Skip to main content
Home

Navigation Menu

  • Back
  • About
    • Back
    • About

      Contact Us

      Business Address
      5241 Broad Branch Rd. NW

      Washington , DC 20015
      United States place Map
      Call Us (202) 387-640
    • Who We Are
      • Back
      • Leadership
      • Board & Advisory Committee
      • Initiatives
      • Financial Stewardship
      • Awards & Accolades
      • History
    • Connect with Us
      • Back
      • Outreach & Education
      • Newsletter
      • Yearbook
    • Working at Carnegie

    Contact Us

    Business Address
    5241 Broad Branch Rd. NW

    Washington , DC 20015
    United States place Map
    Call Us (202) 387-6400
  • Research
    • Back
    • Research Areas & Topics
    • Research Areas & Topics
      • Back
      • Research Areas
      • From genomes to ecosystems and from planets to the cosmos, Carnegie Science is an incubator for cutting-edge, interdisciplinary research.
      • Astronomy & Astrophysics
        • Back
        • Astronomy & Astrophysics
        • Astrophysical Theory
        • Cosmology
        • Distant Galaxies
        • Milky Way & Stellar Evolution
        • Planet Formation & Evolution
        • Solar System & Exoplanets
        • Telescope Instrumentation
        • Transient & Compact Objects
      • Earth Science
        • Back
        • Earth Science
        • Experimental Petrology
        • Geochemistry
        • Geophysics & Geodynamics
        • Mineralogy & Mineral Physics
      • Ecology
        • Back
        • Ecology
        • Atmospheric Science & Energy
        • Adaptation to Climate Change
        • Water Quality & Scarcity
      • Genetics & Developmental Biology
        • Back
        • Genetics & Developmental Biology
        • Adaptation to Climate Change
        • Developmental Biology & Human Health
        • Genomics
        • Model Organism Development
        • Nested Ecosystems
        • Symbiosis
      • Matter at Extreme States
        • Back
        • Matter at Extreme States
        • Extreme Environments
        • Extreme Materials
        • Mineralogy & Mineral Physics
      • Planetary Science
        • Back
        • Planetary Science
        • Astrobiology
        • Cosmochemistry
        • Mineralogy & Mineral Physics
        • Planet Formation & Evolution
        • Solar System & Exoplanets
      • Plant Science
        • Back
        • Plant Science
        • Adaptation to Climate Change
        • Nested Ecosystems
        • Photosynthesis
        • Symbiosis
    • Divisions
      • Back
      • Divisions
      • Biosphere Sciences & Engineering
        • Back
        • Biosphere Sciences & Engineering
        • About

          Contact Us

          Business Address
          5241 Broad Branch Rd. NW

          Washington , DC 20015
          United States place Map
          Call Us (202) 387-640
        • Research
        • Culture
        • Path to Pasadena
      • Earth & Planets Laboratory
        • Back
        • Earth & Planets Laboratory
        • About

          Contact Us

          Business Address
          5241 Broad Branch Rd. NW

          Washington , DC 20015
          United States place Map
          Call Us (202) 387-640
        • Research
        • Culture
        • Campus
      • Observatories
        • Back
        • Observatories
        • About

          Contact Us

          Business Address
          5241 Broad Branch Rd. NW

          Washington , DC 20015
          United States place Map
          Call Us (202) 387-640
        • Research
        • Culture
        • Campus
    • Instrumentation
      • Back
      • Instrumentation
      • Our Telescopes
        • Back
        • Our Telescopes
        • Magellan Telescopes
        • Swope Telescope
        • du Pont Telescope
      • Observatories Machine Shop
      • EPL Research Facilities
      • EPL Machine Shop
      • Mass Spectrometry Facility
      • Advanced Imaging Facility
  • People
    • Back
    • People
      Observatory Staff

      Featured Staff Member

      Staff Member

      Staff Member

      Professional Title

      Learn More
      Observatory Staff

      Search For

    • Search All People
      • Back
      • Staff Scientists
      • Leadership
      • Biosphere Science & Engineering People
      • Earth & Planets Laboratory People
      • Observatories People
    Observatory Staff
    Dr. Allan Spradling
    Staff Scientist, Emeritus Director

    Featured Staff Member

    Allan Spradling portait

    Dr. Allan Spradling - HHMI

    Staff Scientist, Emeritus Director

    Learn More
    Observatory Staff
    Dr. Allan Spradling
    Staff Scientist, Emeritus Director

    Allan Spradling and his team focus on the biology of reproduction, particularly oogenesis — the process of egg formation.

