U.S. Department of Energy

Pacific Northwest National Laboratory

Highlights

2018

Researcher Hyun-Seob Song and his colleague, Purdue University’s Doraiswami Ramkrishna, authored a just-released book detailing a computational method that incorporates metabolic regulation into microbial modeling to predict molecular and phenotypic changes.

Beyond a fundamental...

Posted: October 18

Chemist and Integrative Omics scientist Tom Metz delivered one of nine invited talks at the Carousel of Hope Symposium on Oct. 6...

Posted: October 17

“You Can’t Go Home Again,” the title of a 1940 novel by Thomas Wolfe, makes a pronouncement about the past most people follow.

But not Janet Jansson. On Sept. 21, the veteran scientist and Laboratory Fellow...

Posted: September 26

The Science

A boon to natural gas production, hydraulic fracturing or fracking introduces surface microbes thousands of feet below the Earth’s surface. How do they survive? Could they be harnessed to increase energy output? Scientists brought these microbes into the...

Posted: August 27

New paper lays foundation for future studies of the poorly understood organisms.

The Science                      

The bioaccumulation of mercury in plant and animal tissue is strongly linked to mercury methylation in sediments, and poses a significant...

Posted: July 24

Researchers characterize the degradation products of a protein responsible for generating enamel, opening potential avenues to regeneration strategies. 

The Science

The aim of this study in the journal Archives of Oral Biology was to...

Posted: July 16

The Science                      

T-cells that can recognize and destroy cancer are often suppressed inside of tumors. This study identifies a specific sub-population of T-cells—found  only in tumors—whose  presence correlates with patient survival.

The...

Posted: July 13

Linking microscale processes and macroscale fluxes using soil properties in a process-rich simulation.

The Science

Researchers coupled fundamental soil properties with microbial physiology in a pore-scale simulation to predict how microbial respiration...

Posted: July 11

Study investigates a common human exposure coupled with a high-fat diet. 

The Science                      

A study led by Aaron Wright of Pacific National Laboratory determined that high-fat diets lead to dramatic alterations in liver and lung metabolism...

Posted: June 26

Using math to cross spatial scales and combine process-understanding with data.

The Science                      

We used a mathematical analysis of existing soil decomposition models to: 1) inform a statistical analysis of the direct change in soil carbon...

Posted: June 18

Aim: Cover key aspects of microbial interactions and community dynamics

When the New Year kicked off, one of Hyun-Seob Song’s resolutions was to finalize a special issue of the journal, Processes, which published this month. The topic —...

Posted: June 15

Probes facilitate quantification of active enzyme-specific GST response following perturbation, indicative of the capacity for detoxification.

The Science                      

PNNL researchers developed and applied two new activity-based probes that...

Posted: May 31

Researchers use the reliable Neurospora crassaorganism to demonstrate new method.

The Science                      

Researchers at PNNL are now able to predict cellular metabolite concentrations, rate constants, and regulation of enzymes using the...

Posted: May 28

The Science                      

PNNL researchers developed an analytics-based tool that intelligently combines individual and disparate data quality control metrics to identify anomalous instrument analyses faster and more accurately. 

The Impact...

Posted: May 14

Researchers discover how certain bacteria may safeguard plant growth during a drought, making way for strategies to improve crop productivity

The Science

The devastating effects of drought are expected to increase in severity and frequency in the coming...

Posted: April 13

The Science

Detailed analysis of proteins, an important building block for understanding how cells are functioning, has only been possible with samples of thousands to millions of cells. Now scientists have developed a robotically controlled processing platform that...

Posted: March 28

The Science

Hyporheic zones are found within river corridor ecosystems across the world, and represent a dynamic continuum where groundwater (GW) and river water (RW) mix, stimulating biogeochemical activity. This activity has strong influences over the transformation of...

Posted: February 08

The Science

Phototropic microbial mats are compact ecosystems containing hundreds of different organisms that capture and transform energy from the sun. While cyanobacteria are the primary producers in these systems, the exchange of nutrients and recycling of light energy...

Posted:
2017

The Science 

Three discrete biological events (embryo implantation, decidualization, and placentation) are necessary for a successful pregnancy. A disruption in any of these complex events can cause complications that researchers believe could be treated if we fully...

