, BJM Webb-Robertson, BD Thrall, DG Camp, II, RD Smith, JG Pounds, and T Liu.2011."Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size."Proteomics 11(23):4569-4577. doi:10.1002/pmic.201100037
Authors: 
H Zhang
KE Burnum
ML Luna
BO Petritis
JS Kim
W Qian
RJ Moore
A Heredia-Langner
BJM Webb-Robertson
BD Thrall
DG Camp
II
RD Smith
JG Pounds
T Liu
Facility: 
Volume: 
11
Issue: 
23
Pages: 
4569-4577
Publication year: 
2011

Cellular Recognition and Trafficking of Amorphous Silica Nanoparticles by Macrophage Scavenger Receptor A.

Abstract: 

The internalization of engineered nanoparticles (ENPs) into cells is known to involve active transport mechanisms, yet the precise biological molecules involved are poorly understood. We demonstrate that the uptake of amorphous silica ENPs (92 nm) by macrophage cells is strongly inhibited by silencing expression of scavenger receptor A (SR-A). In addition, ENP uptake is augmented by introducing SR-A expression into human cells that are normally non-phagocytic. Confocal fluorescent microscopy analyses show that the majority of single or small clusters of silica ENPs co-localize intracellularly with SR-A and are internalized through a pathway characteristic of clathrin-dependent endocytosis. In contrast, larger silica NP agglomerates (>500 nm) are poorly co-localized with the receptor, suggesting independent trafficking or internalization pathways are involved. SR-A silencing also caused decreased cellular secretion of pro-inflammatory cytokines in response to silica ENPs. As SR-A is expressed in macrophages throughout the reticulo-endothelial system, this pathway is likely an important determinant of the biodistribution of, and cellular response to ENPs.

Citation: 
Orr G, WB Chrisler, KJ Cassens, R Tan, BJ Tarasevich, LM Markillie, RC Zangar, and BD Thrall.2011."Cellular Recognition and Trafficking of Amorphous Silica Nanoparticles by Macrophage Scavenger Receptor A."Nanotoxicology 5(3):296-311. doi:10.3109/17435390.2010.513836
Authors: 
G Orr
WB Chrisler
KJ Cassens
R Tan
BJ Tarasevich
LM Markillie
RC Zangar
BD Thrall
Facility: 
Volume: 
5
Issue: 
3
Pages: 
296-311
Publication year: 
2011

7 Å Resolution in Protein 2-Dimentional-Crystal X-Ray Diffraction at Linac Coherent Light Source.

Abstract: 

Membrane proteins arranged as two-dimensional (2D) crystals in the lipid en- vironment provide close-to-physiological structural information, which is essential for understanding the molecular mechanisms of protein function. X-ray diffraction from individual 2D crystals did not represent a suitable investigation tool because of radiation damage. The recent availability of ultrashort pulses from X-ray Free Electron Lasers (X-FELs) has now provided a mean to outrun the damage. Here we report on measurements performed at the LCLS X-FEL on bacteriorhodopsin 2D crystals mounted on a solid support and kept at room temperature. By merg- ing data from about a dozen of single crystal diffraction images, we unambiguously identified the diffraction peaks to a resolution of 7 °A, thus improving the observable resolution with respect to that achievable from a single pattern alone. This indicates that a larger dataset will allow for reliable quantification of peak intensities, and in turn a corresponding increase of resolution. The presented results pave the way to further X-FEL studies on 2D crystals, which may include pump-probe experiments at subpicosecond time resolution.

Citation: 
Pedrini B, CJ Tsai, G Capitani, C Padeste, M Hunter, NA Zatsepin, A Barty, H Benner, S Boutet, GK Feld, S Hau-Riege, R Kirian, C Kupitz, M Messerschmidt, JI Ogren, T Pardini, B Segelke, GJ Williams, JC Spence , R Abela, MA Coleman, JE Evans, G Schertler, M Frank, and XD Li.2014."7 Å Resolution in Protein 2-Dimentional-Crystal X-Ray Diffraction at Linac Coherent Light Source."Philosophical Transactions of the Royal Society of London Series B, Biological Sciences 369(1647):Article No. 20130500. doi:10.1098/rstb.2013.0500
Authors: 
B Pedrini
CJ Tsai
G Capitani
C Padeste
M Hunter
NA Zatsepin
A Barty
H Benner
S Boutet
GK Feld
S Hau-Riege
R Kirian
C Kupitz
M Messerschmidt
JI Ogren
T Pardini
B Segelke
GJ Williams
JC Spence
R Abela
MA Coleman
JE Evans
G Schertler
M Frank
XD Li
Instruments: 
Publication year: 
2014

In situ molecular imaging of hydrated biofilm in a microfluidic reactor by ToF-SIMS.