    Search For

    Search All Staff
  • Events
    • Back
    • Events
    • Search All Events
      • Back
      • Biosphere Science & Engineering Events
      • Earth & Planets Laboratory Events
      • Observatories Events

    Upcoming Events

    Events

    Events

    People sit on the shore at sunset.
    Workshop

    Seventh Workshop on Trait-based Approaches to Ocean Life

    Pacific Grove, CA

    August 4

    9:00pm PDT

    A gray-true color Mercury next to a colorized Mercury that combines visible and near infrared light to highlight the differences in surface composition.
    Public Program

    Mercury beyond MESSENGER: Recent Progress from the Earth and Planets Laboratory

    Anne Pommier, Staff Scientist, EPL

    June 5

    6:30pm EDT

    brian-yurasits-EQlwRGr5sqk-unsplash.jpg
    Seminar

    Microenvironmental ecology and symbiosis

    Dr. Michael Kühl

    May 14

    11:00am PDT

  • News
    • Back
    • News
    • Search All News
      • Back
      • Biosphere Science & Engineering News
      • Earth & Planets Laboratory News
      • Observatories News
      • Carnegie Science News
    News

    Recent News

    News

    Read all News
    Vera Rubin at Carnegie Science’s former Department of Terrestrial Magnetism, now part of the Earth and Planets Laboratory, in 1972 usi
    Breaking News
    June 18, 2025

    10 Iconic Photographs of Vera Rubin

    Vera Rubin at Lowell Observatory, 69-inch [i.e., 72-inch] Telescope (Kent Ford in white helmet)
    Breaking News
    June 17, 2025

    Things Named After Carnegie Astronomer Vera Rubin

    A gray-true color Mercury next to a colorized Mercury that combines visible and near infrared light to highlight the differences in surface composition.
    Breaking News
    June 17, 2025

    Inside Mercury: What Experimental Geophysics Is Revealing About Our Strangest Planet

  • Donate
    • Back
    • Donate
      - ,

    • Make a Donation
      • Back
      • Support Scientific Research
      • The Impact of Your Gift
      • Planned Giving
    Jo Ann Eder

    I feel passionately about the power of nonprofits to bolster healthy communities.

    - Jo Ann Eder , Astronomer and Alumna

    Header Text

    Postdoctoral alumna Jo Ann Eder is committed to making the world a better place by supporting organizations, like Carnegie, that create and foster STEM learning opportunities for all. 

