Microscopy

Advancement in energy, environment and biology research relies heavily on micro-, nano- and atomic-scale chemical and structural imaging. Many microscopy instruments have high-resolution imaging capabilities including complementary chemical, structural and phase information, in-situ imaging in native environments and imaging of dynamic processes with high temporal-resolution.

Resources and Techniques

  • Nanoscale and sub-nanoscale imaging allows users to elucidate chemical processes and acquire structural data for a variety of samples such as nanostructures and cell-surface proteins.
  • Tomography yields three-dimensional reconstruction of transmission electron microscopy images generated for biological samples as well as for soft materials and samples with 3D structural heterogeneity.
  • Environmental particle analysis offers knowledge about non-volatile atmospheric particle composition and hydration properties using high-pressure scanning electron microscopy equipped with energy-dispersive x-ray analysis capability.
  • Environmental mode imaging techniques enable sample preservation to eliminate extensive preparation procedures that can introduce artifacts and make possible live-cell imaging and in situ imaging in liquids or controlled gas environments with high resolution microscopy.
  • Dynamic imaging capability enables real-time studies of nanosecond-scale dynamic processes with unprecedented spatial resolution, such as protein-protein interactions, with contrast at the single-molecule level.

In 2014, EMSL anticipates debuting its Dynamic Transmission Electron Microscope (DTEM) for the broad scientific community. It will enable dynamic in suit observation of cellular systems and components at near-atomic spatial resolution and nanosecond time resolution.

Quiet Wing for Advanced Microscopy
Seven microscopes are housed in the Quiet Wing, a space specially designed to reduce external factors, such as vibrations and electromagnetic fields, that can impede capture of high-resolution images. Read more about the Quiet Wing and its instrumentation.

Capability Details

• Electron microscopes with tomography, cryo, scanning, photoemission and high-resolution (sub-nanometer) imaging capabilities
• Focused ion beam/scanning electron microscopes for specialized sample preparation and three-dimensional topographic and chemical imaging
• Nuclear magnetic resonance microscopy with 10-40-_m resolution to study the anatomy, metabolism and transport processes of live cell cultures, biofilms and tissue samples
• Dual Raman confocal microscope for analysis of radiological samples
• Single-molecule fluorescence tools to study molecular interactions in real time
• Scanning probe microscopy with capabilities ranging from examination of dynamic nanoscale processes in condensed environments to high resolution studies of catalysis materials in ultra-high vacuum.

 

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
The LEAP® 4000 XHR local electrode atom probe tomography instrument enabled the first-ever comprehensive and accurate 3-D chemical imaging studies...
This FEI Tecnai T-12 cryo-transmission electron microscope (TEM) complements EMSL's broader microscopy suite and JEOL 2010 analytical high-...
Custodian(s): Alice Dohnalkova
The environmental scanning electron microscope (ESEM) is a new-generation SEM that can image samples under controlled environments and temperatures...
Custodian(s): Alexander Laskin, Scott Lea
It has been increasingly recognized that understanding and predicting the behaviors of nanoparticles is often limited by the degree to which the...
The electronic absorption and emission spectra of freeUO2Cl2 and its Ar-coordinated complexes below 27 000 cm-1 are investigated at the levels of ab...
The plastic substrates, reflective layers, dyes, and adhesives of four archival-grade DVDs and one standard-grade recordable DVD were analyzed to...
Ion mobility spectrometry in conjunction with liquid chromatography separations and mass spectrometry offers a range of new possibilities for...
Applying surface coatings to alloying anodes for Li-ion batteries can improve rate capability and cycle life, but it is unclear how this second phase...
Posted: August 29, 2014
The goal is for the soft nanoparticles to move through the body and attack cancerous cells, destroying only the diseased tissue. The challenge is to...
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: July 09, 2014
Researchers at EMSL, Pacific Northwest National Laboratory and the University of California, San Diego, developed and tested a sponge-like silicon...
Posted: June 17, 2014
The Science Hexavalent chromium is a major environmental contaminant at several Department of Energy (DOE) sites as well as other sites around the...
Posted: May 13, 2014
EMSL and Pacific Northwest National Laboratory scientists isolated two bacterial consortia from a microbial mat in Hot Lake, in north-central...

Advancement in energy, environment and biology research relies heavily on micro-, nano- and atomic-scale chemical and structural imaging. Many microscopy instruments have high-resolution imaging capabilities including complementary chemical, structural and phase information, in-situ imaging in native environments and imaging of dynamic processes with high temporal-resolution.