Abstract: 

The first results of using a novel single channel microfluidic reactor to enable Shewanella biofilm growth and in situ characterization using time-of-flight secondary ion mass spectrometry (ToF-SIMS) in the hydrated environment are presented. The new microfluidic interface allows direct probing of the liquid surface using ToF-SIMS, a vacuum surface technique. The detection window is an aperture of 2 m in diameter on a thin silicon nitride (SiN) membrane and it allows direct detection of the liquid surface. Surface tension of the liquid flowing inside the microchannel holds the liquid within the aperture. ToF-SIMS depth profiling was used to drill through the SiN membrane and the biofilm grown on the substrate. In situ 2D imaging of the biofilm in hydrated state was acquired, providing spatial distribution of the chemical compounds in the biofilm system. This data was compared with a medium filled microfluidic reactor devoid of biofilm and dried biofilm samples deposited on clean silicon wafers. Principle Component Analysis (PCA) was used to investigate these observations. Our results show that imaging biofilms in the hydrated environment using ToF-SIMS is possible using the unique microfluidic reactor. Moreover, characteristic biofilm fatty acids fragments were observed in the hydrated biofilm grown in the microfluidic channel, illustrating the advantage of imaging biofilm in its native environment.

Citation: 
Hua X, XY Yu, Z Wang, L Yang, B Liu, Z Zhu, AE Tucker, WB Chrisler, EA Hill, S Thevuthasan, Y Lin, S Liu, and MJ Marshall.2014."In situ molecular imaging of hydrated biofilm in a microfluidic reactor by ToF-SIMS."Analyst 139:1609-1613. doi:10.1039/C3AN02262E
Authors: 
X Hua
XY Yu
Z Wang
L Yang
B Liu
Z Zhu
AE Tucker
WB Chrisler
EA Hill
S Thevuthasan
Y Lin
S Liu
MJ Marshall
Instruments: 
Publication year: 
2014

Current Understanding and Remaining Challenges in Modeling Long-Term Degradation of Borosilicate Nuclear Waste Glasses.

Abstract: 

Chemical durability is not a single material property that can be uniquely measured. Instead it is the response to a host of coupled material and environmental processes whose rates are estimated by a combination of theory, experiment, and modeling. High-level nuclear waste (HLW) glass is perhaps the most studied of any material yet there remain significant technical gaps regarding their chemical durability. The phenomena affecting the long-term performance of HLW glasses in their disposal environment include surface reactions, transport properties to and from the reacting glass surface, and ion exchange between the solid glass and the surrounding solution and alteration products. The rates of these processes are strongly influenced and are coupled through the solution chemistry, which is in turn influenced by the reacting glass and also by reaction with the near-field materials and precipitation of alteration products. Therefore, those processes must be understood sufficiently well to estimate or bound the performance of HLW glass in its disposal environment over geologic time-scales. This article summarizes the current state of understanding of surface reactions, transport properties, and ion exchange along with the near-field materials and alteration products influences on solution chemistry and glass reaction rates. Also summarized are the remaining technical gaps along with recommended approaches to fill those technical gaps.

Citation: 
Vienna JD, JV Ryan, S Gin, and Y Inagaki.2013."Current Understanding and Remaining Challenges in Modeling Long-Term Degradation of Borosilicate Nuclear Waste Glasses."International Journal of Applied Glass Science 4(4):283-294. doi:10.1111/ijag.12050
Authors: 
JD Vienna
JV Ryan
S Gin
Y Inagaki
Instruments: 
Volume: 
4
Issue: 
4
Pages: 
283-294
Publication year: 
2013

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