Posted: December 01

The Science                      

Many Land System Models (LSMs) do not consider lateral transport of water, leaving out a cross-sectional view and understanding of the coupling of surface water with groundwater along rivers, streams, and other water bodies. And yet,...

Posted: November 17

The Science                      

Researchers improved the predictive capabilities of subsurface flow models by developing new, more efficient equations that account for length scales at which predictions are made and the hydrological measurements that are made in the...

Posted: November 01

The Science

Benthic aquatic habitats—in the sea, in freshwater lakes, and in hypersaline aquatic environments —support one of the most widespread ecosystems on earth. These habitats play critical roles in global biogeochemical cycling, and those operating in the euphotic...

Posted: October 17

The Science                      

Near‐term land management and policy decisions depend on proxies, which are used as surrogates for soil features and processes and that affect long‐term projections of earth system responses to change. In a new paper led by soil ecologist...

Posted: October 09

The Science

Soil organic matter (SOM) sustains terrestrial ecosystems, provides food and fiber, and retains the largest pool of actively cycling carbon (C). Over 75% of the soil organic carbon (SOC) in the top meter of soil is directly affected by human land use practices...

Posted: October 05

The Science                      

River corridors exist worldwide and are comprised of multiple interacting components, all of them significant for their influences on biogeochemical cycling and microbial interactions. For example, the fluvial zone is the river itself,...

Posted: September 21

The Science 

Hydrologic exchange between rivers and subsurface zones is a crucial component of the water cycle. From centimeter to kilometer scales, the magnitude of exchange affects biogeochemical and ecological processes that occur in the hyporheic zone at a river’s...

Posted: September 15

The Science                      

Scientists need a systematic understanding of cellular functioning to metabolically engineer microbes that produce biofuels and other high-value products, and to design drugs that combat pathogens and cancers. Metabolic networks are...

Posted: August 01

The Science                      

Researchers used gene sequencing on the bacteria Rhodopseudomonas palustristo determine which genes are absolutely necessary for phototrophic growth. 

The Impact

The list of genes identified in the...

Posted: July 05

The Science

In a recent studypublished in Advances in Water Resources, researchers performed a set of well-controlled drainage and imbibition experiments using six identically manufactured microfluidic cells to study the reproducibility of multiphase flow experiments. The...

Posted: July 01

The Science                      

Due to its respiratory versatilityShewanella oneidensisMR-1 has been widely investigated as a model organism for heavy metal and radionuclide bioremediation. In this studyPNNL researchers developed a...

Posted: June 29

The Science                      

The yeast Yarrowia lipolyticais considered a promising “microbial cell factory” for producing biofuels and oleochemicals, but researchers need to understand how the yeast’s lipid metabolism is regulated so that they can...

Posted: June 20

The Science 

Root water uptake is one of the most important processes in subsurface flow and transport modeling. It is driven by transpiration caused by the water potential gradient between the atmosphere and the plant. But the mechanisms of root water uptake are poorly...

Posted: June 01

The Science

There is a key bottleneck in lipidomics studies based on liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS): Researchers are unable to process spectral data in a high-throughput manner and at the same time confidently identify and...

Posted: June 01

The Science                      

In this paper, the authors describe how and why a form of quantitative proteomics they call redox proteomics could be  an indispensable tool for redox biology, which investigates cellular oxygen levels. Quantitative proteomics as a whole...

Posted: May 02

The Science

Soils and nearshore sediments comprise a reservoir of carbon (C) 3.2 times larger than all the carbon stored in the atmosphere. Terrestrial C (e.g., from falling leaves and roots growing underground) is increasingly transported into aquatic systems due to...

Posted: April 19

The Science

The hyporheic zone (HZ) is the subsurface zone where river water and groundwater exchange and mix. Researchers used multiple laboratory columns containing sediments from the Columbia River HZ to examine how dynamic changes in groundwater and surface water...

Posted: April 09

The Science        

Soil has networks of pores and channels that weave through it like interconnected straws. They’re formed underground by the different minerals that compose soil and as a result of movements or growth by roots, insects, and other living organisms. The...

