Lawrence Livermore National Laboratory



May 2018


New publication on multimodal LA-ICP-MS and nanoSIMS imaging

NanoSIMS image of copper and phosphorus signals in the zebrafish embryo retina, showing copper is enriched in puncta in the outer nuclear layer

NanoSIMS image of copper and phosphorus signals in the zebrafish embryo retina, showing copper is enriched in puncta in the outer nuclear layer.

We are developing high sensitivity, high spatial resolution methods to image essential metals in biological systems. Here, we collaborated with the C. Chang Lab at UC Berkeley to standardize our NanoSIMS copper measurements and apply the method to analysis of copper metabolism in zebrafish. Using this method, we were able to demonstrate that the fish metal distribution system prioritizes delivering copper to the eye, despite a severe copper deficit caused by a genetic mutation which mimics a human copper dysregulation disorder, Menkes disease.

[Ackerman CM, Weber PK, Xiao T, Thai B, Kuo TJ, Zhang E, Pett-Ridge J, Chang CJ. Multimodal LA-ICP-MS and nanoSIMS imaging enables copper mapping within photoreceptor megamitochondria in a zebrafish model of Menkes disease. Metallomics 2018 10(3):474-85.]



Greenhouse at LLNL now open!

The LLNL greenhouse

Our new greenhouse facility is now operational. It is a new IGC Arch Series 6500 greenhouse (1800 sf) with full temperature and light controls. It will eventually house an array of Coy isotope labeling chambers for plant 13CO2 isotope labeling and our Picarro portable Cavity Ring-Down Spectroscopy (CRDS) analyzer. We are currently setting up a series of plant-AMF inoculations.




Invited seminar on computational systems biology research

Presenter with his powerpoint slide on the wall behind him.

SFA team member Ali Navid recently gave an invited seminar as part of the LLNL’s and nearby Las Positas College student science and engineering seminar series. His talk, given to a large audience of community college science students and faculty, was titled “Computational Systems Biology: Simulating life from microbes to humans.” He discussed the state of computational systems biology in general and particularly at LLNL and presented examples of different types of modeling (e.g., constraint-based genome-scale, dynamic pharmacology, and 3D microbial biophysics models) that span multiple time and spatial scales from his SFA and biosecurity-related research.






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April 2018


New Publication: Quantitative isotope incorporation reveals substrate partitioning in a coastal microbial community

Taxon-specific Chip-SIP isotope incorporation data mapped onto the degradation pathway of various phytoplankton-derived organic substrates.

Taxon-specific Chip-SIP isotope incorporation data mapped onto the degradation pathway of various phytoplankton-derived organic substrates

SFA team members Xavier Mayali and Peter Weber have a new publication, supported by the Biofuels SFA, on the use of the Chip-SIP method (NanoSIMS and microarrays) to quantify the taxon-specific incorporation of algal-derived organic components by bacteria and eukaryotes. They carried out simultaneous incubations with 14 different stable isotope labeled substrates to examine phylogenetic signal of resource utilization and mixotrophy. The unique aspect of examining such a high number of substrates enabled them to identify substrate partitioning, and the data showed that two thirds of the taxa exhibited unique incorporation patterns, with strategies ranging from generalists to specialists.

[X. Mayali and P.K. Weber, Quantitative isotope incorporation reveals substrate partitioning in a coastal microbial community, FEMS Micro Ecol 94 (5), fiy047 (2018), doi:10.1093/femsec/fiy047]


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March 2018


SFA team members attend annual JGI user meeting

Xavier Mayali accepts the “Outside the Box Poster Award” from JGI Director Nigel Mouncey.

Xavier Mayali accepts the “Outside the Box Poster Award” from JGI Director Nigel Mouncey.

Five SFA team members presented at the 13th annual Department of Energy Joint Genome Institute (JGI) “Genomics of Energy and Environment” meeting in San Francisco, CA. Three posters were presented: Chris Ward, “Towards an integrative understanding of chytrid parasitism and its drivers in mass algal culture,” Jeff Kimbrel, “Combining multiple functional annotation tools increases completeness of metabolic annotation,” and Xavier Mayali, “Nanoscale Stable Isotope Tracing to Investigate Interactions between Bacteria and Biofuel-producing Algae.” Mayali’s poster won the “Outside the Box Poster Award.” The LLNL team also presented two invited talks: “Exploring Microbial Ecology with Isotopes and Imaging” by Jennifer Pett-Ridge and “Exploring Metabolite Production from Tryptophan Precursors in Two Algal Associated Bacteria, Algoriphagus sp. ARW1R1 and Marinobacter sp. 19DW” by Ty Samo.

