NMR and EPR

Molecular systems important to biology, environmental remediation and sustainability are studied using a suite of nuclear magnetic resonance (NMR) spectrometers with frequencies ranging from 300 to 850 MHz. A pair of electron paramagnetic resonance (EPR) spectrometers complement the capability.

Interfacial and in situ biology—Innovative NMR instrumentation and techniques for probing properties of macromolecular cellular assemblies and in situ and ex situ metabolic processes, as well as for exploring biological membrane proteins in the solid state. Unique EPR and variable-temperature NMR approaches to explore structure and properties of redox metal centers critical to cell biology.

Environmental chemistry— EMSL offers a unique NMR system for radiological studies. Users can perform magic angle spinning of highly radioactive samples with a novel hermetically sealed 3.2mm NMR probe. These tools allow users to apply NMR techniques to critical areas of radiological research, including the study of radioactive waste processing and storage.

Interfacial and in situ chemistry—Leading-edge solid-state NMR probe technology to analyze and quantify properties of advanced energy materials, fuel cells and real-time catalytic processes. High power pulsed field gradient diffusion capabilities for liquid and solid samples.

 EMSL offers unique and custom NMR and EPR tools, including probes for specialized studies.

  • NMR spectrometers, ranging from 100 MHz to 850 MHz for high-field liquid-state, solid-state and micro-imaging techniques
  • W- and X-band pulsed EPR spectrometers for probing metal centers in biological and materials systems
  • NMR metabolomics capabilities
  • Extreme-temperature probes, both high and low temperatures
  • Virtual NMR tools for remote access to spectrometer systems.
Research applications Samples containing paramagnetics Soils (SOM and NOM) Metal oxide materials for catalysis applications Researchers may operate...
Custodian(s): Herman M Cho
Highlighted Research Applications Characterization of natural and soil organic matter (NOM and SOM) CO2 sequestration investigations via high-...
Highlighted Research Applications EMSL's Bruker 500-MHz WB spectrometer is uniquely tailored for in vivo studies: Microbial biofilms relevant to...
Type of Instrument:
Nuclear Magnetic Resonance Spectrometer (NMR)
Highlighted Research Applications Dynamics studies via 2H NMR Characterization of quadrupolar nuclei for materials and biological samples In situ...
Custodian(s): Andrew S Lipton
Highlighted Research Applications Structural biology Protein structure and dynamics Nuclei acid structure and dynamics. Metabolomics Eukaryotic and...
The effects of acid identity on CH₃OH dehydration are examined here using density functional theory (DFT) estimates of acid strength (as...
A facultative iron-reducing (Fe(III)-reducing) Paenibacillus sp. strain was isolated from Hanford 300A subsurface sediment biofilms that was capable...
Liquid chromatography-mass spectrometry (LC-MS)-based quantitative proteomics has become increasingly applied for a broad range of biological...
Nations producing borosilicate glass as an immobilization material for radioactive wastes resulting from spent nuclear fuel reprocessing have...
Strong upconversion luminescence is observed from colloidal CdS and CdZnS quantum dots dispersed in hexanes. The nanocrystals were synthesized via...
Posted: August 14, 2014
Industry uses zeolites as an ion exchange material and solid acid to catalyze a broad range of chemical reactions. Zeolites are also promising...
Posted: June 23, 2014
Congratulations to Pacific Northwest National Laboratory and EMSL researchers on being named highly cited authors for 2012-2013 by the Journal of...
Posted: November 12, 2013
Tiny electrical wires protrude from some bacteria and contribute to rock and dirt formation. Researchers studying the protein that makes up one such...
Posted: May 22, 2013
Bacteria can move electrons at least half a millimeter across a scaffolding made by themselves, of themselves, even under starving conditions. This...
Posted: March 04, 2013
Using EMSL’s electron paramagnetic resonance spectrometer, University of Connecticut and Pacific Northwest National Laboratory scientists measured...

Molecular systems important to biology, environmental remediation and sustainability are studied using a suite of nuclear magnetic resonance (NMR) spectrometers with frequencies ranging from 300 to 850 MHz. A pair of electron paramagnetic resonance (EPR) spectrometers complement the capability.

Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass.