    Learn more arrow_forward
  • Home

Abstract
Soil dissolved organic matter (DOM) is the most reactive pool of soil organic matter. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) is a powerful tool for obtaining molecular-level DOM information. The ongoing atmospheric nitrogen (N) deposition could cause some negative effects on tropical and subtropical forest ecosystems, and biochar is considered to be an effective soil ameliorator. However, few studies have evaluated the effects of biochar and N deposition, either separately or in combination, on the molecular composition of soil DOM. In this study, we conducted a pot experiment using Chinese fir seedlings amended with biochar (0, 12, and 36 t biochar ha-1, prepared from corn stover at 450 C) and inorganic N (NH4NO3: 0, 40, and 80 kg N ha-1 y-1) in a full factorial design (four replications per treatment) and characterized soil DOM using FTICR-MS. A total of 6084 types of formulas were identified in this study. All 36 samples had 2109 types of formulas in common, which had much lower N/C and P/C ratios than the bulk DOM samples. Permutation-based multivariate analysis of variance revealed that both N addition and biochar application had a significant impact on DOM chemodiversity. N addition increased the relative abundance of lignins and lipids, which may be a way for Chinese fir to acclimate to an acidic environment by expanding roots and fixing N. Biochar amendment increased the relative abundance of carbohydrates and tannins in soil DOM at each N application level. Soil pH is a key soil variable controlling DOM composition, and an increase in pH after biochar amendment contributed greatly to the occurrence of DOM compounds with an O/C > 0.5, which are easily degradable. In particular, lignins associated with low N/C were more abundant at higher pH. Biochar application also improved the efficiency of roots in acquiring nutrients, reduced the relative biomass of roots, and decreased the relative content of lignins or lipids, which primarily originated from the roots. In summary, biochar amendment effectively alleviated the negative effects of N addition by investing more N into the production of easily degradable DOM compounds and stimulating the biogeochemical cycle of N.
View Full Publication open_in_new
Abstract
Increasingly frequent and intense heatwaves threaten ecosystem health in a warming climate. However, plant responses to heatwaves are poorly understood. A key uncertainty concerns the intensification of transpiration when heatwaves suppress photosynthesis, known as transpiration-photosynthesis decoupling. Field observations of such decoupling are scarce, and the underlying physiological mechanisms remain elusive. Here, we use carbonyl sulphide (COS) as a leaf gas exchange tracer to examine potential mechanisms leading to transpiration-photosynthesis decoupling on a coast live oak in a southern California woodland in spring 2013. We found that heatwaves suppressed both photosynthesis and leaf COS uptake but increased transpiration or sustained it at non-heatwave levels throughout the day. Despite statistically significant decoupling between transpiration and photosynthesis, stomatal sensitivity to environmental factors did not change during heatwaves. Instead, midday photosynthesis during heatwaves was restricted by internal diffusion, as indicated by the lower internal conductance to COS. Thus, increased evaporative demand and nonstomatal limitation to photosynthesis act jointly to decouple transpiration from photosynthesis without altering stomatal sensitivity. Decoupling offered limited potential cooling benefits, questioning its effectiveness for leaf thermoregulation in xeric ecosystems. We suggest that adding COS to leaf and ecosystem flux measurements helps elucidate diverse physiological mechanisms underlying transpiration-photosynthesis decoupling.
View Full Publication open_in_new
Abstract
TurboID-based proximity labeling coupled to mass spectrometry (PL-MS) has emerged as a powerful tool for mapping protein-protein interactions in both plant and animal systems. Despite advances in sensitivity, PL-MS studies can still suffer from false negatives, especially when dealing with low abundance bait proteins and their transient interactors. Protein-level enrichment for biotinylated proteins is well developed and popular, but direct detection of biotinylated proteins by peptide-level enrichment and the difference in results between direct and indirect detection remain underexplored. To address this gap, we compared and improved enrichment and data analysis methods using TurboID fused to SPY, a low-abundance O-fucose transferase, using an AAL-enriched SPY target library for cross-referencing. Our results showed that MyOne and M280 streptavidin beads significantly outperformed antibody beads for peptide-level enrichment, with M280 performing best. In addition, while a biotin concentration less than 50 uM is recommended for protein-level enrichment in plants, higher biotin concentrations can be used for peptide-level enrichment, allowing us to improve detection and data quality. MSFragger protein identification and quantification software outperformed Maxquant and Protein Prospector for SPY interactome enrichment due to its superior detection of biotinylated peptides. Our improved washing protocols for protein-level enrichment mitigated bead collapse issues, improving data quality, and reducing experimental time. We found that the two enrichment methods provided complementary results and identified a total of 160 SPY-TurboID-enriched interactors, including 60 previously identified in the AAL-enriched SPY target list and 100 additional novel interactors. SILIA quantitative proteomics comparing WT and spy-4 mutants showed that SPY affects the protein levels of some of the identified interactors, such as nucleoporin proteins. We expect that our improvement will extend beyond TurboID to benefit other PL systems and hold promise for broader applications in biological research.
