Alice Dohnalkova

Electron microscopy imaging and analyses of signs of iron toxicity found in the macrophages of the cardiac tissue

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Alice Dohnalkova

Sudden blockage of coronary artery is a common cause of heart attacks (myocardial infarction, MI). The team of Prof. Rohan Dharmakumar at the Indiana University School of Medicine conduct a NIH…

Establish a Penn State Center for Environmental Kinetics - as part of the Environmental Molecular Science Institute (EMSI) program (NSF/DOE-OBER) [PNNL Scope #47287, Zachara EMSI)

Lead Institution

Pennsylvania State University

Principal Investigator

William Burgos

Project type

Exploratory Research

The National Science Foundation has awarded a team of Penn State researchers $6.7 million to establish a new center for the study of environmental kinetics. Susan L. Brantley, director of the…

3d reconstruction of bacterial extracellular material for investigation of membrane turnover during metal reduction.

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Alice Dohnalkova

Dissimilatory metal reducing bacteria can immobilize soluble metals such as Fe, U or Tc by reducing them into less soluble material. This presents an elegant method for immobilization of motile toxic…

Rhizosphere Underground: Unraveling the Role of Microbes in Stabilizing Carbon Pools in Soils

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Alice Dohnalkova

Microorganisms are fundamental to biogeochemical processes, as microbial metabolism significantly contributes to the regulation of terrestrial carbon and nitrogen cycling. However, the impact of the…

A new capability for high-resolution 3D imaging of soil structure and soil chemistry in the rhizosphere

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Tamas Varga

We aim to answer the following critical questions about the rhizosphere: (i) What is the distribution of important nutrient elements like P in the soil and around the root? (ii) How much of the…

Characterization of novel arsenic-iron precipitates formed during biological iron reduction

Lead Institution

Colorado State University

Principal Investigator

Thomas Borch

Project type

Exploratory Research

Arsenic (As) is a priority pollutant, the fate of which is in part controlled by reactions with ferrous iron. Ferrous iron is capable of mediating solid phase transformations of soil and sediment…

Geobiology of Chemical Weathering: Spatially Explicit Characterization of the Inorganic Chemical Composition of Mycorrhizospheric Biofilms

Lead Institution

Washington State University

Principal Investigator

Chester Keller

Project type

Large-Scale EMSL Research

Rich literatures and recent advances across several fields have set the stage for process-based research into the biogeochemical agency of vascular plants -- in particular, how their physiologies…

Multi-Omics Evaluation of Tripartite Associations in Red Alder Roots: Integrated Transcriptomics, Proteomics, Metabolomics and Metabolite Imaging of Red Alder Symbiotic Associations in Root Tissue

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kim Hixson

This proposal presents the unique opportunity to conduct the first ever integrated multi-omics and imaging evaluation of the Alnus rubra (red alder tree)/Frankia alni (bacteria)/Alpova diplophloeus …

Structure and Chemical Mapping of Soil Organic Matter on Mineral Surfaces

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Ravi Kukkadapu

Secreted and decomposing soil organic matter (SOM) containing carbon, nitrogen, phosphorus, and metals form the basis of many bio/organic matter-mineral interactions in soils. These compounds are …

Host Cell Interactions with Human Infectious Diseases, Straub

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Timothy Straub

Project type

Large-Scale EMSL Research

Pathogenesis is a complex biological process between the human host and the infectious disease agent. In our previous successful collaboration with EMSL scientists (EMSL Project 16297), which lead…

Role of Microenvironments and Transition Zones in Field scale microbial ecology and biogeochemistry

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James McKinley

Project type

Exploratory Research

This is a renewal proposal for a previous collaborative effort between the PNNL Scientific Focus Area (SFA) and EMSL. The research proposed will resolve critical Hanford and basic subsurface science…

Biomineralization and Biosequestration Mechanisms at Life's Upper Temperatures: A Reappraisal using Novel CryoEM Techniques

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Sherry Cady

Though microbes can indirectly and metabolically transform, sequester, and transport (i) ions, (ii) organic and inorganic complexes, and (iii) precipitates via a wide range of mechanisms,…