Abstract: 

Thermophilic bacteria are a potential source of enzymes for the deconstruction of lignocellulosic biomass. However, the complement of proteins used to deconstruct biomass and the specific roles of different microbial groups in thermophilic biomass deconstruction are not well-explored. Here we report on the metagenomic and proteogenomic analyses of a compost-derived bacterial consortium adapted to switchgrass at elevated temperature with high levels of glycoside hydrolase activities. Near-complete genomes were reconstructed for the most abundant populations, which included composite genomes for populations closely related to sequenced strains of Thermus thermophilus and Rhodothermus marinus, and for novel populations that are related to thermophilic Paenibacilli and an uncultivated subdivision of the littlestudied Gemmatimonadetes phylum. Partial genomes were also reconstructed for a number of lower abundance thermophilic Chloroflexi populations. Identification of genes for lignocellulose processing and metabolic reconstructions suggested Rhodothermus, Paenibacillus and Gemmatimonadetes as key groups for deconstructing biomass, and Thermus as a group that may primarily metabolize low molecular weight compounds. Mass spectrometry-based proteomic analysis of the consortium was used to identify .3000 proteins in fractionated samples from the cultures, and confirmed the importance of Paenibacillus and Gemmatimonadetes to biomass deconstruction. These studies also indicate that there are unexplored proteins with important roles in bacterial lignocellulose deconstruction.

Citation: 
D'haeseleer P, JM Gladden, M Allgaier, P Chain, SG Tringe, S Malfatti, JT Aldrich, CD Nicora, EW Robinson, L Pasa-Tolic, P Hugenholtz, BA Simmons, and SW Singer.2013."Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass."PLoS One 8(7):e68465. doi:10.1371/journal.pone.0068465
Authors: 
P D'haeseleer
JM Gladden
M Allgaier
P Chain
SG Tringe
S Malfatti
JT Aldrich
CD Nicora
EW Robinson
L Pasa-Tolic
P Hugenholtz
BA Simmons
SW Singer
Facility: 
Publication year: 
2013

Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1.

Abstract: 

The anaerobic isolate Enterobacter lignolyticus SCF1 was initially cultivated based on anaerobic growth on lignin as sole carbon source. The source of the isolated bacteria was from tropical forest soils that decompose litter rapidly with low and fluctuating redox potentials, making it likely that bacteria using oxygen-independent enzymes play an important role in decomposition. We have examined differential expression of the anaerobic isolate Enterobacter lignolyticus SCF1 during growth on lignin. After 48 hours of growth, we used transcriptomics and proteomics to define the enzymes and other regulatory machinery that these organisms use to degrade lignin, as well as metabolomics to measure lignin degradation and monitor the use of lignin and iron as terminal electron acceptors that facilitate more efficient use of carbon. Proteomics revealed accelerated xylose uptake and metabolism under lignin-amended growth, and lignin degradation via the 4-hydroxyphenylacetate degradation pathway, catalase/peroxidase enzymes, and the glutathione biosynthesis and glutathione S-transferase proteins. We also observed increased production of NADH-quinone oxidoreductase, other electron transport chain proteins, and ATP synthase and ATP-binding cassette (ABC) transporters. Our data shows the advantages of a multi-omics approach, where incomplete pathways identified by genomics were completed, and new observations made on coping with poor carbon availability. The fast growth, high efficiency and specificity of enzymes employed in bacterial anaerobic litter deconstruction makes these soils useful templates for improving biofuel production.

Citation: 
DeAngelis KM, D Sharma, R Varney, BA Simmons, NG Isern, LM Markillie, CD Nicora, AD Norbeck, RC Taylor, JT Aldrich, and EW Robinson.2013."Evidence supporting dissimilatory and assimilatory lignin degradation in Enterobacter lignolyticus SCF1."Frontiers in Microbiology 4:Article No. 280.
Authors: 
KM DeAngelis
D Sharma
R Varney
BA Simmons
NG Isern
LM Markillie
CD Nicora
AD Norbeck
RC Taylor
JT Aldrich
EW Robinson
Facility: 
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

Coregulation of terpenoid pathway genes and prediction of isoprene production in Bacillus subtilis using transcriptomics.

Abstract: 

The isoprenoid pathway converts pyruvate to isoprene and related isoprenoid compounds in plants and some bacteria. Currently, this pathway is of great interest because of the critical role that isoprenoids play in basic cellular processes as well as the industrial value of metabolites such as isoprene. Although the regulation of several pathway genes has been described, there is a paucity of information regarding the system level regulation and control of the pathway. To address this limitation, we examined Bacillus subtilis grown under multiple conditions and then determined the relationship between altered isoprene production and the pattern of gene expression. We found that terpenoid genes appeared to fall into two distinct subsets with opposing correlations with respect to the amount of isoprene produced. The group whose expression levels positively correlated with isoprene production included dxs, the gene responsible for the commitment step in the pathway, as well as ispD, and two genes that participate in the mevalonate pathway, yhfS and pksG. The subset of terpenoid genes that inversely correlated with isoprene production included ispH, ispF, hepS, uppS, ispE, and dxr. A genome wide partial least squares regression model was created to identify other genes or pathways that contribute to isoprene production. This analysis showed that a subset of 213 regulated genes was sufficient to create a predictive model of isoprene production under different conditions and showed correlations at the transcriptional level. We conclude that gene expression levels alone are sufficiently informative about the metabolic state of a cell that produces increased isoprene and can be used to build a model which accurately predicts production of this secondary metabolite across many simulated environmental conditions.