View Full Publication open_in_new
Abstract
Alternative splicing is an important regulatory process in eukaryotes. In plants, the major form of alternative splicing is intron retention. Despite its importance, the global impact of AS on the Arabidopsis proteome has not been investigated. In this study, we address this gap by performing a comprehensive integrated analysis of how changes in AS can affect the Arabidopsis proteome using mutants that disrupt ACINUS and PININ, two evolutionarily conserved alternative splicing factors. We used tandem mass tagging (TMT) with real-time search MS3 (RTS-SPS-MS3) coupled with extensive sample fractionations to achieve very high coverage and accurate protein quantification. We then integrated our proteomic data with transcriptomic data to assess how transcript changes and increased intron retention (IIR) affect the proteome. For differentially expressed transcripts, we have observed a weak to moderate correlation between transcript changes and protein changes. Our studies revealed that some IIRs have no effect on either transcript or protein levels, while some IIRs can significantly affect protein levels. Surprisingly, we found that IIRs have a much smaller effect on increasing protein diversity. Notably, the increased intron retention events detected in the double mutant are also detected in the WT under various biotic or abiotic stresses. We further investigated the characteristics of the retained introns. Our extensive proteomic data help to guide the phenotypic analysis and reveal that collective protein changes contribute to the observed phenotypes of the increased anthocyanin, pale green, reduced growth, and short root observed in the acinus pnn double mutant. Overall, our study provides insight into the intricate regulatory mechanism of intron retention and its impact on protein abundance in plants.
View Full Publication open_in_new
Abstract
Cell polarity is used to guide asymmetric divisions and create morphologically diverse cells. We find that two oppositely oriented cortical polarity domains present during the asymmetric divisions in the Arabidopsis stomatal lineage are reconfigured into polar domains marking ventral (pore-forming) and outward-facing domains of maturing stomatal guard cells. Proteins that define these opposing polarity domains were used as baits in miniTurboID-based proximity labeling. Among differentially enriched proteins, we find kinases, putative microtubule-interacting proteins, and polar SOSEKIs with their effector ANGUSTIFOLIA. Using AI-facilitated protein structure prediction models, we identify potential protein-protein interaction interfaces among them. Functional and localization analyses of the polarity protein OPL2 and its putative interaction partners suggest a positive interaction with mitotic microtubules and a role in cytokinesis. This combination of proteomics and structural modeling with live-cell imaging provides insights into how polarity is rewired in different cell types and cell-cycle stages.
View Full Publication open_in_new
Abstract
Alternative splicing is an important regulatory process in eukaryotes. In plants, the major form of alternative splicing is intron retention. Despite its importance, the global impact of AS on the Arabidopsis proteome has not been investigated. In this study, we address this gap by performing a comprehensive integrated analysis of how changes in AS can affect the Arabidopsis proteome using mutants that disrupt ACINUS and PININ, two evolutionarily conserved alternative splicing factors. We used tandem mass tagging (TMT) with real-time search MS3 (RTS-SPS-MS3) coupled with extensive sample fractionations to achieve very high coverage and accurate protein quantification. We then integrated our proteomic data with transcriptomic data to assess how transcript changes and increased intron retention (IIR) affect the proteome. For differentially expressed transcripts, we have observed a weak to moderate correlation between transcript changes and protein changes. Our studies revealed that some IIRs have no effect on either transcript or protein levels, while some IIRs can significantly affect protein levels. Surprisingly, we found that IIRs have a much smaller effect on increasing protein diversity. Notably, the increased intron retention events detected in the double mutant are also detected in the WT under various biotic or abiotic stresses. We further investigated the characteristics of the retained introns. Our extensive proteomic data help to guide the phenotypic analysis and reveal that collective protein changes contribute to the observed phenotypes of the increased anthocyanin, pale green, reduced growth, and short root observed in the acinus pnn double mutant. Overall, our study provides insight into the intricate regulatory mechanism of intron retention and its impact on protein abundance in plants.
View Full Publication open_in_new
Abstract