Extracellular Research Thrust for EMSL SSA

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

Here we propose to address the basic geochemical and biogeochemical interactions that mediate organic-mineral interactions. Identifying binding mechanisms at the organic matter-mineral interface will…

Special Projects in Electron Microscopy

Lead Institution

David Heil Associates Corporation

Principal Investigator

James Young

Project type

Exploratory Research

WSU-TriCities course offering for practical training in one or more areas of electron microscopy: TEM, SEM, ultramicrotomy, specimen processing, darkroom procedures and light microscopy. Involves…

Correlative High-Resolution Imaging and Spectroscopy to Characterize the Structure and Biogeochemical Function of Microbial Biofilms

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Matthew Marshall

Project type

Exploratory Research

This proposal leverages knowledge and experience gained from DOE-funded research to elucidate the mechanisms involved in dissimilatory metal reduction, as well as, microscale imaging and analytical…

Hydro-Biogeochemical Process Dynamics in the Groundwater-Surface Water Interaction Zone

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Zachara

This is a renewal proposal for a previous collaborative effort between the PNNL Scientific Focus Area (SFA) and EMSL.PNNL Scientific Focus Area. The PNNL SFA will develop a predictive understanding…

Extracellular Research Thrust for EMSL SSA

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Kirsten Hofmockel

This project will develop a conceptual framework that defines the biotic and abiotic mechanisms regulating the persistence of mineral associated organic matter (OM). The specific goals are to…

Electron microscopy imaging of cyanobacteria Synechcystis sp.

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Alice Dohnalkova

Project type

Grand Challenge

As a part of Grand Challenges in Membrane biology, Synechocystis sp. will be investigated in regards of cell morphology and elemental analysis of minerals associated with their outer and inner…

Novel flow based biomolecule immobilization on nanoporous scaffolds
for enhanced biosensor performance and drug delivery applications

Lead Institution

University of Washington

Principal Investigator

Amy Shen

Project type

Exploratory Research

Biosensors play indispensible roles in disease diagnosis, drug screening, and forensic applications. One important area of biosensor research is the immobilization of biomolecules (i.e. enzyme, DNA)…

Rhizosphere Underground:
Unraveling the Role of Microbes in Stabilizing Carbon Pools in Soils

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Alice Dohnalkova

Microorganisms are fundamental to biogeochemical cycling, as microbial metabolism significantly contributes to the regulation of terrestrial carbon and nitrogen cycling. However, the impact of the…

Influences of Hydrologic Exchange Flows on River Corridor and Watershed Biogeochemical Function

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James Stegen

We are developing predictive understanding of the processes that govern influences of hydrologic exchange flows on water quality, nutrient dynamics, and ecosystem health in dynamic river corridor…

Microscopic visualization of membrane pores and bacterial foulants

Lead Institution

University of Houston

Principal Investigator

Shankar Chellam

Project type

Exploratory Research

My research is mainly centered on membrane technologies for municipal water purification. We (1) elucidate contaminant transport and membrane fouling mechanisms, (2) devise methods to enhance…

Coupling of Fe and Tc Speciation in Subsurface Sediments: Implications to Long-Term Tc Immobilization (Zachara NABIR-Fe/Tc, PNNL Scope # 40761)

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Zachara

Project type

Exploratory Research

Creating an in-situ bio-barrier containing sediment-bound, biogenic FE(II) to reduce and collect mobile Tc(VII)O4 - The research objective is to provide scientific insights on the rates of reductive…

Carbon, Oxide, Metal Sequestration Mechanisms of Hot Springs Microbial Communities: Establishing a Technical Platform for Chemical Imaging Investigation

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Sherry Cady

Though microbes can indirectly and metabolically transform, sequester, and transport (i) ions, (ii) organic and inorganic complexes, and (iii) precipitates via a wide range of mechanisms,…

Understanding the Complexity of Biogenic Mineral Formation in Microbial Extracellular Polymeric Substances: a 3-d Nano-scale Perspective

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Alice Dohnalkova

Microbial role in sequestration of various metal has been well studied, including PNNL Microbiology group and numerous EMSL user projects. However, the current view of microbial-mineral interactions…

Biogenic Iron Materials

Lead Institution

J. Craig Venter Institute

Principal Investigator

Yuri Gorby

Project type

Exploratory Research

We will image iron minerals produced by the reduction of solid phase ferric oxides. The research will require the use of field emission SEM and TEM.