Citation: 
Hess BM, J Xue, LM Markillie, RC Taylor, HS Wiley, BK Ahring, and BE Linggi.2013."Coregulation of terpenoid pathway genes and prediction of isoprene production in Bacillus subtilis using transcriptomics."PLoS One 8(6):e66104. doi:10.1371/journal.pone.0066104
Authors: 
BM Hess
J Xue
LM Markillie
RC Taylor
HS Wiley
BK Ahring
BE Linggi
Facility: 
Publication year: 
2013

Microbial communities acclimate to recurring changes in soil redox potential status.

Abstract: 

Rapidly fluctuating environmental conditions can significantly stress organisms, particularly when fluctuations cross thresholds of normal physiological tolerance. Redox potential fluctuations are common in humid tropical soils, and microbial community acclimation or avoidance strategies for survival will in turn shape microbial community diversity and biogeochemistry. To assess the extent to which indigenous bacterial and archaeal communities are adapted to changing in redox potential, soils were incubated under static anoxic, static oxic or fluctuating redox potential conditions, and the standing (DNA-based) and active (RNA-based) communities and biogeochemistry were determined. Fluctuating redox potential conditions permitted simultaneous CO₂ respiration, methanogenesis, N₂O production and iron reduction. Exposure to static anaerobic conditions significantly changed community composition, while 4-day redox potential fluctuations did not. Using RNA: DNA ratios as a measure of activity, 285 taxa were more active under fluctuating than static conditions, compared with three taxa that were more active under static compared with fluctuating conditions. These data suggest an indigenous microbialcommunity adapted to fluctuating redox potential.

Citation: 
DeAngelis KM, W Silver, A Thompson, and MK Firestone.2010."Microbial communities acclimate to recurring changes in soil redox potential status."Environmental Microbiology 12(12):3137-3149. doi:10.1111/j.1462-2920.2010.02286.x
Authors: 
KM DeAngelis
W Silver
A Thompson
MK Firestone
Facility: 
Volume: 
12
Issue: 
12
Pages: 
3137-3149
Publication year: 
2010

Complete genome sequence of Enterobacter lignolyticus” SCF1.

Abstract: 

In an effort to discover anaerobic bacteria capable of lignin degradation, we isolated “Ente-robacter lignolyticus” SCF1 on minimal media with alkali lignin as the sole source of carbon. This organism was isolated anaerobically from tropical forest soils collected from the Short Cloud Forest site in the El Yunque National Forest in Puerto Rico, USA, part of the Luquillo Long-Term Ecological Research Station. At this site, the soils experience strong fluctuations in redox potential and are net methane producers. Because of its ability to grow on lignin anae-robically, we sequenced the genome. The genome of “E. lignolyticus” SCF1 is 4.81 Mbp with no detected plasmids, and includes a relatively small arsenal of lignocellulolytic carbohy-drate active enzymes. Lignin degradation was observed in culture, and the genome revealed two putative laccases, a putative peroxidase, and a complete 4-hydroxyphenylacetate degra-dation pathway encoded in a single gene cluster.

Citation: 
DeAngelis KM, P D'Haeseleer, D Chivian, JL Fortney, JI Khudyakov, BA Simmons, H Woo, AP Arkin, KW Davenport, LA Goodwin, A Chen, N Ivanova, NC Kyrpides, K Mavromatis, T Woyke, and TC Hazen.2011."Complete genome sequence of “Enterobacter lignolyticus” SCF1."Standards in Genomic Sciences 5(1):69-85. doi:10.4056/sigs.2104875
Authors: 
KM DeAngelis
P D'Haeseleer
D Chivian
JL Fortney
JI Khudyakov
BA Simmons
H Woo
AP Arkin
KW Davenport
LA Goodwin
A Chen
N Ivanova
NC Kyrpides
K Mavromatis
T Woyke
TC Hazen
Facility: 
Volume: 
5
Issue: 
1
Pages: 
69-85
Publication year: 
2011

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