Posted: April 01

The Science

Phototropic microbial mats are compact ecosystems containing hundreds of different organisms that capture and transform energy from the sun. While cyanobacteria are the primary producers in these systems, the exchange of nutrients and recycling of light energy...

Posted: March 21

The Science                      

In nature, very small communities of microorganisms are present in very large numbers, and therefore mediate key biogeochemical and ecological processes on a global scale. For instance, both terrestrial and aquatic ecosystems shape Earth’...

Posted: March 07

The Science

Microbial biomass is a clean, renewable energy source with the potential to significantly diversify and sustain future energy and transportation fuel requirements. A new paper by researchers at the Pacific Northwest National Laboratory (PNNL) describes a...

Posted: March 01

The Science                      

Vitamin B12 is produced by only a few organisms but is needed by nearly all. Scientists at the Pacific Northwest National Laboratory (PNNL) just published a paper recording further evidence that the water-soluble vitamin (synthesized in...

Posted: February 14

In nature’s benthic microscopic realms, microbial communities gather in lattice-like mats that allow a variety of microorganisms to do the work of cooperative survival within a spatially organized environment. Photosynthetically active “primary producers” typically occupy the top of these...

Posted: February 11

The Science                      

In a recent study, scientists at Pacific Northwest National Laboratory (PNNL) observed two microbial communities to determine how they support diverse members unable to produce vitamin B-related enzyme cofactors, which are necessary for...

Posted: February 10

The Science

Microbial communities are like our own societies. In their natural environments, where they’re comfortable and acclimated, both microbes and humans tend to thrive. They know how to navigate their surroundings, how to survive, and they concentrate their energy...

Posted:

The Science

Longitudinal studies of disease require collecting biofluids, preferentially blood. But acquiring blood samples in the form of serum requires a professional, and storing thousands of such samples at -80 degrees C requires energy and freezer space. These...

Posted:
2016

The Science                      

There is a great demand for chemical probes that can mimic and react analogously to biological molecules, and that can be used to investigate cellular processes. One class of chemical probes are non-canonical amino acids that can be...

Posted: December 26

The Science

The hyporheic zone (HZ) is a subsurface environment where groundwater and river water mix, causing various physical, chemical, and microbial processes to occur simultaneously. Dynamic river flow conditions can lead to fluctuations in the delivery of oxygen and...

Posted: December 20

The Science                               

Ecological processes govern seasonal changes in microbial communities living along rivers in the hyporheic zone, where groundwater and surface water mix. These processes have been well-studied in plant and animal communities. But...

Posted: December 16

Biologists often envision their hypotheses within a set of protein interactions, networks, and pathways. In turn, their experiments may focus on measuring an explicit subset of these proteins, corresponding to a targeted proteomics experiment.  To date, however, designing a targeted proteomics...

Posted: November 27

The Science                      

Researchers at The Ohio State University, Lawrence Berkeley National Laboratory, and Pacific Northwest National Laboratory assessed how seasonal changes affect microbial populations in the Colorado River, a snowmelt-dominated fluvial...

Posted: November 18

The Science                      

Researchers at the Pacific Northwest National Laboratory recently studied how moisture influences soil heterotrophic respiration, the process by which microbes convert dead organic carbon in the soil to carbon dioxide. Their cost-...

Posted: November 15

Leaf cutter ants area classic example of foraging herbivores that use symbiotic microbes to get energy and nutrients from plant material. According to researchers, a spongy fungal species known as L. gongylophorus,has cooperated with leaf cutter ants for the last 23 million years.

...
Posted: October 01

The Science

Some minerals abundant in soils and in aquatic and subsurface sediments electronically support microbial growth by supplying electrons or storing them as “environmental batteries,” according to this new review article. Microbial cells derive chemical energy...

Posted: August 30

The Science                                

Microbial communities within subsurface aquifers are metabolically influenced by the mineral mixes that bind them. Communities like this also exchange gases on such a vast scale that they influence the composition of the Earth’s...

Posted: July 29
2015

The Science                      

Hydrogen gas (H2) is a zero-emission alternative fuel that can be produced by microbes. One promising platform for H2production is the cyanobacteria Cyanothece51442. A new paper by researchers at the Pacific...

Posted: November 03
| Pacific Northwest National Laboratory