The Role of Microenvironments and Physicochemical Subsurface Components on Field Scale Biogeochemistry and Contaminant Mobility

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James McKinley

Project type

Exploratory Research

This is a renewal proposal for a previous collaborative effort between the PNNL Scientific Focus Area (SFA) and EMSL. The research proposed will resolve critical Hanford and basic subsurface science…

Uranium Biomineralization by Caulobacter crescentus

Lead Institution

Lawrence Livermore National Laboratory

Principal Investigator

Yongqin Jiao

Project type

Large-Scale EMSL Research

The research goal of this proposal is to understand and evaluate the potential of using the aerobic bacterium Caulobacter crescentus for the application of uranium bioremediation. Previous work by…

Influences of Hydrologic Exchange Flows on River Corridor and Watershed Biogeochemical Function

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James Stegen

We are developing predictive understanding of the processes that govern influences of hydrologic exchange flows on water quality, nutrient dynamics, and ecosystem health in dynamic river corridor…

The in vivo localization and interactions between structural components of the Shewanella oneidensis MR-1 metal reducing system by high resolution transmission electron microscopy.

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Matthew Marshall

Project type

Grand Challenge

To understand the mechanisms of anaerobic metal oxide reduction, important issues regarding the subcellular localization and the outer membrane architecture of the iron-reducing respiratory chain…

EMSL/FCSD Scientific Partner Proposal on the Dynamics of Biological and Catalytic Systems

Lead Institution

University of Liverpool

Principal Investigator

Nigel Browning

Project type

Scientific Partner

The goal of this Scientific Partner Proposal is to develop the capability to observe “live” biological and catalytic processes in the dynamic transmission electron microscope (DTEM). Live biological…

Rhizosphere Underground: Unraveling the Role of Microbes in Stabilizing Carbon Pools in Soils

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Alice Dohnalkova

A team of researchers representing selected state-of-the-art EMSL capabilities and the expertise in environmental microbiology, biogeochemistry, molecular biology, soil dynamics and hydrology have…

The role of microbes in biomineral polymorph selection

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Alice Dohnalkova

Biologically precipitated minerals are commonly present in very close association with biomineralizing microbes. Microbe-mineral interactions are complex in that they are often reciprocal in nature…

Electrochemical analyses of the electron transfer rates of MtrC and OmcA to hematite

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Liang Shi

Project type

Large-Scale EMSL Research

Decaheme c-type cytochromes MtrC and OmcA of Shewanella oneidensis MR-1 are hypothesized as terminal reductases to the insoluble forms of iron and manganese oxides [Fe(III)/Mn(III/IV)] because they…

Role of Microenvironments and Transition Zones in Subsurface Reactive Contaminant Transport

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

James McKinley

This is a renewal proposal for a previous collaborative effort between the PNNL Scientific Focus Area (SFA) and EMSL. The research proposed will resolve critical Hanford and basic subsurface science…

Hydro-Biogeochemical Process Dynamics in the Groundwater-Surface Water Interaction Zone

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Zachara

This is a renewal proposal for a previous collaborative effort between the PNNL Scientific Focus Area (SFA) and EMSL.PNNL Scientific Focus Area. The PNNL SFA will develop a predictive understanding…

Revealing Mechanism for Stabilizing Organic Carbon - Innovative Chemical Imaging

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Alice Dohnalkova

Microbial interactions with soil minerals lead to production of stabilized soil organic matter (SOM) [1]. We hypothesize that mineralization of microbial extracellular polymeric substances (EPS) is…

Microscale and spectroscopic investigations in geochemical and microbiological systems

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

John Zachara

Project type

Large-Scale EMSL Research

Apply experimental manipulation and field investigations to understanding the behavior of selected chemical and microbial components in natural systems. The research is targeted towards compounds…