Resources and Techniques

  • Nanoscale and sub-nanoscale imaging allows users to elucidate chemical processes and acquire structural data for a variety of samples such as nanostructures and cell-surface proteins.
  • Tomography yields three-dimensional reconstruction of transmission electron microscopy images generated for biological samples as well as for soft materials and samples with 3D structural heterogeneity.
  • Environmental particle analysis offers knowledge about non-volatile atmospheric particle composition and hydration properties using high-pressure scanning electron microscopy equipped with energy-dispersive x-ray analysis capability.
  • Environmental mode imaging techniques enable sample preservation to eliminate extensive preparation procedures that can introduce artifacts and make possible live-cell imaging and in situ imaging in liquids or controlled gas environments with high resolution microscopy.
  • Dynamic imaging capability enables real-time studies of nanosecond-scale dynamic processes with unprecedented spatial resolution, such as protein-protein interactions, with contrast at the single-molecule level.

In 2014, EMSL anticipates debuting its Dynamic Transmission Electron Microscope (DTEM) for the broad scientific community. It will enable dynamic in suit observation of cellular systems and components at near-atomic spatial resolution and nanosecond time resolution.

Quiet Wing for Advanced Microscopy
Seven microscopes are housed in the Quiet Wing, a space specially designed to reduce external factors, such as vibrations and electromagnetic fields, that can impede capture of high-resolution images. Read more about the Quiet Wing and its instrumentation.

The Toxoplasma gondii cyst wall protein CST1 is critical for cyst wall integrity and promotes bradyzoite persistence.

Abstract: 

Toxoplasma gondii infects up to one third of the world’s population. A key to the success of T.gondii is its ability to persist for the life of its host as bradyzoites within tissue cysts. The glycosylated cyst wall is the key structural feature that facilitates persistence and oral transmission of this parasite. We have identified CST1 (TGME49_064660) as a 250 kDa SRS (SAG1 related sequence) domain protein with a large mucin-like domain. CST1 is responsible for the Dolichos biflorus Agglutinin (DBA) lectin binding characteristic of T. gondii cysts. Deletion of CST1 results in a fragile brain cyst phenotype revealed by a thinning and disruption of the underlying region of the cyst wall. These defects are reversed by complementation of CST1. Additional complementation experiments demonstrate that the CST1-mucin domain is necessary for the formation of a normal cyst wall structure, the ability of the cyst to resist mechanical stress and binding of DBA to the cyst wall. RNA-seq transcriptome analysis demonstrated dysregulation of bradyzoite genes within the various cst1 mutants. These results indicate that CST1 functions as a key structural component that reinforces the cyst wall structure and confers essential sturdiness to the T. gondii tissue cyst.

Citation: 
Tomita T, DJ Bzik, YF Ma, BA Fox, LM Markillie, RC Taylor, K Kim, and LM Weiss.2013."The Toxoplasma gondii cyst wall protein CST1 is critical for cyst wall integrity and promotes bradyzoite persistence."PLoS Pathogens 9(12):e1003823. doi:10.1371/journal.ppat.1003823
Authors: 
T Tomita
DJ Bzik
YF Ma
BA Fox
LM Markillie
RC Taylor
K Kim
LM Weiss
Publication year: 
2013

Changes in Translational Efficiency is a Dominant Regulatory Mechanism in the Environmental Response of Bacteria.

Abstract: 

To understand how cell physiological state affects mRNA translation, we used Shewanella oneidensis MR-1 grown under steady state conditions at either aerobic or suboxic conditions. Using a combination of quantitative proteomics and RNA-Seq, we generated high-confidence data on >1000 mRNA and protein pairs. By using a steady state model, we found that differences in protein-mRNA ratios were primarily caused by differences in the translational efficiency of specific genes. When oxygen levels were lowered, 28% of the proteins showed at least a 2-fold change in expression. Altered transcription levels appeared responsible for 26% of the protein changes, altered translational efficiency appeared responsible for 46% and a combination of both were responsible for the remaining 28%. Changes in translational efficiency were significantly correlated with the codon usage pattern of the genes and measurable tRNA pools changed in response to altered O2 levels. Our results suggest that changes in the translational efficiency of proteins, in part caused by altered tRNA pools, is a major determinant of regulated protein expression in bacteria.