At a rapid pace, biologists are learning the many ways in which resident microbes influence, and sometimes even control, their hosts to shape both health and disease. Understanding the biochemistry behind these interactions promises to reveal completely novel and targeted ways of counteracting disease processes. However, in our protocols and publications, we continue to describe these new results using a language that originated in a completely different context. This language developed when microbial interactions with hosts were perceived to be primarily pathogenic, as threats that had to be vanquished. Biomedicine had one dominating thought: winning this war against microorganisms. Today, we know that beyond their defensive roles, host tissues, especially epithelia, are vital to ensuring association with the normal microbiota, the communities of microbes that persistently live with the host. Thus, we need to adopt a language that better encompasses the newly appreciated importance of host-microbiota associations. We also need a language that frames the onset and progression of pathogenic conditions within the context of the normal microbiota. Such a reimagined lexicon should make it clear, from the very nature of its words, that microorganisms are primarily vital to our health, and only more rarely the cause of disease.This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.
View Full Publication open_in_new
Abstract
All animals and plants likely require interactions with microbes, often in strong, persistent symbiotic associations. While the recognition of this phenomenon has been slow in coming, it will impact most, if not all, subdisciplines of biology.
View Full Publication open_in_new
Abstract
The symbiotic relationship between the bioluminescent bacterium Vibrio fischeri and the bobtail squid Euprymna scolopes serves as a valuable system to investigate bacterial growth and peptidoglycan (PG) synthesis within animal tissues. To better understand the growth dynamics of V. fischeri in the crypts of the light-emitting organ of its juvenile host, we showed that, after the daily dawn-triggered expulsion of most of the population, the remaining symbionts rapidly proliferate for 6 h. At that point the population enters a period of extremely slow growth that continues throughout the night until the next dawn. Further, we found that PG synthesis by the symbionts decreases as they enter the slow-growing stage. Surprisingly, in contrast to the most mature crypts (i.e., Crypt 1) of juvenile animals, most of the symbiont cells in the least mature crypts (i.e., Crypt 3) were not expelled and, instead, remained in the slow-growing state throughout the day, with almost no cell division. Consistent with this observation, the expression of the gene encoding the PG-remodeling enzyme, L,D-transpeptidase (LdtA), was greatest during the slowly growing stage of Crypt 1 but, in contrast, remained continuously high in Crypt 3. Finally, deletion of the ldtA gene resulted in a symbiont that grew and survived normally in culture, but was increasingly defective in competing against its parent strain in the crypts. This result suggests that remodeling of the PG to generate additional 3-3 linkages contributes to the bacterium's fitness in the symbiosis, possibly in response to stresses encountered during the very slow-growing stage.
View Full Publication open_in_new
Abstract
Capturing images of the nuclear dynamics within live cells is an essential technique for comprehending the intricate biological processes inherent to plant cell nuclei. While various methods exist for imaging nuclei, including combining fluorescent proteins and dyes with microscopy, there is a dearth of commercially available dyes for live-cell imaging. In Arabidopsis thaliana, we discovered that nuclei emit autofluorescence in the near-infrared (NIR) range of the spectrum and devised a non-invasive technique for the visualization of live cell nuclei using this inherent NIR autofluorescence. Our studies demonstrated the capability of the NIR imaging technique to visualize the dynamic behavior of nuclei within primary roots, root hairs, and pollen tubes, which are tissues that harbor a limited number of other organelles displaying autofluorescence. We further demonstrated the applicability of NIR autofluorescence imaging in various other tissues by incorporating fluorescence lifetime imaging techniques. Nuclear autofluorescence was also detected across a wide range of plant species, enabling analyses without the need for transformation. The nuclear autofluorescence in the NIR wavelength range was not observed in animal or yeast cells. Genetic analysis revealed that this autofluorescence was caused by the phytochrome protein. Our studies demonstrated that nuclear autofluorescence imaging can be effectively employed not only in model plants but also for studying nuclei in non-model plant species.
View Full Publication open_in_new

Pagination

  • Previous page chevron_left
  • …
  • Page 71
  • Page 72
  • Page 73
  • Page 74
  • Current page 75
  • Page 76
  • Page 77
  • Page 78
  • Page 79
  • …
  • Next page chevron_right
Subscribe to

Get the latest

Subscribe to our newsletters.

Privacy Policy
Home
  • Instagram instagram
  • Twitter twitter
  • Youtube youtube
  • Facebook facebook

Science

  • Biosphere Sciences & Engineering
  • Earth & Planets Laboratory
  • Observatories
  • Research Areas
  • Strategic Initiatives

Legal

  • Financial Statements
  • Conflict of Interest Policy
  • Privacy Policy

Careers

  • Working at Carnegie
  • Scientific and Technical Jobs
  • Postdoctoral Program
  • Administrative & Support Jobs
  • Carnegie Connect (For Employees)

Contact Us

  • Contact Administration
  • Media Contacts

Business Address

5241 Broad Branch Rd. NW

Washington, DC 20015

place Map

© Copyright Carnegie Science 2025