Unraveling the role of mycorrhizospheric bacterial biofilms in soil minerals weathering

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Alice Dohnalkova

This is a 5% proposal which will allow me to work on the research part of my dissertation for my PhD at WSU. Proposal 40111 is associated with this work, which was submitted by the WSU Pullman group…

Decreasing the amount of material required for gross biological carbon and nitrogen flux measurements by more than 12 orders of magnitude using ion implantation isotope dilution and stable isotope measurements by NanoSIMS

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

John Cliff

Advances in mass spectrometry coupled to stable isotope probing techniques have profoundly influenced our understanding of process level biology and biogeochemistry. When stable isotope compounds and…

Harnessing Biomineralization Potential of Metal-Oxidizing Bacteria for REE Synthesis

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Alex Beliaev

Although redox reactions and enzymes participating in the extracellular oxidation of Fe and Mn are identified, little is known about the biomineralization mechanisms that facilitate formation…

3-Dimensional Reconstruction and Modeling of Bacterial Extracellular Polymeric Substances (ExPS)

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Alice Dohnalkova

We propose to apply the method of Cryo-electron tomography for fine scale imaging of the bacterial extracellular polymeric substances (ExPS) in its native state. We will create a 3D model of fully…

Membrane Biology Research Campaign: Use of synthetic biology to probe molecular machines in photosynthesis

Lead Institution

Washington University in St. Louis

Principal Investigator

Himadri Pakrasi

Project type

Research Campaign

We have shown in our previous EMSL collaborations our ability to develop systems-level models of cyanobacterial processes. In the present proposal, our objective is to characterize and…

Carbon Sequestration Beneath the Active Zone of the Rhizosphere: Insights from Extremophile Ecosystems

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Sherry Cady

To better understand the ultimate fate of carbon sequestered in the subsurface, we are studying carbon sequestration mechanisms in mineralizing extremophile environments. Such ecosystems provide an…

Proteomic studies of growth and metabolism in Corynebacterium glutamicum R

Lead Institution

Research Institute of Innovative Technology for the Earth

Principal Investigator

Hideaki Yukawa

Project type

Exploratory Research

Corynebacterium glutamicum is a soil bacterium isolated in Japan in the 1950's as an L-glutamic acid producer (Kinoshita, et al., 1957). Strains derived from C. glutamicum are used in a number…

Cryo-TEM investigation of polyketide synthase megacomplexes in Candidatus Endobugula sertula and Teredinibacter turnerae

Lead Institution

Oregon Health & Science University

Principal Investigator

Margo Haygood

Project type

Capability Research

This Biological and Life Sciences, Biological Interactions and Interfaces Theme, Standard, General, Non-Proprietary project proposal for use of the EMSL cryo-TEM and tomography facility will focus on…

Rhizosphere Research Campaign: The plant-soil interface - understanding dynamic interactions in the context of environmental change

Lead Institution

University of Missouri - Columbia

Principal Investigator

Gary Stacey

Project type

Research Campaign

The ultimate, long-term goal is to determine what drives source-sink relationships that control the cycling of plant nutrients belowground. To fully appreciate the complexities of this dynamic…

Follow-up work on Rhizosphere Underground project (proposal 49147), and work in support of brief one-time exploratory projects within PNNL.

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

Alice Dohnalkova

The EMSL Seed LDRD Rhizosphere project has been closed, but I still need to finish some things for 2 publications. I will use the Cryo TEM after hours, or if there is not conflict with the scheduled…

Functional Materials for Separation and Sensing

Lead Institution

Pacific Northwest National Laboratory

Principal Investigator

Jay Grate

Project type

Large-Scale EMSL Research

A large number of mission areas of the US. DOE demand functional materials that will meet the operational requirements of targeted applications. Indeed, innovative solutions to pressing national…

Untangling the complexity of phototroph-heterotroph interactions in the lab and in the field

Lead Institution

Environmental Molecular Sciences Laboratory

Principal Investigator

H Wiley

Project type

Large-Scale EMSL Research

Despite the fact that ubiquitous microbial interspecies interactions form the foundation of energy flow as well as the biogeochemical cycling of carbon and other elements within natural environments,…