16 Works

Additional file 2 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 2: Supplemental Table S1. Impact of adding different concentrations of non-ionic detergents to the SIP gradient medium on percent DNA recovery (n=3).

Additional file 2 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 2: Supplemental Table S1. Impact of adding different concentrations of non-ionic detergents to the SIP gradient medium on percent DNA recovery (n=3).

Additional file 4 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 4: Supplemental Table S3. Assembly statistics, taxonomic lineage, and atom percent excess (APE) of the metagenome amplified genomes (MAGs) created in this study.

Additional file 5 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 5: Supplemental Table S4. Number of CAZyme family domains in the highly enriched MAGs (>10 atom% excess 13C). AOA = archaeal ammonia oxidizer, Fibro = Fibrobacterota, Myxo = Myxococcota (Myxococcaceae).

Additional file 6 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 6: Supplemental Table S5. Genomic abundance of MEROPS proteae gene per MAG. Columns indicate MEROPS protease families. APE = atom percent excess.

Additional file 7 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 7: Supplemental Table S6. CAZymes for the Myxococcota MAGs. Fen-1088 MAGs are highlighted in yellow. MAGs are sorted by increasing atom percent excess (APE) 13C.

Additional file 5 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 5: Supplemental Table S4. Number of CAZyme family domains in the highly enriched MAGs (>10 atom% excess 13C). AOA = archaeal ammonia oxidizer, Fibro = Fibrobacterota, Myxo = Myxococcota (Myxococcaceae).

Additional file 8 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 8: Supplemental Table S7. Number of CAZy gene homologs that can potentially target a particular substrate. Substrate assignments based off of the Glycoside Hydrolase categories from Berlemonte and Martiny 2015.

Additional file 3 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 3: Supplemental Table S2. Assembly metrics using single fraction assembly (metaspades) verses co-assembly of all fractions (MetaHipMer2).

Restoring function: positive responses of carbon and nitrogen to 20 years of hydrologic restoration in montane meadows

Cody Reed, Cody Reed, Asmeret Berhe, Kimber Moreland, Jim Wilcox & Benjamin Sullivan
Montane meadows are highly productive ecosystems that contain high densities of soil carbon (C) and nitrogen (N). However, anthropogenic disturbances that lead to channel incision and disconnected floodplain hydrology have altered the C balance of many meadows, converting them from net C sinks to net sources of C to the atmosphere. Restoration efforts designed to reconnect floodplain hydrology may slow rates of soil C loss from degraded meadows and restore conditions for C sequestration and...

Additional file 4 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 4: Supplemental Table S3. Assembly statistics, taxonomic lineage, and atom percent excess (APE) of the metagenome amplified genomes (MAGs) created in this study.

Additional file 6 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 6: Supplemental Table S5. Genomic abundance of MEROPS proteae gene per MAG. Columns indicate MEROPS protease families. APE = atom percent excess.

Additional file 7 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 7: Supplemental Table S6. CAZymes for the Myxococcota MAGs. Fen-1088 MAGs are highlighted in yellow. MAGs are sorted by increasing atom percent excess (APE) 13C.

Additional file 8 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 8: Supplemental Table S7. Number of CAZy gene homologs that can potentially target a particular substrate. Substrate assignments based off of the Glycoside Hydrolase categories from Berlemonte and Martiny 2015.

Additional file 3 of HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

Erin E. Nuccio, Steven J. Blazewicz, Marissa Lafler, Ashley N. Campbell, Anne Kakouridis, Jeffrey A. Kimbrel, Jessica Wollard, Dariia Vyshenska, Robert Riley, Andy Tomatsu, Rachel Hestrin, Rex R. Malmstrom, Mary Firestone & Jennifer Pett-Ridge
Additional file 3: Supplemental Table S2. Assembly metrics using single fraction assembly (metaspades) verses co-assembly of all fractions (MetaHipMer2).

Systemic racial disparities in funding rates at the National Science Foundation

Christine Chen, Sara Kahanamoku, Aradhna Tripati, Rosanna Alegado, Vernon Morris, Karen Andrade & Justin Hosbey
Concerns about systemic racism at academic and research institutions have increased over the past decade. Here, we investigate data from the National Science Foundation (NSF), a major funder of research in the United States, and find evidence for pervasive racial disparities. In particular, white principal investigators (PIs) are consistently funded at higher rates than most non-white PIs. Funding rates for white PIs have also been increasing relative to annual overall rates with time. Moreover, disparities...

Registration Year

  • 2022
    16

Resource Types

  • Dataset
    16

Affiliations

  • Lawrence Livermore National Laboratory
    16
  • University of California, Merced
    15
  • University of California, Berkeley
    15
  • University of Massachusetts Amherst
    14
  • Lawrence Berkeley National Laboratory
    14
  • Joint Genome Institute
    14
  • University of Nevada Reno
    1
  • University of Hawaii at Manoa
    1
  • Arizona State University
    1
  • University of California Los Angeles
    1