Visit the JGI website for more information.



LLNL’s Biofuels SFA is hiring!

We have a position for a postdoc to examine host-microbe metabolic interactions and exchange in microalgae and perennial grasses using metabolomics, stable isotope probing, and proteogenomic approaches. For more information, see position 103155 at https://jobs.llnl.gov. If you have questions, feel free to contact Michael Thelen at thelen1@llnl.gov.


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February 2018


New publication: High initial sputter rate found for Vaccinia virions using isotopic labeling, NanoSIMS, and AFM

Five correlated AFM and SIMS images of Vaccinia virions showing colocalization in the two instruments and general nature of virion surface erosion during sputtering.

Correlated AFM and SIMS images of Vaccinia virions showing colocalization in the two instruments and general nature of virion surface erosion during sputtering. The AFM image (A) is a contrast-enhanced height image that corresponds to the region in the SIMS images (B–E). The sequence of SIMS images detail the distribution of the 12C14N- species counts during each scan. SIMS image (B), (C), (D), and (E) correspond to scan number 1, 15, 25, and 39, respectively. The decrease in species counts as a function of scan number is a result of lateral erosion caused by sputtering. Scale bar: 500 nm.

New research supported by the LLNL Biofuels Scientific Focus Area (SFA) shows the promise and challenge of studying the role of viruses in microbial systems. Viruses are known to be ubiquitous and infect all forms of life, including microbes. As such, they are thought to have major roles in carbon and nutrient cycling, but to date, these rates have been unexplored in most systems. With this research, SFA researchers Peter Weber and Ben Stewart and colleagues explored the potential to use high-spatial resolution secondary ion mass spectrometry (SIMS) with a NanoSIMS 50 to characterize nutrient transfer from host to virus using isotopically labeled DNA as a tracer. Their work showed the expected transfer of isotopic label, which is promising for future application of SIMS to virus ecology, but they also found that at the start of SIMS analysis, these tiny structures eroded 100 times faster than previously expected. For the relatively large Vaccinia virus in this study, this was not a major problem, but for bacterial phage, which are as small as 20 nm in diameter, new methods may be necessary to ensure quality measurements of nutrient uptake and cycling.

[S. Gates, R.C. Condit, N. Moussatche, B.J. Stewart, A.J. Malkin, and P.K. Weber, High Initial Sputter Rate Found for Vaccinia Virions Using Isotopic Labeling, NanoSIMS, and AFM, Anal. Chem. 90 (3), 1613 (2018), doi: 10.1021/acs.analchem.7b02786]


SFA team members present at 2018 Ocean Sciences meeting

An ion image generated from the NanoSIMS.

An ion image generated from the NanoSIMS illustrates the high spatial resolution visualization of algal and bacterial biomass, as determined from 12C 14N ion masses. Using these images, exchanges of C and N between algae and bacteria as a function of their spatial interactions can be measured.

SFA members Xavier Mayali and Ty Samo attended the 2018 Ocean Sciences meeting in Portland, Oregon in February to present some of their work on algal-bacterial interactions using stable isotope probing and NanoSIMS. Ty presented a talk entitled “Stable Isotope Probing and NanoSIMS Reveals Effects of Physical Association on Mutualisms Between Individual Bacterial Cells and Two Species of Phytoplankton” in the session “Bridging Microbial, Stable Isotope, and Micronutrient Approaches to Marine Carbon and Nitrogen Recycling.” Xavier presented a talk entitled “Investigating C transfer between diatoms and phycosphere-associated bacteria with stable isotopes and NanoSIMS” in the session “Phytoplankton-Bacteria Interactions: From Microscales to Ocean Scales.”

Learn more about the conference on the 2018 Ocean Sciences Meeting site.



What Can Algae Do For Us?

In this video, SFA scientists help explain what algae are and what they can do for us.

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