Citation: 
Taylor RC, BJM Webb-Robertson, LM Markillie, MH Serres, BE Linggi, JT Aldrich, EA Hill, MF Romine, MS Lipton, and HS Wiley.2013."Changes in Translational Efficiency is a Dominant Regulatory Mechanism in the Environmental Response of Bacteria."Integrative Biology 5(11):1393-1406. doi:10.1039/C3IB40120K
Authors: 
RC Taylor
BJM Webb-Robertson
LM Markillie
MH Serres
BE Linggi
JT Aldrich
EA Hill
MF Romine
MS Lipton
HS Wiley
Facility: 
Volume: 
5
Issue: 
11
Pages: 
1393-1406
Publication year: 
2013

Field evidence of selenium bioreduction in a uranium-contaminated aquifer.

Abstract: 

Removal of selenium from groundwater was documented during injection of acetate into a uraniumcontaminated aquifer near Rifle, Colorado (USA). Bioreduction of aqueous selenium to its elemental form (Se0) concentrated it within mineralized biofilms affixed to tubing used to circulate acetate-amended groundwater. Scanning and transmission electron microscopy revealed close association between Se0 precipitates and cell surfaces, with Se0 aggregates having a diameter of 50-60 nm. Accumulation of Se0 within biofilms occurred over a three-week interval at a rate of c. 9 mg Se0m-2 tubing day-1. Removal was inferred to result from the activity of a mixed microbial community within the biofilms capable of coupling acetate oxidation to the reduction of oxygen, nitrate and selenate. Phylogenetic analysis of the biofilm revealed a community dominated by strains of Dechloromonas sp. and Thauera sp., with isolates exhibiting genetic similarity to the latter known to reduce selenate to Se0. Enrichment cultures of selenate-respiring microorganisms were readily established using Rifle site groundwater and acetate, with cultures dominated by strains closely related to D. aromatica (96-99% similarity). Predominance of Dechloromonas sp. in recovered biofilms and enrichments suggests this microorganism may play a role in the removal of selenium oxyanions present in Se-impacted groundwaters and sediments.

Citation: 
Williams KH, MJ Wilkins, AL N'Guessan, BW Arey, EN Dodova, A Dohnalkova, D Holmes, DR Lovley, and PE Long.2013."Field evidence of selenium bioreduction in a uranium-contaminated aquifer."Environmental Microbiology Reports 5(3):444-452. doi:10.1111/1758-2229.12032
Authors: 
Williams
MJ Wilkins
AL N'Guessan
BW Arey
EN Dodova
A Dohnalkova
D Holmes
DR Lovley
PE Long
Facility: 
Volume: 
5
Issue: 
3
Pages: 
444-452
Publication year: 
2013

Discovery of a Splicing Regulator Required for Cell Cycle Progression.

Abstract: 

In the G1 phase of the cell division cycle, eukaryotic cells prepare many of the resources necessary for a new round of growth including renewal of the transcriptional and protein synthetic capacities and building the machinery for chromosome replication. The function of G1 has an early evolutionary origin and is preserved in single and multicellular organisms, although the regulatory mechanisms conducting G1 specific functions are only understood in a few model eukaryotes. Here we describe a new G1 mutant from an ancient family of apicomplexan protozoans. Toxoplasma gondii temperature-sensitive mutant 12-109C6 conditionally arrests in the G1 phase due to a single point mutation in a novel protein containing a single RNA-recognition-motif (TgRRM1). The resulting tyrosine to asparagine amino acid change in TgRRM1 causes severe temperature instability that generates an effective null phenotype for this protein when the mutant is shifted to the restrictive temperature. Orthologs of TgRRM1 are widely conserved in diverse eukaryote lineages, and the human counterpart (RBM42) can functionally replace the missing Toxoplasma factor. Transcriptome studies demonstrate that gene expression is downregulated in the mutant at the restrictive temperature due to a severe defect in splicing that affects both cell cycle and constitutively expressed mRNAs. The interaction of TgRRM1 with factors of the tri-SNP complex (U4/U6 & U5 snRNPs) indicate this factor may be required to assemble an active spliceosome. Thus, the TgRRM1 family of proteins is an unrecognized and evolutionarily conserved class of splicing regulators. This study demonstrates investigations into diverse unicellular eukaryotes, like the Apicomplexa, have the potential to yield new insights into important mechanisms conserved across modern eukaryotic kingdoms.

Citation: 
Suvorova ES, M Croken, S Kratzer, LM Ting, M Conde de Felipe, B Balu, LM Markillie, LM Weiss, K Kim, and MW White.2013."Discovery of a Splicing Regulator Required for Cell Cycle Progression."PLoS Genetics 9(2):Article No. e1003305. doi:10.1371/journal.pgen.1003305
Authors: 
ES Suvorova
M Croken
S Kratzer
LM Ting
M Conde de Felipe
B Balu
LM Markillie
LM Weiss
K Kim
MW White
Publication year: 
2013

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